■移动元件(ME)构成灵长类动物和其他高等真核生物基因组的主要部分,它们在基因组进化和基因功能中起着重要作用。MEs可以分为两个根本不同的类别:DNA转座子,以“剪切和粘贴”的方式在基因组中转座,和逆转录转座子通过涉及转录和逆转录的过程以“复制和粘贴”方式传播。在灵长类动物基因组中,DNA转座子大多死了,而许多反转录转座子仍然很活跃。我们在这里报告一组独特的ME的识别,我们称之为“复古DNA”,这两个根本不同的ME类的组合特征。
■使用比较计算基因组方法分析了由五只猿组成的10种灵长类动物的参考基因组序列,四只猴子,还有Marmoset.
■根据我们的分析,我们确定了总共1,750个逆转录DNA,代表包括人类在内的10种灵长类动物基因组中的748个独特插入事件。这些逆转录DNA含有DNA转座子序列,但缺乏末端反向重复序列(TIR),DNA转座子的标志.相反,它们显示反转录转座子的特征,比如polyA尾巴,更长的目标站点重复(TSD),和“TT/AAAA”插入站点主题,建议使用基于L1的靶引物逆转录(TPRT)机制。这些逆转录DNA中至少有40%位于基因区域,呈现影响基因功能的潜力。更有趣的是,一些复古的DNA,以及他们的父网站,表现出一定的表达水平,这表明它们有可能在目前的灵长类动物基因组中产生更多的逆转录DNA拷贝。
■虽然数量很少,这些retro-DNAs的鉴定揭示了在没有活性经典DNA转座子活性的灵长类动物基因组中繁殖DNA转座子的新方法。我们的数据还表明,TPRT机制可能会转置基因组中更多种类的DNA序列。
UNASSIGNED: Mobile elements (MEs) constitute a major portion of the genome in primates and other higher eukaryotes, and they play important role in genome evolution and gene function. MEs can be divided into two fundamentally different classes: DNA transposons which transpose in the genome in a \"cut-and-paste\" style, and retrotransposons which propagate in a \"copy-and-paste\" fashion via a process involving transcription and reverse-transcription. In primate genomes, DNA transposons are mostly dead, while many retrotransposons are still highly active. We report here the identification of a unique group of MEs, which we call \"retro-DNAs\", for their combined characteristics of these two fundamentally different ME classes.
UNASSIGNED: A comparative computational genomic approach was used to analyze the reference genome sequences of 10 primate species consisting of five apes, four monkeys, and marmoset.
UNASSIGNED: From our analysis, we identified a total of 1,750 retro-DNAs, representing 748 unique insertion events in the genomes of ten primate species including human. These retro-DNAs contain sequences of DNA transposons but lack the terminal inverted repeats (TIRs), the hallmark of DNA transposons. Instead, they show characteristics of retrotransposons, such as polyA tails, longer target-site duplications (TSDs), and the \"TT/AAAA\" insertion site motif, suggesting the use of the L1-based target- primed reverse transcription (TPRT) mechanism. At least 40% of these retro-DNAs locate into genic regions, presenting potentials for impacting gene function. More interestingly, some retro-DNAs, as well as their parent sites, show certain levels of expression, suggesting that they have the potential to create more retro-DNA copies in the present primate genomes.
UNASSIGNED: Although small in number, the identification of these retro-DNAs reveals a new mean for propagating DNA transposons in primate genomes without active canonical DNA transposon activity. Our data also suggest that the TPRT machinery may transpose a wider variety of DNA sequences in the genomes.