Genomic regions with distinct genomic distance conservation in vertebrate genomes
文献类型：期刊论文
| 作者 | Liu,Wei5; Li,Yixue4,6; Sun,Hong2,4,5,6; Zheng,Xiaohui1; Skogerb?,Geir3 |
| 刊名 | BMC Genomics
 |
| 出版日期 | 2009-03-27 |
| 卷号 | 10期号:1 |
| ISSN号 | 1471-2164 |
| DOI | 10.1186/1471-2164-10-133 |
| 英文摘要 | AbstractBackgroundA number of vertebrate highly conserved elements (HCEs) have been detected and their genomic interval distances have been reported to be more conserved than protein coding genes among mammalian genomes. A characteristic of the human – non-mammalian comparisons is a bimodal distribution of relative distance difference of conserved consecutive HCE pairs; and it is difficult to attribute such profile to a random assortment. We therefore undertook an analysis of the human genomic regions confined by consecutive HCE pairs common to eight genomes (human, mouse, rat, chicken, frog, zebrafish, tetradon and fugu).ResultsAmong HCE pairs, we found that some consistently preserve highly conserved interval distance among genomes while others have relatively low distance conservation. Using a partition method, we detected two groups of inter-HCE regions (IHRs) with distinct distance conservation pattern in vertebrate genomes: IHR1s that are bordered by HCE pairs with relative small distance variation, and IHR2s with larger distance difference values. Compared to random background, annotated repeat sequences are significantly less frequent in IHR1s than IHR2s, which reflects a correlation between repeat sequences and the length expansion of IHRs. Both groups of IHRs are unexpectedly enriched in human indel (i.e. insertion and deletion) polymorphism-variations than random background. The correlation between the percentage of conserved sequence and human IHR length was stronger for IHR1 than IHR2. Both groups of IHRs are significantly enriched for CpG islands.ConclusionThe data suggest that subsets of HCE pairs may undergo different evolutionary paths in light of their genomic distance conservation, and that sets of genomic regions pertain to HCEs, as well as the region in which HCEs reside, should be treated as integrated domains. |
| 语种 | 英语 |
| WOS记录号 | BMC:10.1186/1471-2164-10-133 |
| 出版者 | BioMed Central |
| 源URL | [http://119.78.100.204/handle/2XEOYT63/4107]  |
| 专题 | 中国科学院计算技术研究所期刊论文_2009年英文 |
| 通讯作者 | Liu,Wei; Li,Yixue |
| 作者单位 | 1.Hetian Peoples' Hospital 2.Zhongxin Biotechnology Shanghai Co Ltd 3.Chinese Academy of Sciences; Bioinformatics Laboratory and National Laboratory of Biomacromolecules, Institute of Biophysics 4.Shanghai Center for Bioinformation Technology 5.Wyeth Research; Biological Technologies 6.Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences; Key Laboratory of Systems Biology |
| 推荐引用方式 GB/T 7714 | Liu,Wei,Li,Yixue,Sun,Hong,et al. Genomic regions with distinct genomic distance conservation in vertebrate genomes[J]. BMC Genomics,2009,10(1). |
| APA | Liu,Wei,Li,Yixue,Sun,Hong,Zheng,Xiaohui,&Skogerb?,Geir.(2009).Genomic regions with distinct genomic distance conservation in vertebrate genomes.BMC Genomics,10(1). |
| MLA | Liu,Wei,et al."Genomic regions with distinct genomic distance conservation in vertebrate genomes".BMC Genomics 10.1(2009). |
入库方式： OAI收割
来源：计算技术研究所
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