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Mapping regulatory elements using signatures of open chromatin in Arabidopsis thaliana

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 reported genome-wide high resolution maps of DNase I hypersensitive (DH) sites from both seedling and flower tissues of Arabidopsis from the Columbia (Col) ecotype and the corresponding ddm1 (deficient in DNA methylation 1) mutant. We identified 38,290, 41,193, 38,313, and 38,153 DH sites in leaf (Col), flower (Col), ddm1 leaf, and ddm1 flower tissues, respectively. Approximately 45% of the DH sites in all tissue types were located within 1 kb of a transcription start site (TSS), which represents a putative promoter region. Pairwise comparisons of the DH sites derived from different tissue types revealed DH sites specific to each tissue. DH sites are significantly associated with long non-coding RNAs (lncRNAs) and conserved non-coding sequences (CNSs). The binding sites of MADS-domain transcription factors AP1 and SEP3 are highly correlated with DH sites.

ORGANISM(S): Arabidopsis thaliana

PROVIDER: GSE34318 | GEO | 2012/07/06

SECONDARY ACCESSION(S): PRJNA151473

REPOSITORIES: GEO

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Mapping regulatory elements using signatures of open chromatin in Arabidopsis thaliana

Project description: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 reported genome-wide high resolution maps of DNase I hypersensitive (DH) sites from both seedling and flower tissues of Arabidopsis from the Columbia (Col) ecotype and the corresponding ddm1 (deficient in DNA methylation 1) mutant. We identified 38,290, 41,193, 38,313, and 38,153 DH sites in leaf (Col), flower (Col), ddm1 leaf, and ddm1 flower tissues, respectively. Approximately 45% of the DH sites in all tissue types were located within 1 kb of a transcription start site (TSS), which represents a putative promoter region. Pairwise comparisons of the DH sites derived from different tissue types revealed DH sites specific to each tissue. DH sites are significantly associated with long non-coding RNAs (lncRNAs) and conserved non-coding sequences (CNSs). The binding sites of MADS-domain transcription factors AP1 and SEP3 are highly correlated with DH sites. To map the DH sites in A. thaliana, we constructed a total of five DNase-seq libraries using leaf and flower tissues from the Columbia (Col) ecotype and a ddm1 (deficient in DNA methylation 1) mutant of Columbia. These libraries were sequenced using the Illumina Genome Analyzer. We obtained a total of 190 million (M) sequence reads from these libraries. Approximately 114 M reads had a single sequence match in the A. thaliana genome

2012-07-05 | E-GEOD-34318 | biostudies-arrayexpress

ChIP-seq to identify the positions of three histone modifications in the rice genome

Project description: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. To do associated analysis with DNase I hypersensitive sites in rice, we performed ChIP-seq to identify the positions of three histone modifications (H3K4me2, H3K36me3 and H4K12ac) in the rice genome (leaf tissue only - not callus). The ChIP DNA from seedling of each experiment was sequenced on one lane of Illumina Genome Analyzer.

2011-11-09 | E-GEOD-26733 | biostudies-arrayexpress

ChIP-seq to identify the positions of three histone modifications in the rice genome

Project description: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.

2011-11-09 | GSE26733 | GEO

DNase I hypersensitive sites in two tissues of rice

Project description: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. For RNA-seq used in this project, please check GEO data GSE33265.

2011-11-09 | GSE26610 | GEO

DNase I hypersensitive sites in two tissues of rice

Project description: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.

2011-11-09 | E-GEOD-26610 | biostudies-arrayexpress

Identification of genes regulated by the MADS transcription factor (TF), SEPALLATA3, in the context of the double sep1sep2 and triple sep1sep2sep3 mutant background, by RNA-Seq analysis

Project description:These analyses allowed the identification of more than 2000 genes regulated by the MADS TF, SEPALLATA3 (SEP3). Although the involvement of SEP3 in all flower organ development is well established, the single sep3 mutant shows no flower phenotype, due to redundancy with other SEPALLATA genes. The triple mutant, sep1sep2sep3, shows no floral organ development except sepals, while the sep1sep2 mutant showed characteristic WT flower with, from the outer to the inner whorl of the flower, 4 sepals, 4 petals, 6 stamens and one gynoecium. We performed RNA-seq analysis on sep1sep2, sep1sep2sep3 and on sep1sep2sep3 lines complemented with SEP3 to highlight genes involved in floral organ development and controlled by SEP3. For this purpose we compared gene expression between the triple and the double mutant, and between triple mutant lines complemented with SEP3 and the triple mutant. Genes were considered regulated by SEP3 when the log FC was between 1 and -1 and the FDR <0.05. Using these criteria, we obtained a list of >2000 genes regulated by SEP3.

