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Systematic mapping of 3D enhancer interactions reveals lineage specific regulatory networks during early mouse developmental decisions [Hi-C]

ABSTRACT: Systematic mapping of 3D enhancer interactions reveals lineage specific regulatory networks during early mouse developmental decisions [Hi-C]

PROVIDER: PRJNA878696 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR21497123_1.fastq.gz	Fastqsanger.gz
	SRR21497123_2.fastq.gz	Fastqsanger.gz
	SRR21497124_1.fastq.gz	Fastqsanger.gz
	SRR21497124_2.fastq.gz	Fastqsanger.gz
	SRR21497125_1.fastq.gz	Fastqsanger.gz

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Systematic mapping of 3D enhancer interactions reveals lineage specific regulatory networks during early mouse developmental decisions

Project description:Systematic mapping of 3D enhancer interactions reveals lineage specific regulatory networks during early mouse developmental decisions

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Systematic mapping of 3D enhancer interactions reveals lineage specific regulatory networks during early mouse developmental decisions [Hi-C]

Project description:To model and characterize the chromatin regulatory landscape of the very first developmental cell fates, we made use of three previously derived and well-characterized Trophoblast Stem Cell (TSCs), Embryonic Stem Cell (ESC) and Extra Embryonic Stem Cell lines (XENs) We performed HiC to map large-scale 3D architectural rewiring in ESC, TSC and XEN

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Systematic mapping of 3D enhancer interactions reveals lineage specific regulatory networks during early mouse developmental decisions [ATAC-Seq]

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Systematic mapping of 3D enhancer interactions reveals lineage specific regulatory networks during early mouse developmental decisions [RNA-Seq]

Project description:Systematic mapping of 3D enhancer interactions reveals lineage specific regulatory networks during early mouse developmental decisions [RNA-Seq]

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Systematic mapping of 3D enhancer interactions reveals lineage specific regulatory networks during early mouse developmental decisions [ChIP-Seq]

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Systematic evaluation of chromosome conformation capture assays [Hi-C]

Project description:Chromosome conformation capture (3C)-based assays are used to map chromatin interactions genome-wide. Quantitative analyses of chromatin interaction maps can lead to insights into the spatial organization of chromosomes and the mechanisms by which they fold. A number of protocols such as in situ Hi-C and Micro-C are now widely used and these differ in key experimental parameters including cross-linking chemistry and chromatin fragmentation strategy. To understand how the choice of experimental protocol determines the ability to detect and quantify aspects of chromosome folding we have performed a systematic evaluation of experimental parameters of 3C-based protocols. We find that different protocols capture different 3D genome features with different efficiencies. First, the use of crosslinkers such as DSG in addition to formaldehyde improves signal-to-noise allowing detection of thousands of additional loops and strengthening compartment signal. Second, fragmenting chromatin to the level of nucleosomes using MNase allows detection of more loops. On the other hand, protocols that generate larger multi-kb fragments produce stronger compartmentalization signals. We confirmed our results in multiple cell states such as pluripotent and differentiated cells as well as cell cycle stages; Mitosis and G1. Based on these insights we developed Hi-C 3.0, a single protocol that can be used to both efficiently detect chromatin loops and to quantify compartmentalization. Finally, this study produced ultra-deeply sequenced reference interaction maps using in situ Hi-C, Micro-C and Hi-C 3.0 for commonly cell lines in the 4D Nucleome Project.

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