GEO DataSets

(Submitter supplied) We conducted genome-wide identification of R-loops followed by integrative analyses of R-loops with relation to gene expressionand epigenetic signatures in the rice genome. We found that the correlation between gene expression levels and profiled R-looppeak levels was dependent on the positions of R-loops within gene structures (hereafter named 'genic position'). Both antisenseonly (ASO)-R-loops and sense/antisense(S/AS)-R-loops sharply peaked around transcription start sites (TSSs), and these peaklevels corresponded positively with transcript levels of overlapping genes. more...

Organism:

Oryza sativa

Type:

Methylation profiling by high throughput sequencing; Other

Platforms:

GPL24468 GPL19290

10 Samples

Download data: BED, TXT

(Submitter supplied) Histone lysine crotonylation (Kcr) is a newly discovered post-translational modification (PTM) existing in mammalian. To assess relevance in histone Kcr and genome, we performed on genomic localization analysis of histone Kcr by ChIP-seq analysis.

Organism:

Oryza sativa Japonica Group

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL18525

4 Samples

Download data: TXT

(Submitter supplied) In eukaryotic cells, DNA is tightly packed in the nucleus in chromatin which has histones as its main protein component. Histones are subject to a large number of distinct post-translational modifications, whose sequential or combinatorial action affects genome function. Here, we report the identification of acetylation at lysine 36 in histone H3 (H3K36ac) as a modification in Arabidopsis thaliana. H3K36ac was found to be an evolutionary conserved modification in seed plants. It is highly enriched in euchromatin and very low in heterochromatin. Genome-wide ChIP-seq experiments revealed that H3K36ac is generally found at the 5’ end of genes. Independently of gene length, H3K36ac covers about 500 bp, about two to three nucleosomes, immediately downstream of the transcriptional start. H3K36ac overlaps with H3K4me3 and the H2A.Z histone variant. The histone acetyl transferase GCN5 and the histone deacetylase HDA19 are required for normal steady state levels of H3K36ac in plants. There is negative crosstalk between H3K36ac and H3K36me3, mediated by the histone methyl transferase SDG8 and GCN5. H3K36ac levels are associated with transcriptional activity but show no linear relation. Instead, H3K36ac is a binary indicator of transcription

Organism:

Arabidopsis thaliana

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL13222

29 Samples

Download data: BW

(Submitter supplied) We systematically analyze the basic features of chromatin interaction mediated by RNAP2, H3K4me3 and H3K9me2. All interactions further aggregated into higher-order clusters and modular interacting domains with distinct genomic and transcriptional properties. Together, our strategy provides hierarchical and modular 3D genome architecture for transcription regulation in rice.

Organism:

Oryza sativa Indica Group

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL26667

12 Samples

Download data: BED

(Submitter supplied) Bidirectional gene pairs tend to be highly coregulated and function in similar biological processes in eukaryotic genomes. Structural features and functional consequences of BDPs have received considerable attention among diverse species. However, the underlying mechanisms responsible for bidirectional transcription and coexpression of BDPs remain poorly understood in plants. In this study, we integrated DNase-seq, RNA-seq, ChIP-seq and nucleosome positioning data and investigated the effect of DHSs on transcription of rice BDPs. more...

Organism:

Oryza sativa

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL9316

6 Samples

Download data: BED, WIG

(Submitter supplied) We present high-resolution maps of DNA methylation and H3K4 di- and tri-methylation of two entire chromosomes and two fully sequenced centromeres in rice shoots and cultured cells. Most transposable elements have highly methylated DNA but no H3K4 methylation whereas over half of protein-coding genes have both methylated DNA and di- and/or tri-methylated H3K4. Methylation of DNA but not H3K4 correlates with suppressed transcription. more...

Organism:

Oryza sativa

Type:

Genome binding/occupancy profiling by genome tiling array; Methylation profiling by genome tiling array

Platforms:

GPL6285 GPL6286

32 Samples

Download data: TXT

(Submitter supplied) Histone modifications play an integral role in plant development, but have been poorly studied in woody plants. Investigating chromatin organization in wood-forming tissue and its role in regulating gene expression allows us to understand the mechanisms underlying cellular differentiation during xylogenesis (wood formation) and identify novel functional regions in plant genomes. However, woody tissue poses unique challenges for using high-throughput chromatin immunoprecipitation (ChIP) techniques for studying genome-wide histone modifications in vivo. more...

Organism:

Eucalyptus grandis

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL20030

5 Samples

Download data: BEDGRAPH

(Submitter supplied) The behavior of transcriptomes and epigenomes in hybrids of heterotic parents is of fundamental interest. Here we report highly integrated maps of the epigenome, mRNA and small RNA transcriptomes of two rice subspecies and their reciprocal hybrids. We found that gene activity was correlated with DNA methylation and both active and repressive histone modifications in transcribed regions. Differential epigenetic modifications correlated with changes in transcript levels among hybrids and parental lines. more...

Organism:

Oryza sativa

Type:

Non-coding RNA profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing; Expression profiling by high throughput sequencing; Methylation profiling by high throughput sequencing

Platform:

GPL9147

24 Samples

Download data: BED, TAR

(Submitter supplied) We report the genome localization of R-loops in early and late-stage embryos relative to Drosophila cultured cells. We demonstrate that proper absolute R-loop levels chage during embryogenesis and that resolution of R-loops is critical for embryonic development. R-loop mapping by strand-specific DRIP-seq revealed that R-loop localization is plastic across development, both in the genes which form R-loops and where they localize relative to gene bodies. more...

