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Methods for comparative ChIA-PET and Hi-C data analysis.
Methods 2019M

Abstract

The three-dimensional architecture of chromatin in the nucleus is important for genome regulation and function. Advanced high-throughput sequencing-based methods have been developed for capturing chromatin interactions (Hi-C, genome-wide chromosome conformation capture) or enriching for those involving a specific protein (ChIA-PET, chromatin interaction analysis with paired-end tag sequencing). There is widespread interest in utilizing and interpreting ChIA-PET and Hi-C. We review methods for comparative ChIA-PET and Hi-C data analysis and visualization. The topics reviewed include: downloading ChIA-PET and Hi-C data from the ENCODE and 4DN portals; processing ChIA-PET data using ChIA-PIPE; processing Hi-C data using Juicer or distiller and cooler; viewing 2D contact maps using Juicebox or Higlass; viewing peaks, loops, and domains using BASIC Browser; annotating convergent and tandem CTCF loops.

Authors+Show Affiliations

The Jackson Laboratory for Genomic Medicine, Farmington, Connecticut, USA.The Jackson Laboratory for Genomic Medicine, Farmington, Connecticut, USA.The Jackson Laboratory for Genomic Medicine, Farmington, Connecticut, USA; Department of Genetics and Genome Sciences, University of Connecticut Health Center, Farmington, Connecticut, USA. Electronic address: yijun.ruan@jax.org.

Pub Type(s)

Journal Article
Review

Language

eng

PubMed ID

31629084

Citation

Capurso, Dan, et al. "Methods for Comparative ChIA-PET and Hi-C Data Analysis." Methods (San Diego, Calif.), 2019.
Capurso D, Tang Z, Ruan Y. Methods for comparative ChIA-PET and Hi-C data analysis. Methods. 2019.
Capurso, D., Tang, Z., & Ruan, Y. (2019). Methods for comparative ChIA-PET and Hi-C data analysis. Methods (San Diego, Calif.), doi:10.1016/j.ymeth.2019.09.019.
Capurso D, Tang Z, Ruan Y. Methods for Comparative ChIA-PET and Hi-C Data Analysis. Methods. 2019 Oct 16; PubMed PMID: 31629084.
* Article titles in AMA citation format should be in sentence-case
TY - JOUR T1 - Methods for comparative ChIA-PET and Hi-C data analysis. AU - Capurso,Dan, AU - Tang,Zhonghui, AU - Ruan,Yijun, Y1 - 2019/10/16/ PY - 2019/03/19/received PY - 2019/09/27/revised PY - 2019/09/28/accepted PY - 2019/10/20/entrez PY - 2019/10/20/pubmed PY - 2019/10/20/medline JF - Methods (San Diego, Calif.) JO - Methods N2 - The three-dimensional architecture of chromatin in the nucleus is important for genome regulation and function. Advanced high-throughput sequencing-based methods have been developed for capturing chromatin interactions (Hi-C, genome-wide chromosome conformation capture) or enriching for those involving a specific protein (ChIA-PET, chromatin interaction analysis with paired-end tag sequencing). There is widespread interest in utilizing and interpreting ChIA-PET and Hi-C. We review methods for comparative ChIA-PET and Hi-C data analysis and visualization. The topics reviewed include: downloading ChIA-PET and Hi-C data from the ENCODE and 4DN portals; processing ChIA-PET data using ChIA-PIPE; processing Hi-C data using Juicer or distiller and cooler; viewing 2D contact maps using Juicebox or Higlass; viewing peaks, loops, and domains using BASIC Browser; annotating convergent and tandem CTCF loops. SN - 1095-9130 UR - https://www.unboundmedicine.com/medline/citation/31629084/Methods_for_comparative_ChIA-PET_and_Hi-C_data_analysis L2 - https://linkinghub.elsevier.com/retrieve/pii/S1046-2023(19)30100-8 DB - PRIME DP - Unbound Medicine ER -