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CSA and CSB proteins are known to act in transcription-coupled DNA repair (TCR). Cockayne syndrome (CS) is a devastating multifactorial disease caused by mutations in CSA and CSB ; however the occurrence of features, for example, progeria and neurological dysfunctionalities in CS and not in the DNA repair syndrome xeroderma pigmentosum and UV-sensitive syndrome, suggests that their functions extend far beyond DNA repair. CSA and CSB function in various cellular processes, including transcription and cell cycle regulation, thus determining the need to find a common mechanism of action. We propose that, due to their involvement in ubiquitination, a key mechanism enabling the precise control of protein function and turnover, CSA and CSB act as broad regulators of essential cellular mechanisms, thus explaining the impact of their mutation in CS symptomatology. To face genotoxic stress, eukaryotic cells evolved extremely refined mechanisms. Defects in counteracting the threat imposed by DNA damage underlie the rare disease Cockayne syndrome (CS), which arises from mutations in the CSA and CSB genes. Although initially defined as DNA repair proteins, recent work shows that CSA and CSB act instead as master regulators of the integrated response to genomic stress by coordinating DNA repair with transcription and cell division. CSA and CSB exert this function through the ubiquitination of target proteins, which are effectors/regulators of these processes. This review describes how the ubiquitination of target substrates is a common denominator by which CSA and CSB participate in different aspects of cellular life and how their mutation gives rise to the complex disease CS. [ABSTRACT FROM AUTHOR]

Enhancers are regulatory elements that determine the temporal and spatial specificity of gene transcription. Enhancers serve as hubs for the transient assembly of transcription factor/coactivator clusters during the induction of transcriptional bursting. Transcriptional activation by enhancers does not always accompany an increased physical proximity to target promoters. The formation of higher-order genome architectures fosters ultra-long-range enhancer–promoter communication during cell fate determination. Enhancers are noncoding regulatory elements that instruct spatial and temporal specificity of gene transcription in response to a variety of intrinsic and extrinsic signals during development. Although it has long been postulated that enhancers physically interact with target promoters through the formation of stable loops, recent studies have changed this static view: sequence-specific transcription factors (TFs) and coactivators are dynamically recruited to enhancers and assemble so-called transcription hubs. Dynamic assembly of transcription hubs appears to serve as a key scaffold to integrate regulatory information encoded by surrounding genome and biophysical properties of transcription machineries. In this review, we outline emerging new models of transcriptional regulation by enhancers and discuss future perspectives. [ABSTRACT FROM AUTHOR]

WNT signaling is central to spatial tissue arrangement and regulating stem cell activity, and it represents the hallmark of gastrointestinal cancers. Although its role in driving intestinal tumors is well characterized, WNT's role in gastric tumorigenesis remains elusive. We have developed mouse models to control the specific expression of an oncogenic form of β-catenin (CTNNB1) in combination with MYC activation in Lgr5 + cells of the gastric antrum. We used multiomics approaches applied in vivo and in organoid models to characterize their cooperation in driving gastric tumorigenesis. We report that constitutive β-catenin stabilization in the stomach has negligible oncogenic effects and requires MYC activation to induce gastric tumor formation. Although physiologically low MYC levels in gastric glands limit β-catenin transcriptional activity, increased MYC expression unleashes the WNT oncogenic transcriptional program, promoting β-catenin enhancer invasion without a direct transcriptional cooperation. MYC activation induces a metabolic rewiring that suppresses lysosomal biogenesis through mTOR and ERK activation and MiT/TFE inhibition. This prevents EPCAM degradation by macropinocytosis, promoting β-catenin chromatin accumulation and activation of WNT oncogenic transcription. Our results uncovered a new signaling framework with important implications for the control of gastric epithelial architecture and WNT-dependent oncogenic transformation. [Display omitted] WNT mutations are a hallmark of gastrointestinal cancer, but low MYC activity represents a barrier for stomach adenoma formation. MYC regulates metabolic processes that allow WNT activation of oncogenic programs. [ABSTRACT FROM AUTHOR]

Mast cell–derived mediators induce vasodilatation and fluid extravasation, leading to cardiovascular failure in severe anaphylaxis. We previously revealed a synergistic interaction between the cytokine IL-4 and the mast cell–derived mediator histamine in modulating vascular endothelial (VE) dysfunction and severe anaphylaxis. The mechanism by which IL-4 exacerbates histamine-induced VE dysfunction and severe anaphylaxis is unknown. We sought to identify the IL-4–induced molecular processes regulating the amplification of histamine-induced VE barrier dysfunction and the severity of IgE-mediated anaphylactic reactions. RNA sequencing, Western blot, Ca2+ imaging, and barrier functional analyses were performed on the VE cell line (EA.hy926). Pharmacologic degraders (selective proteolysis-targeting chimera) and genetic (lentiviral short hairpin RNA) inhibitors were used to determine the roles of signal transducer and activator of transcription 3 (STAT3) and STAT6 in conjunction with in vivo model systems of histamine-induced hypovolemic shock. IL-4 enhancement of histamine-induced VE barrier dysfunction was associated with increased VE-cadherin degradation, intracellular calcium flux, and phosphorylated Src levels and required transcription and de novo protein synthesis. RNA sequencing analyses of IL-4–stimulated VE cells identified dysregulation of genes involved in cell proliferation, cell development, and cell growth, and transcription factor motif analyses revealed a significant enrichment of differential expressed genes with putative STAT3 and STAT6 motif. IL-4 stimulation in EA.hy926 cells induced both serine residue 727 and tyrosine residue 705 phosphorylation of STAT3. Genetic and pharmacologic ablation of VE STAT3 activity revealed a role for STAT3 in basal VE barrier function; however, IL-4 enhancement and histamine-induced VE barrier dysfunction was predominantly STAT3 independent. In contrast, IL-4 enhancement and histamine-induced VE barrier dysfunction was STAT6 dependent. Consistent with this finding, pharmacologic knockdown of STAT6 abrogated IL-4–mediated amplification of histamine-induced hypovolemia. These studies unveil a novel role of the IL-4/STAT6 signaling axis in the priming of VE cells predisposing to exacerbation of histamine-induced anaphylaxis. [ABSTRACT FROM AUTHOR]

Phages are the most prevalent and diverse entities in the biosphere and represent the simplest systems that are capable of self-replication. Many fundamental concepts of transcriptional regulation were revealed through phage studies. The replication of phages within bacteria entails the hijacking of the host transcription machinery. Typically, this is accomplished through proteins and RNAs encoded by the phage genome that bind to the host RNA polymerase and modify its characteristics. Understanding these processes offers valuable insights into the mechanisms of bacterial transcription itself. Historically, X-ray crystallography has been the major tool for elucidating the structural basis of phage transcriptional regulation. In recent years, the application of cryoelectron microscopy has not only allowed the exploration of protein-protein and protein-nucleic acid interactions at near-atomic resolution but also captured transient intermediate states, further expanding our mechanistic understanding of phage transcriptional regulation. In this review, He et al. describe the various strategies phages have adopted to modulate transcription initiation, transcription elongation, and transcription termination from a structural perspective. They also discuss potential applications of these findings and future directions of research. [ABSTRACT FROM AUTHOR]

The clinicopathological risk factors in the prognosis of stage IV gastric cancer have been comprehensively studied. However, the influencing factors of stage IV gastric cancer prognosis at genomic and transcriptional levels have not been well defined. The mutational and transcriptional data, along with demographic, clinicopathological and prognostic information of 44 stage IV gastric cancer patients were downloaded from the TCGA database. Univariate and multivariate analyses were performed to identify the significant risk factors and a Nomogram model was established to predict the patient prognosis. TTN, TP53, FLG, LRP1B, SYNE1 and ARID1A were among the top mutated genes without hot-spot mutations. The mutational status of AHNAK2, ASCC3, DNAH3, DOP1A, MYLK, SIPA1L1, SORBS2, SYNE1 and ANF462 significantly stratified the patient prognosis. The transcription of several genes, such as AQP10, HOXC8/9/10, COL10A1/COL11A1, WNT7B, KRT17 and KLK6 was significantly up-regulated or down-regulated. Enrichment analysis on mutations and transcription revealed cell skeleton and membrane function, extracellular matrix function, HPV infection, and several cancer-related pathways as the main aberrancies. Univariate analyses revealed a series of significant factors stratifying patient prognosis, mainly including cancer location, several mutated genes and many up- or down-regulated genes. However, subsequent multivariate analysis revealed SYNE1 mutation, DNAH3 mutation, COMMD3 transcription level, and cancer location as the independent risk factors. A Nomogram model has been established with these significant risk factors to predict the patient prognosis. Further validation is needed to ensure the effectiveness of the model in real clinical practice. Cancer location, along with the mutational status of SYNE1 and DNAH3 and the transcriptional level of COMMD3 were independent risk factors of stage IV gastric cancer. A Nomogram model was established with these factors for prognosis prediction. [ABSTRACT FROM AUTHOR]

