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| 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
Other
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| 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.
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| 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).
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| Contributor(s) |
Li G, Ruan X |
| Citation(s) |
22265404, 23103170 |
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| Submission date |
Nov 14, 2011 |
| Last update date |
Aug 16, 2019 |
| Contact name |
Guoliang Li |
| E-mail(s) |
ligl@gis.a-star.edu.sg
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| Organization name |
Genome Institute of Singapore
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| Department |
Computational and Systems Biology
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| Street address |
60 Biopolis Street, #02-01, Genome
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| City |
Singapore |
| ZIP/Postal code |
138672 |
| Country |
Singapore |
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| Platforms (1) |
| GPL10999 |
Illumina Genome Analyzer IIx (Homo sapiens) |
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| Samples (10)
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| GSM832456 |
gisChiaPet_MCF7_RNAPII_pilot_rep1 |
| GSM832457 |
gisChiaPet_MCF7_RNAPII_pilot_rep2 |
| GSM832458 |
gisChiaPet_MCF7_RNAPII_saturated_rep1 |
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| Relations |
| SRA |
SRP009419 |
| BioProject |
PRJNA148637 |
| 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) |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
| Processed data are available on Series record |
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