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Mus musculus

ABSTRACT: YY1 is a structural regulator of enhancer-promoter loops [ChIA-PET]

PROVIDER: PRJNA388694 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR5634343_1.fastq.gz	Fastqsanger.gz
	SRR5634343_2.fastq.gz	Fastqsanger.gz
	SRR5634344_1.fastq.gz	Fastqsanger.gz
	SRR5634344_2.fastq.gz	Fastqsanger.gz
	SRR5634345_1.fastq.gz	Fastqsanger.gz

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Project description:High resolution mapping of enhancer-promoter interactions [ChIA-PET]

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Dynamic chromatin connectivity maps reveal lineage specific regulation

Project description:Using genome-wide Chromatin Interaction Analysis with Paired-End-Tag sequencing, we mapped long-range chromatin interactions associated with RNA polymerase II in three different mouse cell lines and uncovered widespread promoter-centered interactions. These interactions further aggregated into higher-order clusters, in which proximal and distant genes are engaged through enhancer-promoter interactions. Comparative analyses of different cell lines imply that cell specific enhancer interactions are dynamic among different cell specific transcription, and suggest significant enrichment of enhancer-promoter interactions for cell specific manner. Overall, our study provides novel insights into the three-dimensional basis of transcription activity in mouse cells. RNA polymerase II (RNAPII) guided chromatin interactions were discovered by Chromatin Interaction Analysis with Paired-End Tag (ChIA-PET) sequencing, in order to study genome-wise the enhancer-promoter interactions. Three cell lines, namely mouse embryonic stem cell E14, Neural stem cell NS5 and neuroshpere cells were grown under standard culture conditions and harvested at log phase. Harvested cells were cross-linked using 1% formaldehyde followed by neutralization with 0.2M glycine. Chromatin was isolated and subjected to ChIA-PET protocol as described in Fullwood et al, 2009. The ChIA-PET sequence reads were processed and analyzed using ChIA-PET Tool (Li et al, 2010)

2013-11-04 | E-GEOD-44067 | biostudies-arrayexpress

YY1 is a structural regulator of enhancer-promoter loops [scRNA-seq]

Project description:There is considerable evidence that chromosome structure plays important roles in gene control, but we have limited understanding of the proteins that contribute to structural interactions between gene promoters and their enhancer elements. Large DNA loops that encompass genes and their regulatory elements depend on CTCF-CTCF interactions, but most enhancer-promoter interactions do not depend on this structural protein. Here we show that the transcription factor Yin Yang 1 (YY1) contributes to enhancer-promoter structural interactions in a manner analogous to DNA interactions mediated by CTCF. YY1 binds to active enhancers and promoter-proximal elements in all cells examined. YY1 forms dimers that can facilitate DNA interactions. Deletion of YY1 binding sites or depletion of YY1 can disrupt enhancer-promoter looping and normal gene expression. We propose that YY1-mediated enhancer-promoter interactions are a general feature of mammalian gene control.

2017-11-16 | GSE103574 | GEO