70
views
0
recommends
+1 Recommend
0 collections
    0
    shares
      • Record: found
      • Abstract: found
      • Article: found
      Is Open Access

      Gene function correlates with potential for G4 DNA formation in the human genome

      research-article
      1 , 1 , 2 , 3 , *
      Nucleic Acids Research
      Oxford University Press

      Read this article at

      Bookmark
          There is no author summary for this article yet. Authors can add summaries to their articles on ScienceOpen to make them more accessible to a non-specialist audience.

          Abstract

          G-rich genomic regions can form G4 DNA upon transcription or replication. We have quantified the potential for G4 DNA formation (G4P) of the 16 654 genes in the human RefSeq database, and then correlated gene function with G4P. We have found that very low and very high G4P correlates with specific functional classes of genes. Notably, tumor suppressor genes have very low G4P and proto-oncogenes have very high G4P. G4P of these genes is evenly distributed between exons and introns, and it does not reflect enrichment for CpG islands or local chromosomal environment. These results show that genomic structure undergoes selection based on gene function. Selection based on G4P could promote genomic stability (or instability) of specific classes of genes; or reflect mechanisms for global regulation of gene expression.

          Related collections

          Most cited references42

          • Record: found
          • Abstract: found
          • Article: not found

          Gene Ontology: tool for the unification of biology

          Genomic sequencing has made it clear that a large fraction of the genes specifying the core biological functions are shared by all eukaryotes. Knowledge of the biological role of such shared proteins in one organism can often be transferred to other organisms. The goal of the Gene Ontology Consortium is to produce a dynamic, controlled vocabulary that can be applied to all eukaryotes even as knowledge of gene and protein roles in cells is accumulating and changing. To this end, three independent ontologies accessible on the World-Wide Web (http://www.geneontology.org) are being constructed: biological process, molecular function and cellular component.
            Bookmark
            • Record: found
            • Abstract: found
            • Article: not found

            Genome-wide analysis of mammalian promoter architecture and evolution.

            Mammalian promoters can be separated into two classes, conserved TATA box-enriched promoters, which initiate at a well-defined site, and more plastic, broad and evolvable CpG-rich promoters. We have sequenced tags corresponding to several hundred thousand transcription start sites (TSSs) in the mouse and human genomes, allowing precise analysis of the sequence architecture and evolution of distinct promoter classes. Different tissues and families of genes differentially use distinct types of promoters. Our tagging methods allow quantitative analysis of promoter usage in different tissues and show that differentially regulated alternative TSSs are a common feature in protein-coding genes and commonly generate alternative N termini. Among the TSSs, we identified new start sites associated with the majority of exons and with 3' UTRs. These data permit genome-scale identification of tissue-specific promoters and analysis of the cis-acting elements associated with them.
              Bookmark
              • Record: found
              • Abstract: found
              • Article: not found

              Fragile X mental retardation protein targets G quartet mRNAs important for neuronal function.

              Loss of fragile X mental retardation protein (FMRP) function causes the fragile X mental retardation syndrome. FMRP harbors three RNA binding domains, associates with polysomes, and is thought to regulate mRNA translation and/or localization, but the RNAs to which it binds are unknown. We have used RNA selection to demonstrate that the FMRP RGG box binds intramolecular G quartets. This data allowed us to identify mRNAs encoding proteins involved in synaptic or developmental neurobiology that harbor FMRP binding elements. The majority of these mRNAs have an altered polysome association in fragile X patient cells. These data demonstrate that G quartets serve as physiologically relevant targets for FMRP and identify mRNAs whose dysregulation may underlie human mental retardation.
                Bookmark

                Author and article information

                Journal
                Nucleic Acids Res
                Nucleic Acids Research
                Nucleic Acids Research
                Oxford University Press
                0305-1048
                1362-4962
                2006
                2006
                10 August 2006
                : 34
                : 14
                : 3887-3896
                Affiliations
                1Molecular and Cellular Biology Graduate Program, University of Washington School of Medicine 1959 NE Pacific Street, Seattle, WA 98195-7650, USA
                2Department of Immunology, University of Washington School of Medicine 1959 NE Pacific Street, Seattle, WA 98195-7650, USA
                3Department of Biochemistry, University of Washington School of Medicine 1959 NE Pacific Street, Seattle, WA 98195-7650, USA
                Author notes
                *To whom correspondence should be addressed. Tel: +1 206 221 6876; Fax: +1 206 221 6781; Email: maizels@ 123456u.washington.edu
                Article
                10.1093/nar/gkl529
                1557811
                16914419
                40845ef0-3a17-4240-aebe-20c8fd85b2eb
                © 2006 The Author(s).

                This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License ( http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commerical use, distribution, and reproduction in any medium, provided the original work is properly cited.

                History
                : 13 June 2006
                : 09 July 2006
                : 10 July 2006
                Categories
                Genomics

                Genetics
                Genetics

                Comments

                Comment on this article