Literature DB >> 27643841

HiChIP: efficient and sensitive analysis of protein-directed genome architecture.

Maxwell R Mumbach1,2,3, Adam J Rubin2, Ryan A Flynn1,2, Chao Dai1,2, Paul A Khavari2, William J Greenleaf1,3,4, Howard Y Chang1,2.   

Abstract

Genome conformation is central to gene control but challenging to interrogate. Here we present HiChIP, a protein-centric chromatin conformation method. HiChIP improves the yield of conformation-informative reads by over 10-fold and lowers the input requirement over 100-fold relative to that of ChIA-PET. HiChIP of cohesin reveals multiscale genome architecture with greater signal-to-background ratios than those of in situ Hi-C.

Entities:  

Mesh：

Substances：

Year:  2016        PMID： 27643841      PMCID： PMC5501173          DOI： 10.1038/nmeth.3999

Source DB:  PubMed          Journal:  Nat Methods        ISSN： 1548-7091            Impact factor:   28.547


  26 in total

1.  Structural organization of the inactive X chromosome in the mouse.

Authors:  Luca Giorgetti; Bryan R Lajoie; Ava C Carter; Mikael Attia; Ye Zhan; Jin Xu; Chong Jian Chen; Noam Kaplan; Howard Y Chang; Edith Heard; Job Dekker
Journal:  Nature       Date:  2016-07-18       Impact factor: 49.962

2.  Mango: a bias-correcting ChIA-PET analysis pipeline.

Authors:  Douglas H Phanstiel; Alan P Boyle; Nastaran Heidari; Michael P Snyder
Journal:  Bioinformatics       Date:  2015-06-01       Impact factor: 6.937

3.  Transposition of native chromatin for fast and sensitive epigenomic profiling of open chromatin, DNA-binding proteins and nucleosome position.

Authors:  Jason D Buenrostro; Paul G Giresi; Lisa C Zaba; Howard Y Chang; William J Greenleaf
Journal:  Nat Methods       Date:  2013-10-06       Impact factor: 28.547

4.  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

5.  Mediator and cohesin connect gene expression and chromatin architecture.

Authors:  Michael H Kagey; Jamie J Newman; Steve Bilodeau; Ye Zhan; David A Orlando; Nynke L van Berkum; Christopher C Ebmeier; Jesse Goossens; Peter B Rahl; Stuart S Levine; Dylan J Taatjes; Job Dekker; Richard A Young
Journal:  Nature       Date:  2010-08-18       Impact factor: 49.962

6.  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

7.  Systematic discovery and characterization of regulatory motifs in ENCODE TF binding experiments.

Authors:  Pouya Kheradpour; Manolis Kellis
Journal:  Nucleic Acids Res       Date:  2013-12-13       Impact factor: 16.971

8.  Model-based analysis of ChIP-Seq (MACS).

Authors:  Yong Zhang; Tao Liu; Clifford A Meyer; Jérôme Eeckhoute; David S Johnson; Bradley E Bernstein; Chad Nusbaum; Richard M Myers; Myles Brown; Wei Li; X Shirley Liu
Journal:  Genome Biol       Date:  2008-09-17       Impact factor: 13.583

9.  Comparison of Hi-C results using in-solution versus in-nucleus ligation.

Authors:  Takashi Nagano; Csilla Várnai; Stefan Schoenfelder; Biola-Maria Javierre; Steven W Wingett; Peter Fraser
Journal:  Genome Biol       Date:  2015-08-26       Impact factor: 13.583

10.  HiC-Pro: an optimized and flexible pipeline for Hi-C data processing.

Authors:  Nicolas Servant; Nelle Varoquaux; Bryan R Lajoie; Eric Viara; Chong-Jian Chen; Jean-Philippe Vert; Edith Heard; Job Dekker; Emmanuel Barillot
Journal:  Genome Biol       Date:  2015-12-01       Impact factor: 13.583
View more
  337 in total

1.  Computational methods for predicting 3D genomic organization from high-resolution chromosome conformation capture data.

