Ontology highlight
ABSTRACT:
PROVIDER: PRJNA745462 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR15114300_1.fastq.gz | Fastqsanger.gz | |||
| SRR15114300_2.fastq.gz | Fastqsanger.gz | |||
| SRR15114301_1.fastq.gz | Fastqsanger.gz | |||
| SRR15114301_2.fastq.gz | Fastqsanger.gz | |||
| SRR15114302_1.fastq.gz | Fastqsanger.gz |
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Project description:Scaffold or matrix attachment regions (S/MARs) are found in all eukaryotes. The pattern of distribution and genomic context of S/MARs is thought to be important for processes such as chromatin organization and modulation of gene expression. Despite the importance of such processes, much is unknown about the large-scale distribution and sequence content of S/ MARs in vivo. Here, we report the use of tiling microarrays to map 1358 S/MARs on Arabidopsis thaliana chromosome 4 (chr4). S/MARs occur throughout chr4, spaced much more closely than in the large plant and animal genomes that have been studied to date. Arabidopsis S/MARs can be divided into five clusters based on their association with other genomic features, suggesting a diversity of functions. While some Arabidopsis S/MARs may define structural domains, most occur near the transcription start sites of genes. Genes associated with these S/MARs have an increased probability of expression, which is particularly pronounced in the case of transcription factor genes. Analysis of sequence motifs and 6-mer enrichment patterns show that S/MARs are preferentially enriched in poly(dA:dT) tracts, sequences that resist nucleosome formation, and the majority of S/MARs contain at least one nucleosome-depleted region. This global view of S/MARs provides a framework to begin evaluating genome-scale models for S/MAR function. Contrast between DNA bound to nuclear scaffold/matrix and total genomic DNA in Arabidopsis Chr4 excluding the constitutive heterochromatin. Total of three biological replicates with two independent hybridizations on custom-designed NimbleGen high-density microarrays that include duplicate spots for each probe.
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