Genomics

Dataset Information

0

Apparent loss of PRC2 chromatin occupancy as an artefact of RNA depletion


ABSTRACT: RNA has been implicated in the recruitment of chromatin modifiers, and previous studies have provided evidence in favour and against this idea. RNase treatment of chromatin is a prevalent tool for the study of RNA-mediated regulation of chromatin modifiers, but the limitations of this approach remain unclear. One of the most studied chromatin modifiers in the context of RNA-mediated regulation is the H3K27me3 methyltransferase Polycomb Repressive Complex 2 (PRC2). RNase A treatment during chromatin immunoprecipitation (rChIP) reduces the occupancy of PRC2 on chromatin. This led to suggestions of an “RNA bridge" between PRC2 and chromatin. Here we show that RNase A treatment during chromatin immunoprecipitation leads to the apparent loss of all facultative heterochromatin, including both PRC2 and its H3K27me3 mark genome-wide. This phenomenon persists in mouse embryonic stem cells, human cancer cells and human-induced pluripotent stem cells. We track this observation to a global gain of chromatin that artificially reduces ChIP signals from facultative heterochromatin. Our results point to substantial limitations in RNase A treatment for mapping RNA-dependent chromatin occupancy and invalidate conclusions that were previously established for PRC2 based on this assay.

ORGANISM(S): Mus musculus Homo sapiens

PROVIDER: GSE240079 | GEO | 2024/02/21

REPOSITORIES: GEO

Dataset's files

Source:
Action DRS
Other
Items per page:
1 - 1 of 1

Similar Datasets

2024-02-22 | GSE240380 | GEO
2022-01-20 | PXD029403 | Pride
2022-01-19 | PXD027966 | Pride
2021-01-05 | GSE150758 | GEO
2020-05-31 | GSE128135 | GEO
2020-03-09 | PXD017806 | Pride
| phs000830 | dbGaP
2016-06-09 | E-GEOD-78822 | biostudies-arrayexpress
2016-06-09 | E-GEOD-78820 | biostudies-arrayexpress
2024-09-05 | GSE263441 | GEO