Although the defining events of meiosis are highly conserved, such as genetic recombination and ploidy reduction, the regulation of meiotic entry and divisions is distinct between species and sexes. In mammals, the complex cellular milieu dictates the developmental timing and duration of meiosis and hinges on complex signaling from somatic cells. The unique and dramatic chromosomal events of meiosis and gametogenesis require diverse mechanisms of regulation of gene expression and cell cycle progression. The functional study of meiotic regulatory elements in animals is markedly hampered by the inability to efficiently recapitulate the entire process in cell culture paradigms. However, increasingly powerful genomic analyses are illuminating key aspects of meiotic gene expression such as transcription control, transcriptome epigenetics, and post-transcriptional regulation. Meiosis is essential for gamete production in all sexually reproducing organisms. It entails two successive cell divisions without DNA replication, producing haploid cells from diploid ones. This process involves complex morphological and molecular differentiation that varies across species and between sexes. Specialized genomic events like meiotic recombination and chromosome segregation are tightly regulated, including preparation for post-meiotic development. Research in model organisms, notably yeast, has shed light on the genetic and molecular aspects of meiosis and its regulation. Although mammalian meiosis research faces challenges, particularly in replicating gametogenesis in vitro , advances in genetic and genomic technologies are providing mechanistic insights. Here we review the genetics and molecular biology of meiotic gene expression control, focusing on mammals. [ABSTRACT FROM AUTHOR]

• Transcription had a strong constraining effect on composition quality and productivity. • Transcription moderates the relation between oral language and composition quality. • No signification moderation of transcription on the oral language-composition productivity relation. In the present study we examined the contributions of transcription and foundational oral language skills to written composition outcomes in a sample of kindergartners. Two hundred and eighty-two kindergarten students from 49 classrooms participated in this study. Children's writing-related skills were examined using various tasks. Latent structural equation modeling was used to test the hypothesis that transcription moderates the relation between foundational oral language and compositional productivity and quality for kindergarten writers. This hypothesis is one possible manifestation of the Developmental Constraints Hypothesis (DCH). In support of the DCH, transcription had a strong constraining effect on both composition quality and productivity. Additionally, transcription moderated the relation between foundational oral language skills and composition quality, although the moderation was negative. There was no signification moderation of transcription on the foundational oral language -composition productivity relation. Implications of the findings and future directions are discussed including challenges assessing composition in young, beginning writers. [ABSTRACT FROM AUTHOR]

The finding that animals with circadian gene mutations exhibit diet-induced obesity and metabolic syndrome with hypoinsulinemia revealed a distinct role for the clock in the brain and peripheral tissues. Obesogenic diets disrupt rhythmic sleep/wake patterns, feeding behavior, and transcriptional networks, showing that metabolic signals reciprocally control the clock. Providing access to high-fat diet only during the sleep phase (light period) in mice accelerates weight gain, whereas isocaloric time-restricted feeding during the active period enhances energy expenditure due to circadian induction of adipose thermogenesis. This perspective focuses on advances and unanswered questions in understanding the interorgan circadian control of healthful metabolism. [ABSTRACT FROM AUTHOR]

Despite significant progress in our understanding of promoter melting dynamics, underlying principles of the process remain elusive, with opposing views on key aspects held by many in the field. Here, I discuss the mechanistic logic behind the interplay of thermal and deterministic forces acting to create transcriptionally competent promoter complexes. [ABSTRACT FROM AUTHOR]

Gene regulation and chromosome architecture are intimately linked. Genes with prominent roles in cell identity are often regulated by clusters of enhancer elements. By contrast, a recent study shows housekeeping genes are often regulated through clustering of promoters. We discuss here new regulatory insights for these two types of genes. [ABSTRACT FROM AUTHOR]

A recent report by Chervova, Molliex, et al. shows redundant functions for the transcription factors (TFs) ESRRB and NR5A2 as mitotic bookmarkers in mouse embryonic stem (ES) cells. These occupy some of their target sites in mitotic chromatin, ensuring their robust reactivation after cell division, including markers and regulators of pluripotency. [ABSTRACT FROM AUTHOR]

In a recent study, Oliveira and colleagues revealed how growth arrest and DNA damage-inducible protein 34 (GADD34), an effector of the integrated stress response, initiates the translation of synaptic plasticity-related mRNAs following brain-derived neurotrophic factor (BDNF) stimulation. This work suggests that GADD34 may link transcriptional products with translation control upon neuronal activation, illuminating how protein synthesis is orchestrated in neuronal plasticity. [ABSTRACT FROM AUTHOR]

Endogenous oxidative DNA breaks arise at non-coding regulatory DNA regions such as enhancers and promoters. The oxidative demethylation of DNA and histones is a potential source of DNA breaks at non-coding regulatory regions. Nuclear mitotic apparatus (NuMA, also known as NUMA1) promotes transcriptional responses and repair of oxidative breaks at enhancers and promoters. The failure in repair disrupts gene transcription and interferes with normal physiology. DNA breaks at protein-coding sequences are well-established threats to tissue homeostasis and maintenance. They arise from the exposure to intracellular and environmental genotoxins, causing damage in one or two strands of the DNA. DNA breaks have been also reported in non-coding regulatory regions such as enhancers and promoters. They arise from essential cellular processes required for gene transcription, cell identity and function. One such process that has attracted recent attention is the oxidative demethylation of DNA and histones, which generates abasic sites and DNA single-strand breaks. Here, we discuss how oxidative DNA breaks at non-coding regulatory regions are generated and the recently reported role of NuMA (nuclear mitotic apparatus) protein in promoting transcription and repair at these regions. [ABSTRACT FROM AUTHOR]

Regular exercise leads to many adaptations, including changes to protein abundance, which serve to blunt subsequent homeostatic threats generated by future skeletal muscle contractions. The exercise biology field has developed its own dogma, which proposes that transient changes in mRNA after a single session of exercise can provide insights into both the direction and magnitude of protein changes likely to occur following training. However, there are examples of contraction-induced changes in mRNA without any subsequent change in encoded proteins, and, conversely, proteins with increased abundance in response to exercise training without a corresponding change in respective mRNA levels. We propose an alternative view that there is not always a direct relationship between exercise-induced changes in mRNA levels and the abundance of proteins they encode. The ability of skeletal muscle to adapt to repeated contractile stimuli is one of the most intriguing aspects of physiology. The molecular bases underpinning these adaptations involve increased protein activity and/or expression, mediated by an array of pre- and post-transcriptional processes, as well as translational and post-translational control. A longstanding dogma assumes a direct relationship between exercise-induced increases in mRNA levels and subsequent changes in the abundance of the proteins they encode. Drawing on the results of recent studies, we dissect and question the common assumption of a direct relationship between changes in the skeletal muscle transcriptome and proteome induced by repeated muscle contractions (e.g., exercise). [ABSTRACT FROM AUTHOR]

Plant virology has been at the forefront of major discoveries in RNA biology for over a century. Recent discoveries in gene expression strategies to bypass the monocistronic mRNA dogma have expanded our insights and led to biotechnological applications of viral elements. Work with plant viruses has spearheaded the discoveries of RNA silencing and its suppression. Plant viruses are versatile gene vector tools for various application, including gene editing. Key principles pertaining to RNA biology not infrequently have their origins in plant virology. Examples have arisen from studies on viral RNA-intrinsic properties and the infection process from gene expression, replication, movement, and defense evasion to biotechnological applications. Since RNA is at the core of the central dogma in molecular biology, how plant virology assisted in the reinforcement or adaptations of this concept, while at other instances shook up elements of the doctrine, is discussed. Moreover, despite the negative effects of viral diseases in agriculture worldwide, plant viruses can be considered a scientific treasure trove. Today they remain tools of discovery for biotechnology, studying evolution, cell biology, and host–microbe interactions. [ABSTRACT FROM AUTHOR]

