title: Shotgun bisulphite sequencing of the Arabidopsis genome reveals DNA methylation patterning.
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.
authors.affiliation: Department of Molecular, Cell, and Developmental Biology, University of California at Los Angeles, Los Angeles, California 90095, USA.
authors.forename: Shawn J
authors.initials: SJ
authors.lastname: Cokus
authors.forename: Suhua
authors.initials: S
authors.lastname: Feng
authors.forename: Xiaoyu
authors.initials: X
authors.lastname: Zhang
authors.forename: Zugen
authors.initials: Z
authors.lastname: Chen
authors.forename: Barry
authors.initials: B
authors.lastname: Merriman
authors.forename: Christian D
authors.initials: CD
authors.lastname: Haudenschild
authors.forename: Sriharsa
authors.initials: S
authors.lastname: Pradhan
authors.forename: Stanley F
authors.initials: SF
authors.lastname: Nelson
authors.forename: Matteo
authors.initials: M
authors.lastname: Pellegrini
authors.forename: Steven E
authors.initials: SE
authors.lastname: Jacobsen
mesh_terms: D044503:5-Methylcytosine / Q000378:metabolism; D000818:Animals; D017360:Arabidopsis / Q000235:genetics*; D001483:Base Sequence; D019295:Computational Biology; D003596:Cytosine / Q000378:metabolism; D019175:DNA Methylation; D018506:Gene Expression Regulation, Plant / Q000235:genetics; D015723:Gene Library; D018745:Genome, Plant / Q000235:genetics*; D051379:Mice; D009154:Mutation / Q000235:genetics; D011401:Promoter Regions, Genetic / Q000235:genetics; D015203:Reproducibility of Results; D017422:Sequence Analysis, DNA / Q000379:methods*; D013447:Sulfites / Q000378:metabolism*; D014498:Uracil / Q000378:metabolism
chemical_list: D013447:Sulfites; D014498:Uracil; D044503:5-Methylcytosine; D003596:Cytosine; C009279:sodium bisulfite