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Marine Organism Cell Biology and Regulatory Sequence Discoveryin Comparative Functional Genomics

The use of bioinformatics to integrate phenotypic and genomic data from mammalian models is well established as a means of understanding human biology and disease. Beyond direct biomedical applications of these approaches in predicting structure–function relationships between coding sequences and pr...

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Autores principales: Barnes, David W., Mattingly, Carolyn J., Parton, Angela, Dowell, Lori M., Bayne, Christopher J., Forrest, John N.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Kluwer Academic Publishers 2005
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3449718/
https://www.ncbi.nlm.nih.gov/pubmed/19003267
http://dx.doi.org/10.1007/s10616-005-1719-5
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author Barnes, David W.
Mattingly, Carolyn J.
Parton, Angela
Dowell, Lori M.
Bayne, Christopher J.
Forrest, John N.
author_facet Barnes, David W.
Mattingly, Carolyn J.
Parton, Angela
Dowell, Lori M.
Bayne, Christopher J.
Forrest, John N.
author_sort Barnes, David W.
collection PubMed
description The use of bioinformatics to integrate phenotypic and genomic data from mammalian models is well established as a means of understanding human biology and disease. Beyond direct biomedical applications of these approaches in predicting structure–function relationships between coding sequences and protein activities, comparative studies also promote understanding of molecular evolution and the relationship between genomic sequence and morphological and physiological specialization. Recently recognized is the potential of comparative studies to identify functionally significant regulatory regions and to generate experimentally testable hypotheses that contribute to understanding mechanisms that regulate gene expression, including transcriptional activity, alternative splicing and transcript stability. Functional tests of hypotheses generated by computational approaches require experimentally tractable in vitro systems, including cell cultures. Comparative sequence analysis strategies that use genomic sequences from a variety of evolutionarily diverse organisms are critical for identifying conserved regulatory motifs in the 5′-upstream, 3′-downstream and introns of genes. Genomic sequences and gene orthologues in the first aquatic vertebrate and protovertebrate organisms to be fully sequenced (Fugu rubripes, Ciona intestinalis, Tetraodon nigroviridis, Danio rerio) as well as in the elasmobranchs, spiny dogfish shark (Squalus acanthias) and little skate (Raja erinacea), and marine invertebrate models such as the sea urchin (Strongylocentrotus purpuratus) are valuable in the prediction of putative genomic regulatory regions. Cell cultures have been derived for these and other model species. Data and tools resulting from these kinds of studies will contribute to understanding transcriptional regulation of biomedically important genes and provide new avenues for medical therapeutics and disease prevention.
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spelling pubmed-34497182012-10-31 Marine Organism Cell Biology and Regulatory Sequence Discoveryin Comparative Functional Genomics Barnes, David W. Mattingly, Carolyn J. Parton, Angela Dowell, Lori M. Bayne, Christopher J. Forrest, John N. Cytotechnology Article The use of bioinformatics to integrate phenotypic and genomic data from mammalian models is well established as a means of understanding human biology and disease. Beyond direct biomedical applications of these approaches in predicting structure–function relationships between coding sequences and protein activities, comparative studies also promote understanding of molecular evolution and the relationship between genomic sequence and morphological and physiological specialization. Recently recognized is the potential of comparative studies to identify functionally significant regulatory regions and to generate experimentally testable hypotheses that contribute to understanding mechanisms that regulate gene expression, including transcriptional activity, alternative splicing and transcript stability. Functional tests of hypotheses generated by computational approaches require experimentally tractable in vitro systems, including cell cultures. Comparative sequence analysis strategies that use genomic sequences from a variety of evolutionarily diverse organisms are critical for identifying conserved regulatory motifs in the 5′-upstream, 3′-downstream and introns of genes. Genomic sequences and gene orthologues in the first aquatic vertebrate and protovertebrate organisms to be fully sequenced (Fugu rubripes, Ciona intestinalis, Tetraodon nigroviridis, Danio rerio) as well as in the elasmobranchs, spiny dogfish shark (Squalus acanthias) and little skate (Raja erinacea), and marine invertebrate models such as the sea urchin (Strongylocentrotus purpuratus) are valuable in the prediction of putative genomic regulatory regions. Cell cultures have been derived for these and other model species. Data and tools resulting from these kinds of studies will contribute to understanding transcriptional regulation of biomedically important genes and provide new avenues for medical therapeutics and disease prevention. Kluwer Academic Publishers 2005-11-30 2004-10 /pmc/articles/PMC3449718/ /pubmed/19003267 http://dx.doi.org/10.1007/s10616-005-1719-5 Text en © Springer 2005
spellingShingle Article
Barnes, David W.
Mattingly, Carolyn J.
Parton, Angela
Dowell, Lori M.
Bayne, Christopher J.
Forrest, John N.
Marine Organism Cell Biology and Regulatory Sequence Discoveryin Comparative Functional Genomics
title Marine Organism Cell Biology and Regulatory Sequence Discoveryin Comparative Functional Genomics
title_full Marine Organism Cell Biology and Regulatory Sequence Discoveryin Comparative Functional Genomics
title_fullStr Marine Organism Cell Biology and Regulatory Sequence Discoveryin Comparative Functional Genomics
title_full_unstemmed Marine Organism Cell Biology and Regulatory Sequence Discoveryin Comparative Functional Genomics
title_short Marine Organism Cell Biology and Regulatory Sequence Discoveryin Comparative Functional Genomics
title_sort marine organism cell biology and regulatory sequence discoveryin comparative functional genomics
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3449718/
https://www.ncbi.nlm.nih.gov/pubmed/19003267
http://dx.doi.org/10.1007/s10616-005-1719-5
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