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Unraveling the DNA methylation landscape in dog blood across breeds.

Authors :
Nakamura, Miyuki
Matsumoto, Yuki
Yasuda, Keiji
Nagata, Masatoshi
Nakaki, Ryo
Okumura, Masahiro
Yamazaki, Jumpei
Source :
BMC Genomics. 11/15/2024, Vol. 25 Issue 1, p1-15. 15p.
Publication Year :
2024

Abstract

Background: DNA methylation is a covalent bond modification that is observed mainly at cytosine bases in the context of CG pairs. DNA methylation patterns reflect the status of individual tissues, such as cell composition, age, and the local environment, in mammals. Genetic factors also impact DNA methylation, and the genetic diversity among various dog breeds provides a valuable platform for exploring this topic. Compared to those in the human genome, studies on the profiling of methylation in the dog genome have been less comprehensive. Results: Our study provides extensive profiling of DNA methylation in the whole blood of three dog breeds using whole-genome bisulfite sequencing. The difference in DNA methylation between breeds was moderate after removing CpGs overlapping with potential genetic variation. However, variance in methylation between individuals was common and often occurred in promoters and CpG islands (CGIs). Moreover, we adopted contextual awareness methodology to characterize DNA primary sequences using natural language processing (NLP). This method could be used to effectively separate unmethylated CGIs from highly methylated CGIs in the sequences that are identified by the conventional criteria. Conclusions: This study presents a comprehensive DNA methylation landscape in the dog blood. Our observations reveal the similar methylation patterns across dog breeds, while CGI regions showed high variations in DNA methylation level between individuals. Our study also highlights the potential of NLP approach for analyzing low-complexity DNA sequences, such as CGIs. [ABSTRACT FROM AUTHOR]

Details

Language :
English
ISSN :
14712164
Volume :
25
Issue :
1
Database :
Academic Search Index
Journal :
BMC Genomics
Publication Type :
Academic Journal
Accession number :
180933731
Full Text :
https://doi.org/10.1186/s12864-024-10963-2