pubmed.ncbi.nlm.nih.gov

Spatiotemporal expression control correlates with intragenic scaffold matrix attachment regions (S/MARs) in Arabidopsis thaliana - PubMed

Review

Spatiotemporal expression control correlates with intragenic scaffold matrix attachment regions (S/MARs) in Arabidopsis thaliana

Igor V Tetko et al. PLoS Comput Biol. 2006 Mar.

Erratum in

  • PLoS Comput Biol. 2006 Jun 30;2(6):e67

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.

PubMed Disclaimer

Conflict of interest statement

Competing interests. The authors have declared that no competing interests exist.

Figures

Figure 1
Figure 1. Median Expression Values of S/MAR− and S/MAR+ Genes in Different Organs, Root Tissues, and Flower Tissues

MPSS data recorded in five different organs are shown (Table 1, dataset 1) (A); for Affymetrix-based measurements (B–D), median values for five root tissues (Table 1, dataset 2) (B), ten organs (Table 1, dataset 4) (C), and five flower tissues (Table 1, 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.

Figure 2
Figure 2. DEXP Values of S/MAR− and S/MAR+ Genes for Different Organs and Tissues

(A) DEXP for MPSS data recorded in five different organs (Table 1, dataset 1). (B) DEXP for five root tissues (Table 1, dataset 2). (C) DEXP for ten organs (Table 1, dataset 4). (D) DEXP for five flower tissues (Table 1, dataset 6). There are different scales for different experiments. The 5% confidence intervals are shown as error bars.

Figure 3
Figure 3. Median Expression and DEXP Values for Different Developmental Stages of Root and Flower

The median expression values and the DEXP values for three different developmental stages of the root (A and C) and four developmental stages of the flower (B and D) are given. The respective stage classifier is given on the x-axis. The differences in DEXP values of S/MAR+ and S/MAR− genes decrease with the increasing age of the tissues. The 5% confidence intervals for all values are shown.

Figure 4
Figure 4. DEXP Values for S/MAR+ and S/MAR− TF Genes for Different Datasets

The 5% confidence intervals for all values are shown.

Figure 5
Figure 5. DEXP Values for S/MAR− Genes and as a Function of the Position of the S/MAR within S/MAR+ Genes

The 5% confidence intervals are shown.

Similar articles

Cited by

References

    1. Chernov IP, Akopov SB, Nikolaev LG. [Structure and function of nuclear matrix associated regions (S/MARs)] Bioorg Khim. 2004;30:3–14. - PubMed
    1. Allen GC, Spiker S, Thompson WF. Use of matrix attachment regions (MARs) to minimize transgene silencing. Plant Mol Biol. 2000;43:361–376. - PubMed
    1. Bode J, Stengert-Iber M, Kay V, Schlake T, Dietz-Pfeilstetter A. Scaffold/matrix-attached regions: Topological switches with multiple regulatory functions. Crit Rev Eukaryot Gene Expr. 1996;6:115–138. - PubMed
    1. Michalowski SM, Allen GC, Hall GE, Jr., Thompson WF, Spiker S. Characterization of randomly-obtained matrix attachment regions (MARs) from higher plants. Biochemistry. 1999;38:12795–12804. - PubMed
    1. Butaye KM, Goderis IJ, Wouters PF, Pues JM, Delaure SL, et al. Stable high-level transgene expression in Arabidopsis thaliana using gene silencing mutants and matrix attachment regions. Plant J. 2004;39:440–449. - PubMed

Publication types

MeSH terms

Substances