RDM16 and STA1 regulate differential usage of exon/intron in RNA directed DNA methylation pathway.
The splicing factors RDM16 and STA1 have been reported to play a role in the RNA directed DNA Methylation (RdDM) pathway. In this pathway, small interfering RNAs guide de-novo methylation of homologous DNA sequences. DNA methylation is epigenetic marks, which can suppress transposable elements, repeat sequences and genes. It also affects the chromatin structure. Upon deletion of RDM16 and STA1, previous studies based on gene level analysis were unable to find differentially spliced events implicated in RdDM pathway. In this study, RNA-seq data from RDM16 &STA1 mutants were analyzed. Differential expression analysis was performed at exon and intron level. This analysis revealed 3474 genes with potential differential expression events in the RDM16 mutant and 3058 in the STA1 mutant. We found 17 genes that have been reported to be involved in the RdDM pathway. These results suggest involvement of RDM16 and STA1 by influencing the expression of key gene components such as MORC6 in the RdDM pathway. Therefore, this study increases the understanding of the role of RDM16 and STA1 splicing factors in DNA methylation.
Centre for Microbial and Plant Genetics, KU Leuven, 3000, Belgium; Amity institute of Biotechnology and Amity institute of Integrative Sciences and Health, Amity University Haryana, NH-8, Panchgaon, Gurgaon 122413, India. Electronic address: ravidattasharma@gmail.com.
Ravi Datta
RD
Sharma
Centre for Microbial and Plant Genetics, KU Leuven, 3000, Belgium.
Bert
B
Bogaerts
School of Life Sciences, Jawaharlal Nehru University, New Delhi 110067, India.
Neha
N
Goyal
D017360:Arabidopsis / Q000235:genetics*; D029681:Arabidopsis Proteins / Q000378:metabolism*; D019175:DNA Methylation; D004268:DNA-Binding Proteins / Q000378:metabolism*; D005091:Exons; D007438:Introns; D009687:Nuclear Proteins / Q000378:metabolism*; D012326:RNA Splicing
D029681:Arabidopsis Proteins; D004268:DNA-Binding Proteins; D009687:Nuclear Proteins; C549271:RDM1 protein, Arabidopsis; C519660:STA1 protein, Arabidopsis
Alternative splicing; Arabidopsis thaliana; RNA directed DNA methylation; RNA-seq