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Regional regulation of transcription in the chicken genome

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

Author Affiliations

Animal Breeding and Genomics Centre, Wageningen University, Marijkeweg 40, 6709 PG, Wageningen, the Netherlands

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BMC Genomics 2010, 11:28  doi:10.1186/1471-2164-11-28

Published: 14 January 2010



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.


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.


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: webcite