Mapping Human Epigenomes

被引：386

作者：

Rivera, Chloe M. ^{[1
,2
]}

Ren, Bing ^{[1
,3
]}

机构：

[1] Univ Calif San Diego, Sch Med, UCSD Moores Canc Ctr, Ludwig Inst Canc Res, La Jolla, CA 92093 USA

[2] Univ Calif San Diego, Sch Med, UCSD Moores Canc Ctr, Inst Genom Med,Biomed Sci Grad Program, La Jolla, CA 92093 USA

[3] Univ Calif San Diego, Sch Med, UCSD Moores Canc Ctr, Inst Genom Med,Dept Cellular & Mol Med, La Jolla, CA 92093 USA

来源：

CELL | 2013年 / 155卷 / 01期

关键词：

DNA METHYLATION; CHROMATIN STATE; SINGLE-MOLECULE; HISTONE MODIFICATIONS; NUCLEOSOME POSITIONS; DYNAMIC REGULATION; TET PROTEINS; GENOME; TRANSCRIPTION; ENHANCERS;

D O I：

10.1016/j.cell.2013.09.011

中图分类号：

Q5 [生物化学]; Q7 [分子生物学];

学科分类号：

071010 ; 081704 ;

摘要：

As the second dimension to the genome, the epigenome contains key information specific to every type of cells. Thousands of human epigenome maps have been produced in recent years thanks to rapid development of high throughput epigenome mapping technologies. In this review, we discuss the current epigenome mapping toolkit and utilities of epigenome maps. We focus particularly on mapping of DNA methylation, chromatin modification state, and chromatin structures, and emphasize the use of epigenome maps to delineate human gene regulatory sequences and developmental programs. We also provide a perspective on the progress of the epigenomics field and challenges ahead.

引用

页码：39 / 55

页数：17

共 158 条

[31] DNase I sensitivity QTLs are a major determinant of human expression variation [J].

Degner, Jacob F. ;

Pai, Athma A. ;

Pique-Regi, Roger ;

Veyrieras, Jean-Baptiste ;

Gaffney, Daniel J. ;

Pickrell, Joseph K. ;

De Leon, Sherryl ;

Michelini, Katelyn ;

Lewellen, Noah ;

Crawford, Gregory E. ;

Stephens, Matthew ;

Gilad, Yoav ;

Pritchard, Jonathan K. .

NATURE, 2012, 482 (7385) :390-394

[32] Capturing chromosome conformation [J].

Dekker, J ;

Rippe, K ;

Dekker, M ;

Kleckner, N .

SCIENCE, 2002, 295 (5558) :1306-1311

[33] Exploring the three-dimensional organization of genomes: interpreting chromatin interaction data [J].

Dekker, Job ;

Marti-Renom, Marc A. ;

Mirny, Leonid A. .

NATURE REVIEWS GENETICS, 2013, 14 (06) :390-403

[34] The genomic landscape of cohesin-associated chromatin interactions [J].

DeMare, Laura E. ;

Leng, Jing ;

Cotney, Justin ;

Reilly, Steven K. ;

Yin, Jun ;

Sarro, Richard ;

Noonan, James P. .

GENOME RESEARCH, 2013, 23 (08) :1224-1234

[35]

Diep D, 2012, NAT METHODS, V9, P270, DOI [10.1038/NMETH.1871, 10.1038/nmeth.1871]

[36] Topological domains in mammalian genomes identified by analysis of chromatin interactions [J].

Dixon, Jesse R. ;

Selvaraj, Siddarth ;

Yue, Feng ;

Kim, Audrey ;

Li, Yan ;

Shen, Yin ;

Hu, Ming ;

Liu, Jun S. ;

Ren, Bing .

NATURE, 2012, 485 (7398) :376-380

[37] Chromosome Conformation Capture Carbon Copy (5C): A massively parallel solution for mapping interactions between genomic elements [J].

Dostie, Josee ;

Richmond, Todd A. ;

Arnaout, Ramy A. ;

Selzer, Rebecca R. ;

Lee, William L. ;

Honan, Tracey A. ;

Rubio, Eric D. ;

Krumm, Anton ;

Lamb, Justin ;

Nusbaum, Chad ;

Green, Roland D. ;

Dekker, Job .

