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Series GSE33664 Query DataSets for GSE33664
Status Public on Jan 20, 2012
Title Extensive promoter-centered chromatin interactions provide a topological basis for transcription regulation
Organism Homo sapiens
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Summary Higher-order chromosomal organization for transcription regulation is poorly understood in eukaryotes. Using genome-wide Chromatin Interaction Analysis with Paired-End-Tag sequencing (ChIA-PET), we mapped long-range chromatin interactions associated with RNA polymerase II in human cells and uncovered widespread promoter-centered intragenic, extragenic, and intergenic interactions. These interactions further aggregated into higher-order clusters, wherein proximal and distal genes were engaged through promoter-promoter interactions. Most genes with promoter-promoter interactions were active and transcribed cooperatively, and some interacting promoters could influence each other implying combinatorial complexity of transcriptional controls. Comparative analyses of different cell lines showed that cell-specific chromatin interactions could provide structural frameworks for cell-specific transcription, and suggested significant enrichment of enhancer-promoter interactions for cell-specific functions. Furthermore, genetically-identified disease-associated noncoding elements were found to be spatially engaged with corresponding genes through long-range interactions. Overall, our study provides insights into transcription regulation by three-dimensional chromatin interactions for both housekeeping and cell-specific genes in human cells.
Overall design RNA polymerase II (RNAPII) bound chromatin interactions were extracted with Chromatin Interaction Analysis with Paired-End Tag (ChIA-PET) sequencing, in order to study the transcription regulations with RNAPII-associated long-range chromatin interactions. Five cell lines, namely MCF7 (ATCC# HTB-22), K562 (ATCC# CCL-243), HCT116 (ATCC# CCL-247), HeLa (ATCC# CCL-2.2), and NB4 (Roussel and Lanotte, 2001) (provided by Dr. Sherman Weissman, Yale University), were grown under standard culture conditions and harvested at log phase. Harvested cells were cross-linked using 1% formaldehyde followed by neutralization with 0.2M glycine. Chromatin was isolated and subjected to ChIA-PET protocol as described in Fullwood et al (Fullwood et al: An oestrogen-receptor-alpha-bound human chromatin interactome. Nature 2009, 462(7269):58-64). The ChIA-PET sequence reads were processed and analyzed using ChIA-PET Tool (Li et al: ChIA-PET tool for comprehensive chromatin interaction analysis with paired-end tag sequencing. Genome Biol 2010, 11(2):R22).
Contributor(s) Li G, Ruan X
Citation(s) 22265404, 23103170
Submission date Nov 14, 2011
Last update date Aug 16, 2019
Contact name Guoliang Li
Organization name Genome Institute of Singapore
Department Computational and Systems Biology
Street address 60 Biopolis Street, #02-01, Genome
City Singapore
ZIP/Postal code 138672
Country Singapore
Platforms (1)
GPL10999 Illumina Genome Analyzer IIx (Homo sapiens)
Samples (10)
GSM832456 gisChiaPet_MCF7_RNAPII_pilot_rep1
GSM832457 gisChiaPet_MCF7_RNAPII_pilot_rep2
GSM832458 gisChiaPet_MCF7_RNAPII_saturated_rep1
SRA SRP009419
BioProject PRJNA148637

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SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE33664_GSM832456_CHM040T_hg19.hg19.bam 1.9 Gb (ftp)(http) BAM
GSE33664_GSM832457_CHM053T.hg19.bam 1.2 Gb (ftp)(http) BAM
GSE33664_GSM832458_CHM160M_L2_lane11.hg19.bam 764.1 Mb (ftp)(http) BAM
GSE33664_GSM832459_CHM160M_L2_lane23.hg19.bam 750.9 Mb (ftp)(http) BAM
GSE33664_GSM832460_CHH524T.hg19.bam 767.2 Mb (ftp)(http) BAM
GSE33664_GSM832461_IHH025T_hg19.hg19.bam 896.9 Mb (ftp)(http) BAM
GSE33664_GSM832462_IHN009T_hg19.hg19.bam 625.1 Mb (ftp)(http) BAM
GSE33664_GSM832463_CHK004T_hg19.hg19.bam 1.3 Gb (ftp)(http) BAM
GSE33664_GSM832464_CHK019_3r69_t1.hg19.bam 638.6 Mb (ftp)(http) BAM
GSE33664_GSM832465_CHK019_3r69_t2.hg19.bam 645.1 Mb (ftp)(http) BAM
GSE33664_RAW.tar 1.6 Gb (http)(custom) TAR (of BED, BW, TXT)
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Raw data are available in SRA
Processed data provided as supplementary file
Processed data are available on Series record

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