Dataset Information

Chromatin Interaction Analysis with Paired-End Tag (ChIA-PET) sequencing technology and application.

ABSTRACT:

Background

Long-range chromatin interactions play an important role in transcription regulation. Chromatin Interaction Analysis with Paired-End-Tag sequencing (ChIA-PET) is an emerging technology that has unique advantages in chromatin interaction analysis, and thus provides insight into the study of transcription regulation.

Results

This article introduces the experimental protocol and data analysis process of ChIA-PET, as well as discusses some applications using this technology. It also unveils the direction of future studies based on this technology.

Conclusions

Overall we show that ChIA-PET is the cornerstone to explore the three-dimensional (3D) chromatin structure, and certainly will lead the forthcoming wave of 3D genomics studies.

SUBMITTER: Li G

PROVIDER: S-EPMC4303937 | biostudies-literature | 2014

REPOSITORIES: biostudies-literature

ACCESS DATA

Publications

Chromatin Interaction Analysis with Paired-End Tag (ChIA-PET) sequencing technology and application.

Li Guoliang G Cai Liuyang L Chang Huidan H Hong Ping P Zhou Qiangwei Q Kulakova Ekaterina V EV Kolchanov Nikolay A NA Ruan Yijun Y

BMC genomics 20141219

<h4>Background</h4>Long-range chromatin interactions play an important role in transcription regulation. Chromatin Interaction Analysis with Paired-End-Tag sequencing (ChIA-PET) is an emerging technology that has unique advantages in chromatin interaction analysis, and thus provides insight into the study of transcription regulation.<h4>Results</h4>This article introduces the experimental protocol and data analysis process of ChIA-PET, as well as discusses some applications using this technology ...[more]

PMID: 25563301

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Project description:This data was generated by ENCODE. If you have questions about the data, contact the submitting laboratory directly (Yijun Ruan mailto:ruanyj@gis.a-star.edu.sg). If you have questions about the Genome Browser track associated with this data, contact ENCODE (mailto:genome@soe.ucsc.edu). 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 (ERa), RNA polymerase II (RNAPII), and CCCTC binding factor (CTCF). For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf 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. Chromatin interactions identified by ChIA-PET have been validated by 3C, ChIP-3C, 4C and DNA-FISH (Fullwood et al., 2009).

Dataset Information

Chromatin Interaction Analysis with Paired-End Tag (ChIA-PET) sequencing technology and application.

Background

Results

Conclusions

Publications

Chromatin Interaction Analysis with Paired-End Tag (ChIA-PET) sequencing technology and application.

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