GENOME RESEARCH, 2006, 16 (10) :1299-1309

[38] A Bayesian deconvolution strategy for immunoprecipitation-based DNA methylome analysis [J].

Down, Thomas A. ;

Rakyan, Vardhman K. ;

Turner, Daniel J. ;

Flicek, Paul ;

Li, Heng ;

Kulesha, Eugene ;

Graf, Stefan ;

Johnson, Nathan ;

Herrero, Javier ;

Tomazou, Eleni M. ;

Thorne, Natalie P. ;

Backdahl, Liselotte ;

Herberth, Marlis ;

Howe, Kevin L. ;

Jackson, David K. ;

Miretti, Marcos M. ;

Marioni, John C. ;

Birney, Ewan ;

Hubbard, Tim J. P. ;

Durbin, Richard ;

Tavare, Simon ;

Beck, Stephan .

NATURE BIOTECHNOLOGY, 2008, 26 (07) :779-785

[39] An integrated encyclopedia of DNA elements in the human genome [J].

Dunham, Ian ;

Kundaje, Anshul ;

Aldred, Shelley F. ;

Collins, Patrick J. ;

Davis, CarrieA. ;

Doyle, Francis ;

Epstein, Charles B. ;

Frietze, Seth ;

Harrow, Jennifer ;

Kaul, Rajinder ;

Khatun, Jainab ;

Lajoie, Bryan R. ;

Landt, Stephen G. ;

Lee, Bum-Kyu ;

Pauli, Florencia ;

Rosenbloom, Kate R. ;

Sabo, Peter ;

Safi, Alexias ;

Sanyal, Amartya ;

Shoresh, Noam ;

Simon, Jeremy M. ;

Song, Lingyun ;

Trinklein, Nathan D. ;

Altshuler, Robert C. ;

Birney, Ewan ;

Brown, James B. ;

Cheng, Chao ;

Djebali, Sarah ;

Dong, Xianjun ;

Dunham, Ian ;

Ernst, Jason ;

Furey, Terrence S. ;

Gerstein, Mark ;

Giardine, Belinda ;

Greven, Melissa ;

Hardison, Ross C. ;

Harris, Robert S. ;

Herrero, Javier ;

Hoffman, Michael M. ;

Iyer, Sowmya ;

Kellis, Manolis ;

Khatun, Jainab ;

Kheradpour, Pouya ;

Kundaje, Anshul ;

Lassmann, Timo ;

Li, Qunhua ;

Lin, Xinying ;

Marinov, Georgi K. ;

Merkel, Angelika ;

Mortazavi, Ali .

NATURE, 2012, 489 (7414) :57-74

[40] An assessment of histone-modification antibody quality [J].

Egelhofer, Thea A. ;

Minoda, Aki ;

Klugman, Sarit ;

Lee, Kyungjoon ;

Kolasinska-Zwierz, Paulina ;

Alekseyenko, Artyom A. ;

Cheung, Ming-Sin ;

Day, Daniel S. ;

Gadel, Sarah ;

Gorchakov, Andrey A. ;

Gu, Tingting ;

Kharchenko, Peter V. ;

Kuan, Samantha ;

Latorre, Isabel ;

Linder-Basso, Daniela ;

Luu, Ying ;

Ngo, Queminh ;

Perry, Marc ;

Rechtsteiner, Andreas ;

Riddle, Nicole C. ;

Schwartz, Yuri B. ;

Shanower, Gregory A. ;

Vielle, Anne ;

Ahringer, Julie ;

Elgin, Sarah C. R. ;

Kuroda, Mitzi I. ;

Pirrotta, Vincenzo ;

Ren, Bing ;

Strome, Susan ;

Park, Peter J. ;

Karpen, Gary H. ;

Hawkins, R. David ;

Lieb, Jason D. .

NATURE STRUCTURAL & MOLECULAR BIOLOGY, 2011, 18 (01) :91-+

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