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RNA polymerase II and PARP1 shape enhancer-promoter contacts [ChRO-seq]

ABSTRACT: RNA polymerase II and PARP1 shape enhancer-promoter contacts [ChRO-seq]

PROVIDER: PRJNA848812 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR19643020_1.fastq.gz	Fastqsanger.gz
	SRR19643020_2.fastq.gz	Fastqsanger.gz
	SRR19643021_1.fastq.gz	Fastqsanger.gz
	SRR19643021_2.fastq.gz	Fastqsanger.gz
	SRR19643022_1.fastq.gz	Fastqsanger.gz

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Project description:Poly(ADP-ribose) polymerase 1 (PARP1) is a highly conserved nuclear protein in multicellular organisms that modulates chromatin opening, and by doing so, it plays a significant role in gene expression regulation during development and differentiation. Despite its significance, all reported Parp1 total knockout mice strains are viable and fertile with no developmental anomalies. It was previously believed that functional redundancy with other PARP family members explain such a controversy. PARP2 is the main candidate to fulfill PARP1 functions in Parp1 knockout mice. Indeed, Parp1 Parp2 double knockout mice are arrested early in development and unable to proceed through gastrulation. However, while PARP2 has similar catalytic domain to PARP1, it lacks other domains that play important regulatory roles, thus making the lack of developmental problems in Parp1 mice total knockouts highly unlikely. To address this question, we checked the best investigated and publicly available Parp1 knockout mice strain. We found that Parp1 is still expressed in these mice, based on the presence of its mRNA transcript. Contrary to prior assumptions, we identified persistent mRNA expression in knockout mice, albeit at reduced levels. Detailed transcript analysis revealed an alternatively spliced PARP1 variant lacking exon two with introduced artificial cassette. Subsequent protein analysis confirmed the existence of a truncated PARP1 protein in knockout mice. We established embryonic stem cell lines from knockout mice and revealed the presence of pADPr. The decreased level of pADPr was detected in knockout ES cells with Western Blotting analysis, but immunofluorescence staining didn’t detect any difference in distribution or level of pADPr in nuclei of knockout ES cells compared to control ones. Moreover, in double Parp1 Parg mutant ES cells the accumulation of pADPr greatly exceeded its amount in normal and even in hypomorph Parg mutant ES cells, suggesting the presence of functionally active PARP1. Therefore, our findings challenge the conventional understanding of PARP1 depletion effects.

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RNA polymerase II and PARP1 shape enhancer-promoter contacts [ChRO-seq]

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