Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

DNase I hypersensitive sites in two tissues of rice

ABSTRACT: Gene expression is controlled by the complex interaction of transcription factors binding to promoters and other regulatory DNA elements. One common characteristic of the genomic regions associated with regulatory proteins is a pronounced sensitivity to DNase I digestion. We generated genome-wide high resolution maps of DNase I hypersensitive (DH) sites from both seedling and callus tissues of rice. Approximately 25% of the DH sites from both tissues were found in the putative promoters, indicating that the vast majority of gene regulatory elements in rice are not located at promoter regions. We found 58% more DH sites in callus than in seedling. For DH sites detected in both seedling and callus, 31% displayed significantly different levels of DNase I sensitivity within the two tissues. Genes that were differentially expressed in seedling and callus were frequently associated with DH sites in both tissues. The DNA sequences contained within the DH sites were hypomethylated, consistent with what is known about active gene regulatory elements. Interestingly, tissue-specific DH sites located in the promoters showed an elevated level of DNA methylation. A distinct elevation of H3K27me3 was associated with intergenic DH sites. These results suggest that epigenetic modifications play a role in the dynamic changes of the numbers and DNase I sensitivity of DH sites during development. Generation of genome-wide high resolution maps of DNase I hypersensitive sites in two tissues of rice. For seedling, we constructed 3 libraries (biological replicates) and sequenced a lane of Illumina Genome Analyzer for each library. For callus, we constructed 2 libraries (biological replicates). We sequenced two lanes for one library and one lane for another library.

ORGANISM(S): Oryza sativa

SUBMITTER: Yufeng Wu

PROVIDER: E-GEOD-26610 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Publications

High-resolution mapping of open chromatin in the rice genome.

Zhang Wenli W Wu Yufeng Y Schnable James C JC Zeng Zixian Z Freeling Michael M Crawford Gregory E GE Jiang Jiming J

Genome research 20111122 1

Gene expression is controlled by the complex interaction of transcription factors binding to promoters and other regulatory DNA elements. One common characteristic of the genomic regions associated with regulatory proteins is a pronounced sensitivity to DNase I digestion. We generated genome-wide high-resolution maps of DNase I hypersensitive (DH) sites from both seedling and callus tissues of rice (Oryza sativa). Approximately 25% of the DH sites from both tissues were found in putative promote ...[more]

PMID: 22110044

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Project description:Distant enhancer elements are a major source of specificity in mammalian gene expression. Although enhancers that regulate broad developmental decisions and inducible gene expression have been studied extensively, little is known about regulatory elements that govern monogenic and monoallelic expression. Here, using high throughput epigenetic and genetic techniques we identified a plethora of distant enhancers that regulate monoallelic olfactory receptor (OR) gene expression. Potential OR enhancers have unique, cell type specific epigenetic marks that distinguish them from other neuronal enhancers and correlate with enhancer activity in vivo. Using sequence capture to enrich for these sequences we identified Dnase-protected footprints that reveal novel regulatory sequences and transcription factors required for OR gene activation. Our experiments provide insight to the regulation of OR expression, and describe novel principles and methodologies towards the understanding of transcriptional mechanisms that generate cellular diversity. In vivo examination of H3K79me3 enrichment and DNAse protected footprints on olfactory receptor enhancer sequences. We performed ChIP-seq on native chromatin isolated from the mouse olfactory epithelium using antibodies against H3K79me3. To sequence accessible regions of the genome we treated nuclei with limiting amounts of DNAse I to digest accessible chromatin and perform Dnase Hypersensitivity (DHS)-seq. In the olfactory epithelium, the H enhancer – the first described enhancer for olfactory receptors has a well-defined DNAse I hypersensitivity peak and is flanked by high levels of H3K79me3. We find other intergenic sequences nearby olfactory receptor genes that share the same chromatin signature, and test their function in vivo. TO uncover transcription factor footprints on olfactory receptor enhancers we performed sequence capture of the DHS-seq library to enrich for these sequences. We find multiple DNAse-protected sequences and perform motif analysis on transcription factor footprints to reveal factors involved in olfactory receptor gene regulation.

Dataset Information

DNase I hypersensitive sites in two tissues of rice

Publications

High-resolution mapping of open chromatin in the rice genome.

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