The genomic binding sites of a noncoding RNA

被引：312

作者：

Simon, Matthew D. ^{[1
]}

Wang, Charlotte I. ^{[2
]}

Kharchenko, Peter V. ^{[3
,4
]}

West, Jason A. ^{[1
]}

Chapman, Brad A. ^{[1
]}

Alekseyenko, Artyom A. ^{[2
]}

Borowsky, Mark L. ^{[1
]}

Kuroda, Mitzi I. ^{[2
]}

Kingston, Robert E. ^{[1
]}

机构：

[1] Harvard Univ, Sch Med, Dept Genet, Dept Mol Biol,Massachusetts Gen Hosp, Boston, MA 02114 USA

[2] Harvard Univ, Sch Med, Div Genet, Dept Med,Brigham & Womens Hosp, Boston, MA 02115 USA

[3] Harvard Univ, Sch Med, Ctr Biomed Informat, Boston, MA 02115 USA

[4] Childrens Hosp, Informat Program, Boston, MA 02115 USA

来源：

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA | 2011年 / 108卷 / 51期

基金：

美国国家卫生研究院;

关键词：

chromatin-associated RNAs; chromatin-modifying complexes; RNase H mapping; DROSOPHILA DOSAGE COMPENSATION; MALE X-CHROMOSOME; ANALYSIS REVEALS; GENE-EXPRESSION; HEAT-SHOCK; CHROMATIN; COMPLEX; CELLS; TRANSCRIPTION; PROTEINS;

D O I：

10.1073/pnas.1113536108

中图分类号：

O [数理科学和化学]; P [天文学、地球科学]; Q [生物科学]; N [自然科学总论];

学科分类号：

07 ; 0710 ; 09 ;

摘要：

Long noncoding RNAs (lncRNAs) have important regulatory roles and can function at the level of chromatin. To determine where lncRNAs bind to chromatin, we developed capture hybridization analysis of RNA targets (CHART), a hybridization-based technique that specifically enriches endogenous RNAs along with their targets from reversibly cross-linked chromatin extracts. CHART was used to enrich the DNA and protein targets of endogenous lncRNAs from flies and humans. This analysis was extended to genome-wide mapping of roX2, a well-studied ncRNA involved in dosage compensation in Drosophila. CHART revealed that roX2 binds at specific genomic sites that coincide with the binding sites of proteins from the male-specific lethal complex that affects dosage compensation. These results reveal the genomic targets of roX2 and demonstrate how CHART can be used to study RNAs in a manner analogous to chromatin immunoprecipitation for proteins.

引用

页码：20497 / 20502

页数：6

共 66 条

[1] High-resolution ChIP-chip analysis reveals that the Drosophila MSL complex selectively identifies active genes on the male X chromosome [J].

Alekseyenko, AA ;

Larschan, E ;

Lai, WR ;

Park, PJ ;

Kuroda, MI .

GENES & DEVELOPMENT, 2006, 20 (07) :848-857

[2] A sequence motif within chromatin entry sites directs MSL establishment on the Drosophila X chromosome [J].

Alekseyenko, Artyom A. ;

Peng, Shouyong ;

Larschan, Erica ;

Gorchakov, Andrey A. ;

Lee, Ok-Kyung ;

Kharchenko, Peter ;

McGrath, Sean D. ;

Wang, Charlotte I. ;

Mardis, Elaine R. ;

Park, Peter J. ;

Kuroda, Mitzi I. .

CELL, 2008, 134 (04) :599-609

[3] Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project [J].

Birney, Ewan ;

Stamatoyannopoulos, John A. ;

Dutta, Anindya ;

Guigo, Roderic ;

Gingeras, Thomas R. ;

Margulies, Elliott H. ;

Weng, Zhiping ;

Snyder, Michael ;

Dermitzakis, Emmanouil T. ;

Stamatoyannopoulos, John A. ;

Thurman, Robert E. ;

Kuehn, Michael S. ;

Taylor, Christopher M. ;

Neph, Shane ;

Koch, Christoph M. ;

Asthana, Saurabh ;

Malhotra, Ankit ;

Adzhubei, Ivan ;

Greenbaum, Jason A. ;

Andrews, Robert M. ;

Flicek, Paul ;

Boyle, Patrick J. ;

Cao, Hua ;

Carter, Nigel P. ;

Clelland, Gayle K. ;

Davis, Sean ;

Day, Nathan ;

Dhami, Pawandeep ;

Dillon, Shane C. ;

Dorschner, Michael O. ;

Fiegler, Heike ;

Giresi, Paul G. ;

Goldy, Jeff ;

Hawrylycz, Michael ;

Haydock, Andrew ;

Humbert, Richard ;

James, Keith D. ;

Johnson, Brett E. ;

Johnson, Ericka M. ;

Frum, Tristan T. ;

Rosenzweig, Elizabeth R. ;

Karnani, Neerja ;

Lee, Kirsten ;

Lefebvre, Gregory C. ;

Navas, Patrick A. ;

Neri, Fidencio ;

Parker, Stephen C. J. ;

Sabo, Peter J. ;

Sandstrom, Richard ;

Shafer, Anthony .

NATURE, 2007, 447 (7146) :799-816

[4] Long-range chromatin regulatory interactions in vivo [J].

Carter, D ;

Chakalova, L ;

Osborne, CS ;

Dai, YF ;

Fraser, P .

NATURE GENETICS, 2002, 32 (04) :623-626

[5] Altered Nuclear Retention of mRNAs Containing Inverted Repeats in Human Embryonic Stem Cells: Functional Role of a Nuclear Noncoding RNA [J].

Chen, Ling-Ling ;

Carmichael, Gordon G. .

MOLECULAR CELL, 2009, 35 (04) :467-478

[6] Genomic Maps of Long Noncoding RNA Occupancy Reveal Principles of RNA-Chromatin Interactions [J].

Chu, Ci ;

Qu, Kun ;

Zhong, Franklin L. ;

Artandi, Steven E. ;

Chang, Howard Y. .

MOLECULAR CELL, 2011, 44 (04) :667-678

[7] The Reality of Pervasive Transcription [J].

Clark, Michael B. ;

Amaral, Paulo P. ;

Schlesinger, Felix J. ;

Dinger, Marcel E. ;

Taft, Ryan J. ;

Rinn, John L. ;

Ponting, Chris P. ;

Stadler, Peter F. ;

Morris, Kevin V. ;

Morillon, Antonin ;

Rozowsky, Joel S. ;

Gerstein, Mark B. ;

Wahlestedt, Claes ;

Hayashizaki, Yoshihide ;

Carninci, Piero ;

Gingeras, Thomas R. ;

Mattick, John S. .

PLOS BIOLOGY, 2011, 9 (07)

[8] An Architectural Role for a Nuclear Noncoding RNA: NEAT1 RNA Is Essential for the Structure of Paraspeckles [J].

Clemson, Christine M. ;

Hutchinson, John N. ;

Sara, Sergio A. ;

Ensminger, Alexander W. ;

Fox, Archa H. ;

Chess, Andrew ;

Lawrence, Jeanne B. .

MOLECULAR CELL, 2009, 33 (06) :717-726

[9] HITS-CLIP: panoramic views of protein-RNA regulation in living cells [J].

Darnell, Robert B. .

WILEY INTERDISCIPLINARY REVIEWS-RNA, 2010, 1 (02) :266-286

[10] Purification of Proteins Associated with Specific Genomic Loci [J].

Dejardin, Jerome ;

Kingston, Robert E. .

CELL, 2009, 136 (01) :175-186

← 1 2 3 4 5 6 7 →