Repetitive element-mediated recombination as a mechanism for new gene origination in Drosophila.
Repetitive element-mediated recombination as a mechanism for new gene origination in Drosophila.
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DOI：
10.1371/journal.pgen.0040003
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发表时间：
2008-01
期刊：
影响因子：
4.5
通讯作者：
Wang W
中科院分区：
文献类型：
--
作者：
Yang S;Arguello JR;Li X;Ding Y;Zhou Q;Chen Y;Zhang Y;Zhao R;Brunet F;Peng L;Long M;Wang W
以前的研究重复元件（RE）在产生新的嵌合基因的机械作用。这些例子与依赖于非同源重组的外显子改组的经典模型一致。然而，最近的染色体畸变的模式生物的数据表明，异位同源依赖性重组也可能是重要的。缺乏一个数据集，包括实验验证的年轻的重复，阻碍了这些模型的有效检查，以及调查的序列功能，介导的重排。在这里，我们使用117，000个cDNA探针（1112，000个原始图像）来筛选黑腹果蝇亚组中的8个物种，并在过去的12个月内通过异位重组产生17个重复。其中大多数是功能性的，并已进化出不同的表达模式和新的嵌合结构。对它们的侧翼序列的检查揭示了过量的重复序列，其中大多数属于与新基因相关的转座因子DNAREP 1家族。我们的数据集强烈表明RE在这些物种内嵌合基因的产生中起着重要作用。在许多生物体中，已经发现许多新的基因起源于分散的基因复制和外显子/结构域改组。在复制和改组过程中涉及什么样的重组机制？缺乏在同源序列之间共享足够序列同一性的重组中间产物，或新基因所来源的亲本序列，通常使得回答这些问题变得困难。我们确定了一些年轻的基因，起源于最近分歧的分支在进化树的8个果蝇亚组物种，通过使用荧光原位杂交与多线染色体。我们分析了17个新的分散的重复基因周围的基因组区域，并观察到这些基因中的大多数是侧翼的重复元件（RE），包括一个大的和分歧的转座因子家族，DNAREP 1。这些RE的几个拷贝保留在新基因和亲本基因区域中，并且它们的退化与所鉴定的新基因的年龄增加相关。这些数据表明，RE介导的重组负责新基因的起源。
Previous studies of repetitive elements (REs) have implicated a mechanistic role in generating new chimerical genes. Such examples are consistent with the classic model for exon shuffling, which relies on non-homologous recombination. However, recent data for chromosomal aberrations in model organisms suggest that ectopic homology-dependent recombination may also be important. Lack of a dataset comprising experimentally verified young duplicates has hampered an effective examination of these models as well as an investigation of sequence features that mediate the rearrangements. Here we use ∼7,000 cDNA probes (∼112,000 primary images) to screen eight species within the Drosophila melanogaster subgroup and identify 17 duplicates that were generated through ectopic recombination within the last 12 mys. Most of these are functional and have evolved divergent expression patterns and novel chimeric structures. Examination of their flanking sequences revealed an excess of repetitive sequences, with the majority belonging to the transposable element DNAREP1 family, associated with the new genes. Our dataset strongly suggests an important role for REs in the generation of chimeric genes within these species. In numerous organisms, many new genes have been found to originate through dispersed gene duplication and exon/domain shuffling. What recombination mechanisms were involved in the duplication and the shuffling processes? Lack of the intermediate products of recombination that share adequate sequence identity between homologous sequences, or the parental sequences from which the new genes were derived, often makes answering these questions difficult. We identified a number of young genes that originated in recently diverged branches in the evolutionary tree of the eight Drosophila melanogaster subgroup species, by using fluorescence in situ hybridization with polytene chromosomes. We analyzed the genomic regions surrounding 17 new dispersed duplicate genes and observed that most of these genes are flanked by repetitive elements (REs), including a large and diverged transposable element family, DNAREP1. Several copies of these REs are kept in both new and parental gene regions, and their degeneration is correlated with the increasing ages of the identified new genes. These data suggest that REs mediate the recombination responsible for the new gene origination.
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影响因子：
56.9
作者：
Gao, LZ;Innan, H
通讯作者：
Innan, H
影响因子：
7
作者：
Ciccarelli, FD;von Mering, C;Bork, P
通讯作者：
Bork, P
影响因子：
7
作者：
Babcock, M;Pavlicek, A;Morrow, BE
通讯作者：
Morrow, BE
DOI：
10.1073/pnas.0605426103
发表时间：
2006-11-21
影响因子：
11.1
作者：
Johnson, Matthew E.;Cheng, Ze;Eichler, Evan E.
通讯作者：
Eichler, Evan E.
影响因子：
10.7
作者：
Katju, V;Lynch, M
通讯作者：
Lynch, M