Animal Breeding and Genomics Centre, Wageningen University, Marijkeweg 40, 6709 PG, Wageningen, the Netherlands.
BMC Genomics. 2010 Jan 14;11:28. doi: 10.1186/1471-2164-11-28.
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: http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?token=tjwjpscyceqawjk&acc=GSE17108.
在过去的几年中，已经在许多不同的脊椎动物基因组中研究了基因转录与染色体位置之间的关系。在几个不同的物种中已经发现了基因表达的区域差异。鸡基因组作为与哺乳动物最接近的测序基因组，是研究鸟类转录的区域效应以及通过比较分析研究染色体进化的区域动态的重要资源。
我们使用基因表达数据调查了 8 种鸡组织，并为所有鸡染色体创建了转录组图谱。结果显示，存在两种截然不同的染色体区域类型，其特征是高度或低度表达基因簇。此外，这些区域与许多基因组特征高度相关。与低度表达基因簇相比，高度表达基因簇的区域具有更高的基因密度、更短的基因、更短的平均内含子和更高的 GC 含量。使用类似组织面板构建的鸡和人转录组图谱的比较分析表明，高度表达基因簇的区域在两个基因组之间相对保守。
我们的结果揭示了鸡基因组存在影响基因表达的更高阶组织，证实了其他物种的类似观察结果。这些结果将有助于进一步了解染色体进化的区域动态。本分析中使用的微阵列数据已提交给 NCBI GEO 数据库，注册号为 GSE17108。评审员访问链接为：http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi？token=tjwjpscyceqawjk&acc=GSE17108。
