Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

Deciphering the relationship between polycomb repression and stochastic gene expression from single-cell RNA-seq data

ABSTRACT: Polycomb repressive complexes are important histone modifiers, which silence gene expression, yet there exists a subset of polycomb-bound genes actively transcribed by RNA polymerase II. To investigate the switching between polycomb-repressed and active states, we sequence mRNA from OS25 mouse embryonic stem cells cultured in serum/LIF. To validate our finding that polycomb modulates stochastic gene expression and transcriptional bursting, we perform knockout experiments and we sequence mRNA from Ring1A knockout (untreated) and Ring1A/B double knockout cells with constitutive Ring1A knockout and tamoxifen-inducible conditional Ring1B knockout.

INSTRUMENT(S): Illumina HiSeq 2000

ORGANISM(S): Mus musculus

SUBMITTER: Gozde Kar

PROVIDER: E-MTAB-5661 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Publications

Flipping between Polycomb repressed and active transcriptional states introduces noise in gene expression.

Kar Gozde G Kim Jong Kyoung JK Kolodziejczyk Aleksandra A AA Natarajan Kedar Nath KN Torlai Triglia Elena E Mifsud Borbala B Elderkin Sarah S Marioni John C JC Pombo Ana A Teichmann Sarah A SA

Nature communications 20170626 1

Polycomb repressive complexes (PRCs) are important histone modifiers, which silence gene expression; yet, there exists a subset of PRC-bound genes actively transcribed by RNA polymerase II (RNAPII). It is likely that the role of Polycomb repressive complex is to dampen expression of these PRC-active genes. However, it is unclear how this flipping between chromatin states alters the kinetics of transcription. Here, we integrate histone modifications and RNAPII states derived from bulk ChIP-seq da ...[more]

PMID: 28652613

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Project description:Two distinct Polycomb complexes, PRC1 and PRC2, collaborate to maintain epigenetic repression of key developmental loci in embryonic stem cells (ESCs). PRC1 and PRC2 have histone modifying activities, catalyzing mono-ubiquitination of histone H2A (H2AK119u1) and trimethylation of H3 lysine 27 (H3K27me3) respectively. Compared to H3K27me3, localization and role of H2AK119ub1 is not fully understood in ESCs. Here we present genome-wide H2AK119u1 maps in ESCs and identify a group of genes at which H2AK119u1 is deposited in a Ring1-dependent manner. These genes are a distinctive subset of genes with H3K27me3 enrichment and are the central targets of Polycomb silencing that are required to maintain ESC identity. We further show that the H2A ubiquitination activity of PRC1 is dispensable for its target binding and its activity to compact chromatin at Hox loci, but is indispensable for efficient repression of target genes and thereby ESC maintenance. These data demonstrate that multiple effector mechanisms including H2A ubiquitination and chromatin compaction combine to mediate PRC1-dependent repression of genes that are crucial for the maintenance of ESC identity. Utilization of these diverse effector mechanisms might provide a means to maintain a repressive state that is robust yet highly responsive to developmental cues during ES cell self-renewal and differentiation. This SuperSeries is composed of the following subset Series: GSE38224: Expression data from Ring1A(-/-);Ring1B(fl/fl);R26::CreERT2 ES cells expressing either of mock, WT or mutant Ring1B construct before or after OHT treatment GSE38504: ChIP-on-chip analysis of Ring1B, Ring1A, H2AK119u1 and H3K27me3 in mouse ES cells Total RNAs were extracted from the respective ES cells, and were subjected to microarray analysis using Affymetrix GeneChip Mouse Genome 430A 2.0 arrays. ChIP on chip analysis was carried out using the Mouse Promoter ChIP-on-chip Microarray Set (G4490A, Agilent, Palo Alto, Calif., USA). MEFs were subjected to ChIP assay using various antibodies. Purified immunoprecipitated and input DNA was subjected to T7 RNA polymerase-based amplification. Labeling, hybridization and washing were carried out according to the Agilent mammalian ChIP-on-chip protocol (ver.9.0). Scanned images were quantified with Agilent Feature Extraction software under standard conditions.

Dataset Information

Deciphering the relationship between polycomb repression and stochastic gene expression from single-cell RNA-seq data

Publications

Flipping between Polycomb repressed and active transcriptional states introduces noise in gene expression.

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