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Review
. 2024 Oct 3;84(19):3627-3643.
doi: 10.1016/j.molcel.2024.08.021.

An RNA-centric view of transcription and genome organization

Jonathan E Henninger  1 , Richard A Young  2
Affiliations
Review

An RNA-centric view of transcription and genome organization

Jonathan E Henninger et al. Mol Cell. .

Abstract

Foundational models of transcriptional regulation involve the assembly of protein complexes at DNA elements associated with specific genes. These assemblies, which can include transcription factors, cofactors, RNA polymerase, and various chromatin regulators, form dynamic spatial compartments that contribute to both gene regulation and local genome architecture. This DNA-protein-centric view has been modified with recent evidence that RNA molecules have important roles to play in gene regulation and genome structure. Here, we discuss evidence that gene regulation by RNA occurs at multiple levels that include assembly of transcriptional complexes and genome compartments, feedback regulation of active genes, silencing of genes, and control of protein kinases. We thus provide an RNA-centric view of transcriptional regulation that must reside alongside the more traditional DNA-protein-centric perspectives on gene regulation and genome architecture.

Keywords: RNA; RNA-binding proteins; biomolecular condensates; feedback; gene expression; genome organization; transcription; transcription factors.

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Conflict of interest statement

Declaration of interests R.A.Y. is a founder and shareholder of Syros Pharmaceuticals, Camp4 Therapeutics, Omega Therapeutics, Dewpoint Therapeutics, and Paratus Sciences; has consulting or advisory roles at Precede Biosciences and Novo Nordisk; and is on the advisory board of Molecular Cell.

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