Epigenetic Regulation: Chromatin Modeling and Small RNAs

Abstract

Epigenetic mechanisms, namely histone modifications and DNA methylation induced changes in the chromatin, give rise to epigenomes, which add diversity and complexity to the genome of organisms. Epigenetic modifications play a pivotal role in genomic imprinting, paramutation, defense against transposon proliferation and regulation of gene expression. Specific combinations of histone N-tail modifications can be considered a histone code, which determines the chromatin structure and thus regulates transcription. Cytosine methylation of DNA is a ubiquitous epigenetic mark in diverse species. Asymmetric methylation is re-established after every mitosis cycle, whereas symmetric methylation can be maintained through mitosis and may even be transmitted through meiosis. Abiotic stresses and plant hormones induce epigenetic changes, which can lead to altered gene expression and recombination. ABA induces chromatin remodeling by histone H3 acetylation and methylation to regulate gene expression and abiotic stress-induced growth arrest. Submergence-stress induces the expression of alcohol dehydrogenase (ADH1) and pyruvate decarboxylase (PDC1) genes in rice through histone H3 trimethylation and acetylation. Further, Arabidopsis HOS15, a component of the chromatin repression complex involved in histone deacetylation, plays a key role in freezing stress tolerance. Besides these histone modifications, abiotic stresses also induce a change in DNA methylation. Cold, osmotic, salt, heavy-metal stresses and plant hormones can induce DNA demethylation or hypermethylation at specific loci. Abiotic stresses and plant hormones may also induce the transposition of transposons through DNA hypomethylation. Small RNAs can guide posttranscriptional or transcriptional gene silencing. Stresses like UV-C radiation or the biotic factor - flagellin induces a high frequency of somatic homologous recombination in Arabidopsis and this change is transmitted meiotically across generations probably through epigenetic processes such as DNA hypomethylation. Stress memory, through the epigenetic process, might help plants more effectively combat subsequent incidences of stresses within a generation and might confer an adaptive advantage when meiotically inherited. Further studies on abiotic stress regulated epigenetic processes will help to better understand abiotic stress tolerance of plants.