S/MARt DB
NAR Molecular Biology Database Collection entry number 309
Liebich I.1 and Wingender E.1,2
1BIOBASE GmbH, Halchtersche Straße 33, D-38304 WolfenbÜttel, Germany
2Department of Bioinformatics, UKG, University of GÖttingen, Goldschmidtstrasse 1, D-37077 GÖttingen, Germany
2Department of Bioinformatics, UKG, University of GÖttingen, Goldschmidtstrasse 1, D-37077 GÖttingen, Germany
Database Description
The nuclear organization of metaphase and interphase cells has been studied over several decades and increasing evidence supports the concept upon which the eukaryotic chromatin is organized in the form of functional independent loop domains [1; 2]. Scaffold/matrix attached regions (S/MARs) are DNA sequences that mediate the tight contact of the chromatin with the proteinaceous scaffold within the nucleus. They have shown to be necessary for chromatin loops to form [3] and they were observed at the base of chromatin loops [4]. S/MARs have also been assigned to function in gene expression. Recently it has been shown that S/MARs can serve as landing platforms for several chromatin remodeling factors and thereby influence gene expression [5]. S/MARs were also attributed a fundamental role in carcinogenesis [6].
S/MARt DB is a curated database which collects information about S/MARs and nuclear proteins which are involved in the interaction of these elements with the nuclear scaffold [7]. Its wet-lab verified data are compiled predominantly from publications in peer-reviewed journals. The database equipped with tools for searching and browsing is freely accessible through WWW (http://smartdb.bioinf.med.uni-goettingen.de/) for users from non-profit organizations.
The data presented as three hyperlinked files for the use via the internet come mainly from animal and plant species.
S/MARt DB has been enlarged by new entries to 500 S/MAR entries in the recent release and improved further by updating of already existing entries in each of its tables. With release 2.2 the database was complemented by hyperlinks to EntrezGene and Ensembl, respectively. They serve to incorporate S/MARt DB into a European network of biological databases which is going to be build up in the context of the TEMBLOR project.
S/MARt DB is a curated database which collects information about S/MARs and nuclear proteins which are involved in the interaction of these elements with the nuclear scaffold [7]. Its wet-lab verified data are compiled predominantly from publications in peer-reviewed journals. The database equipped with tools for searching and browsing is freely accessible through WWW (http://smartdb.bioinf.med.uni-goettingen.de/) for users from non-profit organizations.
The data presented as three hyperlinked files for the use via the internet come mainly from animal and plant species.
S/MARt DB has been enlarged by new entries to 500 S/MAR entries in the recent release and improved further by updating of already existing entries in each of its tables. With release 2.2 the database was complemented by hyperlinks to EntrezGene and Ensembl, respectively. They serve to incorporate S/MARt DB into a European network of biological databases which is going to be build up in the context of the TEMBLOR project.
Acknowledgements
We are grateful to our colleagues for technical support. This work was supported by grants of the German Federal Ministry of Education, Science and Research (BMBF, project no. 01SF9988/4).
References
1. Gasser, S. M. and Laemmli, U. K. (1987) A glimpse at chromosomal order, Trends Genet. 3, 16-22.
2. Heng, H. H. Q., Krawetz, S. A., Lu, W., Bremer, S., Liu, G. and Ye, C. J. (2001) Re-defining the chromatin loop domain, Cytogenet. Cell Genet.. 93, 1551-1561.
3. Heng, H. H. Q., Goetze, S., Ye, C. J., Liu, G., Stevens, J. B., Bremer, S. W., Wykes, S. M., Bode, J. and Krawetz, S. A. (2004) Chromatin loops are selectively anchored using scaffold/matrix-attachment regions, J. Cell Sci. 117, 999-1008.
4. Cai, S., Han, H.-J. and Kohwi-Shigematsu, T. (2003) Tissue-specific nuclear architecture and gene expression regulated by SATB1, Nat. Genet. 34, 42-51
5. Yasui, D., Miyano, M., Cai, S., Varga-Weisz, P. and Kohwi-Shigematsu, T. (2002) SATB1 _targets chromatin remodelling to regulate genes over long distances, Nature 419, 641-645.
6. Will,K., Warnecke,G., Albrechtsen,N., Boulikas,T. and Deppert,W. (1998) High affinity MAR-DNA binding is a common property of murine and human mutant p53. J. Cell. Biochem. 69, 260-270.
7. Liebich,I. Bode,J., Frisch,M. and Wingender,E. (2002) S/MARt DB: a database on scaffold/matrix attached regions. Nucleic Acids Res. 30, 372-374.
2. Heng, H. H. Q., Krawetz, S. A., Lu, W., Bremer, S., Liu, G. and Ye, C. J. (2001) Re-defining the chromatin loop domain, Cytogenet. Cell Genet.. 93, 1551-1561.
3. Heng, H. H. Q., Goetze, S., Ye, C. J., Liu, G., Stevens, J. B., Bremer, S. W., Wykes, S. M., Bode, J. and Krawetz, S. A. (2004) Chromatin loops are selectively anchored using scaffold/matrix-attachment regions, J. Cell Sci. 117, 999-1008.
4. Cai, S., Han, H.-J. and Kohwi-Shigematsu, T. (2003) Tissue-specific nuclear architecture and gene expression regulated by SATB1, Nat. Genet. 34, 42-51
5. Yasui, D., Miyano, M., Cai, S., Varga-Weisz, P. and Kohwi-Shigematsu, T. (2002) SATB1 _targets chromatin remodelling to regulate genes over long distances, Nature 419, 641-645.
6. Will,K., Warnecke,G., Albrechtsen,N., Boulikas,T. and Deppert,W. (1998) High affinity MAR-DNA binding is a common property of murine and human mutant p53. J. Cell. Biochem. 69, 260-270.
7. Liebich,I. Bode,J., Frisch,M. and Wingender,E. (2002) S/MARt DB: a database on scaffold/matrix attached regions. Nucleic Acids Res. 30, 372-374.
Category: Nucleotide Sequence Databases
Subcategory: Coding and non-coding DNA
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