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Bioinformatics. 2017 Jun 1;33(11):1591-1595. doi: 10.1093/bioinformatics/btx040.

Genome-wide analysis of DNA methylation profiles in a senescence-accelerated mouse prone 8 brain using whole-genome bisulfite sequencing.

Zhang S1,2,3, Qin C1,2,3, Cao G1,2,3, Guo L1,2,3, Feng C1,2,3, Zhang W1,2,3,4.

Author information

1
Beijing Area Major Laboratory of Protection and Utilization of Traditional Chinese Medicine, Beijing Normal University, Beijing, China.
2
Engineering Research Center of Natural Medicine, Ministry of Education, Beijing Normal University, Beijing, China.
3
College of Resources Science Technology, Beijing Normal University, Beijing, China.
4
National and Local United Engineering Research Center for Sanqi Resources Protection and Utilization Technology, Kunming, China.

Abstract

Motivation:

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.

Availability and Implementation:

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.

Contact:

zws@bnu.edu.cn.

Supplementary information:

Supplementary data are available at Bioinformatics online.

PMID:
28130229
DOI:
10.1093/bioinformatics/btx040
[Indexed for MEDLINE]

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