Characterizing gene interactions and microRNA nodes in Arabidopsis thaliana gene regulatory networks

Date
2023-08
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Abstract

RNA metabolism is focused on RNA molecules and encompasses all the crucial processes an RNA molecule may or will undergo throughout its life cycle. It is an essential cellular process that allows all cells to function effectively. The transcriptomic landscape of a cell is shaped by the interaction of processes such as RNA biosynthesis, maturation (RNA processing, folding, and modification), intra- and inter-cellular transport, small RNA (sRNA)-mediated RNA silencing (both post-transcriptional and transcriptional), and catabolic decay. All these processes interact with one another and are important in terms of RNA homeostasis. Overlapping pathways like sRNA-mediated RNA silencing, mRNA decay, and epigenetic transcriptional silencing interact closely with one another and play an important role in regulating plant growth and development. Although the interaction of various effectors of both pathways has been documented for the model plant Arabidopsis thaliana, little is known about the potential interactions (direct or indirect/genetic) of ABA-HYPERSENSITIVE1/ABH1/CAP BINDING PROTEIN80/CBP80 and SUPPRESSOR OF GENE SILENCING3/SGS3, which regulate post-transcriptional and transcriptional processes respectively, and potentially both. My investigation focused on developmental abnormalities and RNA-Seq and small RNA-seq data analysis across various developmental stages of abh1/sgs3 homozygous double mutant. My results demonstrate a synergistic genetic interaction between ABH1 and SGS3 on miRNA-mediated Post Transcriptional Gene Silencing (PTGS) activities in Arabidopsis thaliana. microRNAs (miRNAs), a class of sRNAs directly affected by abh1/cbp80 and sgs3 mutants, are considered as nodes in gene network models and play a significant role in crosstalk mechanisms for observed pleiotropic effects of miRNA mutants on plant growth and development as well as stress responses. miRNA-mediated gene regulation occurs at the post-transcriptional and translational levels, characterized in plants by a set of sequence-based rules widely accepted by the scientific community, where qualified miRNA:target mRNA interactions are considered ‘canonical.’ However, there have been several recent reports showing evidences for ‘non-canonical’ exceptions, opening up a new area for discovery. I show by multiple independent degradome slicing evidences 43 novel miRNA:target interactions in Arabidopsis, four of which were considered canonical and 39 of which were considered non-canonical. Significantly, some of these novel interactions were found to be up-regulated in miRNA biogenesis and PTGS mutants, including abh1 and/or sgs3, and were observed to be evolutionarily conserved in other plant species. My studies raise new questions about non-canonical miRNA functions as possible links to well-known but poorly understood pleotropic effects caused by derangement of MIRNA expressions. The broader potential significance of my findings is a better understanding of crosstalk between PTGS and transcriptional gene silencing pathways.


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Keywords
Arabidopsis thaliana, plant development, microRNAs, small interfering RNAs, novel miRNA-target modules, novel non-canonical targets, cleavage tags
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