Abnormally activated CDK9 participates in the super-enhancer mediated transcription of short-lived proteins required for cancer cell survival. Targeting CDK9 has shown potent anti-tumor activity in clinical trials among different cancers. However, the study and knowledge on drug resistance to CDK9 inhibitors are very limited. In this study, we established an AML cell line with acquired resistance to a highly selective CDK9 inhibitor BAY1251152. Through genomic sequencing, we identified in the kinase domain of CDK9 a mutation L156F, which is also a coding SNP in the CDK9 gene. By knocking in L156F into cancer cells using CRISPR/Cas9, we found that single CDK9 L156F could drive the resistance to CDK9 inhibitors, not only ATP competitive inhibitor but also PROTAC degrader. Mechanistically, CDK9 L156F disrupts the binding with inhibitors due to steric hindrance, further, the mutation affects the thermal stability and catalytic activity of CDK9 protein. To overcome the drug resistance mediated by the CDK9-L156F mutation, we discovered a compound, IHMT-CDK9-36 which showed potent inhibition activity both for CDK9 WT and L156F mutant. Together, we report a novel resistance mechanism for CDK9 inhibitors and provide a novel chemical scaffold for the future development of CDK9 inhibitors. Here we report a resistance mechanism for CDK9 inhibitors mediated by a CDK9 coding SNP and provide a novel chemical scaffold for future development of CDK9 inhibitors. [Display omitted] [ABSTRACT FROM AUTHOR]

In aged animals from worms to humans, transcriptional elongation rates are faster, leading to changes in transcript quality and alternative splicing. Recent work by Debès et al. shows how interventions that slow elongation rates, such as mutating RNA polymerase II (Pol II) or increasing nucleosome density to impose transcriptional 'traffic', delay senescence and promote longevity. In aged animals from worms to humans, transcriptional elongation rates are faster, leading to changes in transcript quality and alternative splicing. Recent work by Debès et al. shows how interventions that slow elongation rates, such as mutating RNA polymerase II (Pol II)or increasing nucleosome density to impose transcriptional 'traffic', delay senescence and promote longevity. [ABSTRACT FROM AUTHOR]

Innate stereotypical behaviors show 'behavioral canalization', defined as robustness in the face of environmental change. Behavioral canalization is achieved through positive selection on central alleles in transcriptional niches which stabilize genetic networks by reducing variation in the expression of interconnected genes. The genetic architecture that underlies innate behaviors can be protected from deleterious mutations by suppressing epistasis. Epistatically suppressed mutations provide a reservoir of cryptic genetic variation that can be released when epistatic suppression is relaxed under environmental pressure to enable behavioral adaptation. Behaviors are components of fitness and contribute to adaptive evolution. Behaviors represent the interactions of an organism with its environment, yet innate behaviors display robustness in the face of environmental change, which we refer to as 'behavioral canalization'. We hypothesize that positive selection of hub genes of genetic networks stabilizes the genetic architecture for innate behaviors by reducing variation in the expression of interconnected network genes. Robustness of these stabilized networks would be protected from deleterious mutations by purifying selection or suppressing epistasis. We propose that, together with newly emerging favorable mutations, epistatically suppressed mutations can generate a reservoir of cryptic genetic variation that could give rise to decanalization when genetic backgrounds or environmental conditions change to allow behavioral adaptation. [ABSTRACT FROM AUTHOR]

Protein-glutaminase (EC 3.5.1.44, PG) derived from Chryseobacterium proteolyticum can significantly improve the solubility, emulsification and foaming properties of food proteins and is a promising deaminase. PG has broad application prospects in the food industry. However, the low yield of the enzyme is not sufficient for industrial applications. Mutagenesis and molecular breeding can improve PG yield, which consumes considerable time and has high costs. In contrast, it is a feasible way to achieve high PG yields to optimize the fermentation conditions of the strains. In this work, amino acids were screened to improve PG production. The addition of 0.80 g/L leucine (Leu) could increase PG production by 27.80%. Then, through the response surface method, it was found that under the combination of 1.60 g/L Leu, 5.65 g/L MgSO 4 .7 H 2 O and 5.13 g/L KH 2 PO 4 , PG production reached 2.93 U/mL, which was 1.87 times that of the original medium. The growth and metabolism curves of Chryseobacterium proteolyticum were measured under this formula. The effect of Leu on PG production was further investigated by measuring the transcription of the PG gene, the conductivity of fermentation fluid and the morphological characteristics of cells. This work lays a foundation for the industrial production of PG. [Display omitted] • Protein-glutaminase yield was increased by 87% by optimizing the fermentation medium with leucine. • The addition of leucine accelerated the growth of Chryseobacterium proteolyticum. • The addition of leucine may increase the permeability of the cell membrane. [ABSTRACT FROM AUTHOR]

Cells must coordinate their individual activities toward multicellular goals, which requires efficient information processing mechanisms. Bioelectrical signals encode instructive rules at multiple scales, from the individual cell to the tissue and organ levels, because patterns of cell potentials are locally coupled to transcription and morphogenesis via biochemical downstream processes. We review here biophysical models that suggest how bi-stable and oscillatory bioelectrical memories defined at the single-cell and multicellular scales can constitute pattern memories that are instructive for morphological outcomes. Multicellular aggregates are open to the external microenvironment and typically show spatio-temporal distributions of potassium and calcium ions, neurotransmitters, and specific transcription activators that are correlated with electric potential patterns. This correlation results in patterns composed of dynamic subsystems (modules) with cells that share the same bioelectrical state. The particular integration–segregation topology of the different modules defines a multicellular pattern memory. By acting on these separate modules and their particular integration, pattern memories can be retrieved or externally rewritten, with morphological consequences. Thus, the simulations give further support to recent experimental findings and suggest new opportunities for external actions at the intermediate scale characteristic of endogenous multicellular fields. [Display omitted] • Local transcription correlates with bioelectricity in aggregates of non-excitable cells. • Cell potentials modulate transcription via biochemical downstream processes. • Biophysical models use ion channels and intercellular junctions act as bioelectrical units. • Multicellular patterns are instructive in development, regeneration, and tumorigenesis. • Pattern memories emerge from the integration-segregation of bioelectrical modules. [ABSTRACT FROM AUTHOR]

Plant secondary metabolites are vital for human health leading to the gain the access to natural products. The quality of crops is the result of the interaction of different biotic and abiotic factors. Abiotic stresses during plant growth may reduce the crop performance and quality of the produce. However, abiotic stresses can result in numerous physiological, biochemical, and molecular responses in plants, aiming to deal with these conditions. Abiotic stresses are also elicitors of the biosynthesis of plant secondary metabolites in plants which possess plant defense mechanisms as well as human health benefits such as anti-inflammatory, antioxidative properties etc. Plants either synthesize new compounds or alter the concentration of bioactive compounds. Due to increasing attention towards the production of bioactive compounds, the understanding of crop responses to abiotic stresses in relation to the biosynthesis of bioactive compounds is critical. Plants alter their metabolism at the genetic level in response to different abiotic stresses resulting the changes in secondary metabolite production. Transcriptional factors regulate genes responsible for secondary metabolite biosynthesis in several plants under stress conditions. Understanding the signaling pathways involved in the secondary metabolite biosynthesis has become easy with the use of molecular biology. Therefore, aim of writing the review is to focus on secondary metabolite production in vegetable crops, their health benefits and transcription regulation under various abiotic stresses. • Abiotic stress induced biosynthesis of secondary metabolites in vegetables is discussed. • Pathways involved in the secondary metabolite biosynthesis are discussed. • Health benefits of plant secondary metabolites are reviewed. • Technological advances such as sensor-based system and transcriptional regulation are presented. [ABSTRACT FROM AUTHOR]

