title: Genome-wide in silico mapping of scaffold/matrix attachment regions in Arabidopsis suggests correlation of intragenic scaffold/matrix attachment regions with gene expression.
abstract: We carried out a genome-wide prediction of scaffold/matrix attachment regions (S/MARs) in Arabidopsis. Results indicate no uneven distribution on the chromosomal level but a clear underrepresentation of S/MARs inside genes. In cases where S/MARs were predicted within genes, these intragenic S/MARs were preferentially located within the 5'-half, most prominently within introns 1 and 2. Using Arabidopsis whole-genome expression data generated by the massively parallel signature sequencing methodology, we found a negative correlation between S/MAR-containing genes and transcriptional abundance. Expressed sequence tag data correlated the same way with S/MAR-containing genes. Thus, intragenic S/MARs show a negative correlation with transcription level. For various genes it has been shown experimentally that S/MARs can function as transcriptional regulators and that they have an implication in stabilizing expression levels within transgenic plants. On the basis of a genome-wide in silico S/MAR analysis, we found a significant correlation between the presence of intragenic S/MARs and transcriptional down-regulation.
authors.affiliation: Munich Information Center for Protein Sequences/Institute for Bioinformatics, GSF-National Research Center for Environment and Health, 85764 Neuherberg, Germany.
authors.forename: Stephen
authors.initials: S
authors.lastname: Rudd
authors.forename: Matthias
authors.initials: M
authors.lastname: Frisch
authors.forename: Korbinian
authors.initials: K
authors.lastname: Grote
authors.forename: Blake C
authors.initials: BC
authors.lastname: Meyers
authors.forename: Klaus
authors.initials: K
authors.lastname: Mayer
authors.forename: Thomas
authors.initials: T
authors.lastname: Werner
mesh_terms: D017360:Arabidopsis / Q000235:genetics*; D020224:Expressed Sequence Tags; D018506:Gene Expression Regulation, Plant; D018745:Genome, Plant; D045170:Matrix Attachment Regions / Q000235:genetics*; D020161:Physical Chromosome Mapping / Q000379:methods*; D014157:Transcription Factors / Q000235:genetics
chemical_list: D014157:Transcription Factors