Grover Deepak, Mukerji Mitali, Bhatnagar Pankaj, Kannan K, Brahmachari Samir K
Functional Genomics Unit, Institute of Genomics and Integrative Biology (IGIB), CSIR, Mall Road, Delhi 110007, India.
Bioinformatics. 2004 Apr 12;20(6):813-7. doi: 10.1093/bioinformatics/bth005. Epub 2004 Jan 29.
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.
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.
转座子衍生的Alu重复序列仅与灵长类基因组相关。近年来，它们已变得相当重要，有证据表明它们参与基因调控的各个方面，例如可变剪接、核小体定位、CpG甲基化、转录因子和激素受体的结合位点等。本研究的目的是调查影响Alu重复元件在人类基因组中分布的因素。这种分析有望深入了解灵长类动物基因调控的各个方面。
对人类基因组构建32（于2003年1月发布）的Alu重复序列分布分析表明，它们占据了测序区域近十分之一的部分。在整个基因组中观察到Alu频率存在巨大差异，其中19号染色体的Alu密度最高，Y染色体的Alu密度最低。分析的重点如下：（1）基因组中四分之三的基因与Alu相关。（2）除19号和22号染色体外，所有染色体上基因中的Alu密度均高于基因间区域。（3）人类基因组中的Alu密度与GC含量、基因密度和内含子密度高度相关，与其他两者相比，GC含量是主要的决定因素。（4）Alu密度与基因密度的相关性高于内含子密度，表明Alu插入到外显子的非翻译区域。
