Genome-wide in silico mapping of scaffold/matrix attachment regions in Arabidopsis suggests correlation of intragenic scaffold/matrix attachment regions with gene expression.
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.
Rudd
Stephen
S
Munich Information Center for Protein Sequences/Institute for Bioinformatics, GSF-National Research Center for Environment and Health, 85764 Neuherberg, Germany.
Frisch
Matthias
M
Grote
Korbinian
K
Meyers
Blake C
BC
Mayer
Klaus
K
Werner
Thomas
T
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
D014157:Transcription Factors