Literature DB >> 36066718

Hi-C Analysis to Identify Genome-Wide Chromatin Structural Aberration in Cancer.

Atsushi Okabe1, Atsushi Kaneda2.   

Abstract

Hi-C is a method that analyzes genome-wide chromatin structure using next-generation sequencer. Chromatin structure is crucial for regulating transcription or replication, and Hi-C has revealed the hierarchical chromatin structures, such as loop, domain , and compartment structures. Aberrant alteration of these structures causes disease, and a number of structural aberrations in cancer cells have been reported recently. Besides, Hi-C can identify chromosome rearrangements that frequently occurred in cancer. Therefore, Hi-C is a powerful technique to analyze epigenomic and genomic aberrations in tumorigenesis. Here we will introduce the basic protocol of Hi-C in experimental and analytical aspects.
© 2023. The Author(s), under exclusive license to Springer Science+Business Media, LLC, part of Springer Nature.

Entities:  

Keywords:  Cancer; Chromatin structure; Chromosome conformation capture; Chromosome rearrangement; Genome architecture; Hi-C

Mesh：

Substances：

Year:  2023        PMID： 36066718     DOI： 10.1007/978-1-0716-2433-3_15

Source DB:  PubMed          Journal:  Methods Mol Biol        ISSN： 1064-3745


  36 in total

1.  Circular chromosome conformation capture (4C) uncovers extensive networks of epigenetically regulated intra- and interchromosomal interactions.

Authors:  Zhihu Zhao; Gholamreza Tavoosidana; Mikael Sjölinder; Anita Göndör; Piero Mariano; Sha Wang; Chandrasekhar Kanduri; Magda Lezcano; Kuljeet Singh Sandhu; Umashankar Singh; Vinod Pant; Vijay Tiwari; Sreenivasulu Kurukuti; Rolf Ohlsson
Journal:  Nat Genet       Date:  2006-10-08       Impact factor: 38.330

2.  Capturing chromosome conformation.

Authors:  Job Dekker; Karsten Rippe; Martijn Dekker; Nancy Kleckner
Journal:  Science       Date:  2002-02-15       Impact factor: 47.728

3.  Enhancer connectome in primary human cells identifies target genes of disease-associated DNA elements.

Authors:  Maxwell R Mumbach; Ansuman T Satpathy; Evan A Boyle; Chao Dai; Benjamin G Gowen; Seung Woo Cho; Michelle L Nguyen; Adam J Rubin; Jeffrey M Granja; Katelynn R Kazane; Yuning Wei; Trieu Nguyen; Peyton G Greenside; M Ryan Corces; Josh Tycko; Dimitre R Simeonov; Nabeela Suliman; Rui Li; Jin Xu; Ryan A Flynn; Anshul Kundaje; Paul A Khavari; Alexander Marson; Jacob E Corn; Thomas Quertermous; William J Greenleaf; Howard Y Chang
Journal:  Nat Genet       Date:  2017-09-25       Impact factor: 38.330

4.  Organization and function of the 3D genome.

Authors:  Boyan Bonev; Giacomo Cavalli
Journal:  Nat Rev Genet       Date:  2016-10-31       Impact factor: 53.242

5.  Spatial partitioning of the regulatory landscape of the X-inactivation centre.

Authors:  Elphège P Nora; Bryan R Lajoie; Edda G Schulz; Luca Giorgetti; Ikuhiro Okamoto; Nicolas Servant; Tristan Piolot; Nynke L van Berkum; Johannes Meisig; John Sedat; Joost Gribnau; Emmanuel Barillot; Nils Blüthgen; Job Dekker; Edith Heard
Journal:  Nature       Date:  2012-04-11       Impact factor: 49.962

6.  The 4D nucleome project.

Authors:  Job Dekker; Andrew S Belmont; Mitchell Guttman; Victor O Leshyk; John T Lis; Stavros Lomvardas; Leonid A Mirny; Clodagh C O'Shea; Peter J Park; Bing Ren; Joan C Ritland Politz; Jay Shendure; Sheng Zhong
Journal:  Nature       Date:  2017-09-13       Impact factor: 49.962

7.  An oestrogen-receptor-alpha-bound human chromatin interactome.

Authors:  Melissa J Fullwood; Mei Hui Liu; You Fu Pan; Jun Liu; Han Xu; Yusoff Bin Mohamed; Yuriy L Orlov; Stoyan Velkov; Andrea Ho; Poh Huay Mei; Elaine G Y Chew; Phillips Yao Hui Huang; Willem-Jan Welboren; Yuyuan Han; Hong Sain Ooi; Pramila N Ariyaratne; Vinsensius B Vega; Yanquan Luo; Peck Yean Tan; Pei Ye Choy; K D Senali Abayratna Wansa; Bing Zhao; Kar Sian Lim; Shi Chi Leow; Jit Sin Yow; Roy Joseph; Haixia Li; Kartiki V Desai; Jane S Thomsen; Yew Kok Lee; R Krishna Murthy Karuturi; Thoreau Herve; Guillaume Bourque; Hendrik G Stunnenberg; Xiaoan Ruan; Valere Cacheux-Rataboul; Wing-Kin Sung; Edison T Liu; Chia-Lin Wei; Edwin Cheung; Yijun Ruan
Journal:  Nature       Date:  2009-11-05       Impact factor: 49.962

Review 8.  The hierarchy of the 3D genome.

Authors:  Johan H Gibcus; Job Dekker
Journal:  Mol Cell       Date:  2013-03-07       Impact factor: 17.970

9.  Comprehensive mapping of long-range interactions reveals folding principles of the human genome.

Authors:  Erez Lieberman-Aiden; Nynke L van Berkum; Louise Williams; Maxim Imakaev; Tobias Ragoczy; Agnes Telling; Ido Amit; Bryan R Lajoie; Peter J Sabo; Michael O Dorschner; Richard Sandstrom; Bradley Bernstein; M A Bender; Mark Groudine; Andreas Gnirke; John Stamatoyannopoulos; Leonid A Mirny; Eric S Lander; Job Dekker
Journal:  Science       Date:  2009-10-09       Impact factor: 47.728

10.  Topological domains in mammalian genomes identified by analysis of chromatin interactions.

Authors:  Jesse R Dixon; Siddarth Selvaraj; Feng Yue; Audrey Kim; Yan Li; Yin Shen; Ming Hu; Jun S Liu; Bing Ren
Journal:  Nature       Date:  2012-04-11       Impact factor: 49.962
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