HNF1β (HNF1B) is a transcription factor frequently mutated in patients with developmental renal disease. It binds to mitotic chromatin and reactivates gene expression after mitosis, a phenomenon referred to as bookmarking. Using a crosslinking method that circumvents the artifacts of formaldehyde, we demonstrate that HNF1β remains associated with chromatin in a sequence-specific way in both interphase and mitosis. We identify an HNF1β-interacting protein, BTBD2, that enables the interaction and activation of Topoisomerase 1 (TOP1) exclusively during mitosis. Our study identifies a shared microhomology domain between HNF1β and TOP1, where a mutation, found in "maturity onset diabetes of the young" patients, disrupts their interaction. Importantly, HNF1β recruits TOP1 and induces DNA relaxation around HNF1β mitotic chromatin sites, elucidating its crucial role in chromatin remodeling and gene reactivation after mitotic exit. These findings shed light on how HNF1β reactivates target gene expression after mitosis, providing insights into its crucial role in maintenance of cellular identity. [Display omitted] • HNF1β mitotic site binding is preserved with a specific methanol/formaldehyde ChIP • BTBD2, an HNF1β partner, mediates mitosis-specific interaction with TOP1 • HNF1β recruits TOP1 and induces DNA relaxation around bookmarked HNF1β sites • An HNF1β mutation, found in MODY patients, disrupts the interaction with TOP1 Bagattin et al. developed a ChIP methodology that strongly improves the identification of HNF1β-bound mitotic regions. They demonstrate that HNF1β remains associated with mitotic chromatin and recruits TOP1 on bookmarked sites in order to resolve DNA topological constraints. An HNF1β mutation, found in MODY patients, prevents the interaction with TOP1. [ABSTRACT FROM AUTHOR]

Quiescence is an important non-pathological state in which cells pause cell cycle progression temporarily, sometimes for decades, until they receive appropriate proliferative stimuli. Quiescent cells make up a significant proportion of the body, and maintaining genomic integrity during quiescence is crucial for tissue structure and function. While cells in quiescence are spared from DNA damage associated with DNA replication or mitosis, they are still exposed to various sources of endogenous DNA damage, including those induced by normal transcription and metabolism. As such, it is vital that cells retain their capacity to effectively repair lesions that may occur and return to the cell cycle without losing their cellular properties. Notably, while DNA repair pathways are often found to be downregulated in quiescent cells, emerging evidence suggests the presence of active or differentially regulated repair mechanisms. This review aims to provide a current understanding of DNA repair processes during quiescence in mammalian systems and sheds light on the potential pathological consequences of inefficient or inaccurate repair in quiescent cells. • Quiescent cells in a state of reversible growth arrest retain the ability to repair DNA damage. • DNA repair mechanisms are often channelled to restore specific regions of the genome. • DNA repair factors may have different functions in cycling and non-cycling cells. • DNA repair in quiescent cells has important implications for human disease. [ABSTRACT FROM AUTHOR]

• Light promotes the transcription level of MAP30. • McHY5 and McHY5-X1 activate MAP30 expression mainly under light conditions. • McPIF1-X1 and McPIF3 are negative regulators for MAP30 transcription. • McHY5/McHY5-X1 and McPIF1-X1/McPIF3 antagonistically regulate MAP30 expression. MAP30, a ribosome-inactivating protein mainly isolated from the fruits and seeds of bitter gourd (Momordica charantia), has many pharmacological properties, such as anti-HIV and anti-tumor activities. Using qPCR analysis, we found that MAP30 transcription was higher in light, but drastically reduced in darkness. However, the molecular mechanism by which MAP30 is regulated remains unclear. Using yeast one-hybrid (Y1H) library screening, we found that McHY5, a homolog of AtHY5, bound to the MAP30 promoter. In addition, McHY5 and its homolog McHY5-X1 are identified as positive regulators binding to the MAP30 promoter by using Y1H, Electrophoretic mobility shift assay (EMSA) and Dual-Luciferase Reporter (DLR) assay. Due to MAP30 is not present in Arabidopsis we transformed pMAP30:MAP30 to Col and obtained transgenic line 18. Compared with pMAP30:MAP30/Col 18#, MAP30 transcription was largely reduced in pMAP30:MAP30 18#/Athy5–215 whether under light or dark conditions. Moreover, approximately 70 % of the tested bitter gourd germplasms showed consistent expression patterns of McHY5 / McHY5-X1 and MAP30 under light conditions. In contrast to McHY5, McPIF1-X1 and McPIF3 acted as inactivators to inhibit MAP30 transcription. In this study, we found that MAP30 transcription was activated by McHY5 and McHY5-X1 in light, while McPIF1-X1 and McPIF3 inhibited MAP30 transcription mainly in darkness. Conclusively, we established the antagonistic module of McHY5/McHY5-X1 and McPIF1-X1/McPIF3 in MAP30 transcription regulation. This work expands our understanding of the regulatory mechanism of MAP30 and provides a valuable conceptual guidance for cultivating high pharmacological activity bitter gourd varieties with high MAP30 protein levels. [ABSTRACT FROM AUTHOR]

MicroRNAs (miRNAs) play crucial roles in physiological functions and disease, but the regulation of their nuclear biogenesis remains poorly understood. Here, BioID on Drosha, the catalytic subunit of the microprocessor complex, reveals its proximity to splicing factor proline- and glutamine (Q)-rich (SFPQ), a multifunctional RNA-binding protein (RBP) involved in forming paraspeckle nuclear condensates. SFPQ depletion impacts both primary and mature miRNA expression, while other paraspeckle proteins (PSPs) or the paraspeckle scaffolding RNA NEAT1 do not, indicating a paraspeckle-independent role. Comprehensive transcriptomic analyses show that SFPQ loss broadly affects RNAs and miRNA host gene (HG) expression, influencing both their transcription and the stability of their products. Notably, SFPQ protects the oncogenic miR-17∼92 polycistron from degradation by the nuclear exosome targeting (NEXT)-exosome complex and is tightly linked with its overexpression across a broad variety of cancers. Our findings reveal a dual role for SFPQ in regulating miRNA HG transcription and stability, as well as its significance in cancers. [Display omitted] • SFPQ is a regulator of miRNA biogenesis via two paraspeckle-independent mechanisms • SFPQ represses the transcriptional elongation of a subset of miRNA host genes • SFPQ stabilizes miRNA primary transcripts by repressing the NEXT nuclear exosome • SFPQ is a major determinant for miR-17∼92 oncogenic expression across cancer types Thivierge et al. integrate multiple transcriptomic analyses to reveal a function for the multifunctional protein SFPQ in the biogenesis of microRNAs (miRNAs) by controlling host genes' transcriptional elongation and stabilizing primary transcripts. They show a genome-wide footprint of SFPQ in miRNA expression and a role in oncogenic overexpression of miR-17∼92. [ABSTRACT FROM AUTHOR]

LoaP is a member of the universal NusG protein family. Previously, we reported that unlike other characterized homologs, LoaP binds RNA sequence-specifically, recognizing a stem-loop in the 5′-untranslated region of operons it regulates. To elucidate how this NusG homolog acquired this ability, we now determined the co-crystal structure of Thermoanaerobacter pseudethanolicus LoaP bound to its cognate 26-nucleotide dfn RNA element. Our structure reveals that the LoaP C-terminal KOW domain recognizes the helical portion of the RNA by docking into a broadened major groove, while a protruding β-hairpin of the N-terminal NusG-like domain binds the UNCG tetraloop capping the stem-loop. Major-groove RNA recognition is unusual and is made possible by conserved features of the dfn hairpin. Superposition with structures of other NusG proteins implies that LoaP can bind concurrently to the dfn RNA and the transcription elongation complex, suggesting a new level of co-transcriptional regulation by proteins of this conserved family. [Display omitted] • Unique among NusG family transcription factors, LoaP binds RNA sequence-specifically • The cocrystal structure of LoaP reveals both of its conserved domains recognizing RNA • LoaP makes specific interactions with a broad major groove, and also a UNCG tetraloop • LoaP may be able to bind simultaneously to its cognate RNA and the elongation complex Uniquely among the universal NusG family of transcription factors, LoaP binds a cognate RNA. The structure of LoaP solved by Elghondakly et al. reveals LoaP recognizing both the stem and terminal UNCG tetraloop of its target RNA, and suggests it may function by simultaneously binding to the transcription elongation complex. [ABSTRACT FROM AUTHOR]

