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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

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.



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.


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.


Supplementary information:

Supplementary data are available at Bioinformatics online.

[Indexed for MEDLINE]

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