S/MARt DB: A database on chromatin organizing S/MAR regions

I. Liebich, J. Bode and E. Wingender

INTRODUCTION

Within the past 20 years (approximately) the model of the interphase nucleus underwent radical changes from a bag of chromatin immersed in homogeneous nucleoplasm to an anchored loop domain model in which chromatin is organized into large domains or loops fastened by a nonchromatin matrix [Gasser and Laemmli, 1986; Berezney, 1991]. The nuclear matrix is believed to correspond to the protein framework that resists extraction of nuclei with high­salt or lithium diiodosalicylate and DNA digestion [Mirkovitch et al., 1984]. A variety of functions have been assigned to the nuclear matrix. It has been suggested that the nuclear matrix may play a role in genome organization as well as in replication and gene expression [Amati and Gasser, 1990; Levi­Wilson and Fortier, 1989; Bode et al., 1995]. These functions are supposed to be mediated by scaffold or matrix attached regions (S/MARs).

S/MARt DB

S/MARs (scaffold or matrix attached regions) are elements of the DNA that attach the chromatin fiber to the proteinaceous network of the nucleus, the nuclear matrix or scaffold. Thereby they subdivide the eukaryotic genome into structural and functional domains. They are found at the base of the chromatin loops into which the eukaryotic genome appears to be organized. We have developed a relational model for a new database module called S/MARt DB (saffold/matrix attached region transaction database). This database collects information about S/MARs and the nuclear matrix proteins that are supposed be involved in the interaction of these elements with the nuclear matrix. These data are mainly extracted from original publications, but direct submissions are accepted as well if sufficient experimental evidence is provided to keep it as up­to­date as possible. The information on proteins involved in S/MAR attachment include, for example, molecular mass, amino acid sequence, structural and functional features as well as the modes by which binding to a S/MAR has been shown. The data collected on S/MAR elements include the method(s) by which a S/MAR has been defined, their sequence, structural and several functional features, e.g. binding strength, as far as this information is available. The chromosomal location of the S/MAR element as well as the notion of nearby genes, which may be influenced by them, will also be kept. This kind of information allows the modelling of functional and/or structural domains. The S/MARt DB database module is closely linked to the the TRANSFAC database [Heinemeyer et al., 1999]. It has been designed to make optimal use of structures and resources that are already present in the TRANSFAC database simultaneously extending TRANSFAC to another level of gene regulation. S/MARt DB is freely accessible through WWW [http:/transfac.gbf.de/SMART/] for non­profit research.

ACKNOWLEDGEMENT

This work has been supported by a grant of the German Ministry of Education, Science, Research and Technology (BMBF; Projekt­Nr. 0311640).

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