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DNA methylation state is associated with the formation of loops and links in hematopoietic stem cells [RNA-seq]

ABSTRACT: We present the high resolution HiC study of genome folding in primary hematopoietic stem and progenitor cells. We investigated the relationship of chromosomal contacts with other epigenetic marks, particularly DNA methylation which is known to be important for appropriate stem cell differentiation.

ORGANISM(S): Homo sapiens

PROVIDER: GSE107149 | GEO | 2017/11/24

SECONDARY ACCESSION(S): PRJNA419463

REPOSITORIES: GEO

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DNA methylation state is associated with the formation of loops and links in hematopoietic stem cells [HiC]

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Cohesin HiChIP datasets of pluripotent and surface ectoderm cells with and without p63

Project description:Purpose: Assess changes in the three-dimensional (3D) chromatin architecture during surface ectoderm commitment and evaluate changes in 3D chromatin architecture in human embryonic stem cells and surface ectoderm cells with and without p63. Methods: Cohesin HiChIP profiles for human embryonic stem cells and surface ectoderm cells with and without p63 were generated in triplicate with deep sequencing on the Illumina HiSeq 4000 sequencer. Using HiC-Pro, paired end reads were aligned to hg19, duplicate reads were removed, and then were assigned to MboI restriction fragments, filtered for valid interactions, and used to generate binned interaction matrices of 10 kb resolution. Contacts were called using FitHiC and filtered for counts >= 10 and FDR < 0.001. Results: The greatest change in 3D chromatin architecture was observed between human embryonic stem cells and surface ectoderm cells, while moderate changes were observed in human embryonic stem cells with and without p63, and limited changes were observed in surface ectoderm cells with and without p63. Conclusion: Both p63 and the surface ectoderm morphogens direct changes in chromatin folding to establish the 3D chromatin landscape in the surface ectoderm.

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