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Massively multiplex single-molecule oligonucleosome footprinting

ABSTRACT: Massively multiplex single-molecule oligonucleosome footprinting

PROVIDER: PRJNA681807 | ENA |

REPOSITORIES: ENA

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			Action	DRS
		Other
	SRR13173518_subreads.fastq.gz	Fastqsanger.gz
	SRR13173519_subreads.fastq.gz	Fastqsanger.gz
	SRR13173520_subreads.fastq.gz	Fastqsanger.gz
	SRR13173521_subreads.fastq.gz	Fastqsanger.gz

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Massively multiplex single-molecule oligonucleosome footprinting

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Project description:Single Molecule Footprinting (SMF) data from Sonmezer et al., 2020. SMF data is obtained by treating isolated nuclei with methyltransferases, where binding of proteins on DNA, e.g. nucleosomes and TFs, leave behind unmethylated cytosines as footprints. Data in this experiment comprises SMF data obtained from ES cells and various derivatives of ES cells, such DNMT-null, REST-knockout ES cells, neural progenitors and ES cells treated with NRF1 sirNA.

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Project description:Emerging 3D genome mapping efforts suggest complex chromosomal folding structures. However, the true multiplex nature of chromatin interactions has yet to be fully explored. Here, we describe a chromatin interaction analysis by droplet-based sequencing (ChIA-Drop). In ChIA-Drop, individual chromatin complexes are partitioned into droplets that contain a gel bead of DNA-barcoded primers, such that tethered chromatin DNA fragments are uniquely indexed and amplified for sequencing and mapping to demarcate multiplex chromatin contacts. Thus, ChIA-Drop can identify complex chromatin interactions with unprecedented single-molecule precision, which is not possible using methods that analyze pairwise contacts via proximity ligation. We demonstrate that multiplex chromatin interactions predominantly contribute to topologically associated domains with high heterogeneity, and that multivalent promoter-centered interactions provide a topological model for gene transcription.

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