Description

This track was produced as part of the ENCODE Project. It shows the locations of protein factor mediated chromatin interactions determined by Chromatin Interaction Analysis with Paired-End Tag (ChIA-PET) data (Fullwood et al., 2010) extracted from five different human cancer cell lines (K562 (chronic myeloid leukemia), HCT116 (colorectal cancer), HeLa-S3 (cervical cancer), MCF-7 (breast cancer), and NB4 (promyelocytic)). A chromatin interaction is defined as the association of 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, ChIA-PET experiments generate transcription factor 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. The protein factors displayed in the track include estrogen receptor alpha (ERα), RNA polymerase II (RNAPII), and CCCTC binding factor (CTCF).

Display Conventions and Configuration

In the graphical display, the PETs are represented by two blocks one for each end. These blocks are connected by a horizontal line if both ends are in the same chromosome. If the two ends are on different chromosomes, only one block will display. PET sequences that overlap at both ends form PET clusters. The number of PETs in a cluster reflects the strength of a chromatin interaction. Singleton PETs (PETs without a cluster) are potentially false positives, whereas PET clusters of more than 3 PETs could indicate genuine chromatin interactions. The density graph of the tags shows the ChIP enrichment at different points of genome, and high peaks indicate transcription factor binding sites.

To show only selected subtracks, uncheck the boxes next to the tracks that you wish to hide.

Interactions

ChIA-PET Chromatin Interaction PET clusters: Two different genomic regions in the chromatin are genomically far from each other or in different chromosomes, but are spatially close to each other in the nucleus and interact with each other for regulatory functions. BED12 format is used to represent the data.

Signal

Density graph (wiggle) of signal enrichment based on aligned read density.

Metadata for a particular subtrack can be found by clicking the down arrow in the list of subtracks.

Methods

Chromatin interaction analysis with paired-end tag sequencing (ChIA-PET) is a global de novo high-throughput method for characterizing the 3-dimensional structure of chromatin in the nucleus. In the ChIA-PET protocol, samples were cross-linked and fragmented, then subjected to chromatin immunoprecipitation. The DNA fragments that were brought together by the chromatin interactions were then proximity-ligated. During this proximity-ligation step, the half-linkers (created by the fragmentation) containing flanking MmeI sites (type IIS restriction enzymes) were first ligated to the DNA fragments and then 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. MmeI cuts 20 base pairs away from its recognition site. Tag-linker-tag (paired-end tag, PET) constructs were sequenced by ultra-high-throughput methods (Illumina or SOLiD paired-end sequencing). ChIA-PET reads were processed with the ChIA-PET Tool (Li et al., 2010) 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.

Verification

Chromatin interactions identified by ChIA-PET have been validated by 3C, ChIP-3C, 4C and DNA-FISH (Fullwood et al., 2009).

Credits

Genome Institute of Singapore: Guoliang Li, Xiaoan Ruan, Kuljeet Singh Sandhu, Fabianus Hendriyan Mulawadi, Huay Mei Poh, Yufen Goh, Su Qin Peh, Wing-Kin Sung, Yijun Ruan

Stanford University: Raymond Auerbach, Michael Snyder

References

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 et al. An oestrogen-receptor-alpha-bound human chromatin interactome. Nature. 2009 Nov 5;462(7269):58-64.

Li G, Fullwood MJ, Xu H, Mulawadi FH, Velkov S, Vega V, Ariyaratne PN, Mohamed YB, Ooi HS, Tennakoon C et al. ChIA-PET tool for comprehensive chromatin interaction analysis with paired-end tag sequencing. Genome Biol. 2010;11(2):R22.

Publications

Li G, Ruan X, Auerbach RK, Sandhu KS, Zheng M, Wang P, Poh HM, Goh Y, Lim J, Zhang J et al. Extensive promoter-centered chromatin interactions provide a topological basis for transcription regulation. Cell. 2012 Jan 20;148(1-2):84-98.

Data Release Policy

Data users may freely use ENCODE data, but may not, without prior consent, submit publications that use an unpublished ENCODE dataset until nine months following the release of the dataset. This date is listed in the Restricted Until column, above. The full data release policy for ENCODE is available here.