This track is produced as part of the ENCODE Chromatin Interaction Analysis with Paired-End Tag (ChIA-PET) Project. It shows the locations of RNA polymerase II-bound (RNAPII-bound) chromatin interactions determined by Paired-End Tag (PET) sequencing using proximity-ligated chromatin extracts from five different human cell lines (HCT116 (colorectal cancer), HeLa (cervical cancer), K562 (chronic myeloid leukemia), MCF7 (breast cancer), and NB4 (promyelocytic)). A chromatin interaction is defined as two regions of the genome that are far apart in terms of genomic distance, but are spatially proximate to each other in the 3-dimensional cellular nucleus.
Additionally, the RNAPII ChIA-PET experiment generates RNAPII binding sites. A binding site is defined as a region of the genome that is highly enriched by specific Chromatin ImmunoPrecipitation (ChIP) against a transcription factor, which indicates that the transcription factor binds specifically to this region. Generally, a chromatin interaction is more likely to connect two RNAPII binding sites together.
Chromosome Conformation Capture Carbon Copy (5C) (Dostie 2006) maps genomic interactions. The three-dimensional organization of chromosomes and chromatin domains is obtained by cross-linking, digestion, ligation and then detection (Dekker 2002). These data have not been engineered to display in the UCSC Genome Browser. Two 5C data sets are available for download, one from Washington University and the other from University of Massachusetts.
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Chromatin Interaction Analysis with Paired-End Tag (ChIA-PET) Sequencing is a global, de novo, high-throughput method for characterizing the 3-dimensional structure of chromatins in the nucleus. In the ChIA-PET protocol, cells were cross-linked, fragmented, and chromatin immunoprecipitated. The DNA fragments which are brought close together by the chromatin interactions were then proximity-ligated. During this proximity ligation step, the half-linkers containing flanking MmeI sites (type IIS restriction enzymes) were first ligated to the DNA fragments; then, the half-linkers were ligated to each other to form full linkers. Full linkers bridge either two ends of a self-circularized fragment, or two ends of two different chromatin fragments. The material was then reverse cross-linked, purified, and digested with MmeI. As MmeI cuts 20 base pairs away from its recognition site, tag-linker-tag (Paired-End Tag, PET) constructs were obtained, which was then sequenced by ultra-high-throughput methods (Illumina or SOLiD paired end sequencing). ChIA-PET reads were processed with ChIA-PET Tool by the following steps: linker filtering, short reads mapping, PET classification, binding site identification, and interaction cluster identification. The high-confidence binding sites and chromatin interaction clusters were reported.
Chromatin interactions identified by ChIA-PET have been validated by 3C, ChIP-3C, 4C and DNA-FISH (Fullwood et al ).
Guoliang Li, Xiaoan Ruan, Kuljeet Singh Sandhu, Fabianus Hendriyan Mulawadi, Huay Mei Poh, Yufen Goh, Su Qin Peh, Wing-Kin Sung, Yijun Ruan, Genome Institute of Singapore.
Collaborators: Raymond Auerbach, Michael Snyder, Department of Genetics, Stanford University, Stanford
Contact: Yijun Ruan
Dekker, J., Rippe, K., Dekker, M., and Kleckner, N. (2002). Capturing Chromosome Conformation. Science, 295, 1306-1311.
Dostie J, Richmond TA, Arnaout RA, Selzer RR, Lee WL, Honan TA, Rubio ED, Krumm A, Lamb J, Nusbaum C, Dekker J. Chromosome Conformation Capture Carbon Copy (5C): a massively parallel solution for mapping interactions between genomic elements. Genome Research 2006; 16(10):1299-1309.
Li G, Fullwood MJ, Xu H, Mulawadi FH, Velkov S, Vega V, Ariyaratne PN, Mohamed YB, Ooi HS, Tennakoon C, Wei CL, Ruan Y, Sung WK. ChIA-PET tool for comprehensive chromatin interaction analysis with paired-end tag sequencing. Genome Biol. 2010 Feb 25;11(2):R22.
Fullwood MJ, Han Y, Wei CL, Ruan X, Ruan Y. Chromatin interaction analysis using paired-end tag sequencing. Curr Protoc Mol Biol. 2010 Jan;Chapter 21:Unit 21 15 1-25.
Fullwood MJ, Liu MH, Pan YF, Liu J, Xu H, Mohamed YB, Orlov YL, Velkov S, Ho A, Mei PH, Chew EG, Huang PY, Welboren WJ, Han Y, Ooi HS, Ariyaratne PN, Vega VB, Luo Y, Tan PY, Choy PY, Wansa KD, Zhao B, Lim KS, Leow SC, Yow JS, Joseph R, Li H, Desai KV, Thomsen JS, Lee YK, Karuturi RK, Herve T, Bourque G, Stunnenberg HG, Ruan X, Cacheux-Rataboul V, Sung WK, Liu ET, Wei CL, Cheung E, Ruan Y. An oestrogen-receptor-alpha-bound human chromatin interactome. Nature. 2009 Nov 5;462(7269):58-64.
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