Abstract
Drought stress response is a complex trait regulated at multiple levels. Changes in the epigenetic and miRNA regulatory landscape can dramatically alter the outcome of a stress response. However, little is known about the scope and extent of these regulatory factors on drought related cellular processes and functions. To this end, we selected a list of 5468 drought responsive genes (DRGs) of rice identified in multiple microarray studies and mapped the DNA methylation regions found in a genome wide methylcytosine immunoprecipitation and sequencing (mCIP-Seq) study to their genic and promoter regions, identified the chromatin remodeling genes and the genes that are targets of miRNAs. We found statistically significant enrichment of DNA methylation reads and miRNA target sequences in DRGs compared to a random set of genes. About 75% of the DRGs annotated to be involved in chromatin remodeling were downregulated. We found one-third of the DRGs are targeted by two-thirds of all known/predicted miRNAs in rice which include many transcription factors targeted by more than five miRNAs. Clustering analysis of the DRGs with epigenetic and miRNA features revealed, upregulated cluster was enriched in drought tolerance mechanisms while the downregulated cluster was enriched in drought resistance mechanisms evident by their unique gene ontologies (GOs), protein-protein interactions (PPIs), specific transcription factors, protein domains and metabolic pathways. Further, we analyzed the proteome of two weeks old young rice plants treated with a global demethylating agent, 5-azacytidine (5-azaC), subjected to drought stress and identified 56 protein spots that are differentially expressed. Out of the 56 spots, 35 were differently expressed in the sample with both demethylation and drought stress treatments and 28 (50%) were part of DRGs considered in the bioinformatic analysis.
Highlights
In plants, epigenetic mechanisms including DNA methylation, histone modifications and certain small RNA mediated pathways regulate gene expression, chromatin structure and genome stability [1]
The average gene length of the drought responsive genes (DRGs) with at least one methylation read in their genic regions was 4725 bases and those without any methylation reads in their genic regions was 2735 bases
We found 678 DRGs (12.3%) with one or two methylcytosine immunoprecipitation (mCIP)-reads mapped to their promoter regions (Fig. 2A)
Summary
Epigenetic mechanisms including DNA methylation, histone modifications and certain small RNA (sRNA) mediated pathways regulate gene expression, chromatin structure and genome stability [1]. Genome-wide high resolution maps of DNase I hypersensitive (DH) sites from seedling and callus tissues of rice, which correlate with open chromatin structure revealed majority of DH sites to be located outside promoter regions and found 58% more DH sites in callus than in seedling [3]. While majority of sRNA in plants are small interfering RNAs (siRNAs) regulating transcriptional gene silencing, micro RNAs (miRNAs) play a key role in posttranscriptional gene silencing. Integration and analysis of data on differential gene expression, epigenetic and sRNA mediated regulation would reveal a comprehensive picture of the dynamics of stress responsive genome in generating phenotypic diversity and could have significant implications in agriculture
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