Literature DB >> 22101853

Sensitive and specific single-molecule sequencing of 5-hydroxymethylcytosine.

Chun-Xiao Song1, Tyson A Clark, Xing-Yu Lu, Andrey Kislyuk, Qing Dai, Stephen W Turner, Chuan He, Jonas Korlach.   

Abstract

We describe strand-specific, base-resolution detection of 5-hydroxymethylcytosine (5-hmC) in genomic DNA with single-molecule sensitivity, combining a bioorthogonal, selective chemical labeling method of 5-hmC with single-molecule, real-time (SMRT) DNA sequencing. The chemical labeling not only allows affinity enrichment of 5-hmC-containing DNA fragments but also enhances the kinetic signal of 5-hmC during SMRT sequencing. We applied the approach to sequence 5-hmC in a genomic DNA sample with high confidence.

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Year:  2011        PMID： 22101853      PMCID： PMC3646335          DOI： 10.1038/nmeth.1779

Source DB:  PubMed          Journal:  Nat Methods        ISSN： 1548-7091            Impact factor:   28.547


  16 in total

1.  Genome-wide regulation of 5hmC, 5mC, and gene expression by Tet1 hydroxylase in mouse embryonic stem cells.

Authors:  Yufei Xu; Feizhen Wu; Li Tan; Lingchun Kong; Lijun Xiong; Jie Deng; Andrew J Barbera; Lijuan Zheng; Haikuo Zhang; Stephen Huang; Jinrong Min; Thomas Nicholson; Taiping Chen; Guoliang Xu; Yang Shi; Kun Zhang; Yujiang Geno Shi
Journal:  Mol Cell       Date:  2011-04-21       Impact factor: 17.970

2.  TET1 and hydroxymethylcytosine in transcription and DNA methylation fidelity.

Authors:  Kristine Williams; Jesper Christensen; Marianne Terndrup Pedersen; Jens V Johansen; Paul A C Cloos; Juri Rappsilber; Kristian Helin
Journal:  Nature       Date:  2011-04-13       Impact factor: 49.962

3.  DNA demethylation dynamics.

Authors:  Nidhi Bhutani; David M Burns; Helen M Blau
Journal:  Cell       Date:  2011-09-16       Impact factor: 41.582

Review 4.  5-Hydroxymethylcytosine, the sixth base of the genome.

Authors:  Martin Münzel; Daniel Globisch; Thomas Carell
Journal:  Angew Chem Int Ed Engl       Date:  2011-06-17       Impact factor: 15.336

5.  Genome-wide mapping of 5-hydroxymethylcytosine in embryonic stem cells.

Authors:  William A Pastor; Utz J Pape; Yun Huang; Hope R Henderson; Ryan Lister; Myunggon Ko; Erin M McLoughlin; Yevgeny Brudno; Sahasransu Mahapatra; Philipp Kapranov; Mamta Tahiliani; George Q Daley; X Shirley Liu; Joseph R Ecker; Patrice M Milos; Suneet Agarwal; Anjana Rao
Journal:  Nature       Date:  2011-05-08       Impact factor: 49.962

6.  The behaviour of 5-hydroxymethylcytosine in bisulfite sequencing.

Authors:  Yun Huang; William A Pastor; Yinghua Shen; Mamta Tahiliani; David R Liu; Anjana Rao
Journal:  PLoS One       Date:  2010-01-26       Impact factor: 3.240

7.  Conversion of 5-methylcytosine to 5-hydroxymethylcytosine in mammalian DNA by MLL partner TET1.

Authors:  Mamta Tahiliani; Kian Peng Koh; Yinghua Shen; William A Pastor; Hozefa Bandukwala; Yevgeny Brudno; Suneet Agarwal; Lakshminarayan M Iyer; David R Liu; L Aravind; Anjana Rao
Journal:  Science       Date:  2009-04-16       Impact factor: 47.728

8.  Real-time DNA sequencing from single polymerase molecules.

Authors:  John Eid; Adrian Fehr; Jeremy Gray; Khai Luong; John Lyle; Geoff Otto; Paul Peluso; David Rank; Primo Baybayan; Brad Bettman; Arkadiusz Bibillo; Keith Bjornson; Bidhan Chaudhuri; Frederick Christians; Ronald Cicero; Sonya Clark; Ravindra Dalal; Alex Dewinter; John Dixon; Mathieu Foquet; Alfred Gaertner; Paul Hardenbol; Cheryl Heiner; Kevin Hester; David Holden; Gregory Kearns; Xiangxu Kong; Ronald Kuse; Yves Lacroix; Steven Lin; Paul Lundquist; Congcong Ma; Patrick Marks; Mark Maxham; Devon Murphy; Insil Park; Thang Pham; Michael Phillips; Joy Roy; Robert Sebra; Gene Shen; Jon Sorenson; Austin Tomaney; Kevin Travers; Mark Trulson; John Vieceli; Jeffrey Wegener; Dawn Wu; Alicia Yang; Denis Zaccarin; Peter Zhao; Frank Zhong; Jonas Korlach; Stephen Turner
Journal:  Science       Date:  2008-11-20       Impact factor: 47.728

