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Interdependence between histone marks and steps in Pol II transcription [Danko.submission]

ABSTRACT: Interdependence between histone marks and steps in Pol II transcription [Danko.submission]

PROVIDER: PRJNA684511 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR13242100_1.fastq.gz	Fastqsanger.gz
	SRR13242100_2.fastq.gz	Fastqsanger.gz
	SRR13242101_1.fastq.gz	Fastqsanger.gz
	SRR13242101_2.fastq.gz	Fastqsanger.gz
	SRR13242102_1.fastq.gz	Fastqsanger.gz

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Interdependence between histone marks and steps in Pol II transcription

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Interdependence between histone marks and steps in Pol II transcription [Antczak.submission]

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Interdependence between histone marks and steps in Pol II transcription [Danko.submission]

Project description:We trained sensitive machine learning models that decompose maps of primary transcription into ChIP-seq profiles representing 9 distinct histone modifications. We show that transcription measured using precision run-on and sequencing (PRO-seq) can recover the pattern of active histone modifications at nucleosome resolution and with an accuracy that rivals the correlation between independent ChIP-seq experiments in holdout cell types. To define the nature of the causal relationship between histone modifications and transcription, we perturbed transcription and examined the genomic distribution of four active and one repressive histone modification: H3K4me1, H3K4me3, H3K27ac, H3K36me3, H3K27me3.

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Pol II and its associated epigenetic marks are present at pol III-transcribed non-coding RNA genes (II)

Project description:Epigenetic control is an important aspect of gene regulation. Despite detailed understanding of many examples, the transcription of non-coding RNA genes by RNA polymerase (pol) III is less well characterized. Here we profile the epigenetic features of pol III target genes throughout the human genome. This reveals that the chromatin landscape of pol III-transcribed genes resembles that of pol II templates in many ways, although there are also clear differences. Our analysis also discovered an entirely unexpected phenomenon, namely that pol II co-localizes with the majority of genomic loci that are bound by pol III. RNA-seq experiment for total RNA in CD4+ cells.

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Pol II and its associated epigenetic marks are present at pol III-transcribed non-coding RNA genes (II)

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PARG is Essential for Pol-theta-Mediated DNA End-Joining by Removing Repressive Poly-ADP Ribose Marks

Project description:DNA polymerase theta (Pol-theta)-mediated end-joining (TMEJ) repairs DNA double-strand breaks and confers resistance to genotoxic agents. How Pol-theta is regulated at the molecular level to exert TMEJ remains unknown. We find that Pol-theta interacts with and is PARylated by PARP1 in vitro and in cells. PARP1 recruits Pol-theta to the vicinity of DNA damage via PARylation dependent liquid demixing, however, PARylated Pol-theta (PAR-Pol-theta) cannot perform TMEJ due to its inability to bind DNA. PARG-mediated de-PARylation of Pol-theta reactivates its DNA binding and end-joining activities in vitro. Consistent with this, PARG is essential for TMEJ in cells and the temporal recruitment of PARG to DNA damage corresponds with TMEJ activation and dissipation of PARP1 and PAR. These studies support a two-step spatiotemporal mechanism of TMEJ regulation. First, PARP1 PARylates Pol-theta and facilitates its recruitment to DNA damage sites in an inactivated state. PARG subsequently activates TMEJ by removing repressive PAR marks on Pol-theta.

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Pol II and its associated epigenetic marks are present at pol III-transcribed non-coding RNA genes (I)

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Pol II (Rpb3) ChIP-seq in Drosophila melanogaster S2 cells

Project description:Control of RNA transcription is critical for the development and homeostasis of all organisms, and can occur at multiple steps of the transcription cycle, including RNA polymerase II (Pol II) recruitment, initiation, promoter-proximal pausing, and elongation. That Pol II accumulates on many promoters in metazoans implies that steps other than Pol II recruitment are rate-limiting and regulated 1-6. By integrating genome-wide Pol II chromatin immunoprecipition (ChIP) and Global Run-On (GRO) genomic data sets from Drosophila cells, we examined critical features of Pol II near promoters. The accumulation of promoter-proximal polymerase is widespread, occurring on 70% of active genes; and unlike elongating Pol II within the body of genes, promoter Pol II are held paused by factors like NELF, unable to transcribe unless nuclei are treated with strong detergent. Notably, we find that the vast majority of promoter-proximal Pol II detected by ChIP are paused, thereby identifying the biochemical nature of this rate-limiting step in transcription. Finally, we demonstrate that Drosophila promoters do not have the upstream divergent Pol II that is seen so broadly and prominently on mammalian promoters. We postulate this is a consequence of Drosophila’s extensive use of directional core promoter sequence elements, which contrasts with mammals’ lack of directional elements and prevalence of CpG island core promoters. In support of this idea, we show that the fraction of mammalian promoters containing a TATA box core element is dramatically depleted of upstream divergent transcription. ChIP-seq data set for Pol II (rpb3) (2 replicates).

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