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mRNA accessibility within messenger ribonucleoproteins (mRNPs), in contrast to DNA accessibility within chromatin, has not yet been well established as an important determinant of gene expression. Recent work has revealed the importance of the exon junction complex (EJC) as an architectural protein complex that controls mRNP packaging. An important function of EJC-mediated mRNP packaging is to regulate m6A specificity. Structures of nuclear mRNP globules reveal an architecture in which EJCs reside within the inaccessible interior of globules. mRNA exon architecture may be a determinant of mRNA accessibility due to EJC-mediated mRNP packaging. Gene expression is a complex process requiring many control mechanisms to achieve a desired phenotype. DNA accessibility within chromatin is well established as an important determinant of gene expression. By contrast, while mRNA also associates with a complement of proteins, the exact nature of messenger ribonucleoprotein (mRNP) packaging and its functional relevance is not as clear. Recent reports indicate that exon junction complex (EJC)-mediated mRNP packaging renders exon junction-proximal regions inaccessible for m6A methylation, and that EJCs reside within the inaccessible interior of globular transcription and export (TREX) complex-associated nuclear mRNPs. We propose that 'mRNA accessibility' within mRNPs is an important determinant of gene expression that may modulate the specificity of a broad array of regulatory processes including but not limited to m6A methylation. [ABSTRACT FROM AUTHOR]

N6‐methyladenosine (m6A) in messenger RNA (mRNA) regulates immune cells in homeostasis and in response to infection and inflammation. The function of the m6A reader YTHDF2 in the tumor microenvironment (TME) in these contexts has not been explored. We discovered that the loss of YTHDF2 in regulatory T (Treg) cells reduces tumor growth in mice. Deletion of Ythdf2 in Tregs does not affect peripheral immune homeostasis but leads to increased apoptosis and impaired suppressive function of Treg cells in the TME. Elevated tumor necrosis factor (TNF) signaling in the TME promotes YTHDF2 expression, which in turn regulates NF‐κB signaling by accelerating the degradation of m6A‐modified transcripts that encode NF‐κB‐negative regulators. This TME‐specific regulation of Treg by YTHDF2 points to YTHDF2 as a potential target for anti‐cancer immunotherapy, where intratumoral Treg cells can be targeted to enhance anti‐tumor immune response while avoiding Treg cells in the periphery to minimize undesired inflammations. Synopsis: The RNA m6A‐binding protein YTHDF2 regulates NF‐κB signaling to maintain intratumoral Treg survival and function.Deletion of Ythdf2 in Treg cells delays tumor development in mice while maintaining peripheral homeostasis.Ythdf2‐deficient Treg cells have reduced infiltration capacity and impaired function.TNF/NF‐κB signaling elevates the expression of YTHDF2.YTHDF2 accelerates the decay of m6A‐modified transcripts encoding NF‐κB‐negative regulators. [ABSTRACT FROM AUTHOR]

Over 70% land plants live in mutualistic symbiosis with arbuscular mycorrhizal (AM) fungi, and maintenance of symbiosis requires transcriptional and post‐transcriptional regulation. The former has been widely studied, whereas the latter mediated by symbiotic microRNAs (miRNAs) remains obscure, especially in woody plants. Here, we performed high‐throughput sequencing of the perennial woody citrus plant Poncirus trifoliata and identified 3750 differentially expressed genes (DEGs) and 42 miRNAs (DEmiRs) upon AM fungal colonization. By analyzing cis‐regulatory elements in the promoters of the DEGs, we predicted 329 key AM transcription factors (TFs). A miRNA‐mRNA regulatory network was then constructed by integrating these data. Several candidate miRNA families of P. trifoliata were identified whose members target known symbiotic genes, such as miR167h‐AMT2;3 and miR156e‐EXO70I, or key TFs, such as miR164d‐NAC and miR477a‐GRAS, thus are involved in AM symbiotic processes of fungal colonization, arbuscule development, nutrient exchange and phytohormone signaling. Finally, analysis of selected miRNA family revealed that a miR159b conserved in mycorrhizal plant species and a Poncirus‐specific miR477a regulate AM symbiosis. The role of miR477a was likely to target GRAS family gene RAD1 in citrus plants. Our results not only revealed that miRNA‐mRNA network analysis, especially miRNA‐TF analysis, is effective in identifying miRNA family regulating AM symbiosis, but also shed light on miRNA‐mediated post‐transcriptional regulation of AM symbiosis in woody citrus plants. Summary statement: In our study, we integrated miRNA with mRNA analysis, especially specific miRNA‐TF co‐expression node analysis, and attempted to reveal the regulatory links between transcriptional and post‐transcriptional regulatory mechanisms involved in AM symbiosis of woody citrus plants. [ABSTRACT FROM AUTHOR]

