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Direct and indirect transcriptional effects of abiotic stress in Zea mays plants defective in RNA-directed DNA methylation

ABSTRACT: MOP1-mediated regulation of gene expression of plant responses to early ABA induction has transcriptionally and physiologically relevant roles. Homozygous mop1-1 plants are compromised in their ability to recover from water deprivation. Purpose: Genome-wide identification of immediate and direct MOP1-dependent ABA transcriptional responses Methods: mRNA profiles of Mop1 wildtype and mop1-1 mutant V3 stage maize seedlings were subjected to ABA and MS treatments for 1 hour. The trimmed sequence reads were analyzed at the gene level using HISAT2, stringite, and edgeR. Results: we mapped ~33 million, 150 bp, paired-end sequence reads per sample to the B73 version 4 maize genome and identified 1,856 genes in four pairwise-comparisons to be differentially expressed genes (DEGs) with a log2FC ≥ 0.95 and FDR <0.05, 1,119 DEGs were found to be unique to one genotype/treatment comparison. Conclusions: MOP1-mediated regulation of gene expression in maize seedlings in the RdDM (mop1-1) mutant has relevant transcriptional and physiological roles in plants subjected to stress. Our study generated by RNA-seq technology identified genes and biological processes regulated by RdDM and ABA-mediated stress responses, including MOP1-dependent and immediate response genes (MIMs).

ORGANISM(S): Zea mays

PROVIDER: GSE179629 | GEO | 2021/07/08

REPOSITORIES: GEO

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Project description:Transposable elements (TEs) comprise a substantial portion of many eukaryotic genomes and are typically transcriptionally silenced. RNA–dependent RNA polymerase 2 (RDR2) is a component of the RNA–directed DNA methylation (RdDM) silencing pathway. In maize, loss of mediator of paramutation1 (mop1) encoded RDR2 function results in reactivation of transcriptionally silenced Mu transposons and a substantial reduction in the accumulation of 24 nt short-interfering RNAs (siRNAs) that recruit RNA silencing components. An RNA–seq experiment conducted on shoot apical meristems (SAMs) revealed that, as expected based on a model in which RDR2 generates 24 nt siRNAs that suppress expression, most differentially expressed DNA TEs (78%) were up-regulated in the mop1 mutant. In contrast, most differentially expressed retrotransposons (68%) were down-regulated. This striking difference suggests that distinct silencing mechanisms are applied to different silencing templates. In addition, 6,000 genes (24% of analyzed genes), including nearly 80% (286/361) of genes in chromatin modification pathways, were differentially expressed. Overall, two-thirds of differentially regulated genes were down-regulated in the mop1 mutant. This finding suggests that RDR2 plays a significant role in regulating the expression of not only transposons, but also of genes. A re-analysis of existing small RNA data identified both RDR2–sensitive and RDR2–resistant species of 24 nt siRNAs that we hypothesize may at least partially explain the complex changes in the expression of genes and transposons observed in the mop1 mutant. Single sequencing library was constructed for mop1 mutant and non-mutant. Each library was sequenced using 2 lanes on a Solexa flow cell. Processed data file 'ZmB73_4a.53_filtered_genes.fasta' and its README file are linked below as supplementary files. The fasta file contains the gene model ID and corresponding sequence generated from maize genome project. This fasta file was used for the following samples: GSM418173, GSM418174, GSM420173, GSM420174, GSM422828, GSM422829.

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Direct and indirect transcriptional effects of abiotic stress in Zea mays plants defective in RNA-directed DNA methylation

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