The human genome-wide distribution of DNA palindromes
The human genome-wide distribution of DNA palindromes
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DOI：
10.1007/s10142-007-0047-6
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发表时间：
2007-07-01
影响因子：
2.9
通讯作者：
Li, Jinming
中科院分区：
文献类型：
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作者：
Lu, Le;Jia, Hui;Li, Jinming
在这项工作中，我们对人类基因组DNA中存在的完美和非间隔区回文序列进行了系统研究，并调查了回文序列在整个人类基因组和功能区域（如外显子、内含子、基因间和上游区域（翻译起始位点上游2,000 bp））的分布。我们发现，24个回文丰富的间隔大多位于G带，这是凝聚早，复制晚，相对A+T丰富。一般来说，回文在内含子中的代表性过高，但在外显子中的代表性不足。上游区域有丰富的回文分布，回文可以作为转录因子的结合位点。我们创建了一个人类DNA回文数据库（HPALDB），可在http://vhp.ntu.edu.sg/ hpaldb上访问。它包含12，556，994个条目，涵盖了人类基因组中所有长于6 bp的回文序列。可以以不同的方式执行搜索。数据库中的每个条目都与其在NCBI的人类染色体地图查看器上的位置相关联。
In this work, we performed a systematic study of perfect and nonspacer palindromes present in human genomic DNA, and we investigated palindrome distribution over the entire human genome and over the functional regions such as the exon, intron, intergenic, and upstream regions (2,000 bp upstream from translational start site). We found that 24 palindrome-abundant intervals are mostly located on G-bands, which condense early, replicate late, and are relatively A+T rich. In general, palindromes are overrepresented in introns but underrepresented in exons. Upstream region has enriched palindrome distribution, where palindromes can serve as transcription factor binding sites. We created a Human DNA Palindrome Database (HPALDB) which is accessible at http://vhp.ntu.edu.sg/ hpaldb. It contains 12,556,994 entries covering all palindromes in the human genome longer than 6 bp. Queries can be performed in different ways. Each entry in the database is linked to its location on NCBI's human chromosome Map Viewer.