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A certain degree of chromatin openness is necessary for the activity of transcription-regulating regions within the genome, facilitating accessibility to RNA polymerases and subsequent synthesis of regulatory element RNAs (regRNAs) from these regions. The rapidly increasing number of studies underscores the significance of regRNAs across diverse cellular processes and diseases, challenging the paradigm that these transcripts are non-functional transcriptional noise. This review explores the multifaceted roles of regRNAs in human cells, encompassing rather well-studied entities such as promoter RNAs and enhancer RNAs (eRNAs), while also providing insights into overshadowed silencer RNAs and insulator RNAs. Furthermore, we assess notable examples of shorter regRNAs, like miRNAs, snRNAs, and snoRNAs, playing important roles. Expanding our discourse, we deliberate on the potential usage of regRNAs as biomarkers and novel targets for cancer and other human diseases. [Display omitted] • Accessible chromatin necessary for active regulatory elements leads to RNA synthesis. • Transcripts from regulatory elements (regRNA) play key role in various cell processes. • Poorly known insulator and silencer RNAs act alongside enhancer and promoter RNAs. • Small regRNAs employ miRNA, snRNA and snoRNA mechanisms. • regRNAs inherent cell specificity suggests them as biomarkers and therapeutic targets. [ABSTRACT FROM AUTHOR]

Diatoms are a key phytoplankton group in the contemporary ocean, showing extraordinary adaptation capacities to rapidly changing environments. The recent availability of whole genome sequences from representative species has revealed distinct features in their genomes, like novel combinations of genes encoding distinct metabolisms and a significant number of diatom-specific genes. However, the regulatory mechanisms driving diatom gene expression are still largely uncharacterized. Considering the wide variety of fields of study orbiting diatoms, ranging from ecology, evolutionary biology to biotechnology, it is thus essential to increase our understanding of fundamental gene regulatory processes such as transcriptional regulation. To this aim, we explored the functional properties of the 5′-flanking region of the Phaeodatylum tricornutum Lhcf2 gene, encoding a member of the Light Harvesting Complex superfamily and we showed that this region enhances transcription of a GUS reporter gene in an orientation- and distance-independent fashion. This represents the first example of a cis-regulatory sequence with enhancer-like features discovered in diatoms and it is instrumental for the generation of novel genetic tools and diatom exploitation in different areas of study. [ABSTRACT FROM AUTHOR]

An abstract of the article "Regulation effect analysis of lactoferrin gene promoter elements," by Jin Jing and colleagues is presented.

Summary: VNTR (variable number of tandem repeats) has been used extensively for Mycobacterium tuberculosis strain discrimination. In contrast, their biological roles have been rarely investigated. We, herewith, studied whether two VNTR could promote expression of a downstream reporter gene, gfp. The VNTR loci, VNTR0960c and VNTR4052, reside upstream of the translational start sites of Rv0861c (helicase gene, ercc3) and Rv3610c (ftsH), respectively. Both are highly polymorphic among clinical strains of M. tuberculosis. DNA fragments containing various numbers of the repeat units were amplified and inserted upstream of the gfp gene and transformed into M. smegmatis mc2155 and M. tuberculosis H37Ra. The levels of fluorescence were determined by microplate fluorometry and flow cytometry. It was found that VNTR0960c could promote the expression of gfp while VNTR4052 alone could not. However, VNTR4052 was needed for complementing the promoter activity of the downstream sequence. The effects were discernible in M. tuberculosis, even though only the incomplete copy of the repeat was present. The addition of a complete copy of the repeat augmented the promoter activity. The presence of more copies of the repeat had minimal effects or even decreased the expressions. Significance of the effects on the cellular metabolisms of M. tuberculosis warrants further studies. [ABSTRACT FROM AUTHOR]

• Chromatin accessibility analysis of human satellite cells and myoblasts. • Identification of putative loci underlying human satellite cell epigenetic regulation. • Conserved human-mouse loci display enrichment for self-renewal regulators. • Integration of epigenetic and transcriptional data reveals potential PAX7 targets. • PAX7 may control PPARGC1A expression in muscle progenitors. Satellite cells represent the main myogenic population accounting for skeletal muscle homeostasis and regeneration. While our knowledge of the signaling pathways controlling satellite cell regenerative capability is increasing, the underlying epigenetic mechanisms are still not clear, especially in the case of human satellite cells. Here, by performing chromatin accessibility profiling (ATAC-seq) in samples isolated from human and murine muscles, we investigated the changes in the epigenetic landscape occurring during the transition from activated satellite cells to myoblasts. Our analysis identifies a compendium of putative regulatory elements defining human activated satellite cells and myoblasts, respectively. A subset of these differentially accessible loci is shared by both murine and human satellite cells, includes elements associated with known self-renewal regulators, and is enriched for motifs bound by transcription factors participating in satellite cell regulation. Integration of transcriptional and epigenetic data reveals that known regulators of metabolic gene expression, such as PPARGC1A, represent potential PAX7 targets. Through characterization of genomic networks and the underlying effectors, our data represent an important starting point for decoding and manipulating the molecular mechanisms underlying human satellite cell muscle regenerative potential. [ABSTRACT FROM AUTHOR]

Eukaryotic regulons are regulatory units formed by a set of genes under the control of the same transcription factor (TF). Despite the functional plasticity, TFs are highly conserved and recognize the same DNA sequences in different organisms. One of the main factors that confer regulatory specificity is the distribution of the binding sites of the TFs along the genome, allowing the configuration of different transcriptional regulatory networks (TRNs) from the same regulator. A similar scenario occurs between tissues of the same organism, where a TRN can be rewired by epigenetic factors, modulating the accessibility of the TF to its binding sites. In this article we discuss concepts that can help to formulate testable hypotheses about the construction of regulons, exploring the presence and absence of the elements that form a TRN throughout the evolution of an ancestral lineage. This article is part of a Special Issue entitled: Transcriptional Profiles and Regulatory Gene Networks edited by Dr. Federico Manuel Giorgi and Dr. Shaun Mahony. [ABSTRACT FROM AUTHOR]