Genomics

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ATAC-seq profiling of open chromatin with global epigenetic and transcriptional trends in two-line hybrid rice


ABSTRACT: The transcriptional regulatory switches responsible for the mechanism of fertility conversion in two-line system of hybrid rice remain unclear. Here, we employed the ATAC-seq, combined with H3K9ac and H3K4me2 and gene expression analyses, in a rice PTGMS Line Wuxiang S to delineate an integrative chromatin accessibility profiling to uncover the key new regulatory modules in response to temperature fluctuation, which can provide important hypotheses regarding the mechanisms of fertility conversion. Collectively, the potentially active genes with H3K4me2 mark under the permissive state of chromatin can easily be regulated by these transcription factors (TFs). Analyzing TF binding cis-regulatory motifs in differentially accessible chromatin regions identified an ERF-driven regulatory module, that acts as an active transcriptional repressor with temperature-dependent function, specially in WXS(F), which can switch into an activator to control both cell wall development, response to temperature fluctuation, and plant architecture. On the contrary, a MADS/ERF co-regulatory module is unique to the WXS(S) at meiosis period, which tends to directly or indirectly affect various metabolic pathways-related genes to coordinate plant development and growth with proper anther development. Meanwhile, there was a unique accessibility of chromatin on the promoter of UbL40 mRNA in WXS(F), which were found to be regulated by the MADS/ERF module. Our analyses uncovered new TF control modules involved in fertility conversion and shed light on the transcriptional mechanisms as fundamental for further study of genetic manipulations of these transcription factors, in order to prove and elaborate on the specific predictions made by the key model. Overall design: ATAC-seq was performed on nuclei of a novel PTGMS male sterile line Wuxiang S (WXS) generated by our laboratory, which is derived from a mutant tms5 locus in indica rice. All ATAC-seq experiments were performed in two biological replicates. Genome-wide integrated mapping of mRNA transcripts in three biological replicates and two select histone modifications (H3K4me2 and H3K9ac) were performed. All datasets used in the analysis were developed using the panicle of WXS(F) and WXS(S) at meiosis period and uninucleate period.

INSTRUMENT(S): Illumina HiSeq 2000 (Oryza sativa)

ORGANISM(S): Oryza sativa  

SUBMITTER: jin jing  

PROVIDER: GSE114090 | GEO | 2019-12-31

REPOSITORIES: GEO

Dataset's files

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GSE114090_All_gene_counts.list.txt.gz Txt
GSE114090_All_gene_fpkm.list.txt.gz Txt
GSE114090_RAW.tar Raw
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Publications

The transcription factor GATA10 regulates fertility conversion of a two-line hybrid tms5 mutant rice via the modulation of Ub<sub>L40</sub> expression.

Jin Jing J   Gui Songtao S   Li Qian Q   Wang Ying Y   Zhang Hongyuan H   Zhu Zhixuan Z   Chen Hao H   Sun Yueyang Y   Zou Yu Y   Huang Xingguo X   Ding Yi Y  

Journal of integrative plant biology 20191106 7


The thermosensitive genic male sterile 5 (tms5) mutation causes thermosensitive genic male sterility in rice (Oryza sativa) through loss of RNase Z<sup>S1</sup> function, which influences ubiquitin fusion ribosomal protein L40 (Ub<sub>L40</sub> ) messenger RNA levels during male development. Here, we used ATAC-seq, combined with analysis of H3K9ac and H3K4me2, to identify changes in accessible chromatin during fertility conversion of the two-line hybrid rice Wuxiang S (WXS) derived from a mutant  ...[more]