MethylC-seq library preparation for base-resolution whole-genome bisulfite sequencing.
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TLDR
The M methylC-sequencing (MethylC-seq) library preparation method is described, a 2-d protocol that enables the genome-wide identification of cytosine DNA methylation states at single-base resolution.Abstract:
Current high-throughput DNA sequencing technologies enable acquisition of billions of data points through which myriad biological processes can be interrogated, including genetic variation, chromatin structure, gene expression patterns, small RNAs and protein-DNA interactions. Here we describe the MethylC-sequencing (MethylC-seq) library preparation method, a 2-d protocol that enables the genome-wide identification of cytosine DNA methylation states at single-base resolution. The technique involves fragmentation of genomic DNA followed by adapter ligation, bisulfite conversion and limited amplification using adapter-specific PCR primers in preparation for sequencing. To date, this protocol has been successfully applied to genomic DNA isolated from primary cell culture, sorted cells and fresh tissue from over a thousand plant and animal samples.read more
Citations
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Journal ArticleDOI
Epigenomic Diversity in a Global Collection of Arabidopsis thaliana Accessions
Taiji Kawakatsu,Shao-shan Carol Huang,Florian Jupe,Eriko Sasaki,Robert J. Schmitz,Robert J. Schmitz,Mark A. Urich,Rosa Castanon,Joseph R. Nery,Cesar Barragan,Yupeng He,Huaming Chen,Manu J. Dubin,Cheng-Ruei Lee,Congmao Wang,Felix Bemm,Claude Becker,Ryan C. O’Neil,Ronan C. O'Malley,Danjuma Quarless,Nicholas J. Schork,Detlef Weigel,Magnus Nordborg,Joseph R. Ecker,Joseph R. Ecker +24 more
TL;DR: Comparison to cistrome and epicistrome datasets identifies associations between transcription factor binding sites, methylation, nucleotide variation, and co-expression modules in the 1001 Genomes collection of Arabidopsis thaliana.
Journal ArticleDOI
Single-cell methylomes identify neuronal subtypes and regulatory elements in mammalian cortex
Chongyuan Luo,Christopher L. Keown,Laurie Kurihara,Jingtian Zhou,Jingtian Zhou,Yupeng He,Yupeng He,Jun-Hao Li,Rosa Castanon,Jacinta Lucero,Joseph R. Nery,Justin P. Sandoval,Brian Bui,Terrence J. Sejnowski,Terrence J. Sejnowski,Timothy T. Harkins,Eran A. Mukamel,M. Margarita Behrens,Joseph R. Ecker +18 more
TL;DR: A comprehensive map of methylation variation in neuronal cell populations, including a between-species comparison, illustrates how epigenetic diversity plays important roles in neuronal development.
Journal ArticleDOI
Widespread natural variation of DNA methylation within angiosperms.
Chad E. Niederhuth,Adam J. Bewick,Lexiang Ji,Magdy S. Alabady,Kyung Do Kim,Qing Li,Nicholas A. Rohr,Aditi Rambani,John M. Burke,Joshua A. Udall,Chiedozie Egesi,Jeremy Schmutz,Jane Grimwood,Scott A. Jackson,Nathan M. Springer,Robert J. Schmitz +15 more
TL;DR: The extent of variation in DNA methylation in angiosperms is revealed and patterns are shown to be broadly a reflection of the evolutionary and life histories of plant species.
Journal ArticleDOI
Molecular Criteria for Defining the Naive Human Pluripotent State
Thorold W. Theunissen,Marc Friedli,Yupeng He,Yupeng He,Evarist Planet,Ryan C. O’Neil,Ryan C. O’Neil,Styliani Markoulaki,Julien Pontis,Haoyi Wang,Alexandra Iouranova,Michael Imbeault,Julien Duc,Malkiel A. Cohen,Katherine J. Wert,Rosa Castanon,Zhuzhu Zhang,Yanmei Huang,Joseph R. Nery,Jesse Drotar,Tenzin Lungjangwa,Didier Trono,Joseph R. Ecker,Rudolf Jaenisch +23 more
TL;DR: It is shown that transcription of transposable elements provides a sensitive measure of the concordance between pluripotent stem cells and early human development and induction of the naive state is accompanied by genome-wide DNA hypomethylation.
