In Vivo Mapping of Arabidopsis Scaffold/Matrix Attachment Regions Reveals Link to Nucleosome-Disfavoring Poly(dA:dT) Tracts  . Issue 1 (31st January 2014)

• Record Type: Journal Article
• Authors: Pascuzzi, Pete E.; Flores-Vergara, Miguel A.; Lee, Tae-Jin; Sosinski, Bryon; Vaughn, Matthew W.; Hanley-Bowdoin, Linda; Thompson, William F.; Allen, George C.
• Is Part Of: The Plant Cell. Volume 26:Issue 1(2014)
• Page Start: 102
• Page End: 120
• Publication Date: 2014-01-31
• DOI: 10.1105/tpc.113.121194
• Languages: English
• ISSNs: 1040-4651

Abstract

Abstract : This work uses tiling microarrays to map S/MARs on Arabidopsis chromosome 4. S/MARs were found to be spaced more closely than in the large plant and animal genomes studied to date and preferentially enriched in poly(dA:dT) tracts, sequences that resist nucleosome formation. Most S/MARs occur near gene transcription start sites, and these genes show an increased probability of expression. Abstract: 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.