title: Spatiotemporal expression control correlates with intragenic scaffold matrix attachment regions (S/MARs) in Arabidopsis thaliana.
abstract: Scaffold/matrix attachment regions (S/MARs) are essential for structural organization of the chromatin within the nucleus and serve as anchors of chromatin loop domains. A significant fraction of genes in Arabidopsis thaliana contains intragenic S/MAR elements and a significant correlation of S/MAR presence and overall expression strength has been demonstrated. In this study, we undertook a genome scale analysis of expression level and spatiotemporal expression differences in correlation with the presence or absence of genic S/MAR elements. We demonstrate that genes containing intragenic S/MARs are prone to pronounced spatiotemporal expression regulation. This characteristic is found to be even more pronounced for transcription factor genes. Our observations illustrate the importance of S/MARs in transcriptional regulation and the role of chromatin structural characteristics for gene regulation. Our findings open new perspectives for the understanding of tissue- and organ-specific regulation of gene expression.
authors.affiliation: GSF National Research Center for Environment and Health, MIPS, Institute for Bioinformatics, Neuherberg, Germany.
authors.forename: Igor V
authors.initials: IV
authors.lastname: Tetko
authors.forename: Georg
authors.initials: G
authors.lastname: Haberer
authors.forename: Stephen
authors.initials: S
authors.lastname: Rudd
authors.forename: Blake
authors.initials: B
authors.lastname: Meyers
authors.forename: Hans-Werner
authors.initials: HW
authors.lastname: Mewes
authors.forename: Klaus F X
authors.initials: KF
authors.lastname: Mayer
mesh_terms: D017360:Arabidopsis / Q000235:genetics*; D002467:Cell Nucleus / Q000235:genetics; D002843:Chromatin / Q000235:genetics; D018744:DNA, Plant / Q000235:genetics; D018506:Gene Expression Regulation, Plant; D017343:Genes, Plant; D020411:Oligonucleotide Array Sequence Analysis; D014158:Transcription, Genetic
chemical_list: D002843:Chromatin; D018744:DNA, Plant