Regional regulation of transcription in the chicken genome View Full Text


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Article Info

DATE

2010-12

AUTHORS

Haisheng Nie, Richard PMA Crooijmans, John WM Bastiaansen, Hendrik-Jan Megens, Martien AM Groenen

ABSTRACT

BACKGROUND: Over the past years, the relationship between gene transcription and chromosomal location has been studied in a number of different vertebrate genomes. Regional differences in gene expression have been found in several different species. The chicken genome, as the closest sequenced genome relative to mammals, is an important resource for investigating regional effects on transcription in birds and studying the regional dynamics of chromosome evolution by comparative analysis. RESULTS: We used gene expression data to survey eight chicken tissues and create transcriptome maps for all chicken chromosomes. The results reveal the presence of two distinct types of chromosomal regions characterized by clusters of highly or lowly expressed genes. Furthermore, these regions correlate highly with a number of genome characteristics. Regions with clusters of highly expressed genes have higher gene densities, shorter genes, shorter average intron and higher GC content compared to regions with clusters of lowly expressed genes. A comparative analysis between the chicken and human transcriptome maps constructed using similar panels of tissues suggests that the regions with clusters of highly expressed genes are relatively conserved between the two genomes. CONCLUSIONS: Our results revealed the presence of a higher order organization of the chicken genome that affects gene expression, confirming similar observations in other species. These results will aid in the further understanding of the regional dynamics of chromosome evolution.The microarray data used in this analysis have been submitted to NCBI GEO database under accession number GSE17108. The reviewer access link is: http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?token=tjwjpscyceqawjk&acc=GSE17108. More... »

PAGES

28

References to SciGraph publications

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  • 2004-12. Sequence and comparative analysis of the chicken genome provide unique perspectives on vertebrate evolution in NATURE
  • 2001-10. Arrangements of macro- and microchromosomes in chicken cells in CHROMOSOME RESEARCH
  • 2005. limma: Linear Models for Microarray Data in BIOINFORMATICS AND COMPUTATIONAL BIOLOGY SOLUTIONS USING R AND BIOCONDUCTOR
  • 1999-10. Complete sequence and gene map of a human major histocompatibility complex in NATURE
  • 1979-11. Karyology of the primitive slamanders, family hynobiidae in CELLULAR AND MOLECULAR LIFE SCIENCES
  • 2005-09. Replication and transcription: Shaping the landscape of the genome in NATURE REVIEWS GENETICS
  • 2005-12. The genesis and evolution of homeobox gene clusters in NATURE REVIEWS GENETICS
  • 2002-06. Evidence for large domains of similarly expressed genes in the Drosophila genome in BMC BIOLOGY
  • 2005-10. The role of chromatin structure in regulating the expression of clustered genes in NATURE REVIEWS GENETICS
  • 2004-04. The evolutionary dynamics of eukaryotic gene order in NATURE REVIEWS GENETICS
  • 2002-08. Selection for short introns in highly expressed genes in NATURE GENETICS
  • Identifiers

    URI

    http://scigraph.springernature.com/pub.10.1186/1471-2164-11-28

    DOI

    http://dx.doi.org/10.1186/1471-2164-11-28

    DIMENSIONS

    https://app.dimensions.ai/details/publication/pub.1007671504

    PUBMED

    https://www.ncbi.nlm.nih.gov/pubmed/20074332


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