Single-cell epigenomics: powerful new methods for understanding gene regulation and cell identity

被引：222

作者：

Clark, Stephen J. ^{[1
]}

Lee, Heather J. ^{[1
,2
]}

Smallwood, Sebastien A. ^{[1
,3
]}

Kelsey, Gavin ^{[1
,4
]}

Reik, Wolf ^{[1
,2
,4
,5
]}

机构：

[1] Babraham Inst, Epigenet Programme, Cambridge CB22 3AT, England

[2] Wellcome Trust Sanger Inst, Cambridge CB10 1SA, England

[3] Friedrich Miescher Inst Biomed Res, Maulbeerstr 66, CH-4058 Basel, Switzerland

[4] Univ Cambridge, Ctr Trophoblast Res, Cambridge CB2 3EG, England

[5] Univ Cambridge, Dept Physiol Dev & Neurosci, Cambridge CB2 3EG, England

来源：

GENOME BIOLOGY | 2016年 / 17卷

基金：

英国生物技术与生命科学研究理事会; 英国惠康基金;

关键词：

EMBRYONIC STEM-CELLS; GENOME-WIDE DETECTION; RNA-SEQ; DNA METHYLATION; ANALYSIS REVEALS; EPIGENETIC HETEROGENEITY; CHROMATIN ACCESSIBILITY; DYNAMIC REGULATION; BASE-RESOLUTION; HI-C;

D O I：

10.1186/s13059-016-0944-x

中图分类号：

Q81 [生物工程学（生物技术）]; Q93 [微生物学];

学科分类号：

071005 [微生物学]; 090105 [作物生产系统与生态工程];

摘要：

Emerging single-cell epigenomic methods are being developed with the exciting potential to transform our knowledge of gene regulation. Here we review available techniques and future possibilities, arguing that the full potential of single-cell epigenetic studies will be realized through parallel profiling of genomic, transcriptional, and epigenetic information.

引用

页数：10

共 69 条

[1]

High-throughput spatial mapping of single-cell RNA-seq data to tissue of origin [J].

Achim, Kaia ;

Pettit, Jean-Baptiste ;

Saraiva, Luis R. ;

Gavriouchkina, Daria ;

Larsson, Tomas ;

Arendt, Detlev ;

Marioni, John C. .

NATURE BIOTECHNOLOGY, 2015, 33 (05) :503-U215

[2]

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)

[3]

Toward understanding and exploiting tumor heterogeneity [J].

Alizadeh, Ash A. ;

Aranda, Victoria ;

Bardelli, Alberto ;

Blanpain, Cedric ;

Bock, Christoph ;

Borowski, Christine ;

Caldas, Carlos ;

Califano, Andrea ;

Doherty, Michael ;

Elsner, Markus ;

Esteller, Manel ;

Fitzgerald, Rebecca ;

Korbel, Jan O. ;

Lichter, Peter ;

Mason, Christopher E. ;

Navin, Nicholas ;

Pe'er, Dana ;

Polyak, Kornelia ;

Roberts, Charles W. M. ;

Siu, Lillian ;

Snyder, Alexandra ;

Stower, Hannah ;

Swanton, Charles ;

Verhaak, Roel G. W. ;

Zenklusen, Jean C. ;

Zuber, Johannes ;

Zucman-Rossi, Jessica .

NATURE MEDICINE, 2015, 21 (08) :846-853

[4]

Parallel single-cell sequencing links transcriptional and epigenetic heterogeneity [J].

Angermueller, Christof ;

Clark, Stephen J. ;

Lee, Heather J. ;

Macaulay, Iain C. ;

Teng, Mabel J. ;

Hu, Tim Xiaoming ;

Krueger, Felix ;

Smallwood, Sebastien A. ;

Ponting, Chris P. ;

Voet, Thierry ;

Kelsey, Gavin ;

Stegle, Oliver ;

Reik, Wolf .

NATURE METHODS, 2016, 13 (03) :229-+

[5]

Chromatin dynamics during cellular reprogramming [J].

Apostolou, Effie ;

Hochedlinger, Konrad .

NATURE, 2013, 502 (7472) :462-471

[6]

A decade of exploring the cancer epigenome - biological and translational implications [J].

Baylin, Stephen B. ;

Jones, Peter A. .

NATURE REVIEWS CANCER, 2011, 11 (10) :726-734

[7]

Unravelling cancer stem cell potential [J].

Beck, Benjamin ;

Blanpain, Cedric .

NATURE REVIEWS CANCER, 2013, 13 (10) :727-738

[8]

The mammalian epigenome [J].

Bernstein, Bradley E. ;

Meissner, Alexander ;

Lander, Eric S. .

CELL, 2007, 128 (04) :669-681

[9]

Quantitative Sequencing of 5-Methylcytosine and 5-Hydroxymethylcytosine at Single-Base Resolution [J].

Booth, Michael J. ;

Branco, Miguel R. ;

Ficz, Gabriella ;

Oxley, David ;

Krueger, Felix ;

Reik, Wolf ;

Balasubramanian, Shankar .

SCIENCE, 2012, 336 (6083) :934-937

[10]

Uncovering the role of 5-hydroxymethylcytosine in the epigenome [J].

Branco, Miguel R. ;

Ficz, Gabriella ;

Reik, Wolf .

NATURE REVIEWS GENETICS, 2012, 13 (01) :7-13

← 1 2 3 4 5 6 7 →