Alu repeat analysis in the complete human genome: trends and variations with respect to genomic composition
Alu repeat analysis in the complete human genome: trends and variations with respect to genomic composition
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DOI：
10.1093/bioinformatics/bth005
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发表时间：
2004-04-12
期刊：
影响因子：
5.8
通讯作者：
Brahmachari, SK
中科院分区：
文献类型：
--
作者：
Grover, D;Mukerji, M;Brahmachari, SK
动机：转座子衍生的Alu重复序列只与灵长类基因组相关。近年来，有证据表明它们参与基因调控的各个方面，如选择性剪接、核小体定位、CpG甲基化、转录因子和激素受体的结合位点等，它们已经变得相当重要。本研究的目的是探讨影响人类基因组中Alu重复序列元件分布的因素。这样的分析有望深入了解灵长类动物基因调控的各个方面。结果：2003年1月发表的人类基因组32序列的Alu重复序列分布分析表明，它们占据了近十分之一的测序区域。在整个基因组中可以看到Alu频率的巨大差异，其中19号染色体是Alu密集染色体最多的，Y号染色体是Alu密集染色体最少的。分析的亮点如下：(1)基因组中有四分之三的基因与Alus相关。(2)除19号和22号染色体外，其余染色体的Alu密度均高于基因间区。(3)人类基因组中Alu密度与GC含量、基因密度和内含子密度高度相关，GC含量是主要的决定因素。(4) Alu密度与基因密度的相关性大于与内含子密度的相关性，表明Alu在外显子的非翻译区插入。补充资料：在线补充资料可在网站http://www.igib.res.in/manuscriptdata/aluanalysis.html获取。
Motivation: Transposon-derived Alu repeats are exclusively associated with primate genomes. They have gained considerable importance in the recent times with evidence of their involvement in various aspects of gene regulation, e.g. alternative splicing, nucleosome positioning, CpG methylation, binding sites for transcription factors and hormone receptors, etc. The objective of this study is to investigate the factors that influence the distribution of Alu repeat elements in the human genome. Such analysis is expected to yield insights into various aspects of gene regulation in primates.Results: Analysis of Alu repeat distribution for the human genome build 32 (released in January 2003) reveals that they occupy nearly one-tenth portion of the sequenced regions. Huge variations in Alu frequencies were seen across the genome with chromosome 19 being the most and chromosome Y being the least Alu dense chromosomes. The highlights of the analysis are as follows: (1) three-fourth of the total genes in the genome are associated with Alus. (2) Alu density is higher in genes as compared with intergenic regions in all the chromosomes except 19 and 22. (3) Alu density in human genome is highly correlated with GC content, gene density and intron density with GC content being major deterministic factor compared with other two. (4) Alu densities were correlated more with gene density than intron density indicating the insertion of Alus in untranslated regions of exons.Supplementary information: Online supplementary data is available at the web page http://www.igib.res.in/manuscriptdata/aluanalysis.html.