Genome-wide in silico mapping of scaffold/matrix attachment regions in arabidopsis suggests correlation of intragenic scaffold/matrix attachment regions with gene expression

Stephen Rudd, Matthias Frisch, Korbinian Grote, Blake C. Meyers, Klaus Mayer, Thomas Werner

Research output: Contribution to journalArticlepeer-review

34 Scopus citations

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.

Original languageEnglish
Pages (from-to)715-722
Number of pages8
JournalPlant Physiology
Volume135
Issue number2
DOIs
StatePublished - Jun 2004
Externally publishedYes

Fingerprint

Dive into the research topics of 'Genome-wide in silico mapping of scaffold/matrix attachment regions in arabidopsis suggests correlation of intragenic scaffold/matrix attachment regions with gene expression'. Together they form a unique fingerprint.

Cite this