ArticleNucleic acids research2002
Evaluation of sequence motifs found in scaffold/matrix-attached regions (S/MARs).
Article in Nucleic acids research, 2002. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 25 papers.
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Who cites it
25 citing papers in PubMed, 66 citations in OpenAlex.
- Selective DNA-binding of SP120 (rat ortholog of human hnRNP U) is mediated by arginine-glycine rich domain and modulated by RNA.PloS one · 2023Article
- Transposable elements as scaffold/matrix attachment regions: shaping organization and functions in genomes.Frontiers in molecular biosciences · 2023Article
- Dynamics of nuclear matrix attachment regions during 5BMC genomics · 2022Article
- Specific subfamilies of transposable elements contribute to different domains of T lymphocyte enhancers.Proceedings of the National Academy of Sciences of the United States of America · 2020Article
- Comparative Analysis ofInsects · 2019Article
- Mapping of scaffold/matrix attachment regions in human genome: a data mining exercise.Nucleic acids research · 2019Article
- Chimeric 3' flanking regions strongly enhance gene expression in plants.Plant biotechnology journal · 2018Article
- 5' and 3' Untranslated Regions Strongly Enhance Performance of Geminiviral Replicons in Nicotiana benthamiana Leaves.Frontiers in plant science · 2016Article
- In vivo mapping of arabidopsis scaffold/matrix attachment regions reveals link to nucleosome-disfavoring poly(dA:dT) tracts.The Plant cell · 2014Article
- Relationship between DNA replication and the nuclear matrix.Genes to cells : devoted to molecular & cellular mechanisms · 2013Review
- CTCF binds to sites in the major histocompatibility complex that are rapidly reconfigured in response to interferon-gamma.Nucleic acids research · 2012Article
- Mechanisms of unphosphorylated STAT3 transcription factor binding to DNA.The Journal of biological chemistry · 2012Article
- High-level transgene expression by homologous recombination-mediated gene transfer.Nucleic acids research · 2011Article
- A mini review of MAR-binding proteins.Molecular biology reports · 2010Review
- The molecular anatomy of the FIP1L1-PDGFRA fusion gene.Leukemia · 2009Article
- Reconfiguration of genomic anchors upon transcriptional activation of the human major histocompatibility complex.Genome research · 2008Article
- Anchoring the genome.Genome biology · 2008Review
- Genetics and smoking behavior.Current psychiatry reports · 2007Review
- A comparative study of S/MAR prediction tools.BMC bioinformatics · 2007Article
- Molecular evolution of toxin genes in Elapidae snakes.Molecular diversity · 2006Review
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Authors and funding
4 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Based on the contents of the database S/MARt DB, the most comprehensive data collection of scaffold/matrix-attached regions (S/MARs) publicly available thus far, we initiated a systematic evaluation of the stored data. By analyzing the 245 S/MAR sequences presently described in this database, we found that the S/MARs contained in this collection are generally AT-rich, with certain significant exceptions. Comparative analyses showed that most of the AT-rich motifs which were found to be enriched in S/MARs are also enriched in randomized S/MAR sequences of the same AT content. Some sequence patterns previously suggested to be characteristic for S/MARs were also investigated, among them potential binding sites for homeodomain transcription factors. Even though hexanucleotides containing the core motif of homeodomain factors were frequently observed in S/MARs, only a few potential binding sites for these factors were found enriched when compared with regulatory regions or exon sequences. All our analyses indicated that, on average, the observed frequency of motifs in S/MAR elements is largely influenced by the AT content. Our results can serve as a guideline for further improvements in the definition of S/MARs, which are now believed to constitute the functional coordinate system for genomic regulatory regions.
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