Simple Summary: Current treatment strategies for pancreatic cancer (PC) yield poor survival outcomes. It is thus essential to identify factors that orchestrate pancreatic tumorigenesis and contribute to therapeutic resistance. Fat mass and obesity-associated protein (FTO) play a crucial role in demethylating N6-methyladenosine (a known and prevalent modification in eukaryotic RNA). Notably, recent pioneering studies have identified a significant association of FTO overexpression with the cancer progression of various types. Nevertheless, our current understanding of the role of FTO in modulating biological processes relevant to PC is in its infancy. We demonstrate that PC cells expressed higher FTO levels than the normal pancreatic ductal epithelial (HPDE) cells. Furthermore, both lentiviral-mediated genetic and CS1-mediated pharmacological inhibition of FTO impaired PC cell growth, survival, migratory, and invasiveness capabilities. Additionally, FTO loss led to the reversal of EMT traits, impaired tumorsphere formation, and reduced the expression of cancer stem cells (CSC) markers. In agreement, FTO-depleted PC cells displayed impaired tumorigenic capability in a xenograft model. Our study thus demonstrates the functional importance of FTO overexpression in the PC tumorigenicity and maintenance of CSCs via EMT regulation. Therefore, FTO may represent an attractive therapeutic target for PC. N6-methyladenosine (m6A) is the most prevalent post-transcriptional RNA modification regulating cancer self-renewal. However, despite its functional importance and prognostic implication in tumorigenesis, the relevance of FTO, an m6A eraser, in pancreatic cancer (PC) remains elusive. Here, we establish the oncogenic role played by FTO overexpression in PC. FTO is upregulated in PC cells compared to normal human pancreatic ductal epithelial (HPDE) cells. Both RNAi depletion and CS1-mediated pharmacological inhibition of FTO caused a diminution of PC cell proliferation via cell cycle arrest in the G1 phase and p21cip1 and p27kip1 induction. While HPDE cells remain insensitive to CS1 treatment, FTO overexpression confers enhancements in growth, motility, and EMT transition, thereby inculcating tumorigenic properties in HPDE cells. Notably, shRNA-mediated FTO depletion in PC cells impairs their mobility and invasiveness, leading to EMT reversal. Mechanistically, this was associated with impaired tumorsphere formation and reduced expression of CSCs markers. Furthermore, FTO depletion in PC cells weakened their tumor-forming capabilities in nude mice; those tumors had increased apoptosis, decreased proliferation markers, and MET conversion. Collectively, our study demonstrates the functional importance of FTO in PC and the maintenance of CSCs via EMT regulation. Thus, FTO may represent an attractive therapeutic target for PC. [ABSTRACT FROM AUTHOR]

RNA carries a diverse array of chemical modifications that play important roles in the regulation of gene expression. N6‐methyladenosine (m6A), installed onto mRNA by the METTL3/METTL14 methyltransferase complex, is the most prevalent mRNA modification. m6A methylation regulates gene expression by influencing numerous aspects of mRNA metabolism, including pre‐mRNA processing, nuclear export, decay, and translation. The importance of m6A methylation as a mode of post‐transcriptional gene expression regulation is evident in the crucial roles m6A‐mediated gene regulation plays in numerous physiological and pathophysiological processes. Here, we review current knowledge on the mechanisms by which m6A exerts its functions and discuss recent advances that underscore the multifaceted role of m6A in the regulation of gene expression. We highlight advances in our understanding of the regulation of m6A deposition on mRNA and its context‐dependent effects on mRNA decay and translation, the role of m6A methylation of non‐coding chromosomal‐associated RNA species in regulating transcription, and the activities of the RNA demethylase FTO on diverse substrates. We also discuss emerging evidence for the therapeutic potential of targeting m6A regulators in disease. [ABSTRACT FROM AUTHOR]

Objective: To investigate the roles of integrin‐linked kinase (ILK) in mediating the cell migration, proliferation, and apoptosis of human periodontal ligament cells (hPDLCs) in response to cyclic tensile stress. Methods: Primary hPDLCs were obtained through the enzyme digestion and tissue culture method. Short hairpin ILK‐expressing hPDLCs were constructed using a recombinant lentiviral vector that specifically targeted ILK gene expression. The silencing of the ILK gene was identified by quantitative real‐time polymerase chain reaction (qRT‐PCR) and Western blot. The hPDLCs were seeded on a flexible substrate and loaded with cyclic tensile stress at 0.5 Hz for 0, 2, 4, and 8 hr, consecutively, with the Flexcell Tension System. The response of cell migration was tested by the scratch assay. Cell proliferation was characterized by optical density (OD) value of cell counting kit‐8 (CCK‐8) test and Ki67 mRNA expression of qRT‐PCR. Cell apoptosis was determined by flow cytometry and Caspase‐3 mRNA expression of qRT‐PCR. Results: Knocking down ILK substantially reduces migration and proliferation as well as regulates the sensitivity of hPDLCs to apoptosis under cyclic tensile stress. Conclusions: ILK can promote the proliferation and migration as well as inhibit apoptosis of hPDLCs under cyclic tensile stress. [ABSTRACT FROM AUTHOR]

Osteoarthritis (OA) is an aseptic inflammatory disease which is associated with the stromal cell-derived factor 1/C-X-C chemokine receptor type 4 (SDF-1/CXCR4) axis. Accumulating studies have identified numbers of microRNAs (miRNAs) that serve important roles in the pathogenesis of OA. However, whether and how the inhibition of the SDF-1/CXCR4 axis induces alterations in miRNA expression remains largely unclear. miRNA profiling was performed in OA chondrocytes stimulated with SDF-1 alone, or SDF-1 with the CXCR4 antagonist TN14003 by miRNA microarray. Candidate miRNAs were verified by reverse transcription quantitative polymerase chain reaction. Bioinformatic analyses including target prediction, gene ontology (GO) and pathway analysis were performed to explore the potential functions of candidate miRNAs. Notably, 7 miRNAs (miR-146a-5p, miR-221-3p, miR-126-3p, miR-185-5p, miR-155-5p, miR-124-3p and miR-130a-3p) were significantly differentially expressed. GO analysis indicated that miR-146a-5p and its associated genes were enriched in receptor regulatory activity, nuclear factor-kappa-light-chain-enhancer of activated B cells (NF-κB)-inducing kinase activity, cellular response to interleukin-1, cytokine-cytokine receptor interaction, NF-κB signaling pathway and osteoclast differentiation pathways. CXCR4 was predicted to be a target of miR-146a-5p with high importance. The mRNA and protein levels of key factors involved in cartilage degeneration were measured following manipulation of the expression levels of miR-146a-5p in OA chondrocytes. CXCR4 and MMP-3 levels were negatively associated with miR-146a-5p expression, while the levels of type II collagen and aggrecan were positively associated. These data reveal that TN14003 upregulates miR-146a-5p expression, and also pinpoints a novel role of miR-146a-5p in inhibiting cartilage degeneration by directly targeting the SDF-1/CXCR4 axis. [ABSTRACT FROM AUTHOR]