2020-09-07 | GSE150605 | GEO

Characterization of small RNAs and their targets in Amborella trichopoda

Project description:The small RNAs and their targets were characterized in Amborella genome by deep sequencing the small RNA populations of leaf tissue and opened-female flower tissue. The small RNA targets were also validated from degradome populations of leaf tissue and opened-female flower tissue.

2013-07-01 | GSE41811 | GEO

Comparing the targets of distinct RNA Directed DNA Methylation mechanisms in Arabidopsis thaliana

Project description:The diversity of small RNA-directed DNA methylation (RdDM) mechanisms have been underestimated due to the nearly complete transcriptional silencing of transposable elements (TEs) in the wt Col ecotype of Arabidopsis thaliana. In plants mutant for the SWI/SNF2 histone remodeler DDM1, TEs are globally activated due to loss of genome wide heterochromatin condensation. Activated TEs go through additional non-canonical forms of RdDM. However, the global targets of the non-canonical RdDM pathway are unidentified. In an attempt to identify and contrast the targets of canonical and non-canonical RdDM, we sequenced small RNAs from several RdDM mutants in either the TE-silent or the TE-active (ddm1) contexts. Examination of unopened flower bud small RNAs from wild type and various single or double mutant combinations, many of which have biological replicates. Small RNA sequences from wt Col, controls and other mutants shown in the study are available at GSE41755 and GSE57191.

2016-07-22 | E-GEOD-79780 | biostudies-arrayexpress

Genome-wide dynamics of H3K27me3 and H3K4me3 during early flower development [ChIP-seq]

Project description:We studied early events of flower formation with a temporal resolution by employing a floral induction system to drive synchronized flower development from inflorescence meristem-like tissue (Wellmer et al. (2006)). We generated a developmental time series including vegetative leaf tissue, young developing flowers at zero (t0) and two days after induction of flower development (t2), and fully expanded inflorescences. Although we found very similar numbers of H3K27me3 and H3K4me3 target genes, many genes display quantitative changes in those marks, especially between different tissue types (e.g. >60% of target genes change quantitatively from leaf to t0).

2017-07-18 | GSE71564 | GEO

The chromatin remodeler protein DDM1 regulates early seedling growth hybrid vigor by modulating gene expression in Arabidopsis

Project description:Despite of the paramount importance of heterosis in agriculture, the molecular mechanisms underlying heterosis remain elusive. Recent studies in Arabidopsis suggested possible involvement of DNA methylation in heterosis. We tested this hypothesis genetically by crossing homozygous mutants in DNA methylation-related genes in the Columbia (Col) ecotype with homozygous mutants in the same DNA methylation-related genes in the C24 ecotype. When genes in the RNA-directed DNA methylation (RdDM) pathway were mutated, the resultant F1 hybrids did not show appreciable loss of best parent heterosis (BPH) performances in early seedling growth. In contrast, mutations in the putative chromatin remodeling protein DECREASE OF DNA METHYLATION 1 (DDM1) caused ddm1-Col like growth pattern of ddm1-F1 hybrids, a mid-parent heterosis (MPH) performance. To understand the underlying molecular mechanisms, we compared the transcriptomes of the parental plants and reciprocal F1 hybrids in the wild type and ddm1 mutant backgrounds, and identified 183 non-additively expressed (NAE) genes, which were functionally enriched in defense response, a group of genes negatively associated with plant size. Interestingly, for the expression levels of the NAE genes, WT-F1 hybrids were enriched in the Golden Ration between mid-parent values (MPVs) and Col parents in WT, but ddm1-F1 hybrids were comparable to ddm1-Col parent in ddm1 mutant, which explained the MPH performance of ddm1-F1 hybrids. DNA methylation analyses revealed only one third of the NAE genes with highly methylated promoters whose expression is negatively associated with DNA methylation of promoters, strongly suggesting that DDM1 regulates heterosis by multiple epigenetic modifications.

2016-11-07 | GSE74551 | GEO

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