R loops regulate promoter-proximal chromatin architecture and cellular differentiation

Area of Science:

• Molecular Biology
• Epigenetics
• Genomics

Background:

• RNA binding regulates numerous chromatin-remodeling factors, but its functional contexts remain unclear.
• R loops, a structure of RNA-DNA hybrids, are implicated in gene regulation.

Purpose of the Study:

• To investigate the role of R loops in modulating the binding of chromatin-regulatory complexes Tip60-p400 and polycomb repressive complex 2 (PRC2).
• To determine how R loops affect the recruitment of these complexes to chromatin in mouse embryonic stem cells (ESCs).

Main Methods:

• Analysis of Tip60-p400 and PRC2 binding to nascent transcripts in mouse ESCs.
• Genome-wide occupancy profiling of Tip60-p400 and PRC2 in relation to R loop formation.
• Assessment of ESC differentiation potential following R loop disruption.

Main Results:

• Tip60-p400 and PRC2 bind to nascent transcripts, but only Tip60-p400 binding is promoted by transcription.
• Promoter-proximal R loops correlate with higher Tip60-p400 and lower PRC2 occupancy.
• Disrupting R loops globally decreases Tip60-p400 and increases PRC2 occupancy, impairing ESC differentiation.

Conclusions:

• R loops play a dual role, positively and negatively modulating the recruitment of key pluripotency regulators like Tip60-p400 and PRC2.
• R loop integrity is crucial for maintaining proper chromatin regulation and ESC differentiation capacity.