Inhibition of osteoclasts formation and bone resorption by estrogen is very important in the etiology of postmenopausal osteoporosis. The mechanisms of this process are still not fully understood. Recent studies implicated an important role of microRNAs in estrogen‐mediated responses in various cellular processes, including cell differentiation and proliferation. Thus, we hypothesized that these regulatory molecules might be implicated in the process of estrogen‐decreased osteoclasts formation and bone resorption. Western blot, quantitative real‐time polymerase chain reaction, tartrate‐resistant acid phosphatase staining, pit formation assay and luciferase assay were used to investigate the role of microRNAs in estrogen‐inhibited osteoclast differentiation and bone resorption. We found that estrogen could directly suppress receptor activator of nuclear factor B ligand/macrophage colony‐stimulating factor‐induced differentiation of bone marrow‐derived macrophages into osteoclasts in the absence of stromal cell. MicroRNA‐27a was significantly increased during the process of estrogen‐decreased osteoclast differentiation. Overexpressing of microRNA‐27a remarkably enhanced the inhibitory effect of estrogen on osteoclast differentiation and bone resorption, whereas which were alleviated by microRNA‐27a depletion. Mechanistic studies showed that microRNA‐27a inhibited peroxisome proliferator‐activated receptor gamma (PPARγ) and adenomatous polyposis coli (APC) expression in osteoclasts through a microRNA‐27a binding site within the 3′‐untranslational region of PPARγ and APC. PPARγ and APC respectively contributed to microRNA‐27a‐decreased osteoclast differentiation and bone resorption. Taken together, these results showed that microRNA‐27a may play a significant role in the process of estrogen‐inhibited osteoclast differentiation and function. First, we found that microRNA‐27a was significantly increased during the process of estrogen‐decreased osteoclast differentiation. Second, overexpressing of microRNA‐27a remarkably enhanced the inhibitory effect of estrogen on osteoclasts formation and bone resorption, whereas which were alleviated by microRNA‐27a depletion. Third, estrogen might respectively decrease osteoclast differentiation and bone resorption via miR‐27a targeting peroxisome proliferator‐activated receptor gamma and adenomatous polyposis coli. Our results indicate that microRNA‐27a may play a significant role in the process of estrogen‐inhibited osteoclast differentiation and function. [ABSTRACT FROM AUTHOR]

Methylation at the N6 position of adenosine (m6A) is a highly prevalent and reversible modification within eukaryotic mRNAs that has been linked to many stages of RNA processing and fate. Recent studies suggest that m6A deposition and proteins involved in the m6A pathway play a diverse set of roles in either restricting or modulating the lifecycles of select viruses. Here, we report that m6A levels are significantly increased in cells infected with the oncogenic human DNA virus Kaposi’s sarcoma-associated herpesvirus (KSHV). Transcriptome-wide m6A-sequencing of the KSHV-positive renal carcinoma cell line iSLK.219 during lytic reactivation revealed the presence of m6A across multiple kinetic classes of viral transcripts, and a concomitant decrease in m6A levels across much of the host transcriptome. However, we found that depletion of the m6A machinery had differential pro- and anti-viral impacts on viral gene expression depending on the cell-type analyzed. In iSLK.219 and iSLK.BAC16 cells the pathway functioned in a pro-viral manner, as depletion of the m6A writer METTL3 and the reader YTHDF2 significantly impaired virion production. In iSLK.219 cells the defect was linked to their roles in the post-transcriptional accumulation of the major viral lytic transactivator ORF50, which is m6A modified. In contrast, although the ORF50 mRNA was also m6A modified in KSHV infected B cells, ORF50 protein expression was instead increased upon depletion of METTL3, or, to a lesser extent, YTHDF2. These results highlight that the m6A pathway is centrally involved in regulating KSHV gene expression, and underscore how the outcome of this dynamically regulated modification can vary significantly between cell types. [ABSTRACT FROM AUTHOR]

The N 6-methyladenosine (m6A) modification is a highly conserved RNA modification found in eukaryotic messenger RNAs (mRNAs). It plays a vital role in regulating various biological processes. Dysregulation of m6A modifications has been linked to a range of complex genetic diseases in humans. However, there has been a lack of comprehensive characterization and comparison of m6A modifications at the transcriptome-wide level within families. To address this gap, we profiled transcriptome-wide m6A methylation in 18 individuals across 6 Yoruba trio families. The m6A methylomes of these 18 individuals revealed that m6A modifications in children showed greater similarity to each other than to their parents. This suggests that m6A modifications are influenced by multiple factors rather than solely determined by genetic factors. Additionally, we found that mRNAs exhibiting m6A modifications specific to children were enriched in cell cycle control processes, while those with m6A modifications specific to parents were associated with chromatin modifications. Furthermore, our analysis on the interactions between differentially expressed m6A-related regulatory genes and age-related genes suggested that age might be one of the factors influencing m6A modifications. In summary, our study provided a valuable dataset that highlighted the differences and functional diversity of m6A modifications within and between trio families. [ABSTRACT FROM AUTHOR]

Osteoarthritis (OA) is one of the most common diseases affecting older people; however, there remains no effective targeted drug to combat OA. The aims of this study were (1) to explore the effect of T140 in regulating degeneration of articular cartilage in vivo by targeted blocking of the SDF-1/CXCR4 signaling pathway, and (2) to provide experimental evidence for the development of a novel OA-targeted pharmacotherapy. Thirty-six healthy Hartley guinea pigs were randomly divided into three groups: a T140-treated group (n = 12), a phosphate buffer saline control group (n = 12) and an untreated control group (n = 12). At 2, 4, 6, 8, 10 and 12 weeks of treatment, SDF-1 in serum was quantified by enzyme-linked immunosorbent assay. At 12 weeks of treatment, the cartilage from knee tibial plateau in the knee joint was collected for H&E, Safranin-O staining and Mankin grading; measurement for mRNA levels of matrix metalloproteinases (MMP-3, MMP-9 and MMP-13), aggrecan (ACAN) and collagen II (Col II) using RT-PCR; and measurement for Col II protein levels by western blot. Results showed that SDF-1 in serum increased in the T140 group and increased in the control groups. H&E and Safranin-O staining revealed less cartilage loss in T140-treated animals compared to controls. The mRNA levels of MMP-3, MMP-9 and MMP-13 in cartilage were much lower in the T140 group than other groups, but mRNA levels of ACAN and Col II in cartilage were higher in the T140-treated group. Col II protein levels in the T140 group and control groups were different. T140 can downregulate the expression of matrix-degrading enzyme and lessen the degeneration of cartilage by blocking the SDF-1/CRCR4 signaling pathway in vivo. This mechanism may present a pharmacological target for the treatment of OA. [ABSTRACT FROM AUTHOR]

