DNA methylation and its effects on gene expression during primary to secondary growth in poplar stems

BMC Genomics
Yang ZhangZhigang Wei

Abstract

As an important epigenetic mark, 5-methylcytosine (5mC) methylation is involved in many DNA-dependent biological processes and plays a role during development and differentiation of multicellular organisms. However, there is still a lack of knowledge about the dynamic aspects and the roles of global 5mC methylation in wood formation in tree trunks. In this study, we not only scrutinized single-base resolution methylomes of primary stems (PS), transitional stems (TS), and secondary stems (SS) of Populus trichocarpa using a high-throughput bisulfite sequencing technique, but also analyzed the effects of 5mC methylation on the expression of genes involved in wood formation. The overall average percentages of CG, CHG, and CHH methylation in poplar stems were ~ 53.6%, ~ 37.7%, and ~ 8.5%, respectively, and the differences of 5mC in genome-wide CG/CHG/CHH contexts among PS, TS, and SS were statistically significant (p < 0.05). The evident differences in CG, CHG, and CHH methylation contexts among 2 kb proximal promoters, gene bodies, and 2 kb downstream regions were observed among PS, TS, and SS. Further analysis revealed a perceptible global correlation between 5mC methylation levels of gene bodies and transcript levels but failed t...Continue Reading

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Citations

Apr 21, 2021·Food and Chemical Toxicology : an International Journal Published for the British Industrial Biological Research Association·Zhanwei YangWenjun Wang

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Methods Mentioned

BETA
RNA-seq
WGBS
deamination
methylation sequencing
PCR
BS-Seq
methylation profiling

Software Mentioned

Phytozome
Bowtie2
TopHat2
Basic Local Alignment Search Tool ( BLAST )
Cufflinks
SPSS
KOBAS
methyl Kit
BSMAP
BLASTP

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