Unknown,Transcriptomics,Genomics,Proteomics

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Analysis of soybean DNA methylomes shows CHH hypermethylation enhances gene expression in cotyledons of developing seeds [methylome]

ABSTRACT: Cytosine methylation is an important mechanism for dynamical regulation of gene expression and transposon mobility during plant developmental processes. Recently, the variation of DNA methylation has been described between wild type and DNA methylation-related mutants in Arabidopsis thaliana. However, the elaborate representation of soybean DNA methylomes remains lacking. Here, we described the epigenome maps of soybean root, stem, leaf, and cotyledon of developing seed at a single-base resolution. We confirmed the transcription start sites of genes using high-throughput sequencing and reported the DNA methylation patterns in gene and transposon regions. The correlation between gene expression and DNA methylation was revealed through transcriptome sequencing. We found CHH methylation may function in promotion of gene expression and ten cotyledon-preferred genes were identified CHH hypermethylated in cotyledon. Small RNA library sequencing showed that DNA methylation was enhanced by small RNAs not by strand-specific way, and the variation of DNA methylation between the organs was highly related with expression of small RNAs. methylomes of roots, stems, leaves, and cotyledons of developing seeds

ORGANISM(S): Glycine max

SUBMITTER: Jinsong Zhang

PROVIDER: E-GEOD-34849 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Project description:The M-NM-1-proteobacterium Sinorhizobium fredii NGR234 has an exceptionally wide host range as it forms nitrogen-fixing nodules with more legumes than any other known microsymbiont. Within its 6.9 Mbp genome it encodes two N-acyl-homoserine-lactone synthase genes (i.e. traI and ngrI) involved in the biosynthesis of two distinct autoinducer I-type molecules. Here we report on the construction of a NGR234-M-NM-^TtraI and a NGR234-M-NM-^TngrI mutant and the genome wide RNA-seq-based transcriptome analysis in the parent strain and in the two constructed mutants. A high-resolution RNA-seq analysis of early stationary phase cultures in the background of NGR234-M-NM-^TtraI suggested that up to 316 genes (4.9% of all predicted genes) were differentially expressed in the mutant vs. the parent strain. Similarly, in the background of NGR234-M-NM-^TngrI 466 differentially regulated genes (7.3% of all predicted genes) were identified. A considerable overlap in the gene expression pattern was uncovered between both mutants resulting in a common set of 186 genes which were almost identically regulated. Co-regulated genes that were linked to the ngrI- and the traI-dependent autoinducer regulatory circuits included 53 flagella biosynthesis genes and genes linked to EPS succinoglycan biosynthesis. Among the genes and ORFs that were differentially regulated in NGR234-M-NM-^TtraI were those linked to replication of the pNGR234a symbiotic plasmid and cytochrome c-related genes. In the NGR234-M-NM-^TngrI mutant biotin and pyrroloquinoline quinone (PQQ) biosynthesis genes were differentially expressed as well as the entire cluster of 21 genes linked to assembly of the NGR234 type three secretion system II (T3SS-II). We also discovered that genes responsible for octopine catabolism in NGR234 are strongly repressed in the presence of high levels of N-acyl-homoserine-lactones (AHLs). Surprisingly, only few truly symbiosis-related genes were identified that appeared to be quorum sensing regulated. Together with nodulation assays, the RNAseq-based findings suggested that QS-dependent gene regulation appears to be of higher relevance during non-symbiotic growth rather than for life within root nodules. In total 12 samples were analyzed (six different treatments with two independent samples), treatment A: NGR234 wild type strain in stationary phase, treatment B: NGR234 traI-mutant strain in stationary phase, treatment C: NGR234 ngrI-mutant strain in stationary phase, treatment D: NGR234 wild type strain in exponential phase, treatment E: NGR234 wild type supplemented with 0.05 M-BM-5M AHLs in exponential phase, treatment F: NGR234 wild type supplemented with 50 M-BM-5M AHLs in exponential phase

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Analysis of soybean DNA methylomes shows CHH hypermethylation enhances gene expression in cotyledons of developing seeds [methylome]

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