RNA modifications have long been known to be central in the proper function of tRNA and rRNA. While chemical modifications in mRNA were discovered decades ago, their function has remained largely mysterious until recently. Using enrichment strategies coupled to next generation sequencing, multiple modifications have now been mapped on a transcriptome-wide scale in a variety of contexts. We now know that RNA modifications influence cell biology by many different mechanisms — by influencing RNA structure, by tuning interactions within the ribosome, and by recruiting specific binding proteins that intersect with other signaling pathways. They are also dynamic, changing in distribution or level in response to stresses such as heat shock and nutrient deprivation. Here, we provide an overview of recent themes that have emerged from the substantial progress that has been made in our understanding of chemical modifications across many major RNA classes in eukaryotes. [ABSTRACT FROM PUBLISHER]

The reprogramming of cellular memory in specific cell types, and in visceral adipocytes in particular, appears to be a fundamental aspect of obesity and its related negative health outcomes. We explored the hypothesis that adipose tissue contains epigenetically distinct subpopulations of adipocytes that are differentially potentiated to record cellular memories of their environment. Adipocytes are large, fragile, and technically difficult to efficiently isolate and fractionate. We developed fluorescence nuclear cytometry (FNC) and fluorescence activated nuclear sorting (FANS) of cellular nuclei from visceral adipose tissue (VAT) using the levels of the pan-adipocyte protein, peroxisome proliferator-activated receptor gamma-2 (PPARg2), to distinguish classes of PPARg2-Positive (PPARg2-Pos) adipocyte nuclei from PPARg2-Negative (PPARg2-Neg) leukocyte and endothelial cell nuclei. PPARg2-Pos nuclei were 10-fold enriched for most adipocyte marker transcripts relative to PPARg2-Neg nuclei. PPARg2-Pos nuclei showed 2- to 50-fold higher levels of transcripts encoding most of the chromatin-remodeling factors assayed, which regulate the methylation of histones and DNA cytosine (e.g., DNMT1, TET1, TET2, KDM4A, KMT2C, SETDB1, PAXIP1, ARID1A, JMJD6, CARM1, and PRMT5). PPARg2-Pos nuclei were large with decondensed chromatin. TAB-seq demonstrated 5-hydroxymethylcytosine (5hmC) levels were remarkably dynamic in gene bodies of various classes of VAT nuclei, dropping 3.8-fold from the highest quintile of expressed genes to the lowest. In short, VAT-derived adipocytes appear to be more actively remodeling their chromatin than non-adipocytes. [ABSTRACT FROM AUTHOR]

DNA methylation at selective cytosine residues (5-methylcytosine (5mC)) and their removal by TET-mediated DNA demethylation are critical for setting up pluripotent states in early embryonic development. TET enzymes successively convert 5mC to 5-hydroxymethylcytosine (5hmC), 5-formylcytosine (5fC), and 5-carboxylcytosine (5caC), with 5fC and 5caC subject to removal by thymine DNA glycosylase (TDG) in conjunction with base excision repair. Early reports indicate that 5fC and 5caC could be stably detected on enhancers, promoters and gene bodies, with distinct effects on gene expression, but the mechanisms have remained elusive. Here we determined the X-ray crystal structure of yeast elongating RNA polymerase II (Pol II) in complex with a DNA template containing oxidized 5mCs, revealing specific hydrogen bonds between the 5-carboxyl group of 5caC and the conserved epi-DNA recognition loop in the polymerase. This causes a positional shift for incoming nucleoside 5′-triphosphate (NTP), thus compromising nucleotide addition. To test the implication of this structural insight in vivo, we determined the global effect of increased 5fC/5caC levels on transcription, finding that such DNA modifications indeed retarded Pol II elongation on gene bodies. These results demonstrate the functional impact of oxidized 5mCs on gene expression and suggest a novel role for Pol II as a specific and direct epigenetic sensor during transcription elongation. [ABSTRACT FROM AUTHOR]

Cellular RNAs can be chemically modified over a hundred different ways. These modifications were once thought to be static, discrete, and utilized to fine-tune RNA structure and function. However, recent studies have revealed that some modifications, like mRNA methylation, can be reversed, and these reversible modifications may play active roles in regulating diverse biological processes. In this perspective, we summarize examples of dynamic RNA modifications that affect biological functions. We further propose that reversible modifications might occur on tRNA, rRNA, and other noncoding RNAs to regulate gene expression analogous to the reversible mRNA methylation. [ABSTRACT FROM AUTHOR]

Cellular RNAs carry diverse chemical modifications that used to be regarded as static and having minor roles in 'fine-tuning' structural and functional properties of RNAs. In this Review, we focus on reversible methylation through the most prevalent mammalian mRNA internal modification, N6-methyladenosine (m6A). Recent studies have discovered protein 'writers', 'erasers' and 'readers' of this RNA chemical mark, as well as its dynamic deposition on mRNA and other types of nuclear RNA. These findings strongly indicate dynamic regulatory roles that are analogous to the well-known reversible epigenetic modifications of DNA and histone proteins. This reversible RNA methylation adds a new dimension to the developing picture of post-transcriptional regulation of gene expression. [ABSTRACT FROM AUTHOR]

