Literature DB >> 27376768

UMI-4C for quantitative and targeted chromosomal contact profiling.

Omer Schwartzman1,2,3,4, Zohar Mukamel3,4, Noa Oded-Elkayam3,4, Pedro Olivares-Chauvet3,4, Yaniv Lubling3,4, Gilad Landan3,4, Shai Izraeli1,2, Amos Tanay3,4.   

Abstract

We developed a targeted chromosome conformation capture (4C) approach that uses unique molecular identifiers (UMIs) to derive high-complexity quantitative chromosome contact profiles with controlled signal-to-noise ratios. UMI-4C detects chromosomal interactions with improved sensitivity and specificity, and it can easily be multiplexed to allow robust comparison of contact distributions between loci and conditions. This approach may open the way to the incorporation of contact distributions into quantitative models of gene regulation.

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Year:  2016        PMID： 27376768     DOI： 10.1038/nmeth.3922

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


  37 in total

1.  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

2.  Whsc1 links pluripotency exit with mesendoderm specification.

Authors:  Tian V Tian; Bruno Di Stefano; Grégoire Stik; Maria Vila-Casadesús; José Luis Sardina; Enrique Vidal; Alessandro Dasti; Carolina Segura-Morales; Luisa De Andrés-Aguayo; Antonio Gómez; Johanna Goldmann; Rudolf Jaenisch; Thomas Graf
Journal:  Nat Cell Biol       Date:  2019-06-24       Impact factor: 28.824

3.  Determination of local chromatin interactions using a combined CRISPR and peroxidase APEX2 system.

Authors:  Wenqing Qiu; Zhijiao Xu; Min Zhang; Dandan Zhang; Hui Fan; Taotao Li; Qianfeng Wang; Peiru Liu; Zaihua Zhu; Duo Du; Minjia Tan; Bo Wen; Yun Liu
Journal:  Nucleic Acids Res       Date:  2019-05-21       Impact factor: 16.971

Review 4.  Diverse Genome Topologies Characterize Dosage Compensation across Species.

Authors:  William Jordan; Leila E Rieder; Erica Larschan
Journal:  Trends Genet       Date:  2019-02-23       Impact factor: 11.639

5.  Challenges and progress in interpretation of non-coding genetic variants associated with human disease.

Authors:  Yizhou Zhu; Cagdas Tazearslan; Yousin Suh
Journal:  Exp Biol Med (Maywood)       Date:  2017-06-05

Review 6.  How best to identify chromosomal interactions: a comparison of approaches.

Authors:  James O J Davies; A Marieke Oudelaar; Douglas R Higgs; Jim R Hughes
Journal:  Nat Methods       Date:  2017-01-31       Impact factor: 28.547

7.  Capturing pairwise and multi-way chromosomal conformations using chromosomal walks.

Authors:  Pedro Olivares-Chauvet; Zohar Mukamel; Aviezer Lifshitz; Omer Schwartzman; Noa Oded Elkayam; Yaniv Lubling; Gintaras Deikus; Robert P Sebra; Amos Tanay
Journal:  Nature       Date:  2016-11-30       Impact factor: 49.962

8.  Lineage-specific dynamic and pre-established enhancer-promoter contacts cooperate in terminal differentiation.

Authors:  Adam J Rubin; Brook C Barajas; Mayra Furlan-Magaril; Vanessa Lopez-Pajares; Maxwell R Mumbach; Imani Howard; Daniel S Kim; Lisa D Boxer; Jonathan Cairns; Mikhail Spivakov; Steven W Wingett; Minyi Shi; Zhixin Zhao; William J Greenleaf; Anshul Kundaje; Michael Snyder; Howard Y Chang; Peter Fraser; Paul A Khavari
Journal:  Nat Genet       Date:  2017-08-14       Impact factor: 38.330

9.  Genomics in 3D and 4D.

Authors:  Vivien Marx
Journal:  Nat Methods       Date:  2016-09-29       Impact factor: 28.547

10.  In Situ Capture of Chromatin Interactions by Biotinylated dCas9.

Authors:  Xin Liu; Yuannyu Zhang; Yong Chen; Mushan Li; Feng Zhou; Kailong Li; Hui Cao; Min Ni; Yuxuan Liu; Zhimin Gu; Kathryn E Dickerson; Shiqi Xie; Gary C Hon; Zhenyu Xuan; Michael Q Zhang; Zhen Shao; Jian Xu
Journal:  Cell       Date:  2017-08-24       Impact factor: 41.582
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