## Description

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.

## Display Conventions and Configuration

In the graphical display, the tags (ends) are represented by blocks, and connected by a horizontal line if both ends are in the same chromosome and in a viewable window. PET sequences that overlap at both ends form PET clusters and the total count of PETs in a PET cluster reflects the strength of a chromatin interaction. Singleton PETs (PET count = 1 in a PET cluster) are most likely noise, whereas PET clusters with PET count 3 and above could indicate genuine chromatin interactions. A density track of the tags shows the ChIP enrichment at different points of genome, and high peaks indicate RNAPII binding sites. Instructions for configuring multi-view tracks are here.

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. In addition to the two replicates displayed here there are pooled replicates available as downloads.
Alignment densities (currently available only as downloads)
  The Alignment densities view shows reads mapped to the genome. BAM format is used to represent the data. The SAM/BAM tags used are QNAME, FLAG, RNAME, POS, MAPQ, CIGAR, MRNM, MPOS, ISIZE, SEQ and QUAL. For more information about the SAM output and the SAM Format Specification for more information on the SAM/BAM file format.

## Methods

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.

## Verification

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

## Credits

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

## References

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.

## 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 on the track configuration page and the download page. The full data release policy for ENCODE is available here.