Unknown,Transcriptomics,Genomics,Proteomics

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MiR396-OsGRF6 module controls rice inflorescence architecture

ABSTRACT: Developing strategies to increase rice productivity to meet global demand is one of the main challenges for breeders around the world. Here, we report a novel microRNA mediated process that increases rice grain yield in field trials. Expression of target mimicry of microRNA396 (MIM396) significantly increases rice yield by modulating the development of the auxiliary branches and spikelets through promoting the expression of Growth Regulation Factor 6 (OsGRF6). OsGRF6 coordinately induces the expression of several key factors involved in branch and spikelet development, auxin (IAA) biosynthesis, and auxin signaling pathway. Our results demonstrate that the miR396b-GRF6 module acts as a key player in shaping the inflorescence architecture of rice, which could be engineered to generate high-yield rice. This dataset records the profile of the binding peaks of OsGRF6 with GFP antibody in 35S:GRF6-GFP overexpression lines and the differential expressed genes between MIM396 and WT plants. Examination of OsGRF6 regulated genes.

ORGANISM(S): Oryza sativa

SUBMITTER: Wang Kun

PROVIDER: E-GEOD-72694 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Project description:Nucleosome positioning dictates the DNA accessibility for regulatory proteins, and thus is critical for gene expression and regulation. It has been well documented that only a subset of nucleosomes are reproducibly positioned (phased) in eukaryotic genomes. The most prominent example of phased nucleosomes is the context of genes, where phased nucleosomes flank the transcriptional starts sites (TSSs). It is unclear, however, what factors influence nucleosome phasing in regions that are not close to genes. We performed a combinational mapping of nucleosome positioning and DNase I hypersensitive sites (DHSs) across the rice genome. We discovered that DHSs located in a variety of contexts, both genic and intergenic, were flanked by strongly phased nucleosome arrays. Our results support the barrier model for nucleosome organization as a general feature of eukaryote genomes, including plant genomes, and not limited to TSSs. Specifically, regions bound with regulatory proteins, including intergenic regions, can serve as barriers that organize phased nucleosome arrays on both sides. Our results also suggest that rice DHSs often span a single, phased nucleosome, similar to the H2A.Z-containing nucleosomes observed in DHSs in the human genome. We propose that genome-wide nucleosome positioning in the eukaryotic genomes is orchestrated by genomic regions associated with regulatory proteins. Rice chromatin was digested by micrococcal nuclease (MNase) into mono-nucleosome size. Mono-nucleosomal DNA was isolated and sequenced (MNase-seq) using Illumina sequencing platforms. We obtained a total of 38 million (M) single-end reads from our first MNase-seq experiment and mapped ~26 M to unique positions in the rice genome. We also conducted pair-end sequencing of an independent MNase-seq library, obtained 274 M paired-end reads, and mapped ~231 M read pairs to unique positions in the rice genome.We applied a strategy of combinational mapping of nucleosome positioning and DHSs (GSE26610) to examine whether nucleosome positioning is associated with all cis-regulatory elements in the rice genome. All datasets used in the analysis were developed using rice leaf tissue in the same developmental stage

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MiR396-OsGRF6 module controls rice inflorescence architecture

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