Nuclear integrations of mitochondrial DNA in great apes

描述(由申请人提供)-这是一项在人类和类人猿中检查Numts(线粒体DNA基因移位到细胞核)的建议。它将涉及BLAST搜索插入到核基因组中的mtDNA转录本中的高变量1基因(Hv1)。这些基因在大猩猩中的频率较高，已有数百种基因在人类中被描述。即使在体外也有重组的事实表明，这种现象可能并不罕见。首先，该策略是(1)从黑猩猩和大猩猩的BAC文库中筛选Numts以寻找核插入，以及从几个黑猩猩和大猩猩的精子头中搜索核浓缩的DNA噬菌体文库。然后，将这些序列与那些物种先前存在的BLAST调查进行比较。人类Numts将从爆炸搜索中抽出。TE比较工作受到四个问题的推动：(A)大猩猩体内的人类免疫缺陷病毒1整合子是否升高？(B)整合的速度是随着时间的推移而不变的，还是存在系统发育的暴发？(C)线粒体拷贝和核整合拷贝的核苷酸进化速率是否不同？(D)Numts与经典的大猩猩亚种分类相匹配的程度。其次，这个想法是用核侧翼序列和线粒体DNA断裂位点来鉴定插入位点，并确定核中是否有后续的基因复制，解决三个问题：(A)整合位点是随机的，还是序列规则的？(B)整合后重复的比例是多少？(C)是否有特别易于动员或插入的特定序列基序？第三，将尝试使用Numts来重建大猩猩种群历史，因为第一阶段的研究中有大量的数据，解决了两个问题：(A)我们能否使用多态Numts来重建大猩猩种群历史？(B)主要的大猩猩亚种分支在HV1数据中明显吗？线粒体中的主要亚种分支在Numts中也明显吗？基本目的有两个：(A)探索由于我们在以前的工作中无法检测到Numts而造成的各种推理困难，以及(B)确定它们在多大程度上可以用于分类学或种群遗传学目的的优势。

DESCRIPTION (provided by applicant): - This is a proposal to examine Numts (mtDNA genes translocated to the nucleus) in humans and great apes. It will involve blast searches for hypervariable 1 gene (HV1) from mtDNA transcripts, inserted into nuclear genomes. These have elevated frequencies in gorillas, and hundreds have been described for humans. The fact that there is recombination even in vitro suggests that the phenomenon may not be all that rare. First, the strategy is (1) to screen Numts from chimpanzee and gorilla BAC libraries for nuclear insertions, as well as to search nuclear-enriched DNA phage libraries from sperm heads from several chimpanzees and gorillas. Then, these sequences will be compared with the pre-existing BLAST surveys of those species. Human Numts will be drawn from BLAST searches. Te comparative work is motivated by four questions: (a) Are HV1 integrants elevated in gorillas? (b) Is the rate of integration constant over time, or are there phylogenetic bursts? (c) Do rates of nucleotide evolution differ for mitochondrial and nuclear-integrated copies? (d) How well do the Numts match up with the classic gorilla subspecific taxonomy. Second, the idea is to map the insertion sites, using nuclear flanking sequences and mtDNA break sites for identification, and to determine whether there has been subsequent gene duplication in the nucleus, addressing three questions: (a) Are the sites of integration random, or are they sequence-regular? (b) What is the fraction of post-integration duplication? (c) Are there specific sequence motifs that are particularly prone to mobilization or to insertion? Third, an attempt will be made to use the Numts to reconstruct gorilla population history, since there are a great many in hand from the 1st phase of the study, addressing two questions: (a) Can we use polymorphic Numts to reconstruct gorilla population history? (b) Are the major gorilla subspecific clades evident in the HV1 data in the mitochondrion also evident in the Numts? The basic intent is twofold: (a) to explore the sorts of inferential difficulty caused by our inability to detect Numts in previous work, and (b) to determine the extent to which they can used to advantage for taxonomic or population genetic purposes.