• Long noncoding RNA cytochrome B (Lnc CytB), encoded by mtDNA, facilitates mtDNA transcription. • Downregulation of Lnc CytB in diabetes compromises mitochondrial transcription factor binding at mtDNA promoters. • Suboptimal mtDNA-encoded polypeptides dysfunction the electron transport chain. • Dysfunctional/damaged mitochondria accelerate apoptosis, culminating in diabetic retinopathy development. In diabetic retinopathy, mitochondrial DNA (mtDNA) is damaged and mtDNA-encoded genes and long noncoding RNA cytochrome B (Lnc CytB) are downregulated. LncRNAs lack an open reading frame, but they can regulate gene expression by associating with DNA/RNA/protein. Double stranded mtDNA has promoters on both heavy (HSP) and light (LSP) strands with binding sites for mitochondrial transcription factor A (TFAM) between them. The aim was to investigate the role of Lnc CytB in mtDNA transcription in diabetic retinopathy. Using human retinal endothelial cells incubated in high glucose, the effect of regulation of Lnc CytB on TFAM binding at mtDNA promoters was investigated by Chromatin immunoprecipitation, and binding of Lnc CytB at TFAM by RNA immunoprecipitation and RNA fluorescence in situ hybridization. High glucose decreased TFAM binding at both HSP and LSP , and binding of Lnc CytB at TFAM. While Lnc CytB overexpression ameliorated decrease in TFAM binding and transcription of genes encoded by both H- and L- strands, Lnc CytB- siRNA further downregulated them. Maintenance of mitochondrial homeostasis by overexpressing mitochondrial superoxide dismutase or Sirtuin-1 protected diabetes-induced decrease in TFAM binding at mtDNA and Lnc CytB binding at TFAM, and mtDNA transcription. Similar results were obtained from mouse retinal microvessels from streptozotocin-induced diabetic mice. Thus, Lnc CytB facilitates recruitment of TFAM at HSP and LSP , and its downregulation in diabetes compromises the binding, resulting in the downregulation of polypeptides encoded by mtDNA. Regulation of Lnc CytB , in addition to protecting mitochondrial genomic stability, should also help in maintaining the transcription of mtDNA encoded genes and electron transport chain integrity in diabetic retinopathy. [ABSTRACT FROM AUTHOR]

The Eyes Absent family (EYA1–4) are a group of dual function proteins that act as both tyrosine phosphatases and transcriptional co-activators. EYA proteins play a vital role in development, but are also aberrantly overexpressed in cancers, where they often confer an oncogenic effect. Precisely how the EYAs impact cell biology is of growing interest, fuelled by the therapeutic potential of an expanding repertoire of EYA inhibitors. Recent functional studies suggest that the EYAs are important players in the regulation of genome maintenance pathways including DNA repair, mitosis, and DNA replication. While the characterized molecular mechanisms have predominantly been ascribed to EYA phosphatase activities, EYA co-transcriptional activity has also been found to impact the expression of genes that support these pathways. This indicates functional convergence of EYA phosphatase and co-transcriptional activities, highlighting the emerging importance of the EYA protein family at the intersection of genome maintenance mechanisms. In this review, we discuss recent progress in defining EYA protein substrates and transcriptional effects, specifically in the context of genome maintenance. We then outline future directions relevant to the field and discuss the clinical utility of EYA inhibitors. • EYA1–4 are dual function proteins with converging roles in genome maintenance. • The EYAs act as tyrosine phosphatases and can dephosphorylate H2AX, RAD51 and PLK1. • The EYAs also function as co-transcriptional activators of genes involved in genome maintenance. • EYA phosphatase and co-transcriptional inhibitors have emerging potential as cancer therapeutics. [ABSTRACT FROM AUTHOR]

RNA polymerase I (Pol I) is responsible for synthesizing ribosomal RNA, which is the rate limiting step in ribosome biogenesis. We have reported wide variability in the magnitude of the rate constants defining the rate limiting step in sequential nucleotide additions catalyzed by Pol I. in this study we sought to determine if base identity impacts the rate limiting step of nucleotide addition catalyzed by Pol I. To this end, we report a transient state kinetic interrogation of AMP, CMP, GMP, and UMP incorporations catalyzed by Pol I. We found that Pol I uses one kinetic mechanism to incorporate all nucleotides. However, we found that UMP incorporation is faster than AMP, CMP, and GMP additions. Further, we found that endonucleolytic removal of a dimer from the 3′ end was fastest when the 3′ terminal base is a UMP. It has been previously shown that both downstream and upstream template sequence identity impacts the kinetics of nucleotide addition. The results reported here show that the incoming base identity also impacts the magnitude of the observed rate limiting step. [Display omitted] • Pol I employs one universal kinetic mechanism independent of base identity. • UMP is incorporated substantially faster than GMP, CMP, and AMP. • Fast incorporation of UMP may be important for termination. [ABSTRACT FROM AUTHOR]

bZIP transcription factors can function as homodimers or heterodimers through interactions with their disordered coiled-coil domain. Such dimer assemblies are known to influence DNA-binding specificity and/or the recruitment of binding partners, which can cause a functional switch of a transcription factor from being an activator to a repressor. We recently identified the genomic targets of a bZIP transcription factor called CREB3L1 in rat hypothalamic supraoptic nucleus by ChIP-seq. The objective of this study was to investigate the CREB3L1 protein-to-protein interactome of which little is known. For this approach, we created and screened a rat supraoptic nucleus yeast two-hybrid prey library with the bZIP region of rat CREB3L1 as the bait. Our yeast two-hybrid approach captured five putative CREB3L1 interacting prey proteins in the supraoptic nucleus. One interactor was selected by bioinformatic analyses for more detailed investigation by co-immunoprecipitation, immunofluorescent cellular localisation, and reporter assays in vitro. Here we identify dimerisation hub protein Dynein Light Chain LC8-Type 1 as a CREB3L1 interacting protein that in vitro enhances CREB3L1 activation of target genes. • A yeast two-hybrid screen reels in novel CREB3L1 interacting SON prey proteins. • Dimerization hub protein DYNLL1 binding motifs are present in the CREB3 family. • Proximity ligation assays establish the cell locations of CREB3L1-DYNLL1 interactions. • DYNLL1 significantly enhances CREB3L1 activation of target gene promoters. [ABSTRACT FROM AUTHOR]

The histone acetyltransferase HBO1, also known as KAT7, is a major chromatin modifying enzyme responsible for H3 and H4 acetylation. It is found within two distinct tetrameric complexes, the JADE subunit-containing complex and BRPF subunit-containing complex. The HBO1-JADE complex acetylates lysine 5, 8 and 12 of histone H4, and the HBO1-BRPF complex acetylates lysine 14 of histone H3. HBO1 regulates gene transcription, DNA replication, DNA damage repair, and centromere function. It is involved in diverse signaling pathways and plays crucial roles in development and stem cell biology. Recent work has established a strong relationship of HBO1 with the histone methyltransferase MLL/KMT2A in acute myeloid leukemia. Here, we discuss functional and pathological links of HBO1 to cancer, highlighting the underlying mechanisms that may pave the way to the development of novel anti-cancer therapies. • HBO1 acetyltransferase, or KAT7, is a major chromatin modifying enzyme. • HBO1 catalyzes acetylation of histone H3 and H4. • HBO1 regulates gene transcription and genome stability. • HBO1 and MLL complexes cooperate and activate transcription in leukemogenesis. • HBO1 is a potential pharmacological target for a broad spectrum of cancers. [ABSTRACT FROM AUTHOR]

Maintenance of genome integrity is a precise but tedious and complex job for the cell. Several post-translational modifications (PTMs) play vital roles in maintaining the genome integrity. Although ubiquitination is one of the most crucial PTMs, which regulates the localization and stability of the nonhistone proteins in various cellular and developmental processes, ubiquitination of the histones is a pivotal epigenetic event critically regulating chromatin architecture. In addition to genome integrity, importance of ubiquitination of core histones (H2A, H2A, H3, and H4) and linker histone (H1) have been reported in several cellular processes. However, the complex interplay of histone ubiquitination and other PTMs, as well as the intricate chromatin architecture and dynamics, pose a significant challenge to unravel how histone ubiquitination safeguards genome stability. Therefore, further studies are needed to elucidate the interactions between histone ubiquitination and other PTMs, and their role in preserving genome integrity. Here, we review all types of histone ubiquitinations known till date in maintaining genomic integrity during transcription, replication, cell cycle, and DNA damage response processes. In addition, we have also discussed the role of histone ubiquitination in regulating other histone PTMs emphasizing methylation and acetylation as well as their potential implications in chromatin architecture. Further, we have also discussed the involvement of deubiquitination enzymes (DUBs) in controlling histone ubiquitination in modulating cellular processes. • Histone ubiquitination maintains the genome integrity of cells. • Ubiquitination of histone plays a key role in transcription, replication, and DNA damage response. • Histone ubiquitination regulates other PTMs to preserve genome integrity. [ABSTRACT FROM AUTHOR]

