In vivo mapping of arabidopsis scaffold/matrix attachment regions reveals link to nucleosome-disfavoring poly(dA:dT) tracts.
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.
Department of Molecular and Structural Biochemistry, North Carolina State University, Raleigh, North Carolina 27695.
Pete E
PE
Pascuzzi
Miguel A
MA
Flores-Vergara
Tae-Jin
TJ
Lee
Bryon
B
Sosinski
Matthew W
MW
Vaughn
Linda
L
Hanley-Bowdoin
William F
WF
Thompson
George C
GC
Allen
D017360:Arabidopsis / Q000235:genetics*; D029681:Arabidopsis Proteins / Q000235:genetics / Q000378:metabolism / Q000502:physiology*; D002843:Chromatin / Q000378:metabolism; D018506:Gene Expression Regulation, Plant; D045170:Matrix Attachment Regions; D009707:Nucleosomes / Q000378:metabolism*; D059372:Nucleotide Motifs; D011067:Poly dA-dT / Q000378:metabolism*; D014157:Transcription Factors / Q000235:genetics / Q000378:metabolism / Q000502:physiology*
D029681:Arabidopsis Proteins; D002843:Chromatin; D009707:Nucleosomes; D014157:Transcription Factors; D011067:Poly dA-dT