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.

Figure 1.

S/MAR-containing genes are associated with fewer MPSS matches and ESTs than S/MAR-less genes. A, This graph shows the relative coverage of MPSS hits of genes with (S/MAR+) or without (S/MAR−) intragenic S/MARs. A gene was only considered containing an S/MAR when the predicted S/MAR overlapped at least 50 bp with an annotated gene. The number of genes containing an S/MAR (S/MAR+) or without an S/MAR (S/MAR−) for which at least 10 MPSS hits were found is shown as percentage of all genes of this class. The exact values and sd are given above the columns. P < 0.0001. Calculation of expected values is detailed in the methods. B, The graph shows results of an analogous analysis as in A using EST data. P < 0.0001. All values were calculated by InStat3 from GraphPad software (www.graphpad.com).

Figure 2.

Intragenic S/MARs in Arabidopsis are located preferentially in the 5′-half of the genes. This graph shows the relative frequency of an S/MAR overlapping or occurring within a particular intron or exon. A value of 1.0 is indicative of the observed value equaling the expected value; a value greater than 1.0 is indicative of an overrepresentation of S/MAR occurrence with this feature; and a value of less than 1.0 is indicative of an underrepresentation of S/MAR occurrence with this feature. Numbers have been corrected for actual numbers and length of introns and exons.