Integrated Methylome and Transcriptome Analysis between the CMS-D2 Line ZBA and Its Maintainer Line ZB in Upland Cotton

Abstract

DNA methylation is an important epigenetic modification involved in multiple biological processes. Altered methylation patterns have been reported to be associated with male sterility in some plants, but their role in cotton cytoplasmic male sterility (CMS) remains unclear. Here, integrated methylome and transcriptome analyses were conducted between the CMS-D2 line ZBA and its near-isogenic maintainer line ZB in upland cotton. More methylated cytosine sites (mCs) and higher methylation levels (MLs) were found among the three sequence contexts in ZB compared to ZBA. A total of 4568 differentially methylated regions (DMRs) and 2096 differentially methylated genes (DMGs) were identified. Among the differentially expressed genes (DEGs) associated with DMRs (DMEGs), 396 genes were upregulated and 281 genes were downregulated. A bioinformatics analysis of these DMEGs showed that hyper-DEGs were significantly enriched in the “oxidative phosphorylation” pathway. Further qRT-PCR validation indicated that these hypermethylated genes (encoding the subunits of mitochondrial electron transport chain (ETC) complexes I and V) were all significantly upregulated in ZB. Our biochemical data revealed a higher extent of H2O2 production but a lower level of adenosine triphosphate (ATP) synthesis in CMS-D2 line ZBA. On the basis of the above results, we propose that disrupted DNA methylation in ZBA may disrupt the homeostasis of reactive oxygen species (ROS) production and ATP synthesis in mitochondria, triggering a burst of ROS that is transferred to the nucleus to initiate programmed cell death (PCD) prematurely, ultimately leading to microspore abortion. This study illustrates the important role of DNA methylation in cotton CMS.

CD73 facilitates EMT progression and promotes lung metastases in triple-negative breast cancer

“…Furthermore, in line with decreased growth and migration in vitro, cells with suppressed CD73 expression formed significantly smaller tumors and less lung metastases than control cells 13 , 15 , 17 . Similar effects on lung metastases have also been described by other investigators 16 , 40 . Interestingly, we did not detect a significant difference in liver metastases, suggesting that CD73 may mediate specifically lung metastases.…”

“…Moreover, several studies have demonstrated that CD73 has prognostic value in TNBC 13 – 15 . No such correlation was detected among HER2+ or luminal breast cancer subtypes 15 , 16 . CD73-associated poor outcome in TNBC may stem from immune evasion, as adenosine may protect cancer cells from adaptive anti-tumor immune responses 17 – 19 .…”

Prospects for Molecular Breeding in Cotton,Gossypiumspp

“…Many studies have been carried out to identify genes that are differentially expressed, however paucity of the causes of the differential expression, hints us towards epigenetic regulations and transcription factors as the probable cause. Very few methylation studies have been carried out in cotton for fiber quality [79], male sterility [80], cold stress [81], salt tolerance [82], fruiting branch development [83]. Thus, there is huge scope for studies like differential methylation, studies on transcription factor, and correlating them with the differential expression patterns.…”

Physical mapping and InDel marker development for the restorer gene Rf2 in cytoplasmic male sterile CMS-D8 cotton 

“…Reverse transcription was conducted using the PrimeScriptTM RT Reagent Kit (TaKaRa, Beijing, China). TransStartTopGreen qPCRSuperMix (Trans gen, Beijing, China) was used according to the manufacturer's instructions to conduct qRT-PCR of the genes.The internal control gene used for qRT-PCR was the cottonHis3 gene (i.e., histone 3) with primers of GhHIS3F and GhHIS3R, and relative gene expression levels were calculated using the 2-△△CT method [91],as described in detail in previous studies [92][93][94]. Each gene in each sample was analyzed with three replicates and two technical replicates.…”