Organism:

Drosophila melanogaster

Type:

Other

Platform:

GPL25244

15 Samples

Download data: BED

(Submitter supplied) We generated genome-wide high-resolution maps of H4K16ac and H3K23ac in Arabidopsis thaliana and Oryza sativa.

Organism:

Oryza sativa; Arabidopsis thaliana

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platforms:

GPL13222 GPL13160

5 Samples

Download data: BW

(Submitter supplied) To identify the genes regulated by androgen receptor (AR), we performed the profiling array analysis on the CWR22Rv1 cells and determined the differentially expressed genes upon the knockdown of AR.

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL16686

4 Samples

Download data: CEL

(Submitter supplied) Enhancers are important regulators of gene expression, but their identification is a challenge in plants. STARR-seq is a method measuring directly the enhancer activity of millions fragments in parallel, which had been successfully used to identify enhancers in Drosophila and human genomes. Here we present a global map of rice enhancers whose activities are quantitatively determined by STARR-seq.We also predicted intergenic enhancers based on DNase I hypersensitivity as described in a previously published work. more...

Organism:

Oryza sativa Japonica Group

Type:

Other

Platform:

GPL23876

4 Samples

Download data: BED, TXT

(Submitter supplied) Inspired by the important roles of the special chromatin structure R-loops, here we report a new method, ssDRIP-seq, for genome-wide identification of R-loops, and demonstrate its high efficiency, low bias, and strand-specificity when profiling the R-loops in Arabidopsis. Using this single-strand DNA ligation based library construction technique, we find that Arabidopsis R-loops are formed in both the sense and antisense orientations of genes, and prefer both AT and GC skews. more...

Organism:

Arabidopsis thaliana

Type:

Other

Platform:

GPL23157

5 Samples

Download data: BW, NARROWPEAK

(Submitter supplied) In this study, we aim to present a global view of transcriptome dynamics in different rice cultivars (IR64, Nagina 22 and Pokkali) under control and stress conditions. More than 50 million high quality reads were obtained for each tissue sample using Illumina platform. Reference-based assembly was performed for each rice cultivar. The transcriptome dynamics was studied by differential gene expression analyses between stress treatment and control sample.

Organism:

Oryza sativa

Type:

Expression profiling by high throughput sequencing

Platform:

GPL9316

7 Samples

Download data: TXT

(Submitter supplied) Opaque2 (O2) is a transcription factor that plays important roles during maize endosperm development. Mutation of the O2 gene improves the nutritional value of maize seeds, but also confers pleiotropic effects that result in reduced agronomic quality. To reveal the transcriptional regulatory framework of O2, we determined O2 DNA binding targets using chromatin immunoprecipitation coupled to high-throughput sequencing (ChIP-Seq). more...

Organism:

Zea mays

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL15463

2 Samples

Download data: BED, TXT

(Submitter supplied) Analysis of gene expression level. The hypothesis tested in the present study was that opaque2 mutant influence the expression of storage proteins. Results provide important information of the gene expression level regulation of storage proteins and other biological processes.

Organism:

Zea mays

Type:

Expression profiling by high throughput sequencing

Platform:

GPL17628

2 Samples

Download data: TXT

(Submitter supplied) DDX5, XRN2, and PRMT5 have been shown to resolve DNA/RNA hybrids (R-loops) at RNA polymerase II transcription termination sites at few genomic loci. Herein, we perform genome-wide R-loop mapping using classical DNA/RNA immunoprecipitation and high-throughput sequencing (DRIP-seq) of loci regulated by DDX5, XRN2, and PRMT5. We observed hundreds to thousands of R-loop gains and losses at transcribed loci in DDX5-, XRN2-, and PRMT5-deficient U2OS cells. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL24676 GPL20301

26 Samples

Download data: XLSX

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:

Oryza sativa

Type:

Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL19290

16 Samples

Download data: TXT

(Submitter supplied) Plant stress response and tolerance mechanisms are controlled by diverse genes. Transcription factors have been implicated in drought tolerance under drought stress conditions. Identification of target genes of such transcription factors could offer molecular regulatory networks by which the tolerance mechanisms orchestrated. Previously, we generated transgenic rice plants with 4 rice transcription factors OsNAC5, 6, 9, and 10 under the root-specific promoter RCc3 that were tolerant to drought stress with less loss of grain yield under drought conditions. more...

Organism:

Oryza sativa

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL19290

6 Samples

Download data: TXT

(Submitter supplied) To understand the molecular mechanisms of drought tolerance, we performed ChIP-Seq and RNA-Seq analyses to identify direct target genes of the OsNACs using the RCc3:MYC-OsNACs roots. A total of 475 binding loci of 4 OsNACs were identified by cross-referencing the binding occupancy of OsNACs at promoter regions and expression levels of corresponding genes. The binding loci are distributed on promoter regions of 391 target genes that were directly up-regulated by OsNACs in four RCc3:MYC-OsNAC transgenic roots. more...

Organism:

Oryza sativa

Type:

Expression profiling by high throughput sequencing

Platform:

GPL19290

10 Samples

Download data: TXT