Authors:  Kimberly MacKay; Anthony Kusalik
Journal:  Brief Funct Genomics       Date:  2020-07-29       Impact factor: 4.241

2.  Promoter of lncRNA Gene PVT1 Is a Tumor-Suppressor DNA Boundary Element.

Authors:  Seung Woo Cho; Jin Xu; Ruping Sun; Maxwell R Mumbach; Ava C Carter; Y Grace Chen; Kathryn E Yost; Jeewon Kim; Jing He; Stephanie A Nevins; Suet-Feung Chin; Carlos Caldas; S John Liu; Max A Horlbeck; Daniel A Lim; Jonathan S Weissman; Christina Curtis; Howard Y Chang
Journal:  Cell       Date:  2018-05-03       Impact factor: 41.582

Review 3.  3D Chromosomal Landscapes in Hematopoiesis and Immunity.

Authors:  Andreas Kloetgen; Palaniraja Thandapani; Aristotelis Tsirigos; Iannis Aifantis
Journal:  Trends Immunol       Date:  2019-08-15       Impact factor: 16.687

Review 4.  Towards a comprehensive catalogue of validated and target-linked human enhancers.

Authors:  Molly Gasperini; Jacob M Tome; Jay Shendure
Journal:  Nat Rev Genet       Date:  2020-01-27       Impact factor: 53.242

Review 5.  Functional Assays to Screen and Dissect Genomic Hits: Doubling Down on the National Investment in Genomic Research.

Authors:  Kiran Musunuru; Daniel Bernstein; F Sessions Cole; Mustafa K Khokha; Frank S Lee; Shin Lin; Thomas V McDonald; Ivan P Moskowitz; Thomas Quertermous; Vijay G Sankaran; David A Schwartz; Edwin K Silverman; Xiaobo Zhou; Ahmed A K Hasan; Xiao-Zhong James Luo
Journal:  Circ Genom Precis Med       Date:  2018-04

6.  GRID-seq for comprehensive analysis of global RNA-chromatin interactions.

Authors:  Bing Zhou; Xiao Li; Daji Luo; Do-Hwan Lim; Yu Zhou; Xiang-Dong Fu
Journal:  Nat Protoc       Date:  2019-06-07       Impact factor: 13.491

7.  Oncogenic Notch Promotes Long-Range Regulatory Interactions within Hyperconnected 3D Cliques.

Authors:  Jelena Petrovic; Yeqiao Zhou; Maria Fasolino; Naomi Goldman; Gregory W Schwartz; Maxwell R Mumbach; Son C Nguyen; Kelly S Rome; Yogev Sela; Zachary Zapataro; Stephen C Blacklow; Michael J Kruhlak; Junwei Shi; Jon C Aster; Eric F Joyce; Shawn C Little; Golnaz Vahedi; Warren S Pear; Robert B Faryabi
Journal:  Mol Cell       Date:  2019-02-07       Impact factor: 17.970

Review 8.  Blood disease-causing and -suppressing transcriptional enhancers: general principles and GATA2 mechanisms.

Authors:  Emery H Bresnick; Kirby D Johnson
Journal:  Blood Adv       Date:  2019-07-09

Review 9.  When function follows form: Nuclear compartment structure and the epigenetic landscape of the aging neuron.

Authors:  Johannes C M Schlachetzki; Tomohisa Toda; Jerome Mertens
Journal:  Exp Gerontol       Date:  2020-02-14       Impact factor: 4.032

10.  KLF4 is involved in the organization and regulation of pluripotency-associated three-dimensional enhancer networks.

Authors:  Dafne Campigli Di Giammartino; Andreas Kloetgen; Alexander Polyzos; Yiyuan Liu; Daleum Kim; Dylan Murphy; Abderhman Abuhashem; Paola Cavaliere; Boaz Aronson; Veevek Shah; Noah Dephoure; Matthias Stadtfeld; Aristotelis Tsirigos; Effie Apostolou
Journal:  Nat Cell Biol       Date:  2019-09-23       Impact factor: 28.824
View more

北京卡尤迪生物科技股份有限公司 © 2022-2023.