Spatiotemporal Expression Control Correlates with Intragenic Scaffold Matrix Attachment Regions (S/MARs) in Arabidopsis thaliana

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

DEXP Values for S/MAR− Genes and as a Function of the Position of the S/MAR within S/MAR+ Genes

<p>The 5% confidence intervals are shown.</p

Median Expression Values of S/MAR− and S/MAR+ Genes in Different Organs, Root Tissues, and Flower Tissues

<p>MPSS data recorded in five different organs are shown (<a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.0020021#pcbi-0020021-t001" target="_blank">Table 1</a>, dataset 1) (A); for Affymetrix-based measurements (B–D), median values for five root tissues (<a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.0020021#pcbi-0020021-t001" target="_blank">Table 1</a>, dataset 2) (B), ten organs (<a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.0020021#pcbi-0020021-t001" target="_blank">Table 1</a>, dataset 4) (C), and five flower tissues (<a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.0020021#pcbi-0020021-t001" target="_blank">Table 1</a>, dataset 6) (D) are given. For MPSS-based experiments (A), tpm are indicated; for experiments based on the Affymetrix platform (B–D), Affymetrix expression values are plotted. The 5% confidence intervals calculated using bootstrap set for all values are shown.</p

DEXP Values for S/MAR+ and S/MAR− TF Genes for Different Datasets

<p>The 5% confidence intervals for all values are shown.</p