title: Genome-Wide Epigenetic Regulation of Gene Transcription in Maize Seeds.
abstract: BACKGROUND
  Epigenetic regulation is well recognized for its importance in gene expression in organisms. DNA methylation, an important epigenetic mark, has received enormous attention in recent years as it's a key player in many biological processes. It remains unclear how DNA methylation contributes to gene transcription regulation in maize seeds. Here, we take advantage of recent technologies to examine the genome-wide association of DNA methylation with transcription of four types of DNA sequences, including protein-coding genes, pseudogenes, transposable elements, and repeats in maize embryo and endosperm, respectively.
  
  
  RESULTS
  The methylation in CG, CHG and CHH contexts plays different roles in the control of gene expression. Methylation around the transcription start sites and transcription stop regions of protein-coding genes is negatively correlated, but in gene bodies positively correlated, to gene expression level. The upstream regions of protein-coding genes are enriched with 24-nt siRNAs and contain high levels of CHH methylation, which is correlated to gene expression level. The analysis of sequence content within CG, CHG, or CHH contexts reveals that only CHH methylation is affected by its local sequences, which is different from Arabidopsis.
  
  
  CONCLUSIONS
  In summary, we conclude that methylation-regulated transcription varies with the types of DNA sequences, sequence contexts or parts of a specific gene in maize seeds and differs from that in other plant species. Our study helps people better understand from a genome-wide viewpoint that how transcriptional expression is controlled by DNA methylation, one of the important factors influencing transcription, and how the methylation is associated with small RNAs.
authors.affiliation: School of Life Sciences, Qilu Normal University, Jinan, 250200, China; Department of Crop Genomics & Genetic Improvement, Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China.
authors.forename: Xiaoduo
authors.initials: X
authors.lastname: Lu
authors.affiliation: Department of Crop Genomics & Genetic Improvement, Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China; National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI), Beijing, 100081, People's Republic of China.
authors.forename: Weixuan
authors.initials: W
authors.lastname: Wang
authors.affiliation: Maize Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097, China.
authors.forename: Wen
authors.initials: W
authors.lastname: Ren
authors.affiliation: School of Life Sciences, Qilu Normal University, Jinan, 250200, China.
authors.forename: Zhenguang
authors.initials: Z
authors.lastname: Chai
authors.affiliation: Department of Crop Genomics & Genetic Improvement, Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China; National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI), Beijing, 100081, People's Republic of China.
authors.forename: Wenzhu
authors.initials: W
authors.lastname: Guo
authors.affiliation: Department of Crop Genomics & Genetic Improvement, Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China; National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI), Beijing, 100081, People's Republic of China.
authors.forename: Rumei
authors.initials: R
authors.lastname: Chen
authors.affiliation: Department of Crop Genomics & Genetic Improvement, Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China; National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI), Beijing, 100081, People's Republic of China.
authors.forename: Lei
authors.initials: L
authors.lastname: Wang
authors.affiliation: Department of Crop Genomics & Genetic Improvement, Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China; National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI), Beijing, 100081, People's Republic of China.
authors.forename: Jun
authors.initials: J
authors.lastname: Zhao
authors.affiliation: Department of Crop Genomics & Genetic Improvement, Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China; National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI), Beijing, 100081, People's Republic of China.
authors.forename: Zhihong
authors.initials: Z
authors.lastname: Lang
authors.affiliation: Department of Crop Genomics & Genetic Improvement, Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China; National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI), Beijing, 100081, People's Republic of China.
authors.forename: Yunliu
authors.initials: Y
authors.lastname: Fan
authors.affiliation: Maize Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097, China.
authors.forename: Jiuran
authors.initials: J
authors.lastname: Zhao
authors.affiliation: Department of Crop Genomics & Genetic Improvement, Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China; National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI), Beijing, 100081, People's Republic of China.
authors.forename: Chunyi
authors.initials: C
authors.lastname: Zhang
mesh_terms: D019175:DNA Methylation; D044127:Epigenesis, Genetic; D018507:Gene Expression Regulation, Developmental; D018506:Gene Expression Regulation, Plant; D018745:Genome, Plant; D055106:Genome-Wide Association Study; D034741:RNA, Small Interfering / Q000235:genetics; D012639:Seeds / Q000235:genetics*; D014158:Transcription, Genetic; D003313:Zea mays / Q000235:genetics*
chemical_list: D034741:RNA, Small Interfering