Control of Gene Expression by Transcription and Co-transcriptional Processes in Cell Homeostasis and Cell Fate Specification

Dear Colleagues,

All cells properly change their transcriptome in response to various signals and to specify cell fate through the control of gene expression. The first and rate-limiting process in gene expression is transcription, in which RNA polymerase synthesizes RNA from a DNA template. In eukaryotes, RNA polymerase II (Pol II) transcribes all protein-coding and various non-coding RNA (ncRNA) genes. All Pol II-transcribed nascent RNAs need to be further processed and modified to become mature functional RNAs. Additionally, DNA is wrapped around the histone octamer to form nucleosomes, which is intrinsically an obstacle for transcription but is required for higher-order gene regulation.

In the past two decades, increasing evidence has revealed that transcription is intimately coupled with RNA processing and with nucleosomal histone modification through extensive interaction networks. Therefore, understanding the molecular detail and the biological significance of these co-transcriptional processes is essential for deciphering gene control mechanisms in cell homeostasis and cell-fate specification. This Special Issue focuses on gene expression control by transcription and co-transcriptional processes such as RNA processing (5’ capping, splicing, polyadenylation), RNA modification, RNA structural folding, R-loop formation, RNA degradation, RNP (ribonucleoprotein particle) formation, histone modification, chromatin remodeling, heterochromatin formation, and liquid–liquid phase separation (LLPS). We welcome submissions in the form of original research articles, brief reports, reviews, opinions, and methodology reports.

Topics of interest for this Special Issue include, but are not limited to:

• Transcriptional regulation in cell homeostasis;
• Regulation of Pol II-CTD phosphorylation;
• Transcription-coupled RNA processing (5’capping, splicing, polyadenylation, and transport);
• Transcription-coupled RNA chemical modification;
• Transcription-coupled histone modification;
• Physical and functional crosstalk between transcription and RNA processing machineries;
• Methods for detecting co-transcriptional processes;
• Co-transcriptional nascent RNA targeting by ncRNAs (lncRNA, siRNA, miRNA, piRNA).

Dr. Yutaka Hirose
Guest Editor

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• transcription regulation
• RNA polymerase II
• co-transcriptional RNA processing
• chromatin regulation
• epitranscriptome