Chromatin Modifications and RNA-Based Regulation of Gene Expression
A special issue of Genes (ISSN 2073-4425). This special issue belongs to the section "Molecular Genetics and Genomics".
Deadline for manuscript submissions: 25 March 2026 | Viewed by 19
Special Issue Editor
Special Issue Information
Dear Colleagues,
RNA molecules are increasingly recognized as active regulators of transcription, adding new dimensions to classical transcription factor and chromatin-based control. During initiation, nascent RNAs can act as a “trapping mesh”, retaining transcription factors in the vicinity of their DNA binding sites, increasing their binding turnover through a local high concentration effect. Architectural proteins such as CTCF rely on RNA binding to maintain certain chromatin loops, while other transcription factors engage RNA directly through canonical or non-canonical RNA-binding domains. Concurrently, RNA modifications occur co-transcriptionally in chromatin contexts. The m6A writer complex, guided by histone marks such as H3K36me3, deposits methylation on newly synthesized transcripts. These marks, read by nuclear proteins, feed back on chromatin by recruiting histone modifiers, thereby linking RNA methylation with chromatin state and transcriptional output. During elongation, RNA itself modulates the phosphorylation dynamics of RNA polymerase II, influencing the activity of cofactors such as P-TEFb. Transcription-coupled deposition of histone modifications further integrates RNA splicing, as chromatin marks recruit components of the spliceosome, ensuring coordination between RNA processing and elongation. Finally, termination also engages RNA-based mechanisms. RNA helicases help couple RNA modifications with genome stability, while interactions with RNA-binding proteins shape the final stages of transcript maturation. Together, these discoveries establish RNA as an integral partner of chromatin modifications, creating feedback loops that fine-tune gene expression across all stages of transcription.
Dr. Alonso Javier Pardal
Guest Editor
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Keywords
- chromatin modifications
- RNA
- gene expression
- transcription
- chromatin boundaries
- RNA-binding proteins
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