Trac-looping measures genome structure and chromatin accessibility

被引：60

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：

070307 [化学生物学];

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

页码：741 / +

页数：10

共 59 条

[1]

Rapid, low-input, low-bias construction of shotgun fragment libraries by high-density in vitro transposition [J].

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 .

GENOME BIOLOGY, 2010, 11 (12)

[2]

MEME SUITE: tools for motif discovery and searching [J].

Bailey, Timothy L. ;

Boden, Mikael ;

Buske, Fabian A. ;

Frith, Martin ;

Grant, Charles E. ;

Clementi, Luca ;

Ren, Jingyuan ;

Li, Wilfred W. ;

Noble, William S. .

NUCLEIC ACIDS RESEARCH, 2009, 37 :W202-W208

[3]

High-resolution profiling of histone methylations in the human genome [J].

Barski, Artern ;

Cuddapah, Suresh ;

Cui, Kairong ;

Roh, Tae-Young ;

Schones, Dustin E. ;

Wang, Zhibin ;

Wei, Gang ;

Chepelev, Iouri ;

Zhao, Keji .

CELL, 2007, 129 (04) :823-837

[4]

Complex multi-enhancer contacts captured by genome architecture mapping [J].

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 .

NATURE, 2017, 543 (7646) :519-+

[5]

The NIH Roadmap Epigenomics Mapping Consortium [J].

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. .

NATURE BIOTECHNOLOGY, 2010, 28 (10) :1045-1048

[6]

Multiscale 3D Genome Rewiring during Mouse Neural Development [J].

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 .

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 [J].

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. .

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 [J].

Chepelev, Iouri ;

Wei, Gang ;

Wangsa, Dara ;

Tang, Qingsong ;

Zhao, Keji .

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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