|Public on Feb 18, 2015
|Global Reorganization of Chromatin Architecture during Embronic Stem Cell Differentiation
|Genome binding/occupancy profiling by high throughput sequencing
|The 3D organization of the genome is important for regulation of diverse nuclear processes ranging from transcription to DNA replication. Knowledge of the higher order chromatin structure is critical for understanding mechanisms of gene regulation by long-range control elements such as enhancers and insulators. We describe high resolution, genome-wide dynamic chromatin interaction maps in human embryonic stem cells (hESC) as they differentiate into four distinct embryonic cell lineages. Extensive reorganization of higher-order chromatin structure occurs during hESC differentiation. In this process, topological domains remain largely intact but inter-domain association patterns change dramatically, coincident with widespread changes in chromatin state and gene expression. Moreover, using proximity ligation sequencing to generate chromosome span haplotypes, widespread allele biased gene activities are detected. The allelic gene expression patterns can be correlated to epigenetic state at distal enhancers, supporting the role of these elements in regulating gene expression over a distance.
|Two biological replicates of Hi-C experiment and one replicate of CTCF ChIP-Seq experiment in embryonic stem cells and 4 other differentiated cell-types from H1 cell line. Re-analysis of data from GSE16256 in an allele specific manner is linked as supplementary data.
Hi-C data generated in this study can be visualized at www.3dgenome.org.
|Dixon JR, Jung I, Selvaraj S, Ren B
|Nov 18, 2013
|Last update date
|Feb 22, 2021
|Jesse R Dixon
|Salk Institute for Biological Studies
|10010 N. Torrey Pines Rd.
|Illumina HiSeq 2000 (Homo sapiens)
|Illumina HiSeq 2500 (Homo sapiens)
|Hi-C, H1 embryonic stem cells, replicate one
|Hi-C, H1 embryonic stem cells, replicate two
|Hi-C, H1 Mesendoderm cells, replicate one