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

Abstract

Background: As an important epigenetic mark, 5-methylcytosine (5mC) methylation is involved in many DNAdependent 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. Results: 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 to reveal a correlation between 5mC methylation levels of proximal promoter regions and transcript levels. We identified 653 and 858 DMGs and 4978 and 4780 DEGs in PS vs TS and TS vs SS comparisons, respectively. Only 113 genes of 653 DMGs and 4978 DEGs, and 114 genes of 858 DMGs and 4780 DEG were common. Counterparts of some of these common genes in other species, including Arabidopsis thaliana, are known to be involved in secondary cell wall biosynthesis and hormone signaling. This indicates that methylation may directly modulate wood formation genes and indirectly attune hormone signaling genes, which in turn impact wood formation. Conclusions: DNA methylation only marginally affects pathway genes or regulators involved in wood formation, suggesting that further studies of wood formation should lean towards the indirect effects of methylation. The information and data we provide here will be instrumental for understanding the roles of methylation in wood formation in tree species.

Transcriptome-wide identification and characterization of microRNAs in diverse phases of wood formation in Populus trichocarpa

“…The plantlets were planted in humus soil and grown under 16/8 hours day/night photoperiod at 25°C in the greenhouse at Northeast Forestry University for 90 days. Then, Wang and Zhang et al prepared 63 trees as experimental materials for transcriptome and sRNA sequencing, DNA methylation sequencing, qRT-PCR analysis, and anatomical and histological analysis, 9 average trees were selected as material for sequencing among of 63 trees ( Zhang et al 2020 ). According to the study of Prassinos et al (2005) and Dharmawardhana et al (2010) , the IN2, IN4, and IN8 internodes were PS, TS, and SS stages from primary growth to secondary growth of poplar and represent the beginning, middle, and late phases of wood formation, respectively.…”

“…In addition, segments in the middle of PS and SS, where cells synthesize SCW components in the inner part of the primary wall, are transition stems (TS) and represent the middle phase of wood formation. Thus, the different vertical segments of less than 1-year-old poplar trees have been used to investigate the dynamics of gene expression and molecular regulatory mechanisms underlying diverse phases of wood formation ( Prassinos et al 2005 ; Dharmawardhana et al 2010 ; Liu et al 2015a ; Zhang et al 2020 ). Based on the previous research of Zhang et al (2020) , in this study, we concurrently generated the miRNA and mRNA expression profiles in the PS, TS, and SS of Populus trichocarpa using Solexa sequencing.…”

“…Thus, the different vertical segments of less than 1-year-old poplar trees have been used to investigate the dynamics of gene expression and molecular regulatory mechanisms underlying diverse phases of wood formation ( Prassinos et al 2005 ; Dharmawardhana et al 2010 ; Liu et al 2015a ; Zhang et al 2020 ). Based on the previous research of Zhang et al (2020) , in this study, we concurrently generated the miRNA and mRNA expression profiles in the PS, TS, and SS of Populus trichocarpa using Solexa sequencing. This study was designed to collect data and gain insight into three problems: (i) the dynamics of miRNAs associated with diverse phases of wood formation; (ii) the identification of the miRNA-mRNA model associated with diverse phases of wood formation; and (iii) the authentication of the biological functions of miRNAs related to diverse phases of wood formation.…”

Transcriptome-wide identification and characterization of microRNAs in diverse phases of wood formation in Populus trichocarpa

“…Then, Wang et al used 63 trees as experimental materials for transcriptome and small RNA sequencing and qRT-PCR analysis. These materials were sampled and immediately frozen in liquid nitrogen and stored at -80 °C following our previous study [28].…”

“…Additionally, segments in the middle of PS and SS, where cells synthesize SCW components in the inner part of the primary wall, are transition stems (TS) and represent the middle phase of wood formation. Thus, the different vertical segments of less than one-year-old poplar trees have been used to investigate the dynamics of gene expression and molecular regulatory mechanisms underlying diverse phases of wood formation [25][26][27][28]. In this paper, we concurrently generated the miRNA and mRNA expression pro les in the PS, TS, and SS of Populus trichocarpa using Solexa sequencing.…”