Journal ArticleDOI
The genome sequence of segmental allotetraploid peanut Arachis hypogaea
David J. Bertioli,Jerry Jenkins,Josh Clevenger,Olga Dudchenko,Dongying Gao,Guillermo Seijo,Soraya C. M. Leal-Bertioli,Longhui Ren,Andrew Farmer,Manish K. Pandey,Sergio Sebastián Samoluk,Brian Abernathy,Gaurav Agarwal,Carolina Ballén-Taborda,Connor Cameron,Jacqueline D. Campbell,Carolina Chavarro,Annapurna Chitikineni,Ye Chu,Sudhansu Dash,Moaine El Baidouri,Moaine El Baidouri,Baozhu Guo,Wei Huang,Kyung Do Kim,Kyung Do Kim,Walid Korani,Sophie Lanciano,Sophie Lanciano,Christopher Lui,Marie Mirouze,Marie Mirouze,Márcio C. Moretzsohn,Melanie Pham,Jin Hee Shin,Jin Hee Shin,Kenta Shirasawa,Senjuti Sinharoy,Avinash Sreedasyam,Nathan T. Weeks,Xinyou Zhang,Zheng Zheng,Ziqi Sun,Lutz Froenicke,Erez Lieberman Aiden,Richard W Michelmore,Rajeev K. Varshney,C. Corley Holbrook,Ethalinda K. S. Cannon,Brian E. Scheffler,Jane Grimwood,Peggy Ozias-Akins,Steven B. Cannon,Scott A. Jackson,Jeremy Schmutz +54 more
TL;DR: The genome sequence of segmental allotetraploid peanut is reported and suggests that diversity generated by genetic deletions and homeologous recombination helped to favor the domestication of Arachis hypogaea over its diploid relatives.
References
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Human DNA methylomes at base resolution show widespread epigenomic differences
Ryan Lister,Mattia Pelizzola,Robert H. Dowen,R. David Hawkins,Gary C. Hon,Julian Tonti-Filippini,Joseph R. Nery,Leonard Lee,Zhen Ye,Que Minh Ngo,Lee Edsall,Jessica Antosiewicz-Bourget,Jessica Antosiewicz-Bourget,Ron Stewart,Ron Stewart,Victor Ruotti,Victor Ruotti,A. Harvey Millar,James A. Thomson,Bing Ren,Bing Ren,Joseph R. Ecker +21 more
TL;DR: The first genome-wide, single-base-resolution maps of methylated cytosines in a mammalian genome, from both human embryonic stem cells and fetal fibroblasts, along with comparative analysis of messenger RNA and small RNA components of the transcriptome, several histone modifications, and sites of DNA-protein interaction for several key regulatory factors were presented in this article.
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TL;DR: A genomic sequencing method is reported that provides positive identification of 5-methylcytosine residues and yields strand-specific sequences of individual molecules in genomic DNA, which suggests that the high methylation level of single-copy sequences in sperm may be locally modulated by binding of protein factors in germ-line cells.
Journal ArticleDOI
Establishing, maintaining and modifying DNA methylation patterns in plants and animals
Julie A. Law,Steven E. Jacobsen +1 more
TL;DR: Drawing on insights from both plants and animals should deepen the understanding of the regulation and biological significance of DNA methylation.
Journal ArticleDOI
Highly Integrated Single-Base Resolution Maps of the Epigenome in Arabidopsis
Ryan Lister,Ronan C. O'Malley,Julian Tonti-Filippini,Brian D. Gregory,Charles C. Berry,A. Harvey Millar,Joseph R. Ecker +6 more
TL;DR: Deep sequencing of smRNAs revealed a direct relationship between the location of sm RNAs and DNA methylation, perturbation of smRNA biogenesis upon loss of CpG DNA methylisation, and a tendency for smRN as to direct strand-specific DNA methylations in regions of RNA-DNA homology.
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Shotgun bisulphite sequencing of the Arabidopsis genome reveals DNA methylation patterning
Shawn J. Cokus,Suhua Feng,Xiaoyu Zhang,Zugen Chen,Barry Merriman,Christian D. Haudenschild,Sriharsa Pradhan,Stanley F. Nelson,Matteo Pellegrini,Steven E. Jacobsen +9 more
TL;DR: A map at single-base-pair resolution of methylated cytosines for Arabidopsis is generated by combining bisulphite treatment of genomic DNA with ultra-high-throughput sequencing using the Illumina 1G Genome Analyser and Solexa sequencing technology.
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