Coding RNAs with a non-coding function: maintenance of open chromatin structure.

Area of Science:

• Molecular Biology
• Genomics
• Cell Biology

Background:

• Chromatin's multi-layered organization regulates nuclear functions through distinct DNA-associated subcompartments.
• The role of RNA in maintaining chromatin conformation and nuclear activity is not fully understood.

Purpose of the Study:

• To investigate the role of RNA in maintaining decondensed and biologically active interphase chromatin conformation.
• To identify specific RNA molecules involved in chromatin organization.

Main Methods:

• RNase A microinjection and fluorescence microscopy imaging to observe chromatin changes upon RNA digestion.
• High-throughput sequencing to analyze purified nuclear RNA fractions.
• RNA depletion and RNA polymerase II (RNAP II) inhibition experiments.

Main Results:

• Digestion of single-stranded RNAs induced chromatin aggregation in decondensed regions, while pericentric heterochromatin remained resistant.
• A class of coding RNA transcripts, termed 'chromatin-interlinking' RNAs (ciRNAs), was identified as responsible for maintaining active chromatin.
• Restoration of chromatin distribution was achieved using a purified nuclear RNA fraction containing long, spliced, non-polyadenylated RNAP II transcripts with long 3'-UTRs.
• RNA depletion or RNAP II inhibition induced reversible changes in chromatin conformation and RNAP II distribution.

Conclusions:

• ciRNAs act as architectural factors organizing actively transcribed chromatin compartments.
• RNA plays a crucial role in maintaining the decondensed and active state of interphase chromatin.
• The findings reveal a novel mechanism of genome organization mediated by specific RNA molecules.