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ABSTRACT:
PROVIDER: PRJEB13618 | ENA |
REPOSITORIES: ENA
Similar Datasets
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
2014-05-01 | E-GEOD-53027 | biostudies-arrayexpress
Project description:This project aims to analyze rice plasma membrane proteins related to resistance against rice blast infection. We extracted rice plasma membrane proteins before and after M.oryzae infection for 24h, and then used trypsin to digest and iTRAQ to label the peptides, HPLC-MS/MS was used to seperate and identify peptides. 1.1/0.909 fold change with p-value < 0.05 was used as threshold for differentially expressed proteins. 2,977 proteins were identified and 951 of which were found to be responsive to resistance against M. oryzae. Gene Ontology (GO) enrichment analysis, Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis and protein interaction network showed that plenty of proteins were involved in vesicle trafficking with obvious functional tendencies towards transport, vesicle-mediated transport, secretion, endocytosis and phagosome. 10 DEPs were validated at transcript level, and a SNARE protein named NPSN (novel plant-specific SNARE)13 actively responded to M. oryzae infection, and it contributed to rice blast resistance and mainly located at PM.
2022-05-19 | PXD028545 | Pride
Project description:This data set comprises population (47 samples) measurements of transcription factor DNA binding (PU.1 and RPB2) and histone modification (H3K27ac, H3K4me1 and H3k4me3) levels for a subset of the 1000 Genomes Project CEPH samples. This data was generated as part of the following study: - Population Variation and Genetic Control of Modular Chromatin Architecture in Humans. Cell. 2015 Aug 27;162(5):1039-50. doi: 10.1016/j.cell.2015.08.001. Epub 2015 Aug 20. An additional set of 111 samples from the 1000 Genomes Project (GBR and TSI populations) were also assayed for three histone modifications (H3K27ac, H3K4me1 and H3k4me3). This data was generated as part of the following study: - Chromatin 3D interactions mediate genetic effects on regulatory networks.
2019-03-14 | E-MTAB-3657 | biostudies-arrayexpress
Project description:Approximately 73% of rice genomes were annotated with different epigenomic properties. Refinement of promoter regions using open chromatin and H3K4me3-marked regions provided insight into transcriptional regulation. Active and repressed histone modifications and the predicted enhancers varied largely across tissues, whereas inactive chromatin states were relatively stable. Further, we investigated the impact of genetic variants on epigenomic signals and gene expression. Together, these datasets constitute a resource for functional element annotation in rice and indicate the central role of epigenomic information in understanding transcriptional regulation.
2020-04-25 | GSE142569 | GEO
Project description:Approximately 73% of rice genomes were annotated with different epigenomic properties. Refinement of promoter regions using open chromatin and H3K4me3-marked regions provided insight into transcriptional regulation. Active and repressed histone modifications and the predicted enhancers varied largely across tissues, whereas inactive chromatin states were relatively stable. Further, we investigated the impact of genetic variants on epigenomic signals and gene expression. Together, these datasets constitute a resource for functional element annotation in rice and indicate the central role of epigenomic information in understanding transcriptional regulation.
2020-04-25 | GSE142501 | GEO
Project description:Approximately 73% of rice genomes were annotated with different epigenomic properties. Refinement of promoter regions using open chromatin and H3K4me3-marked regions provided insight into transcriptional regulation. Active and repressed histone modifications and the predicted enhancers varied largely across tissues, whereas inactive chromatin states were relatively stable. Further, we investigated the impact of genetic variants on epigenomic signals and gene expression. Together, these datasets constitute a resource for functional element annotation in rice and indicate the central role of epigenomic information in understanding transcriptional regulation.
2020-04-25 | GSE142462 | GEO
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.
2014-05-01 | GSE53027 | GEO
Project description:Copy number variations (CNVs) can create new genes, change gene dosage, reshape gene structures, and modify elements regulating gene expression. As with all types of genetic variation, CNVs may influence phenotypic variation and gene expression. CNVs are thus considered major sources of genetic variation. Little is known, however, about their contribution to genetic variation in rice. To detect CNVs, we used a set of NimbleGen whole-genome comparative genomic hybridization arrays containing 715,851 oligonucleotide probes with a median probe spacing of 500 bp. We compiled a high-resolution map of CNVs in the rice genome, showing 641 CNVs between the genomes of the rice cultivars ‘Nipponbare’ (from O. sativa ssp. japonica) and ‘Guang-lu-ai 4’ (from O. sativa ssp. indica). These CNVs contain some known genes. They are linked to variation among rice varieties, and are likely to contribute to subspecific characteristics.
2012-07-01 | GSE30542 | GEO