9.  Dynamic regulation of 5-hydroxymethylcytosine in mouse ES cells and during differentiation.

Authors:  Gabriella Ficz; Miguel R Branco; Stefanie Seisenberger; Fátima Santos; Felix Krueger; Timothy A Hore; C Joana Marques; Simon Andrews; Wolf Reik
Journal:  Nature       Date:  2011-04-03       Impact factor: 49.962

10.  The nuclear DNA base 5-hydroxymethylcytosine is present in Purkinje neurons and the brain.

Authors:  Skirmantas Kriaucionis; Nathaniel Heintz
Journal:  Science       Date:  2009-04-16       Impact factor: 47.728
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  88 in total

1.  Biochemical characterization of a Naegleria TET-like oxygenase and its application in single molecule sequencing of 5-methylcytosine.

Authors:  June E Pais; Nan Dai; Esta Tamanaha; Romualdas Vaisvila; Alexey I Fomenkov; Jurate Bitinaite; Zhiyi Sun; Shengxi Guan; Ivan R Corrêa; Christopher J Noren; Xiaodong Cheng; Richard J Roberts; Yu Zheng; Lana Saleh
Journal:  Proc Natl Acad Sci U S A       Date:  2015-03-23       Impact factor: 11.205

Review 2.  Advances in the profiling of DNA modifications: cytosine methylation and beyond.

Authors:  Nongluk Plongthongkum; Dinh H Diep; Kun Zhang
Journal:  Nat Rev Genet       Date:  2014-08-27       Impact factor: 53.242

3.  Convergence of DNA methylation and phosphorothioation epigenetics in bacterial genomes.

Authors:  Chao Chen; Lianrong Wang; Si Chen; Xiaolin Wu; Meijia Gu; Xi Chen; Susu Jiang; Yunfu Wang; Zixin Deng; Peter C Dedon; Shi Chen
Journal:  Proc Natl Acad Sci U S A       Date:  2017-04-11       Impact factor: 11.205

Review 4.  Dynamics of DNA methylation in aging and Alzheimer's disease.

Authors:  Hasan A Irier; Peng Jin
Journal:  DNA Cell Biol       Date:  2012-02-07       Impact factor: 3.311

5.  Tracking genomic hydroxymethylation by the base.

Authors:  Gilles Salbert; Michael Weber
Journal:  Nat Methods       Date:  2011-12-28       Impact factor: 28.547

6.  Comparison of Reference Genes for Transcriptional Studies in Postmortem Human Brain Tissue Under Different Conditions.

Authors:  Qing Zhang; Hanlin Zhang; Fan Liu; Qian Yang; Kang Chen; Pan Liu; Tianyi Sun; Chao Ma; Wenying Qiu; Xiaojing Qian
Journal:  Neurosci Bull       Date:  2018-11-07       Impact factor: 5.203

Review 7.  Micro- and nanoscale devices for the investigation of epigenetics and chromatin dynamics.

Authors:  Carlos A Aguilar; Harold G Craighead
Journal:  Nat Nanotechnol       Date:  2013-10       Impact factor: 39.213

Review 8.  5-Hydroxymethylcytosine: generation, fate, and genomic distribution.

Authors:  Li Shen; Yi Zhang
Journal:  Curr Opin Cell Biol       Date:  2013-03-13       Impact factor: 8.382

Review 9.  5-Hydroxymethylcytosine--the elusive epigenetic mark in mammalian DNA.

Authors:  Edita Kriukienė; Zita Liutkevičiūtė; Saulius Klimašauskas
Journal:  Chem Soc Rev       Date:  2012-07-27       Impact factor: 54.564

10.  Tet-mediated covalent labelling of 5-methylcytosine for its genome-wide detection and sequencing.

Authors:  Liang Zhang; Keith E Szulwach; Gary C Hon; Chun-Xiao Song; Beomseok Park; Miao Yu; Xingyu Lu; Qing Dai; Xiao Wang; Craig R Street; Huiping Tan; Jung-Hyun Min; Bing Ren; Peng Jin; Chuan He
Journal:  Nat Commun       Date:  2013       Impact factor: 14.919
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