Epigenetic modifications influence gene expression without alterations to the underlying nucleic acid sequence. In addition to the well-known 5-methylcytosine (5mC), 5-hydroxymethylcytosine (5hmC), 5-formylcytosine (5fC), and 5-carboxycytosine (5caC) have recently been discovered in genomic DNA, which all result from iterative oxidation of 5mC by the TET (Ten-Eleven-Translocate) family of enzymes. Recent studies have proposed the roles of these oxidized cytosines in mediating active demethylation of 5mC. Through affinity-based genome-wide sequencing and oxidation-assisted base-resolution sequencing methods, 5hmC is found to be dynamically regulated during development, and is enriched mainly in distal regulatory elements in human and mouse embryonic cells. Among RNA modifications, N 6-methyladenosine (m6A) is a widespread yet poorly studied base modification in mRNA and non-coding RNA. The recent discovery that m6A in RNA is the major substrate of the fat mass and obesity associated (FTO) protein draws attention to the potential regulatory functions of reversible RNA methylations, which can be dynamic, and could be important in many fundamental cellular functions. [ABSTRACT FROM AUTHOR]

In bacterial two-component regulatory systems ( TCSs), dephosphorylation of phosphorylated response regulators is essential for resetting the activated systems to the pre-activation state. However, in the SaeRS TCS, a major virulence TCS of Staphylococcus aureus, the mechanism for dephosphorylation of the response regulator SaeR has not been identified. Here we report that two auxiliary proteins from the sae operon, SaeP and SaeQ, form a protein complex with the sensor kinase SaeS and activate the sensor kinase's phosphatase activity. Efficient activation of the phosphatase activity required the presence of both SaeP and SaeQ. When SaeP and SaeQ were ectopically expressed, the expression of coagulase, a sae target with low affinity for phosphorylated SaeR, was greatly reduced, while the expression of alpha-haemolysin, a sae target with high affinity for phosphorylated SaeR, was not, demonstrating a differential effect of SaePQ on sae target gene expression. When expression of SaePQ was abolished, most sae target genes were induced at an elevated level. Since the expression of SaeP and SaeQ is induced by the SaeRS TCS, these results suggest that the SaeRS TCS returns to the pre-activation state by a negative feedback mechanism. [ABSTRACT FROM AUTHOR]

Summary: MicroRNAs (miRNAs) control gene expression by promoting degradation or repressing translation of target mRNAs. The components of the miRNA pathway are subject to diverse modifications that can modulate the abundance and function of miRNAs. Iron is essential for fundamental metabolic processes, and its homeostasis is tightly regulated. Here we identified iron chelators as a class of activator of the miRNA pathway that could promote the processing of miRNA precursors. We show that cytosolic iron could regulate the activity of the miRNA pathway through poly(C)-binding protein 2 (PCBP2). PCBP2 is associated with Dicer and promotes the processing of miRNA precursors. Cytosolic iron could modulate the association between PCBP2 and Dicer, as well as the multimerization of PCBP2 and its ability to bind to miRNA precursors, which can alter the processing of miRNA precursors. Our findings reveal a role of iron homeostasis in the regulation of miRNA biogenesis. [ABSTRACT FROM AUTHOR]

One of the recent advances in the epigenetic field is the demonstration that the Tet family of proteins are capable of catalyzing conversion of 5-methylcytosine (5mC) of DNA to 5-hydroxymethylcytosine (5hmC). Interestingly, recent studies have shown that 5hmC can be further oxidized by Tet proteins to generate 5-formylcytosine (5fC) and 5-carboxylcytosine (5caC), which can be removed by thymine DNA glycosylase (TDG). To determine whether Tet-catalyzed conversion of 5mC to 5fC and 5caC occurs in vivo in zygotes, we generated antibodies specific for 5fC and 5caC. By immunostaining, we demonstrate that loss of 5mC in the paternal pronucleus is concurrent with the appearance of 5fC and 5caC, similar to that of 5hmC. Importantly, instead of being quickly removed through an enzyme-catalyzed process, both 5fC and 5caC exhibit replication-dependent dilution during mouse preimplantation development. These results not only demonstrate the conversion of 5mC to 5fC and 5caC in zygotes, but also indicate that both 5fC and 5caC are relatively stable and may be functional during preimplantation development. Together with previous studies, our study suggests that Tet-catalyzed conversion of 5mC to 5hmC/5fC/5caC followed by replication-dependent dilution accounts for paternal DNA demethylation during preimplantation development. [ABSTRACT FROM AUTHOR]

RNA interference (RNAi) is a well-conserved mechanism that uses small noncoding RNAs to silence gene expression posttranscriptionally. Gene regulation by RNAi is now recognized as one of the major regulatory pathways in eukaryotic cells. Although the main components of the RNAi/miRNA pathway have been identified, the molecular mechanisms regulating the activity of the RNAi/miRNA pathway have only begun to emerge within the last couple of years. Recently, high-throughput reporter assays to monitor the activity of the RNAi/miRNA pathway have been developed and used for proof-of-concept pilot screens. Both inhibitors and activators of the RNAi/miRNA pathway have been found. Although still in its infancy, a chemical biology approach using high-throughput chemical screens should open up a new avenue for dissecting the RNAi/miRNA pathway, as well as developing novel RNAi- or miRNA-based therapeutic interventions. [Copyright &y& Elsevier]

Small interfering RNAs (siRNAs) and microRNAs (miRNAs) are sequence-specific post-transcriptional regulators of gene expression. Although major components of the RNA interference (RNAi) pathway have been identified, regulatory mechanisms for this pathway remain largely unknown. Here we demonstrate that the RNAi pathway can be modulated intracellularly by small molecules. We have developed a cell-based assay to monitor the activity of the RNAi pathway and find that the small-molecule enoxacin (Penetrex) enhances siRNA-mediated mRNA degradation and promotes the biogenesis of endogenous miRNAs. We show that this RNAi-enhancing activity depends on the trans-activation-responsive region RNA-binding protein. Our results provide a proof-of-principle demonstration that small molecules can be used to modulate the activity of the RNAi pathway. RNAi enhancers may be useful in the development of research tools and therapeutics. [ABSTRACT FROM AUTHOR]