Xiaoyaosan (XYS), a traditional Chinese medicine formulation, has been used in the treatment of depression. However, no studies have yet identified the active compounds responsible for its antidepressant effects in the brain. We investigated the antidepressants effects of XYS and identified 18β-glycyrrhetinic acid (18β-GA) as the primary compound present in the brain following XYS injection. Furthermore, we explored the molecular mechanisms underlying the antidepressant-like effects of both XYS and 18β-GA. To investigate the antidepressant-like effects of XYS and elucidate the associated molecular mechanisms, we employed various methodologies, including cell cultures, the chronic social defeat stress (CSDS) model, behavioral tests, immunoprecipitation, quantitative PCR (qPCR) assays, Western blotting assays, luciferase assays, chromatin immunoprecipitation (ChIP) assays, immunofluorescence staining, and dendritic spine analysis. We identified 18β-GA as the primary compound in the brain following XYS injection. In vitro , 18β-GA was found to bind with ERK (extracellular signal-regulated kinase), subsequently activating ERK kinase activity toward both c-Jun and cAMP response element binding protein (CREB). Moreover, 18β-GA activated brain-derived neurotrophic factor (BDNF) transcription by stimulating nuclear factor-erythroid factor 2-related factor 2 (Nrf2), c-Jun, and CREB, while also inhibiting methyl CpG binding protein 2 (MeCP2) both in vitro and in vivo. Chronic intraperitoneal (i.p.) administration of 18β-GA exhibited prophylactic antidepressant-like effects in a CSDS model, primarily by activating BDNF transcription in the medial prefrontal cortex (mPFC). Interestingly, a single i.p. injection of 18β-GA produced rapid and sustained antidepressant-like effects in CSDS-susceptible mice by engaging the BDNF-tropomyosin receptor kinase B (TrkB) signaling pathway in the mPFC. These findings suggest that the activation of BDNF transcription in the mPFC underlies the antidepressant-like effects of 18β-GA, a key component of XYS in the brain. [Display omitted] [ABSTRACT FROM AUTHOR]

With the development of epigenetic engineering tools for manipulating DNA methylation at the desired locus, the stable maintenance of targeted methylation status in edited cells after division poses a major obstacle. Transient methylation levels, along with the reversible inhibition of the desired genes, by some epigenetic editing techniques, limit their further application in functional and therapeutic studies of critical regulators in the cancer epigenome. In this study, we utilized CRISPR/Cas9-mediated the homology-directed repair (HDR) pathway following double-strand breaks (DSBs) information to target de novo methylation of the vital epigenetic biomarker, O6-methylguanine-DNA methyltransferase (MGMT). Based on synthetic single and double stranded methylated repair templates, DNA methylation patterns can be incorporated into the endogenous MGMT gene. In addition, we observed upregulation of DNA methyltransferases (DNMTs) in edited HeLa cells. In particular, we employed an optimized method of using the DNA ligase IV inhibitor SCR7 to markedly enhance the insertion efficiency induced by the long methylated repair template, contributing to the induction of stable methylation alterations through epigenetic recombination after cell division. Additionally, our study confirmed that CRISPR/Cas9-mediated target methylation in a site-specific manner enabled the maintenance of gene silencing in vitro and in vivo. Collectively, we show that a combination of CRISPR/Cas9 components, SCR7 treatment, and the long methylated HDR template can enhance CRISPR/Cas9-directed epigenomic editing efficiency and further induce stable effects on methylation modifications and transcriptional suppression. Based on synthetic methylated dsDNA repair template, DNA methylation patterns can be incorporated into the endogenous MGMT using homology, along with the up-regulated expression of DNA methyltransferases (DNMTs). Our results demonstrate that a combination of CRISPR/Cas9 components, SCR7 treatment and methylated homologous template can enhance CRISPR/Cas9-directed epigenetic editing efficiency and further induce stable effects on methylation modifications and transcriptional suppression. [Display omitted] • SCR7 increases the CRISPR/Cas9-mediated epigenetic recombination efficiency. • CRISPR/Cas9-mediated target methylation can be stably maintained after cell division. • CRISPR/Cas9-directed epigenetic silencing of desired gene has potential application in cancer epigenome. [ABSTRACT FROM AUTHOR]

One gene does not equal one RNA or protein. The genomic revolution has revealed numerous different RNA and protein molecules that can be produced from one gene, such as circular RNAs generated by back-splicing, proteins with residues mismatching the genomic encoding because of RNA editing, and proteins extended in the C terminus via stop codon readthrough in translation. Are these diverse products results of exquisite gene regulations or imprecise biological processes? While there are cases where the gene product diversity appears beneficial, genome-scale patterns suggest that much of this diversity arises from nonadaptive, molecular errors. This finding has important implications for studying the functions of diverse gene products and for understanding the fundamental properties and evolution of cellular life. Patterns of gene product diversity suggest that the diversity arises mostly from nonadaptive, molecular errors in gene expression. That gene product diversity largely arises from molecular errors requires the diversity to be considered nonadaptive unless proven otherwise. Natural selection against molecular error is a main force shaping genome-wide trends of features of gene expression. Abundant molecular errors in the expression of genetic information contrast the commonly depicted picture of an orderly and harmonious cellular life, requiring considering the roles of molecular errors in biology, medicine, and evolution. [ABSTRACT FROM AUTHOR]

The histone variant H2A.Z has been extensively studied to understand its manifold DNA-based functions. In the past years, researchers identified its specific binding partners, the 'H2A.Z interactome', that convey H2A.Z-dependent chromatin changes. Here, we summarize the latest findings regarding vertebrate H2A.Z-associated factors and focus on their roles in gene activation and repression, cell cycle regulation, (neuro)development, and tumorigenesis. Additionally, we demonstrate how protein–protein interactions and post-translational histone modifications can fine-tune the complex interplay of H2A.Z-regulated gene expression. Last, we review the most recent results on interactors of the two isoforms H2A.Z.1 and H2A.Z.2.1, which differ in only three amino acids, and focus on cancer-associated mutations of H2A and H2A.Z, which reveal fascinating insights into the functional importance of such minuscule changes. H2A.Z is involved in gene activation and repression, partly through interaction with post-translational modification (PTM) writer and eraser complexes (directly or through mediators). Focusing on PTMs with regard to the histone code hypothesis and the H2A.Z interactome will shed light on H2A.Z's multitude of functions. More studies display distinct functions for H2A.Z.1 and H2A.Z.2.1 partly through specific interactors, even though they only differ in three amino acids. Focusing on how their binding specificity is achieved will highlight the importance of every amino acid. H2A.Z and its interactors [e.g., PWWP Domain Containing 2A (PWWP2A) and ZNF512B] are emerging as novel regulators in early development and neurodevelopment, associate with diseases as well as cancer development, and offer new therapeutic potential. [ABSTRACT FROM AUTHOR]

In eukaryotic cells, the process of gene expression is confined to the nucleus and enabled by multisubunit RNA polymerases (RNAPs). Many viruses make use of the host cellular gene expression apparatus during infection, and hence transfer their genome at least transiently to the host nucleus. However, poxviruses have evolved a different strategy to propagate. Their double-stranded DNA genome is transcribed in the host cytoplasm by a virus-encoded RNAP (vRNAP), which is evolutionarily related to eukaryotic RNA polymerase II. In this Review, we highlight recent high-resolution structures of the poxviral transcription apparatus in different phases of action. These structures, along with biochemical data, now allow the definition of a comprehensive model of poxviral gene expression and its regulation. Poxviruses possess a unique transcription system that works independently from the host nuclear transcription apparatus. The poxviral mRNA is co-transcriptionally capped and polyadenylated and hence can be converted into protein by the translation system of the host. Single particle cryo-electron microscopy has enabled insight into atomic details of the poxviral transcription apparatus and its phylogenetic origin. The enzymatic core of the poxviral transcription system is homologous to eukaryotic multisubunit polymerases, but accessory factors deviate vastly in their function and architecture. Recently solved structures revealed poxviral transcription intermediates that have not (yet) been observed for nuclear polymerases. Structures of poxviral transcription intermediates are attractive targets for rational drug design. [ABSTRACT FROM AUTHOR]

