ArticleGenome research2002
In silico prediction of scaffold/matrix attachment regions in large genomic sequences.
Article in Genome research, 2002. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 32 papers.
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Who cites it
32 citing papers in PubMed, 76 citations in OpenAlex.
- Mapping of scaffold/matrix attachment regions in human genome: a data mining exercise.Nucleic acids research · 2019Article
- Chromosome territories and the global regulation of the genome.Genes, chromosomes & cancer · 2019Review
- Matrix association region/scaffold attachment region: the crucial player in defining the positions of chromosome breaks mediated by bile acid-induced apoptosis in nasopharyngeal epithelial cells.BMC medical genomics · 2019Article
- Genome-WideFrontiers in cellular and infection microbiology · 2016Article
- Genome-wide mapping of matrix attachment regions in Drosophila melanogaster.BMC genomics · 2014Article
- Genome analysis of a major urban malaria vector mosquito, Anopheles stephensi.Genome biology · 2014Article
- BAC-based cellular model for screening regulators of BDNF gene transcription.BMC neuroscience · 2014Article
- Article
- In vivo mapping of arabidopsis scaffold/matrix attachment regions reveals link to nucleosome-disfavoring poly(dA:dT) tracts.The Plant cell · 2014Article
- HMGA regulates the global chromatin state and neurogenic potential in neocortical precursor cells.Nature neuroscience · 2012Article
- The zebrafish IgH locus contains multiple transcriptional regulatory regions.Developmental and comparative immunology · 2011Article
- Article
- Identification of Scaffold/Matrix Attachment (S/MAR) like DNA element from the gastrointestinal protozoan parasite Giardia lamblia.BMC genomics · 2010Article
- Article
- Determination of the in vivo structural DNA loop organization in the genomic region of the rat albumin locus by means of a topological approach.DNA research : an international journal for rapid publication of reports on genes and genomes · 2010Article
- AGAMOUS controls GIANT KILLER, a multifunctional chromatin modifier in reproductive organ patterning and differentiation.PLoS biology · 2009Article
- The molecular anatomy of the FIP1L1-PDGFRA fusion gene.Leukemia · 2009Article
- Association of the matrix attachment region recognition signature with coding regions in Caenorhabditis elegans.BMC genomics · 2007Article
- In silico comparative genomic analysis of GABAA receptor transcriptional regulation.BMC genomics · 2007Article
- A comparative study of S/MAR prediction tools.BMC bioinformatics · 2007Article
Corrections and comments
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Authors and funding
6 authors at 2 institutions in 3 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Scaffold/matrix attachment regions (S/MARs) are essential regulatory DNA elements of eukaryotic cells. They are major determinants of locus control of gene expression and can shield gene expression from position effects. Experimental detection of S/MARs requires substantial effort and is not suitable for large-scale screening of genomic sequences. In silico prediction of S/MARs can provide a crucial first selection step to reduce the number of candidates. We used experimentally defined S/MAR sequences as the training set and generated a library of new S/MAR-associated, AT-rich patterns described as weight matrices. A new tool called SMARTest was developed that identifies potential S/MARs by performing a density analysis based on the S/MAR matrix library (http://www.genomatix.de/cgi-bin/smartest_pd/smartest.pl). S/MAR predictions were evaluated by using six genomic sequences from animal and plant for which S/MARs and non-S/MARs were experimentally mapped. SMARTest reached a sensitivity of 38% and a specificity of 68%. In contrast to previous algorithms, the SMARTest approach does not depend on the sequence context and is suitable to analyze long genomic sequences up to the size of whole chromosomes. To demonstrate the feasibility of large-scale S/MAR prediction, we analyzed the recently published chromosome 22 sequence and found 1198 S/MAR candidates.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.