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Series GSE72816 Query DataSets for GSE72816
Status Public on Dec 11, 2015
Title CTCF-Mediated Human 3D Genome Architecture Reveals Chromatin Topology for Transcription
Organism Homo sapiens
Experiment type Other
Summary Spatial genome organization and its effect on transcription remains a fundamental biological question. We applied an advanced ChIA-PET strategy to comprehensively map higher-order chromosome folding and chromatin interactions mediated by CTCF and RNAPII with haplotype specificity and nucleotide resolution in different human cell lineages. We find that CTCF-mediated interaction anchors serve as structural foci for spatial organization of constitutive genes concordant with CTCF-motif orientation, whereas RNAPII interacts within these structures by selectively drawing cell-type-specific genes towards CTCF-foci and forming RNAPII foci for coordinated transcription. Furthermore, allelic-variants linked to disease susceptibility are found to impact chromatin topology and transcriptional regulation. Importantly, 3D-genome simulation suggested a model of chromatin folding around chromosomal axes, where CTCF involves in defining the interface between condensed and open compartments for structural regulation. Our new 3D-genome strategy thus provides novel insights to explore the topological mechanism of human variations and diseases.
Overall design Investigation of chromatin organization and function by CTCF ChIA-PET
Contributor(s) Luo OJ, Tang Z, Li X, Ruan Y
Citation(s) 26686651, 27625391
Submission date Sep 09, 2015
Last update date May 15, 2019
Contact name Oscar J. Luo
Organization name The Jackson Laboratory for Genomic Medicine
Street address 10 Discovery Dr
City Farmington
State/province CT
ZIP/Postal code 06030
Country USA
Platforms (2)
GPL16791 Illumina HiSeq 2500 (Homo sapiens)
GPL18573 Illumina NextSeq 500 (Homo sapiens)
Samples (6)
GSM1872886 GM12878_CTCF
GSM1872887 GM12878_RNAPII
GSM1872888 HeLa_CTCF
BioProject PRJNA295132
SRA SRP063492

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Supplementary file Size Download File type/resource
GSE72816_RAW.tar 379.1 Mb (http)(custom) TAR (of BW, TXT)
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Raw data are available in SRA
Processed data provided as supplementary file

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