The cAMP response element binding protein 1 (CREB1) is an important nuclear transcription factor in eukaryotes. To explore the potential role of CREB1 on Qinchuan bovine skeletal myoblasts, we investigated the function of CREB1 on proliferation and differentiation. In this study, we found that CREB1 promoted cell proliferation by promoting DNA synthesis in S phase and cell division in G2 phase and promoted myogenic differentiation process in bovine myoblasts. Through dual luciferase experiments, we found that CREB1 can bind to the proximal promoter regions of CCNA2 and MyoG , indicating that CREB1 can play a positive regulatory role in the proliferation and differentiation of myoblasts by mediating the transcription of CCNA2 and MyoG. In addition, through downstream target gene analysis and transcriptome sequencing, we found that CREB1 plays a role in cell proliferation, myogenic differentiation, skeletal muscle repair and other related pathways. [ABSTRACT FROM AUTHOR]

Previously, the Nine amino acid TransActivation Domain (9aaTAD) was identified in the Gal4 region 862–870 (DDVYNYLFD). Here, we identified 9aaTADs in the distal Gal4 orthologs by our prediction algorithm and found their conservation in the family. The 9aaTAD function as strong activators was demonstrated. We identified adjacent Gal4 region 871–811 (DEDTPPNPKKE) as a natural 9aaTAD inhibitory domain located at the extreme Gal4 terminus. Moreover, we identified conserved Gal4 region 172–185 (FDWSEEDDMSDGLP), which was capable to reverse the 9aaTAD inhibition. In conclusion, our results uncover the existence of the cryptic inhibitory domains, which need to be carefully implemented in all functional studies with transcription factors to avoid incorrect conclusions. • Gal4 9aaTAD could be inhibited by adjacent region 862–870 (DEDTPPNPKKE). • The inhibited Gal4 9aaTAD could be reactivated by region 172–185 (FDWSEEDDMSDGLP). • The 9aaTAD activation domains could be identified by our 9aaTAD online prediction algorithm. [ABSTRACT FROM AUTHOR]

In vitro plant culture paves the way for meeting the industrial demand of pharmaceutically valuable secondary metabolites. This study intends to monitor how callus cells of Cannabis indica respond to the simulated microgravity (clinorotation; a Man-made technology). Callus initiation resulted from the culture of the leaf explant in a medium supplemented with kinetin (0.5 mgL−1) and 2, 4-D (2 mgL−1). Calli were treated with microgravity at three exposure times (0, 3, and 5 days). The microgravity treatments increased callus biomass about 2.5-fold. The clinorotation treatments transcriptionally induced the olivetolic acid cyclase (OAC) and olivetol synthase (OLS) genes about 6.2-fold. The tetrahydrocannabinolic acid synthase (THCAS) and cannabidiolic acid synthase (CBDAS) genes displayed a similar upward trend in response to microgravity. The applied treatments also stimulated the expression of the ethylene-responsive element-binding proteins (ERF1B) and WRKY1 transcription factors by an average of 7.6-fold. Moreover, the simulated microgravity triggered epigenetic modification in the DNA methylation profile. The HPLC-based assessment validated the high efficacy of the clinorotation treatments to increase the concentration of cannabinoids, including Cannabigerol (CBG) and Cannabidiol (CBD). However, the clinorotated calli contained a lower concentration of Tetrahydrocannabinol (THC) than the control group. The microgravity treatments increased concentrations of proline (79%), soluble sugars (61.3%), and proteins (21.4%) in calli. The biochemical assessment revealed that the clinorotation treatments slightly increased H 2 O 2 concentration. The upregulation in the activities of peroxidase, catalase, and phenylalanine ammonia-lyase enzymes resulted from the microgravity treatments. Both HPLC and molecular assessments validated the significant efficacy of microgravity to enhance the production of cannabinoids. • The simulated microgravity epigenetically influenced DNA methylome. • Microgravity enhanced the production efficacy of cannabinoids (CBD and CBG). • The clino-rotation treatment improved the callogenesis performance in cannabis. • The involvements of WRKY1 and ERF1B in microgravity signaling are addressed. [ABSTRACT FROM AUTHOR]

[Display omitted] • We constructed a ubiquitination pathway model for Haemonchus contortus. • Conservation, variation and transcription/expression of genes/gene products in this pathway were explored. • Structure modelling of proteins was performed using a machine learning method. • Prospects for fundamental and applied investigations are discussed. The ubiquitin-mediated pathway has been comprehensively explored in the free-living nematode Caenorhabditis elegans , but very little is known about this pathway in parasitic nematodes. Here, we inferred the ubiquitination pathway for an economically significant and pathogenic nematode – Haemonchus contortus – using abundant resources available for C. elegans. We identified 215 genes encoding ubiquitin (Ub; n = 3 genes), ubiquitin-activating enzyme (E1; one), -conjugating enzymes (E2s; 21), ligases (E3s; 157) and deubiquitinating enzymes (DUBs; 33). With reference to C. elegans , Ub, E1 and E2 were relatively conserved in sequence and structure, and E3s and DUBs were divergent, likely reflecting functional and biological uniqueness in H. contortus. Most genes encoding ubiquitination pathway components exhibit high transcription in the egg compared with other stages, indicating marked protein homeostasis in this early developmental stage. The ubiquitination pathway model constructed for H. contortus provides a foundation to explore the ubiquitin–proteasome system, crosstalk between autophagy and the proteasome system, and the parasite-host interactions. Selected E3 and DUB proteins which are very divergent in sequence and structure from host homologues or entirely unique to H. contortus and related parasitic nematodes may represent possible anthelmintic targets. [ABSTRACT FROM AUTHOR]

Cells experiencing proteotoxic stress downregulate the expression of thousands of active genes and upregulate a few stress-response genes. The strategy of downregulating gene expression has conceptual parallels with general lockdown in the global response to the coronavirus disease 2019 (COVID-19) pandemic. The mechanistic details of global transcriptional downregulation of genes, termed stress-induced transcriptional attenuation (SITA), are only beginning to emerge. The reduction in RNA and protein production during stress may spare proteostasis capacity, allowing cells to divert resources to control stress-induced damage. Given the relevance of translational downregulation in a broad variety of diseases, the role of SITA in diseases caused by proteotoxicity should be investigated in future, paving the way for potential novel therapeutics. Acute proteotoxic stress such as heat shock causes significant transcriptional downregulation of about 50–80% of active genes along with upregulation of 2–4% genes in fly, mouse, and human genomes. The large-scale transcriptional downregulation or stress-induced transcriptional attenuation (SITA) is not dependent on heat-shock factor (HSF), the transcription factor that is critical for upregulation of stress-response genes. SITA is regulated at the level of RNA polymerase II elongation in mammalian cells, likely, but not exclusively during transition of promoter-proximal Pol II into elongation phase controlled by negative elongation factor (NELF). NELF forms stress-inducible biomolecular condensates that may facilitate rapid transcriptional downregulation upon stress; the NELF condensates are similar to cytosolic stress granules in terms of stress inducibility and role in downregulation of gene expression. [ABSTRACT FROM AUTHOR]

[Display omitted] • 39 full length MADS box genes were identified from C. sativus transcriptome database. • CstMADS19 encodes an Agamous gene and positively regulates apocarotenoid biosynthesis in Crocus by binding to promoters of pathway genes. • CstMADS19 physically interacts with CstMADS26 and both the genes co-regulate apocarotenoid biosynthesis. Flowers of Crocus sativus L. are immensely important not only for arrangement of floral whorls but more because each floral organ is dominated by a different class of specialized compounds. Dried stigmas of C. sativus flowers form commercial saffron, and are known to accumulate unique apocarotenoids like crocin, picrocrocin and safranal. Inspite of being a high value crop, the molecular mechanism regulating flower development in Crocus remains largely unknown. Moreover, it would be very interesting to explore any co-regulatory mechanism which controls floral architecture and secondary metabolic pathways which exist in specific floral organs. Here we report transcriptome wide identification of MADS box genes in Crocus. A total of 39 full length MADS box genes were identified among which three belonged to type I and 36 to type II class. Phylogeny classified them into 11 sub-clusters. Expression pattern revealed some stigma up-regulated genes among which CstMADS19 encoding an AGAMOUS gene showed high expression. Transient over-expression of CstMADS19 in stigmas of Crocus resulted in increased crocin by enhancing expression of pathway genes. Yeast one hybrid assay demonstrated that CstMADS19 binds to promoters of phytoene synthase and carotenoid cleavage dioxygenase 2 genes. Yeast two hybrid and BiFC assays confirmed interaction of CstMADS19 with CstMADS26 which codes for a SEPALATA gene. Co-overexpression of CstMADS19 and CstMADS26 in Crocus stigmas enhanced crocin content more than was observed when genes were expressed individually. Collectively, these findings indicate that CstMADS19 functions as a positive regulator of stigma based apocarotenoid biosynthesis in Crocus. [ABSTRACT FROM AUTHOR]