Hyperoxic acute lung injury (HALI) is characterized by a cell death response with features of apoptosis and necrosis that is inhibited by IL-11 and other interventions. We hypothesized that Bfl-1/A1, an antiapoptotic Bcl-2 protein, is a critical regulator of HALI and a mediator of IL-11-induced cytoprotection. To test this, we characterized the expression of Al and the oxygen susceptibility of WT and IL-11 Tg(+) mice with normal and null A1 loci. In WT mice, 100% O2 caused TUNEL+ cell death, induction and activation of intrinsic and mitochondrial-death pathways, and alveolar protein leak. Bcl-2 and Bcl-xl were also induced as an apparent protective response. Al was induced in hyperoxia, and in Al-null mice, the toxic effects of hyperoxia were exaggerated, Bcl-2 and Bcl-xl were not induced, and premature death was seen. In contrast, IL-11 stimulated A1, diminished the toxic effects of hyperoxia, stimulated Bcl-2 and Bcl-xl, and enhanced murine survival in 100% O2. In A1-null mice, IL-11-induced protection, survival advantage, and Bcl-2 and Bcl-xl induction were significantly decreased. VEGF also conferred protection via an A1-dependent mechanism. In vitro hyperoxia also stimulated A1, and A1 overexpression inhibited oxidant-induced epithelial cell apoptosis and necrosis. A1 is an important regulator of oxidant-induced lung injury, apoptosis, necrosis, and Bcl-2 and Bcl-xl gene expression and a critical mediator of IL-11- and VEGF-induced cytoprotection. [ABSTRACT FROM AUTHOR]

Although the roles of 5-methylcytosine and 5-hydroxymethylcytosine in epigenetic regulation of gene expression are well established, the functional effects of 5-formylcytosine and 5-carboxylcytosine on the process of transcription are not clear. Here we report a systematic study of the effects of five different forms of cytosine in DNA on mammalian and yeast RNA polymerase II transcription, providing new insights into potential functional interplay between cytosine methylation status and transcription. [ABSTRACT FROM AUTHOR]

N6-methyladenosine (m6A) is the most prevalent internal modification of mRNAs in most eukaryotes. Here we show that RNAs of human respiratory syncytial virus (RSV) are modified by m6A within discreet regions and that these modifications enhance viral replication and pathogenesis. Knockdown of m6A methyltransferases decreases RSV replication and gene expression whereas knockdown of m6A demethylases has the opposite effect. The G gene transcript contains the most m6A modifications. Recombinant RSV variants expressing G transcripts that lack particular clusters of m6A display reduced replication in A549 cells, primary well differentiated human airway epithelial cultures, and respiratory tracts of cotton rats. One of the m6A-deficient variants is highly attenuated yet retains high immunogenicity in cotton rats. Collectively, our results demonstrate that viral m6A methylation upregulates RSV replication and pathogenesis and identify viral m6A methylation as a target for rational design of live attenuated vaccine candidates for RSV and perhaps other pneumoviruses. Here, Xue et al. identify N6-methyladenosine (m6A) modification sites in RNAs of respiratory syncytial virus (RSV) and show that these sites, particularly sites in the transcript encoding for the viral glycoprotein, affect virus replication in primary human cells and cotton rats. [ABSTRACT FROM AUTHOR]

Background: Highly diversified in morphology and structure, feathers have evolved into various forms. Frizzle feathers, which result from a developmental defect of the feather, are observed in several domestic chicken breeds. The frizzle phenotype is consistent with incomplete dominance of a major gene, but the molecular mechanisms that underlie this phenotype remain obscure. Kirin, a Chinese indigenous chicken breed that originated in the Guangdong province, is famous for its frizzle feathers. The KRT75 gene is considered as the dominant gene responsible for the frizzle trait in several chicken breeds, but this is not the case in the Kirin breed. Thus, the objective of our study was to investigate the genomic region and mutation responsible for this phenotype in this particular breed. Results: A resource population was produced by crossing Kirin and Huaixiang chickens to produce F1 and F2 generations. DNA samples from 75 frizzle feather and normal feather individuals were sequenced with double-digest genotyping by sequencing (dd-GBS). After the detection of 525,561 high-quality variants, a genome-wide association analysis was carried out and the gene responsible for the frizzle phenotype was localized within the type II α-keratin cluster on chromosome 33. Sanger sequencing was used to screen for mutations in the exons of five genes of this type II α-keratin cluster. A 15-bp deletion in exon 3 of KRT75L4 that showed complete segregation with the frizzle phenotype was detected within the F2 population. Transcriptome sequencing demonstrated that KRT75L4 was expressed but that the transcript was shorter in Kirin than in Huaixiang chickens. In addition, by using Sanger sequencing, we were able to confirm that the deletion was in complete linkage with frizzle feathers. Conclusions: A deletion in the KRT75L4 gene is responsible for the frizzle feather phenotype in the Kirin chicken. The identification of this mutation, which causes a developmental defect of avian integument appendages, will improve our understanding of the mechanisms that are involved in feather formation. [ABSTRACT FROM AUTHOR]

As the most abundant mRNA modification in eukaryotic cells, N 6 -methyladenosine (m6A) has recently emerged as an important regulator of gene expression. m6A modification can be deposited by m6A methyltransferases, removed by m6A demethylases, and recognized by different reader proteins. Numerous lines of evidence have shown that m6A methylation plays critical roles regulating gene expression in development and disease. In this review, we summarize the molecular and cellular function of m6A and highlight some key results which demonstrate the role of m6A in various cancers. Finally, we discuss future directions for research into m6A and its effects in cancer and the potential for targeting RNA modification in cancer treatment. m6A is the most abundant mRNA modification and it regulates many aspects of RNA metabolism, including RNA splicing, export, translation, and decay. Numerous recent studies indicate an important role for m6A in regulating gene expression in multiple physiologic processes, such as stress responses, stem cell differentiation, gametogenesis, and T cell homeostasis. Aberrant m6A mRNA methylation, through the altered expression of m6A writer, eraser, or reader proteins, has also been associated with several cancers. m6A has been reported to affect gene expression in cancer cells through many different pathways. In some studies, increased m6A methylation appears to contribute to cancer cell tumorigenicity by enhancing translation of oncogenes or degrading tumor suppressor genes. Other studies observe that m6A helps inhibit the expression of oncogenes, suggesting tumor suppressing roles for m6A methylation. [ABSTRACT FROM AUTHOR]

