Evolutionary conservation of regulatory elements in vertebrate HOX gene clusters

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Due to their high degree of conservation, comparisons of DNA sequences among evolutionarily distantly-related genomes permit to identify functional regions in noncoding DNA. Hox genes are optimal candidate sequences for comparative genome analyses, because they are extremely conserved in vertebrates and occur in clusters. We aligned (Pipmaker) the nucleotide sequences of HoxA clusters of tilapia, pufferfish, striped bass, zebrafish, horn shark, human and mouse (over 500 million years of evolutionary distance). We identified several highly conserved intergenic sequences, likely to be important in gene regulation. Only a few of these putative regulatory elements have been previously described as being involved ... continued below

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Santini, Simona; Boore, Jeffrey L. & Meyer, Axel December 31, 2003.

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Due to their high degree of conservation, comparisons of DNA sequences among evolutionarily distantly-related genomes permit to identify functional regions in noncoding DNA. Hox genes are optimal candidate sequences for comparative genome analyses, because they are extremely conserved in vertebrates and occur in clusters. We aligned (Pipmaker) the nucleotide sequences of HoxA clusters of tilapia, pufferfish, striped bass, zebrafish, horn shark, human and mouse (over 500 million years of evolutionary distance). We identified several highly conserved intergenic sequences, likely to be important in gene regulation. Only a few of these putative regulatory elements have been previously described as being involved in the regulation of Hox genes, while several others are new elements that might have regulatory functions. The majority of these newly identified putative regulatory elements contain short fragments that are almost completely conserved and are identical to known binding sites for regulatory proteins (Transfac). The conserved intergenic regions located between the most rostrally expressed genes in the developing embryo are longer and better retained through evolution. We document that presumed regulatory sequences are retained differentially in either A or A clusters resulting from a genome duplication in the fish lineage. This observation supports both the hypothesis that the conserved elements are involved in gene regulation and the Duplication-Deletion-Complementation model.

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  • Journal Name: Genome Research; Journal Volume: 13; Other Information: Journal Publication Date: 2003

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  • Report No.: LBNL--53609
  • Grant Number: AC03-76SF00098
  • Office of Scientific & Technical Information Report Number: 833695
  • Archival Resource Key: ark:/67531/metadc789021

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  • December 31, 2003

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  • Dec. 3, 2015, 9:30 a.m.

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  • April 4, 2016, 3:14 p.m.

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Santini, Simona; Boore, Jeffrey L. & Meyer, Axel. Evolutionary conservation of regulatory elements in vertebrate HOX gene clusters, article, December 31, 2003; Berkeley, California. (digital.library.unt.edu/ark:/67531/metadc789021/: accessed November 19, 2017), University of North Texas Libraries, Digital Library, digital.library.unt.edu; crediting UNT Libraries Government Documents Department.