title: Genome-wide high-resolution mapping of DNA methylation identifies epigenetic variation across embryo and endosperm in Maize (Zea may).
abstract: BACKGROUND
  Epigenetic modifications play important roles in plant and animal development. DNA methylation impacts the transposable element (TE) silencing, gene imprinting and expression regulation.
  
  
  RESULTS
  Through a genome-wide analysis, DNA methylation peaks were characterized and mapped in maize embryo and endosperm genome, respectively. Distinct methylation level was observed across maize embryo and endosperm. The maize embryo genome contained more DNA methylation than endosperm. Totally, 985,478 CG islands (CGIs) were identified and most of them were unmethylated. More CGI shores were methylated than CGIs in maize suggested that DNA methylation level was not positively correlated with CpG density. The promoter sequence and transcriptional termination region (TTR) were more methylated than the gene body (intron and exon) region based on peak number and methylated depth. Result showed that 99% TEs were methylated in maize embryo, but a large portion of them (34.8%) were not methylated in endosperm. Maize embryo and endosperm exhibit distinct pattern/level of methylation. The most differentially methylated region between embryo and endosperm are CGI shores. Our results indicated that DNA methylation is associated with both gene silencing and gene activation in maize. Many genes involved in embryogenesis and seed development were found differentially methylated in embryo and endosperm. We found 41.5% imprinting genes were similarly methylated and 58.5% imprinting genes were differentially methylated between embryo and endosperm. Methylation level was associated with allelic silencing of only a small number of imprinting genes. The expression of maize DEMETER-like (DME-like) gene and MBD101 gene (MBD4 homolog) were higher in endosperm than in embryo. These two genes may be associated with distinct methylation levels across maize embryo and endosperm.
  
  
  CONCLUSIONS
  Through MeDIP-seq we systematically analyzed the methylomes of maize embryo and endosperm and results indicated that the global methylation status of embryo was more than that of the endosperm. Differences could be observed at the total number of methylation peaks, DMRs and specific methylated genes which were tightly associated with development of embryo and endosperm. Our results also revealed that many DNA methylation regions didn't affect transcription of the corresponding genes.
authors.affiliation: Agricultural College, Anhui Agricultural University, Hefei, 230036, PR China. fengqiaoyouzi@126.com.|Bio-Tech Research Center, Shandong Academy of Agricultural Sciences; Shandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and Physiology, Jinan, 250100, PR China. fengqiaoyouzi@126.com.
authors.forename: Pengfei
authors.initials: P
authors.lastname: Wang
authors.affiliation: Bio-Tech Research Center, Shandong Academy of Agricultural Sciences; Shandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and Physiology, Jinan, 250100, PR China. coldxia@126.com.
authors.forename: Han
authors.initials: H
authors.lastname: Xia
authors.affiliation: Bio-Tech Research Center, Shandong Academy of Agricultural Sciences; Shandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and Physiology, Jinan, 250100, PR China. zhangye411@163.com.
authors.forename: Ye
authors.initials: Y
authors.lastname: Zhang
authors.affiliation: Bio-Tech Research Center, Shandong Academy of Agricultural Sciences; Shandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and Physiology, Jinan, 250100, PR China. zhaoshuzhen51@126.com.
authors.forename: Shuzhen
authors.initials: S
authors.lastname: Zhao
authors.affiliation: Bio-Tech Research Center, Shandong Academy of Agricultural Sciences; Shandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and Physiology, Jinan, 250100, PR China. huyjh@126.com.
authors.forename: Chuanzhi
authors.initials: C
authors.lastname: Zhao
authors.affiliation: Bio-Tech Research Center, Shandong Academy of Agricultural Sciences; Shandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and Physiology, Jinan, 250100, PR China. houlei9042@qq.com.
authors.forename: Lei
authors.initials: L
authors.lastname: Hou
authors.affiliation: Bio-Tech Research Center, Shandong Academy of Agricultural Sciences; Shandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and Physiology, Jinan, 250100, PR China. shzyyxgs@126.com.
authors.forename: Changsheng
authors.initials: C
authors.lastname: Li
authors.affiliation: Bio-Tech Research Center, Shandong Academy of Agricultural Sciences; Shandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and Physiology, Jinan, 250100, PR China. liaiqin1970@163.com.
authors.forename: Aiqin
authors.initials: A
authors.lastname: Li
authors.affiliation: Agricultural College, Anhui Agricultural University, Hefei, 230036, PR China. machuanxi@ahau.edu.cn.
authors.forename: Chuanxi
authors.initials: C
authors.lastname: Ma
authors.affiliation: Bio-Tech Research Center, Shandong Academy of Agricultural Sciences; Shandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and Physiology, Jinan, 250100, PR China. xingjunw@hotmail.com.
authors.forename: Xingjun
authors.initials: X
authors.lastname: Wang
mesh_terms: D002874:Chromosome Mapping; D018899:CpG Islands; D019175:DNA Methylation; D004251:DNA Transposable Elements; D056625:Endosperm / Q000235:genetics* / Q000378:metabolism; D044127:Epigenesis, Genetic; D018745:Genome, Plant; D018392:Genomic Imprinting; D059014:High-Throughput Nucleotide Sequencing; D011401:Promoter Regions, Genetic / Q000235:genetics; D012639:Seeds / Q000235:genetics*; D017422:Sequence Analysis, DNA; D003313:Zea mays / Q000235:genetics* / Q000254:growth & development / Q000378:metabolism
chemical_list: D004251:DNA Transposable Elements