Nucleic acids carry a wide range of different chemical modifications. In contrast to previous views that these modifications are static and only play fine-tuning functions, recent research advances paint a much more dynamic picture. Nucleic acids carry diverse modifications and employ these chemical marks to exert essential or critical influences in a variety of cellular processes in eukaryotic organisms. This review covers several nucleic acid modifications that play important regulatory roles in biological systems, especially in regulation of gene expression: 5-methylcytosine (5mC) and its oxidative derivatives, and N 6 -methyladenine (6mA) in DNA; N 6 -methyladenosine (m 6 A), pseudouridine (Ψ), and 5-methylcytidine (m 5 C) in mRNA and long non-coding RNA. Modifications in other non-coding RNAs, such as tRNA, miRNA, and snRNA, are also briefly summarized. We provide brief historical perspective of the field, and highlight recent progress in identifying diverse nucleic acid modifications and exploring their functions in different organisms. Overall, we believe that work in this field will yield additional layers of both chemical and biological complexity as we continue to uncover functional consequences of known nucleic acid modifications and discover new ones. [ABSTRACT FROM AUTHOR]

N 6-methyladenosine (m6A) is a ubiquitous modification in mRNA and other RNAs across most eukaryotes. For many years, however, the exact functions of m6A were not clearly understood. The discovery that the fat mass and obesity-associated protein (FTO) is an m6A demethylase indicates that this modification is reversible and dynamically regulated, suggesting that it has regulatory roles. In addition, it has been shown that m6A affects cell fate decisions in yeast and plant development. Recent affinity-based m6A profiling in mouse and human cells further showed that this modification is a widespread mark in coding and noncoding RNA (ncRNA) transcripts and is likely dynamically regulated throughout developmental processes. Therefore, reversible RNA methylation, analogous to reversible DNA and histone modifications, may affect gene expression and cell fate decisions by modulating multiple RNA-related cellular pathways, which potentially provides rapid responses to various cellular and environmental signals, including energy and nutrient availability in mammals. [ABSTRACT FROM AUTHOR]

Regulation of gene expression plays a fundamental role in cardiac stress-responses. Modification of coding transcripts by adenosine methylation (m6A) has recently emerged as a critical post-transcriptional mechanism underlying heart disease. Thousands of mammalian mRNAs are known to be m6A-modified, suggesting that remodeling of the m6A landscape may play an important role in cardiac pathophysiology. Here we found an increase in m6A content in human heart failure samples. We then adopted genome-wide analysis to define all m6A-regulated sites in human failing compared to non-failing hearts and identified targeted transcripts involved in histone modification as enriched in heart failure. Further, we compared all m6A sites regulated in human hearts with the ones occurring in isolated rat hypertrophic cardiomyocytes to define cardiomyocyte-specific m6A events conserved across species. Our results identified 38 shared transcripts targeted by m6A during stress conditions, and 11 events that are unique to unstressed cardiomyocytes. Of these, further evaluation of select mRNA and protein abundances demonstrates the potential impact of m6A on post-transcriptional regulation of gene expression in the heart. • The m6A landscape remodels in human failing hearts. • Stress responsive m6A modifications target transcripts regulating gene expression. • Few critical m6A sites mark stress response in an evolutionarily conserved way. • mRNA methylation affects transcript translation potential. [ABSTRACT FROM AUTHOR]

RNA modifications have recently emerged as critical posttranscriptional regulators of gene expression programs. They affect diverse eukaryotic biological processes, and the correct deposition of many of these modifications is required for normal development. Messenger RNA (mRNA) modifications regulate various aspects of mRNA metabolism. For example, N6-methyladenosine (m6A) affects the translation and stability of the modified transcripts, thus providing a mechanism to coordinate the regulation of groups of transcripts during cell state maintenance and transition. Similarly, some modifications in transfer RNAs are essential for RNA structure and function. Others are deposited in response to external cues and adapt global protein synthesis and gene-specific translation accordingly and thereby facilitate proper development. [ABSTRACT FROM AUTHOR]

• The first fin regeneration transcriptome analysis of betta fish was performed. • Many pathways and genes related to fin regeneration were identified here. • Pigment gene expression levels of the red and white fins were significantly different. • It provides data source for understanding fin regeneration and color formation of betta fish. The betta fish (Betta splendens), an important ornamental fish, has well-developed and colorful fins. After fin amputation, betta fish can easily regenerate fins similar to the originals in terms of structure and color. The powerful fin regeneration ability and a variety of colors in the betta fish are fascinating. However, the underlying molecular mechanisms are still not fully understood. In this study, tail fin amputation and regeneration experiments were performed on two kinds of betta fish: red and white color betta fish. Then, transcriptome analyses were conducted to screen out fin regeneration and color-related genes in betta fish. Through enrichment analyses of differentially expressed genes (DEGs), we found a series of enrichment pathways and genes related to fin regeneration, including cell cycle (i.e. plcg2), TGF-beta signaling pathway (i.e. bmp6), PI3K-Akt signaling pathway (i.e. loxl2a and loxl2b), Wnt signaling pathway (i.e. lef1), gap junctions (i.e. cx43), angiogenesis (i.e. foxp1), and interferon regulatory factor (i.e. irf8). Meanwhile, some fin color-related pathways and genes were identified in betta fish, especially melanogenesis (i.e. tyr , tyrp1a , tyrp1b, and mc1r) and carotenoid color genes (i.e. pax3 , pax7 , sox10 , and ednrba). In conclusion, this study can not only enrich the research on fish tissue regeneration, but also has a potential significance for the aquaculture and breeding of the betta fish. [ABSTRACT FROM AUTHOR]

