Literature DB >> 30150754

Trac-looping measures genome structure and chromatin accessibility.

Binbin Lai1, Qingsong Tang1, Wenfei Jin2, Gangqing Hu1, Darawalee Wangsa3, Kairong Cui1, Benjamin Z Stanton1, Gang Ren1, Yi Ding1,4, Ming Zhao5, Shuai Liu1, Jiuzhou Song4, Thomas Ried3, Keji Zhao6.   

Abstract

Long-range chromatin interactions play critical roles in genome organization and regulation of transcription. We now report transposase-mediated analysis of chromatin looping (Trac-looping) for simultaneous detection of multiscale genome-wide chromatin interactions among regulatory elements and chromatin accessibility. With this technique, a bivalent oligonucleotide linker is inserted between two interacting regions such that the chromatin interactions are captured without prior chromatin fragmentation and proximity-based ligation. Application of Trac-looping to human CD4+ T cells revealed substantial reorganization of enhancer-promoter interactions associated with changes in gene expression after T cell receptor stimulation.

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Year:  2018        PMID： 30150754      PMCID： PMC7212307          DOI： 10.1038/s41592-018-0107-y

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


  53 in total

1.  Looping and interaction between hypersensitive sites in the active beta-globin locus.

Authors:  Bas Tolhuis; Robert Jan Palstra; Erik Splinter; Frank Grosveld; Wouter de Laat
Journal:  Mol Cell       Date:  2002-12       Impact factor: 17.970

2.  Proximity among distant regulatory elements at the beta-globin locus requires GATA-1 and FOG-1.

Authors:  Christopher R Vakoc; Danielle L Letting; Nele Gheldof; Tomoyuki Sawado; M A Bender; Mark Groudine; Mitchell J Weiss; Job Dekker; Gerd A Blobel
Journal:  Mol Cell       Date:  2005-02-04       Impact factor: 17.970

3.  Multicolor 3D fluorescence in situ hybridization for imaging interphase chromosomes.

Authors:  Marion Cremer; Florian Grasser; Christian Lanctôt; Stefan Müller; Michaela Neusser; Roman Zinner; Irina Solovei; Thomas Cremer
Journal:  Methods Mol Biol       Date:  2008

4.  Klf4 organizes long-range chromosomal interactions with the oct4 locus in reprogramming and pluripotency.

Authors:  Zong Wei; Fan Gao; Sewoon Kim; Hongzhen Yang; Jungmook Lyu; Woojin An; Kai Wang; Wange Lu
Journal:  Cell Stem Cell       Date:  2013-06-06       Impact factor: 24.633

5.  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

6.  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

7.  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

8.  Hi-Corrector: a fast, scalable and memory-efficient package for normalizing large-scale Hi-C data.

Authors:  Wenyuan Li; Ke Gong; Qingjiao Li; Frank Alber; Xianghong Jasmine Zhou
Journal:  Bioinformatics       Date:  2014-11-12       Impact factor: 6.937

9.  Multiscale 3D Genome Rewiring during Mouse Neural Development.

Authors:  Boyan Bonev; Netta Mendelson Cohen; Quentin Szabo; Lauriane Fritsch; Giorgio L Papadopoulos; Yaniv Lubling; Xiaole Xu; Xiaodan Lv; Jean-Philippe Hugnot; Amos Tanay; Giacomo Cavalli
Journal:  Cell       Date:  2017-10-19       Impact factor: 41.582

10.  Multiplexed analysis of chromosome conformation at vastly improved sensitivity.

Authors:  James O J Davies; Jelena M Telenius; Simon J McGowan; Nigel A Roberts; Stephen Taylor; Douglas R Higgs; Jim R Hughes
Journal:  Nat Methods       Date:  2015-11-23       Impact factor: 28.547
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  24 in total

Review 1.  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 2.  Epigenetic reprogramming of immune cells in injury, repair, and resolution.

Authors:  Katarzyna Placek; Joachim L Schultze; Anna C Aschenbrenner
Journal:  J Clin Invest       Date:  2019-07-22       Impact factor: 14.808

Review 3.  Advancements in mapping 3D genome architecture.

Authors:  Daniel J McKay; Alexis V Stutzman; Jill M Dowen
Journal:  Methods       Date:  2019-06-12       Impact factor: 3.608

4.  HiCAR is a robust and sensitive method to analyze open-chromatin-associated genome organization.

Authors:  Xiaolin Wei; Yu Xiang; Derek T Peters; Choiselle Marius; Tongyu Sun; Ruocheng Shan; Jianhong Ou; Xin Lin; Feng Yue; Wei Li; Kevin W Southerland; Yarui Diao
Journal:  Mol Cell       Date:  2022-02-22       Impact factor: 17.970

5.  cLoops2: a full-stack comprehensive analytical tool for chromatin interactions.

Authors:  Yaqiang Cao; Shuai Liu; Gang Ren; Qingsong Tang; Keji Zhao
Journal:  Nucleic Acids Res       Date:  2022-01-11       Impact factor: 16.971

Review 6.  Three-dimensional genome organization in immune cell fate and function.

Authors:  Sergi Cuartero; Grégoire Stik; Ralph Stadhouders
Journal:  Nat Rev Immunol       Date:  2022-09-20       Impact factor: 108.555

7.  Evaluation of 3D Chromatin Interactions Using Hi-C.

Authors:  Gangqing Hu
Journal:  Methods Mol Biol       Date:  2020

Review 8.  Advances in technologies for 3D genomics research.

Authors:  Yan Zhang; Guoliang Li
Journal:  Sci China Life Sci       Date:  2020-05-08       Impact factor: 6.038

9.  Gas chromatography/mass spectrometry-based metabolite profiling of coffee beans obtained from different altitudes and origins with various postharvest processing.

Authors:  Fitri Amalia; Pingkan Aditiawati; Sastia Prama Putri; Eiichiro Fukusaki
Journal:  Metabolomics       Date:  2021-07-12       Impact factor: 4.290

Review 10.  Deciphering the Complexity of 3D Chromatin Organization Driving Lymphopoiesis and Lymphoid Malignancies.

Authors:  Laurianne Scourzic; Eralda Salataj; Effie Apostolou
Journal:  Front Immunol       Date:  2021-05-14       Impact factor: 7.561
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