Literature DB >> 32077696

DNA 5-Methylcytosine-Specific Amplification and Sequencing.

Chang Liu1,2, Xiaolong Cui1,2, Boxuan Simen Zhao3, Pradnya Narkhede4, Yawei Gao5, Jun Liu1,2, Xiaoyang Dou1,2, Qing Dai1,2, Li-Sheng Zhang1,2, Chuan He1,2.   

Abstract

DNA 5-methylcytosine (5mC)-specific mapping has been hampered by severe DNA degradation and the presence of 5-hydroxymethylcytosine (5hmC) using the conventional bisulfite sequencing approach. Here, we present a 5mC-specific whole-genome amplification method (5mC-WGA), with which we achieved 5mC retention during DNA amplification from limited input down to 10 pg scale with limited interference from 5hmC signals, providing DNA 5mC methylome with high reproducibility and accuracy.

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Year:  2020        PMID: 32077696      PMCID: PMC7216556          DOI: 10.1021/jacs.9b12707

Source DB:  PubMed          Journal:  J Am Chem Soc        ISSN: 0002-7863            Impact factor:   15.419


  18 in total

Review 1.  DNA methylation and human disease.

Authors:  Keith D Robertson
Journal:  Nat Rev Genet       Date:  2005-08       Impact factor: 53.242

2.  Bisulfite-free direct detection of 5-methylcytosine and 5-hydroxymethylcytosine at base resolution.

Authors:  Yibin Liu; Paulina Siejka-Zielińska; Gergana Velikova; Ying Bi; Fang Yuan; Marketa Tomkova; Chunsen Bai; Lei Chen; Benjamin Schuster-Böckler; Chun-Xiao Song
Journal:  Nat Biotechnol       Date:  2019-02-25       Impact factor: 54.908

3.  5mC oxidation by Tet2 modulates enhancer activity and timing of transcriptome reprogramming during differentiation.

Authors:  Gary C Hon; Chun-Xiao Song; Tingting Du; Fulai Jin; Siddarth Selvaraj; Ah Young Lee; Chia-An Yen; Zhen Ye; Shi-Qing Mao; Bang-An Wang; Samantha Kuan; Lee E Edsall; Boxuan Simen Zhao; Guo-Liang Xu; Chuan He; Bing Ren
Journal:  Mol Cell       Date:  2014-09-25       Impact factor: 17.970

Review 4.  The DNA methyltransferase family: a versatile toolkit for epigenetic regulation.

Authors:  Frank Lyko
Journal:  Nat Rev Genet       Date:  2017-10-16       Impact factor: 53.242

5.  Quantitative sequencing of 5-methylcytosine and 5-hydroxymethylcytosine at single-base resolution.

Authors:  Michael J Booth; Miguel R Branco; Gabriella Ficz; David Oxley; Felix Krueger; Wolf Reik; Shankar Balasubramanian
Journal:  Science       Date:  2012-04-26       Impact factor: 47.728

Review 6.  Dynamic DNA methylation: In the right place at the right time.

Authors:  Chongyuan Luo; Petra Hajkova; Joseph R Ecker
Journal:  Science       Date:  2018-09-28       Impact factor: 47.728

7.  Single-cell genome-wide bisulfite sequencing for assessing epigenetic heterogeneity.

Authors:  Sébastien A Smallwood; Heather J Lee; Christof Angermueller; Felix Krueger; Heba Saadeh; Julian Peat; Simon R Andrews; Oliver Stegle; Wolf Reik; Gavin Kelsey
Journal:  Nat Methods       Date:  2014-07-20       Impact factor: 28.547

8.  TruePrime is a novel method for whole-genome amplification from single cells based on TthPrimPol.

Authors:  Ángel J Picher; Bettina Budeus; Oliver Wafzig; Carola Krüger; Sara García-Gómez; María I Martínez-Jiménez; Alberto Díaz-Talavera; Daniela Weber; Luis Blanco; Armin Schneider
Journal:  Nat Commun       Date:  2016-11-29       Impact factor: 14.919

9.  MLML: consistent simultaneous estimates of DNA methylation and hydroxymethylation.

Authors:  Jianghan Qu; Meng Zhou; Qiang Song; Elizabeth E Hong; Andrew D Smith
Journal:  Bioinformatics       Date:  2013-08-21       Impact factor: 6.937

10.  Comparison of whole-genome bisulfite sequencing library preparation strategies identifies sources of biases affecting DNA methylation data.

Authors:  Nelly Olova; Felix Krueger; Simon Andrews; David Oxley; Rebecca V Berrens; Miguel R Branco; Wolf Reik
Journal:  Genome Biol       Date:  2018-03-15       Impact factor: 13.583

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  4 in total

Review 1.  RNA m6A Modification in Cancers: Molecular Mechanisms and Potential Clinical Applications.

Authors:  Chang Gu; Xin Shi; Chenyang Dai; Feng Shen; Gaetano Rocco; Jiafei Chen; Zhengyu Huang; Chunji Chen; Chuan He; Tao Huang; Chang Chen
Journal:  Innovation (Camb)       Date:  2020-11-04

2.  Subtraction-free and bisulfite-free specific sequencing of 5-methylcytosine and its oxidized derivatives at base resolution.

Authors:  Yibin Liu; Zhiyuan Hu; Jingfei Cheng; Paulina Siejka-Zielińska; Jinfeng Chen; Masato Inoue; Ahmed Ashour Ahmed; Chun-Xiao Song
Journal:  Nat Commun       Date:  2021-01-27       Impact factor: 14.919

3.  Cellular macromolecules-tethered DNA walking indexing to explore nanoenvironments of chromatin modifications.

Authors:  Feng Chen; Min Bai; Xiaowen Cao; Jing Xue; Yue Zhao; Na Wu; Lei Wang; Dexin Zhang; Yongxi Zhao
Journal:  Nat Commun       Date:  2021-03-30       Impact factor: 14.919

4.  Modular affinity-labeling of the cytosine demethylation base elements in DNA.

Authors:  Fanny Wang; Osama K Zahid; Uday Ghanty; Rahul M Kohli; Adam R Hall
Journal:  Sci Rep       Date:  2020-11-20       Impact factor: 4.379

  4 in total

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