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Architectural RNA is required for heterochromatin organization

Jitendra Thakur, He Fang, Trizia Llagas, Christine M. Disteche, View ORCID ProfileSteven Henikoff
doi: https://doi.org/10.1101/784835
Jitendra Thakur
1Basic Sciences Division, Fred Hutchinson Cancer Research Center, 1100 N. Fairview Ave N, Seattle, WA, 98109
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He Fang
3Department of Pathology, University of Washington, Seattle, WA, 98195, USA
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Trizia Llagas
1Basic Sciences Division, Fred Hutchinson Cancer Research Center, 1100 N. Fairview Ave N, Seattle, WA, 98109
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Christine M. Disteche
3Department of Pathology, University of Washington, Seattle, WA, 98195, USA
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Steven Henikoff
1Basic Sciences Division, Fred Hutchinson Cancer Research Center, 1100 N. Fairview Ave N, Seattle, WA, 98109
2Howard Hughes Medical Institute, USA
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  • ORCID record for Steven Henikoff
  • For correspondence: steveh@fhcrc.org
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Abstract

In addition to its known roles in protein synthesis and enzyme catalysis, RNA has been proposed to stabilize higher-order chromatin structure. To distinguish presumed architectural roles of RNA from other functions, we applied a ribonuclease digestion strategy to our CUT&RUN in situ chromatin profiling method (CUT&RUN.RNase). We find that depletion of RNA compromises association of the murine nucleolar protein Nucleophosmin with pericentric heterochromatin and alters the chromatin environment of CCCTC-binding factor (CTCF) bound regions. Strikingly, we find that RNA maintains the integrity of both constitutive (H3K9me3 marked) and facultative (H3K27me3 marked) heterochromatic regions as compact domains, but only moderately stabilizes euchromatin. To establish the specificity of heterochromatin stabilization by RNA, we performed CUT&RUN on cells deleted for the Firre long non-coding RNA and observed disruption of H3K27me3 domains on several chromosomes. We conclude that RNA maintains local and global chromatin organization by acting as a structural scaffold for heterochromatic domains.

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The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC-ND 4.0 International license.
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Posted September 27, 2019.
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Architectural RNA is required for heterochromatin organization
Jitendra Thakur, He Fang, Trizia Llagas, Christine M. Disteche, Steven Henikoff
bioRxiv 784835; doi: https://doi.org/10.1101/784835
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Architectural RNA is required for heterochromatin organization
Jitendra Thakur, He Fang, Trizia Llagas, Christine M. Disteche, Steven Henikoff
bioRxiv 784835; doi: https://doi.org/10.1101/784835

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