Shotgun bisulphite sequencing of the Arabidopsis genome reveals DNA methylation patterning View Full Text


Ontology type: schema:ScholarlyArticle      Open Access: True


Article Info

DATE

2008-03

AUTHORS

Shawn J. Cokus, Suhua Feng, Xiaoyu Zhang, Zugen Chen, Barry Merriman, Christian D. Haudenschild, Sriharsa Pradhan, Stanley F. Nelson, Matteo Pellegrini, Steven E. Jacobsen

ABSTRACT

Cytosine DNA methylation is important in regulating gene expression and in silencing transposons and other repetitive sequences. Recent genomic studies in Arabidopsis thaliana have revealed that many endogenous genes are methylated either within their promoters or within their transcribed regions, and that gene methylation is highly correlated with transcription levels. However, plants have different types of methylation controlled by different genetic pathways, and detailed information on the methylation status of each cytosine in any given genome is lacking. To this end, we generated a map at single-base-pair resolution of methylated cytosines for Arabidopsis, by combining bisulphite treatment of genomic DNA with ultra-high-throughput sequencing using the Illumina 1G Genome Analyser and Solexa sequencing technology. This approach, termed BS-Seq, unlike previous microarray-based methods, allows one to sensitively measure cytosine methylation on a genome-wide scale within specific sequence contexts. Here we describe methylation on previously inaccessible components of the genome and analyse the DNA methylation sequence composition and distribution. We also describe the effect of various DNA methylation mutants on genome-wide methylation patterns, and demonstrate that our newly developed library construction and computational methods can be applied to large genomes such as that of mouse. More... »

PAGES

215

Journal

TITLE

Nature

ISSUE

7184

VOLUME

452

Identifiers

URI

http://scigraph.springernature.com/pub.10.1038/nature06745

DOI

http://dx.doi.org/10.1038/nature06745

DIMENSIONS

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PUBMED

https://www.ncbi.nlm.nih.gov/pubmed/18278030


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