A novel composite retrotransposon derived from or generated independently of the SVA (SINE/VNTR/Alu) transposon has undergone proliferation in gibbon genomes
A novel composite retrotransposon derived from or generated independently of the SVA (SINE/VNTR/Alu) transposon has undergone proliferation in gibbon genomes
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DOI：
10.1266/ggs.87.181
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发表时间：
2012-06-01
影响因子：
1.1
通讯作者：
Koga, Akihiko
中科院分区：
文献类型：
--
作者：
Hara, Toru;Hirai, Yuriko;Koga, Akihiko
人科（Hominoidea）包括两个科：人科（Hominidae）和长臂猿科（Hylobatidae）。SVA转座子是广泛存在于类人猿中的复合逆转录转座子，并且被认为是通过三种遗传元件的逐步融合产生的：SINE-R，可变数目串联重复（VNTR）序列和Alu。我们鉴定了一种新的转座子，其基本结构与SVA相同，一个显著的区别是存在前列腺素还原酶2（PTGR 2）的一部分代替SINE-R。我们将这种复合转座子命名为PVA，并提出了两种可能的机制。一种是从SVA衍生PVA：通过模板转换将SVA的SINE-R区域替换为PTGR 2片段。另一种是PVA的形成独立于SVA：PTGR 2片段融合到包含VNTR和Alu区域的进化中间体。VNTR和PTGR 2区域之间连接的核苷酸序列支持第二种假设。我们通过基因组序列数据库的分析，在白颊长臂猿Nomeleucogenys中鉴定出PVA，随后的实验分析显示其存在于所有四种长臂猿属中。白颊巨齿鲨在其单倍体基因组中至少有93个PVA拷贝。另一个SVA样复合转座子携带LINE 1和Alu转座子的一部分，以取代SINE-R，命名为LAVA，最近已被报道。PVA发现的意义在于它的取代片段不是来自转座子，而是来自单拷贝基因。PVA应该提供额外的见解，这种类型的复合转座子的转座机制;转座活性被赋予，即使取代的片段是不相关的转座子。
The superfamily Hominoidea (hominoids) comprises two families: Hominidae (hominids) and Hylobatidae (gibbons, also called small apes). The SVA transposon is a composite retrotransposon that occurs widely in hominoids and is considered to have been generated by stepwise fusions of three genetic elements: SINE-R, a variable number of tandem repeat (VNTR) sequence, and Alu. We identified a novel transposon whose basic structure is the same as that of SVA, with one prominent difference being the presence of part of prostaglandin reductase 2 (PTGR2) in place of SINE-R. We designate this composite transposon as PVA and propose two possible mechanisms regarding its generation. One is the derivation of PVA from SVA: the SINE-R region of SVA was replaced with a PTGR2 fragment by template switching. The other is the formation of PVA independently of SVA: a PTGR2 fragment was fused to an evolutionary intermediate comprising the VNTR and Alu regions. The nucleotide sequence of the junction between the VNTR and PTGR2 regions supports the second hypothesis. We identified PVA in the white-cheeked gibbon Nomascus leucogenys by analysis of genome sequence databases, and subsequent experimental analysis revealed its presence in all four gibbon genera. The white-cheeked gibbon harbors at least 93 PVA copies in its haploid genome. Another SVA-like composite transposon carrying parts of the LINE1 and Alu transposons in place of SINE-R, designated as LAVA, has recently been reported. The significance of the discovery of PVA is that its substituted fragment originates not from a transposon but from a single-copy gene. PVA should provide additional insights into the transposition mechanism of this type of composite transposon; the transposition activity is conferred even if the substituted fragment is not related to a transposon.