title: Genome-wide analysis of DNA methylation profiles in a senescence-accelerated mouse prone 8 brain using whole-genome bisulfite sequencing.
abstract: BACKGROUND
  The pathogenesis of AD is complex and contributed by both genetic and environmental factors. Recent work revealed a potential link between DNA methylation and AD. However, a genome-wide study to identify potential DNA methylation sites involved in AD is still at an early stage. WGBS, an up-to-date technology, was used in this study. We investigated mouse brain genome-wide DNA methylation profiles between seven-month-old SAMP8 and SAMR1 models through deep WGBS.
  
  
  RESULTS
  According to the results, the global ML slightly decreased in the SAMP8 mice than in the SAMR1 mice (4.12% versus 4.19%). A total of 1 307 172 280 clean reads were obtained. Subsequently, we identified 63 DMRs from all cases in SAMP8 mice relative to SAMR1 mice. In addition, 26 DMR-related genes were detected. GO analyses revealed that these DMR-related genes were involved in regulating the development of AD from different aspects. Finally, three differentially expressed DMR-related genes ( Dlgap1 , TMEM51 and Eif2ak2 ) that were most likely involved in AD were summarized and listed in detail. Our study provided a systematic exploration of DNA methylation profiles in SAMP8 mouse brain for the first time. These novel methylation sites may be considered strong future candidates to combat this life-threatening disease.
  
  
  METHODS
  The WGBS sequencing clean data and RNA-seq clean data have been deposited in the NCBI Sequence Read Archive (SRA).The accession number of WGBS is SRP097054. The accession number of RNA-seq is SRP096779.
  
  
  BACKGROUND
  zws@bnu.edu.cn.
  
  
  BACKGROUND
  Supplementary data are available at Bioinformatics online.
authors.affiliation: Beijing Area Major Laboratory of Protection and Utilization of Traditional Chinese Medicine, Beijing Normal University, Beijing, China.|Engineering Research Center of Natural Medicine, Ministry of Education, Beijing Normal University, Beijing, China.|College of Resources Science Technology, Beijing Normal University, Beijing, China.
authors.forename: Shuai
authors.initials: S
authors.lastname: Zhang
authors.affiliation: Beijing Area Major Laboratory of Protection and Utilization of Traditional Chinese Medicine, Beijing Normal University, Beijing, China.|Engineering Research Center of Natural Medicine, Ministry of Education, Beijing Normal University, Beijing, China.|College of Resources Science Technology, Beijing Normal University, Beijing, China.
authors.forename: Chunxia
authors.initials: C
authors.lastname: Qin
authors.affiliation: Beijing Area Major Laboratory of Protection and Utilization of Traditional Chinese Medicine, Beijing Normal University, Beijing, China.|Engineering Research Center of Natural Medicine, Ministry of Education, Beijing Normal University, Beijing, China.|College of Resources Science Technology, Beijing Normal University, Beijing, China.
authors.forename: Guoqiong
authors.initials: G
authors.lastname: Cao
authors.affiliation: Beijing Area Major Laboratory of Protection and Utilization of Traditional Chinese Medicine, Beijing Normal University, Beijing, China.|Engineering Research Center of Natural Medicine, Ministry of Education, Beijing Normal University, Beijing, China.|College of Resources Science Technology, Beijing Normal University, Beijing, China.
authors.forename: Limin
authors.initials: L
authors.lastname: Guo
authors.affiliation: Beijing Area Major Laboratory of Protection and Utilization of Traditional Chinese Medicine, Beijing Normal University, Beijing, China.|Engineering Research Center of Natural Medicine, Ministry of Education, Beijing Normal University, Beijing, China.|College of Resources Science Technology, Beijing Normal University, Beijing, China.
authors.forename: Chengqiang
authors.initials: C
authors.lastname: Feng
authors.affiliation: Beijing Area Major Laboratory of Protection and Utilization of Traditional Chinese Medicine, Beijing Normal University, Beijing, China.|Engineering Research Center of Natural Medicine, Ministry of Education, Beijing Normal University, Beijing, China.|College of Resources Science Technology, Beijing Normal University, Beijing, China.|National and Local United Engineering Research Center for Sanqi Resources Protection and Utilization Technology, Kunming, China.
authors.forename: Wensheng
authors.initials: W
authors.lastname: Zhang
mesh_terms: D000375:Aging / Q000235:genetics*; D000544:Alzheimer Disease / Q000235:genetics* / Q000503:physiopathology; D000818:Animals; D001921:Brain / Q000503:physiopathology*; D019175:DNA Methylation; D004195:Disease Models, Animal; D008297:Male; D051379:Mice; D017423:Sequence Analysis, RNA; D000073336:Whole Genome Sequencing