Transcriptional and Epigenetic Regulation of Autophagy in Plants

Coordinated transcriptional upregulation of ATG genes emerges as a general mechanism of autophagy activation in plants. Recent studies unveil several key transcription factors involved in the transcriptional control of plant autophagy. HDA9 functions as an important epigenetic modifier to modulate plant autophagy in response to developmental or stress cues. Genome-wide studies illustrate the enrichment of specific epigenetic marks or nucleobase modifications on ATG loci in plants. Autophagy, a highly conserved quality control mechanism, is essential for maintaining cellular homeostasis and healthy growth of plants. Compared with extensive research in the cytoplasmic control of autophagy, studies regarding the nuclear events involved in the regulation of plant autophagy are just beginning to emerge. Accumulating evidence reveals a coordinated expression of plant autophagy genes in response to diverse developmental states and growth conditions. Here, we summarize recent progress in the identification of tightly controlled transcription factors and histone marks associated with the autophagic process in plants, and propose several modules, consisting of transcription regulators and epigenetic modifiers, as important nuclear players that could contribute to both short-term and long-term controls of plant autophagy at the transcriptional and post-transcriptional levels. Autophagy, a highly conserved quality control mechanism, is essential for maintaining cellular homeostasis and healthy growth of plants. Compared with extensive research in the cytoplasmic control of autophagy, studies regarding the nuclear events involved in the regulation of plant autophagy are just beginning to emerge. Accumulating evidence reveals a coordinated expression of plant autophagy genes in response to diverse developmental states and growth conditions. Here, we summarize recent progress in the identification of tightly controlled transcription factors and histone marks associated with the autophagic process in plants, and propose several modules, consisting of transcription regulators and epigenetic modifiers, as important nuclear players that could contribute to both short-term and long-term controls of plant autophagy at the transcriptional and post-transcriptional levels. a double-membrane structure formed in the cytoplasm responsible for engulfing cytosolic material that is destined for delivery to the vacuole or lysosome. methylation of cytosines in DNA; one epigenetic mechanism that is tightly associated with transcription silencing by influencing DNA accessibility and transcription factor occupancy in the eukaryotic genome. a variety of processes that mediate long-term effects on gene expression programs or heritable alterations of cellular states without changes in DNA sequence. enzymes that remove acetyl groups from histone and/or non-histone lysine residues, thus repressing gene expression or protein activity. a class of covalent post-translational modifications of histone tails, including lysine acetylation, methylation, and ubiquitylation, serine phosphorylation, arginine methylation, and many others, each catalyzed by one or more protein-modifying enzymes. one kind of 18–25-nucleotide (nt) noncoding RNAs derived from endogenous genes, which act as specificity determinants to direct the destruction or translational repression of their mRNA targets. one epigenetic mechanism that fine-tunes gene expression by monitoring RNA processing, such as pre-RNA spicing, RNA metabolism, and mRNA translation, in the eukaryotic genome. RNA transcripts that do not encode proteins but affect gene expression through mechanisms such as chromatin remodeling, control of transcription initiation, and post-transcriptional processing.