Trac-looping measures genome structure and chromatin accessibility

被引：55
作者：
Lai, Binbin [1 ]
Tang, Qingsong [1 ]
Jin, Wenfei [2 ]
Hu, Gangqing [1 ]
Wangsa, Darawalee [3 ]
Cui, Kairong [1 ]
Stanton, Benjamin Z. [1 ]
Ren, Gang [1 ]
Ding, Yi [1 ,4 ]
Zhao, Ming [5 ]
Liu, Shuai [1 ]
Song, Jiuzhou [4 ]
Ried, Thomas [3 ]
Zhao, Keji [1 ]
机构：
[1] NHLBI, Lab Epigenome Biol, Syst Biol Ctr, NIH, Bldg 10, Bethesda, MD 20892 USA
[2] South Univ Sci & Technol China, Dept Biol, Shenzhen, Peoples R China
[3] NCI, Genet Branch, Ctr Canc Res, NIH, Bethesda, MD 20892 USA
[4] Univ Maryland, Dept Anim & Avian Sci, College Pk, MD 20742 USA
[5] NIAID, Prot Chem Core, Res Technol Branch, NIH, Rockville, MD USA
来源：
NATURE METHODS | 2018年 / 15卷 / 09期
关键词：
BETA-GLOBIN LOCUS; HIGH-RESOLUTION; CHROMOSOME CONFORMATION; HUMAN-CELLS; HI-C; YEAST GENOME; MICRO-C; NUCLEOSOME; REVEALS; ORGANIZATION;
D O I：
10.1038/s41592-018-0107-y
中图分类号：
Q5 [生物化学];
学科分类号：
071010 ; 081704 ;
摘要：
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.
引用
收藏
页码：741 / +
页数：10
相关论文
共 59 条
  • [1] Rapid, low-input, low-bias construction of shotgun fragment libraries by high-density in vitro transposition
    Adey, Andrew
    Morrison, Hilary G.
    Asan
    Xun, Xu
    Kitzman, Jacob O.
    Turner, Emily H.
    Stackhouse, Bethany
    MacKenzie, Alexandra P.
    Caruccio, Nicholas C.
    Zhang, Xiuqing
    Shendure, Jay
    [J]. GENOME BIOLOGY, 2010, 11 (12)
  • [2] MEME SUITE: tools for motif discovery and searching
    Bailey, Timothy L.
    Boden, Mikael
    Buske, Fabian A.
    Frith, Martin
    Grant, Charles E.
    Clementi, Luca
    Ren, Jingyuan
    Li, Wilfred W.
    Noble, William S.
    [J]. NUCLEIC ACIDS RESEARCH, 2009, 37 : W202 - W208
  • [3] High-resolution profiling of histone methylations in the human genome
    Barski, Artern
    Cuddapah, Suresh
    Cui, Kairong
    Roh, Tae-Young
    Schones, Dustin E.
    Wang, Zhibin
    Wei, Gang
    Chepelev, Iouri
    Zhao, Keji
    [J]. CELL, 2007, 129 (04) : 823 - 837
  • [4] Complex multi-enhancer contacts captured by genome architecture mapping
    Beagrie, Robert A.
    Scialdone, Antonio
    Schueler, Markus
    Kraemer, Dorothee C. A.
    Chotalia, Mita
    Xie, Sheila Q.
    Barbieri, Mariano
    de Santiago, Ines
    Lavitas, Liron-Mark
    Branco, Miguel R.
    Fraser, James
    Dostie, Josee
    Game, Laurence
    Dillon, Niall
    Edwards, Paul A. W.
    Nicodemi, Mario
    Pombo, Ana
    [J]. NATURE, 2017, 543 (7646) : 519 - +
  • [5] The NIH Roadmap Epigenomics Mapping Consortium
    Bernstein, Bradley E.
    Stamatoyannopoulos, John A.
    Costello, Joseph F.
    Ren, Bing
    Milosavljevic, Aleksandar
    Meissner, Alexander
    Kellis, Manolis
    Marra, Marco A.
    Beaudet, Arthur L.
    Ecker, Joseph R.
    Farnham, Peggy J.
    Hirst, Martin
    Lander, Eric S.
    Mikkelsen, Tarjei S.
    Thomson, James A.
    [J]. NATURE BIOTECHNOLOGY, 2010, 28 (10) : 1045 - 1048
  • [6] Multiscale 3D Genome Rewiring during Mouse Neural Development
    Bonev, Boyan
    Cohen, Netta Mendelson
    Szabo, Quentin
    Fritsch, Lauriane
    Papadopoulos, Giorgio L.
    Lubling, Yaniv
    Xu, Xiaole
    Lv, Xiaodan
    Hugnot, Jean-Philippe
    Tanay, Amos
    Cavalli, Giacomo
    [J]. CELL, 2017, 171 (03) : 557 - +
  • [7] Buenrostro JD, 2013, NAT METHODS, V10, P1213, DOI [10.1038/NMETH.2688, 10.1038/nmeth.2688]
  • [8] Reconstruction of enhancer-target networks in 935 samples of human primary cells, tissues and cell lines
    Cao, Qin
    Anyansi, Christine
    Hu, Xihao
    Xu, Liangliang
    Xiong, Lei
    Tang, Wenshu
    Mok, Myth T. S.
    Cheng, Chao
    Fan, Xiaodan
    Gerstein, Mark
    Cheng, Alfred S. L.
    Yip, Kevin Y.
    [J]. NATURE GENETICS, 2017, 49 (10) : 1428 - +
  • [9] Characterization of genome-wide enhancer-promoter interactions reveals co-expression of interacting genes and modes of higher order chromatin organization
    Chepelev, Iouri
    Wei, Gang
    Wangsa, Dara
    Tang, Qingsong
    Zhao, Keji
    [J]. CELL RESEARCH, 2012, 22 (03) : 490 - 503
  • [10] Cremer Marion, 2008, V463, P205, DOI 10.1007/978-1-59745-406-3_15
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