In the field of molecular diagnostics, the demand for multiplex detection, aimed at reducing overall analysis costs and streamlining procedures, is on the rise, prompting ongoing developments in various technologies. In this study, we developed a novel system, the split T7 promoter-based three-way junction-transcription, coupled with Cas12a/Blocker DNA (T3-CaB), for the multiplex detection of target nucleic acids. The T3-CaB system builds upon the foundation of the T3 system, generating numerous RNA transcripts upon encountering target nucleic acids. Subsequently, these RNA transcripts displace the blocker DNA from reporter DNA, allowing active Cas12a to engage in efficient trans -cleavage reaction on the reporter DNA, resulting in a strong fluorescence signal. Importantly, the proposed system operates at the isothermal condition (37 °C), with the entire analysis completed within 90 min. Further, the detection performance of the proposed system surpasses that of the preceding Cas12a/Blocker DNA system. Model targets, namely the 16S rRNA of Staphylococcus aureus and Escherichia coli , were selected, and a successful demonstration of multiplex detection was achieved. This technology holds promise for broadening the applicability of CRISPR/Cas-based diagnostics, especially in settings necessitating multiplex detection capabilities. [Display omitted] • The optimal blocker DNA is screened in the CaB system by the systematic investigation. • The detection performance surpasses that of the preceding CaB system. • It demonstrates compatibility with various reporters, such as FAM and Cy5. • The T3-CaB system enables simultaneous detection of multiple nucleic acids. • It operates at the isothermal condition, with the entire analysis completed within 90 min. [ABSTRACT FROM AUTHOR]

• G9a deficiency alleviates renal fibrosis through inhibiting ferroptosis. • Slc7a11 is identified as the direct target of G9a. • G9a interacts with transcriptional factor bach1 through IP-MS. • G9a mediated Slc7a11 transcription through impairs the methyltransferase of histones H3K9 on the promoter region of Slc7a11. A high percentage of individuals with renal fibrosis are susceptible to developing chronic kidney disease (CKD), and conventional therapy fails to halt the progression of renal fibrosis and CKD. Here, we assessed the potential functions of G9a in a unilateral ureteral obstruction (UUO)-induced renal fibrosis mouse model. The expression of G9a was significantly increased in the fibrotic kidneys of patients and mice. G9a knockout inhibited inflammatory cytokine production and collagen deposition in mice, whereas its overexpression aggravated renal fibrosis in mice. In vitro , the knockdown of G9a alleviated the production of inflammatory cytokines and renal fibrosis. G9a, a histone methyltransferase, interacts with transcription factor Bach1 and activates ferroptosis by suppressing the transcription of Slc7a11 via dimethylation of histone 3 lysine 9 (H3K9me2) both in vivo and in vitro. Collectively, our findings indicate that G9a could be an attractive therapeutic target for renal fibrosis. [ABSTRACT FROM AUTHOR]

Gastric cancer and diabetes are two complex and interrelated diseases having significant impact on global health. Hyperglycemic condition notably exacerbates cancer by promoting inflammation, angiogenesis, and metastasis. Elevated glucose levels can also upregulate the expression of specific matrix metalloproteinases (MMPs), especially MMP-9, which is associated with cancer cell migration and invasion. However, the molecular mechanism behind such upregulation remains unexplored. In the present study, we have identified the mechanism for hyperglycemia-induced transcriptional activation of MMP-9, in gastric adenocarcinoma (AGS) cells. Using various tools like luciferase-reporter assays with promoter deletion constructs, siRNAs, pharmacological inhibitors, and nuclear translocation experiments, we have identified that the transcriptional activation of MMP-9 under hyperglycemic conditions is predominantly governed by the MAPK pathway, via formation of the AP-1 heterodimer. The p65 NF-κB signaling pathway, although activated, plays no significant role in regulating hyperglycemia-induced MMP-9 expression. Chromatin immunoprecipitation studies indicate that the distal AP-1 binding site is responsible for hyperglycemia-induced MMP-9 transcription; whereas the proximal one accounts for both hyperglycemia-induced and basal MMP-9 transcription. Therefore, binding of AP-1 at both the proximal and distal binding sites on the MMP-9 promoter region is required for hyperglycemia-induced MMP-9 expression. Overall, our study unveils a novel mechanism of MMP-9 transcription under hyperglycemic conditions and also suggests that inhibiting the binding of the AP-1 heterodimer with its distal binding site can potentially reduce the complications developed during gastric cancer-hyperglycemia co-morbidity. A drug designed specifically to inhibit this interaction may prevent hyperglycemia-induced tumor aggressiveness to a considerable extent by impeding MMP-9 transcription. • Hyperglycemia-induced upregulation of MMP-9 is independent of p65 NF-κB pathway and dependent on AP-1 • AP-1 binding to its proximal site on the MMP-9 promoter regulates basal as well as hyperglycemia-induced MMP-9 expression • Distal AP-1 binding site is activated upon hyperglycemia induction and regulates hyperglycemia-induced MMP-9 transcription • Targeting AP-1 binding to the distal binding site may reduce the effect of hyperglycemia on MMP-9 transcription [ABSTRACT FROM AUTHOR]

Studying Rhodococcus erythropolis stress response is of significant scientific interest, since this microorganism is widely used for bioremediation of oil-contaminated sites and is essential for environmental biotechnology. In addition, much less data was published on molecular mechanisms of stress resistance and adaptation to effects of pollutants for Gram-positive oil degraders compared to Gram-negative ones. This study provided an assessment of changes in the transcription level of the soxR , sodA , sodC , oxyR , katE , katG , recA , dinB , sigF, sigH genes in the presence of decane, hexadecane, cyclohexane, benzene, naphthalene, anthracene and diesel fuel. Judging by the changes in the expression of target genes, hydrocarbons as the main carbon source caused oxidative stress in R. erythropolis cells, which resulted in DNA damage. It was documented by enhanced transcription of genes encoding antioxidant enzymes (superoxide dismutase and catalase), SOS response, DNA polymerase IV, and sigma factors of RNA polymerase SigH and SigF. At this, it was likely that in the presence of hydrocarbons, transcription of catalase genes (katE and katG) was coordinated primarily by the sigF regulator. • Alkanes and naphthralene cause superoxide stress in R. erythropolis cells. • Cyclohexane, naphthalene and diesel cause peroxide stress. • Significant SOS induction is caused by diesel and decane. • Benzene and naphthalene cause the strong levels of dinB transcription. • katE and katG expression under hydrocarbon stress is probably sigF -regulated. [ABSTRACT FROM AUTHOR]

● With the rapid development of new breeding techniques, the ecological impacts of transgenic plants receive wide concern again, particularly for potential gene flow from transgenic crops to their relatives. The transgene insertion position, number of gene copies, and flanking sequence of exogenous genes integrated into the recipient genome affect the genetic stability and fitness of offspring. ● We employed hybrids F 1 and F 2 , six backcross generations BC 1 -BC 6 and BC 1 F 1 from transgenic Brassica napus with Bacillus thuringiensis (Bt) cry1Ac gene and its wild relative B. juncea through hand pollination. We detected exogenous gene copies, mRNA transcription, and protein expression by ddPCR, qRT-PCR and ELISA, and the fitness of hybrid and backcross generations. ● Exogenous genes followed Mendelian segregation expectations in hybrid and backcrossed generations, with stable gene copies, mRNA transcription and protein concentration of exogenous genes in offspring. Exogenous gene copies had no significant effects on plant fitness, but had positive effects on mRNA transcription and protein concentration that varied with growth stages in hybrid and backcross generations. ● Our study demonstrated inheritance and ecological effects of exogenous genes from transgenic plants to wild relatives, which will help ecological risk management of biotechnological plants released in the nature. • Performance of cry1Ac gene in offspring of transgenic Brassica napus and its wild relative Brassica juncea is studied. • Exogenous genes followed Mendelian segregation expectations in hybrid and backcrossed generations. • Exogenous gene copies had effects on mRNA transcription and protein concentration in hybrid and backcross generations. [ABSTRACT FROM AUTHOR]