Summary We present a highly sensitive and selective chemical labeling and capture approach for genome-wide profiling of 5-hydroxylmethylcytosine (5hmC) using DNA isolated from ∼1,000 cells (nano-hmC-Seal). Using this technology, we assessed 5hmC occupancy and dynamics across different stages of hematopoietic differentiation. Nano-hmC-Seal profiling of purified Tet2- mutant acute myeloid leukemia (AML) murine stem cells allowed us to identify leukemia-specific, differentially hydroxymethylated regions that harbor known and candidate disease-specific target genes with differential 5hmC peaks compared to normal stem cells. The change of 5hmC patterns in AML strongly correlates with differential gene expression, demonstrating the importance of dynamic alterations of 5hmC in regulating transcription in AML. Together, covalent 5hmC labeling offers an effective approach to study and detect DNA methylation dynamics in in vivo disease models and in limited clinical samples. [ABSTRACT FROM AUTHOR]

5-methylcytosine (5mC) in DNA plays an important role in gene expression, genomic imprinting, and suppression of transposable elements. 5mC can be converted to 5-hydroxymethylcytosine (5hmC) by the Tet (ten eleven translocation) proteins. Here, we show that, in addition to 5hmC, the Tet proteins can generate 5-formylcytosine (5fC) and 5-carboxylcytosine (5caC) from 5mC in an enzymatic activity dependent manner. Furthermore, we reveal the presence of 5fC and 5caC in genomic DNA of mouse embryonic stem cells and mouse organs. The genomic content of 5hmC, 5fC, and 5caC can be increased or reduced through overexpression or depletion of Tet proteins. Thus, we identify two previously unknown cytosine derivatives in genomic DNA as the products of Tet proteins. Our study raises the possibility that DNA demethylation may occur through Tet-catalyzed oxidation followed by decarboxylation. [ABSTRACT FROM AUTHOR]

Accumulation of unfolded or misfolded proteins in the endoplasmic reticulum (ER) lumen triggers an unfolded protein response (UPR) for stress adaptation, the failure of which induces cell apoptosis and tissue/organ damage. The molecular switches underlying how the UPR selects for stress adaptation over apoptosis remain unknown. Here, we discovered that accumulation of unfolded/misfolded proteins selectively induces N 6-adenosine-methyltransferase-14 (METTL14) expression. METTL14 promotes C/EBP-homologous protein (CHOP) mRNA decay through its 3′ UTR N 6-methyladenosine (m6A) to inhibit its downstream pro-apoptotic target gene expression. UPR induces METTL14 expression by competing against the HRD1-ER-associated degradation (ERAD) machinery to block METTL14 ubiquitination and degradation. Therefore, mice with liver-specific METTL14 deletion are highly susceptible to both acute pharmacological and alpha-1 antitrypsin (AAT) deficiency-induced ER proteotoxic stress and liver injury. Further hepatic CHOP deletion protects METTL14 knockout mice from ER-stress-induced liver damage. Our study reveals a crosstalk between ER stress and mRNA m6A modification pathways, termed the ERm6A pathway, for ER stress adaptation to proteotoxicity. [Display omitted] • UPR selectively induces m6A writer METTL14 protein expression • METTL14 suppresses CHOP-induced apoptosis for ER stress adaptation • HRD1 is a METTL14 ubiquitin ligase and UPR suppresses HRD1-mediated METTL14 degradation • CHOP suppression rescues METTL14 null mice from proteotoxic liver damage ERAD is critical for ER-stress adaptation, and its failure triggers cell apoptosis. Wei et al. discovered that ER stress induces N 6-adenosine-methyltransferase METTL14 expression by suppressing HRD1-mediated ubiquitination to promote CHOP mRNA decay for inhibiting CHOP-induced apoptosis. This study defines an ERm6A pathway, underlying how ERAD selects stress adaptation over apoptosis. [ABSTRACT FROM AUTHOR]

Summary N 6 -methyladenosine (m 6 A) regulates mRNA metabolism and translation, serving as an important source of post-transcriptional regulation. To date, the functional consequences of m 6 A deficiency within the adult brain have not been determined. To achieve m 6 A deficiency, we deleted Mettl14 , an essential component of the m 6 A methyltransferase complex, in two related yet discrete mouse neuronal populations: striatonigral and striatopallidal. Mettl14 deletion reduced striatal m 6 A levels without altering cell numbers or morphology. Transcriptome-wide profiling of m 6 A-modified mRNAs in Mettl14 -deleted striatum revealed downregulation of similar striatal mRNAs encoding neuron- and synapse-specific proteins in both neuronal types, but striatonigral and striatopallidal identity genes were uniquely downregulated in each respective manipulation. Upregulated mRNA species encoded non-neuron-specific proteins. These changes increased neuronal excitability, reduced spike frequency adaptation, and profoundly impaired striatal-mediated behaviors. Using viral-mediated, neuron-specific striatal Mettl14 deletion in adult mice, we further confirmed the significance of m 6 A in maintaining normal striatal function in the adult mouse. [ABSTRACT FROM AUTHOR]

Summary The dynamic and reversible N 6 -methyladenosine (m 6 A) RNA modification installed and erased by N 6 -methyltransferases and demethylases regulates gene expression and cell fate. We show that the m 6 A demethylase ALKBH5 is highly expressed in glioblastoma stem-like cells (GSCs). Silencing ALKBH5 suppresses the proliferation of patient-derived GSCs. Integrated transcriptome and m 6 A-seq analyses revealed altered expression of certain ALKBH5 target genes, including the transcription factor FOXM1. ALKBH5 demethylates FOXM1 nascent transcripts, leading to enhanced FOXM1 expression. Furthermore, a long non-coding RNA antisense to FOXM1 (FOXM1-AS) promotes the interaction of ALKBH5 with FOXM1 nascent transcripts. Depleting ALKBH5 and FOXM1-AS disrupted GSC tumorigenesis through the FOXM1 axis. Our work uncovers a critical function for ALKBH5 and provides insight into critical roles of m 6 A methylation in glioblastoma. [ABSTRACT FROM AUTHOR]