Transcriptomics,Genomics,Multiomics

Dataset Information

7

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. 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

OTHER RELATED OMICS DATASETS IN: PRJNA151473

ORGANISM(S): Arabidopsis thaliana  

TISSUE(S): Flower, Leaf

SUBMITTER: Tao Zhang   Yufeng Wu  Wenli Zhang  Jiming Jiang 

PROVIDER: E-GEOD-34318 | ArrayExpress | 2012-07-05

SECONDARY ACCESSION(S): SRP009678GSE34318PRJNA151473

REPOSITORIES: GEO, ArrayExpress, ENA

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Publications

Genome-wide identification of regulatory DNA elements and protein-binding footprints using signatures of open chromatin in Arabidopsis.

Zhang Wenli W   Zhang Tao T   Wu Yufeng Y   Jiang Jiming J  

The Plant cell 20120705 7


Gene expression and regulation in eukaryotes is controlled by orchestrated binding of regulatory proteins, including both activators and repressors, to promoters and other cis-regulatory DNA elements. An increasing number of plant genomes have been sequenced; however, a similar effort to the ENCODE project, which aimed to identify all functional elements in the human genome, has yet to be initiated in plants. Here we report genome-wide high-resolution mapping of DNase I hypersensitive (DH) sites  ...[more]

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