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

DOI: 10.1371/journal.pcbi.0020021 Spatiotemporal Expression Control Correlates with Intragenic Scaffold Matrix Attachment Regions (S/MARs) in Arabidopsis thaliana Igor V. Tetko 0 1 Georg Haberer 0 1 Stephen Rudd 0 1 Blake Meyers 0 1 Hans-Werner Mewes 0 1 Klaus F. X. Mayer 0 1 0 Editor: Philip E. Bourne, University of California San Diego , United States of America 1 1 GSF National Research Center for Environment and Health, MIPS, Institute for Bioinformatics , Neuherberg, Germany , 2 Bioinformatics Group, Turku Centre for Biotechnology , Tykistokatu, Turku , Finland , 3 Department of Genome-Oriented Bioinformatics, Wissenschaftszentrum Weihenstephan, Technische Universita t Mu nchen , Freising, Germany , 4 Department of Plant and Soil Sciences, Delaware Biotechnology Institute , Newark, New Jersey , United States of America 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. - Scaffold/matrix attachment regions (S/MARs) are structural elements of eukaryotic cells [1]. S/MARs are required for the compaction and anchoring of chromatin to the nuclear framework. These regions are approximately 300 base pairs to several kilobases in length, and they are present in all higher eukaryotes, including mammals and plants [2,3]. S/ MARs are defined as DNA elements that specifically bind to the nuclear matrix and as DNA fragments that copurify with the nuclear matrix [4]. Involvement of S/MARs in the regulation of gene activity and in the stabilization of expression has been shown for individual genes and S/MARs [5]. For vertebrates, a striking overlap of conserved noncoding elements and S/MAR functionality has been reported [6]. Glazko and coworkers reported that an excess of conserved vertebrate S/MAR regions was detected in intergenic regions preceding the 59 end of genes, suggesting that these attachment regions might be involved in transcriptional control. These conclusions made for vertebrates are supported by our previous analysis of the correlation of S/MAR elements and expression levels in Arabidopsis thaliana. S/MARcontaining genes (S/MAR genes) have been shown to reach overall significantly lower expression levels compared to genes not associated with S/MARs, or lacking S/MARs (S/ MAR genes) [7]. Thus, intragenic S/MARs show a negative correlation with the transcriptional level of the S/MARcontaining gene and therefore may be involved in regulation of gene expression. It has been hypothesized that, apart from transcriptional control mediated by specific transcription factors (TFs) and their respective cis-regulatory promoter binding sites, higherlevel spatial and temporal chromosome topology within the nucleus and its association with the nuclear matrix exert important regulatory functions. For individual S/MARs, tissue and temporal regulatory roles are well established [1,8,9]. However, thus far, for no organism has a comprehensive and genome scale analysis been undertaken to investigate the implications of S/MAR presence within genes with respect to transcriptional activity. With the availability of a high-quality genome template for Arabidopsis and the localization of S/ MARs on the complete genome [7] as well as the availability of high quality expression data [10 13], it has become feasible to address questions regarding the influence of intragenic S/ MARs on spatiotemporal regulation of transcription. In our analysis, we made use of the available expression data that measure expression within different tissues, organs, and developmental stages. Our results provide evidence that the presence of an intragenic S/MAR not only correlates with the expression levels of genes but also shows a pronounced specificity for tissues, organs, and developmental phases. This allows the conclusion that intragenic S/MARs not only serve as static organizers of nuclear and chromosomal structure but also reflect the presence of potentially dynamic DNA elements that exert important regulatory functions on the expression of individual genes. Scaffold/matrix attachment regions (S/MARs) are AT-rich DNA sequences that mediate structural organization of the chromatin within the nucleus. These elements constitute anchor points of the DNA for the chromatin scaffold and serve to organize the chromatin into structural domains. Studies on individual genes led to the conclusion that the dynamic and complex organization of the chromatin mediated by S/MAR elements plays an important role in the regulation of gene expression. In addition to intergenic S/MARs, which likely exert import insulator effects, more than 2,000 intragenic S/MARs have been shown to be present within the Arabidopsis genome. In this study, the authors set out to analyze the effects of these intragenic S/MAR elements on the regulation of the genes affected. Making use of exhaustive and multidimensional expression datasets available for Arabidopsis, the authors analyzed overall expression differences and correlation of intragenic S/MARs with spatiotemporal expression of genes. On a genome scale, pronounced tissue- and organ-specific and developmental expression patterns of S/MAR-containing genes have been detected. Notably, transcription factor genes contain a significant higher portion of S/MARs. The pronounced difference in expression characteristics of S/MAR-containing genes emphasizes their functional importance and the importance of structural chromosomal characteristics for gene regulation in plants as well as within other eukaryotes. In our analysis, we used S/MARs that were detected as described in our previous analysis [7]. Within this study we showed that S/MAR genes containing S/MAR elements have an overall lower expression level. This has been measured by EST associations as a proxy for expression strength as well as by MPSS (Massive Parallel Sequencing Signature). The MPSS technology produces short sequence signatures produced from a defined position within an mRNA, and the relative abundance of these signatures in a given library represents a quantitati (...truncated)