Krasnov Aleksei, Koskinen Heikki, Afanasyev Sergey, Mölsä Hannu
Institute of Applied Biotechnology, University of Kuopio, P,O,B, 1627, FIN-70211 Kuopio, Finland.
BMC Genomics. 2005 Aug 12;6:107. doi: 10.1186/1471-2164-6-107.
Mobile genetic elements comprise a substantial fraction of vertebrate genomes. These genes are considered to be deleterious, and in vertebrates they are usually inactive. High throughput sequencing of salmonid fish cDNA libraries has revealed a large number of transposons, which remain transcribed despite inactivation of translation. This article reports on the structure and potential role of these genes.
A search of EST showed the ratio of transcribed transposons in salmonid fish (i.e., 0.5% of all unique cDNA sequences) to be 2.4-32 times greater than in other vertebrate species, and 68% of these genes belonged to the Tc1-family of DNA transposons. A phylogenetic analysis of reading frames indicate repeated transposition of distantly related genes into the fish genome over protracted intervals of evolutionary time. Several copies of two new DNA transposons were cloned. These copies showed relatively little divergence (11.4% and 1.9%). The latter gene was transcribed at a high level in rainbow trout tissues, and was present in genomes of many phylogenetically remote fish species. A comparison of synonymous and non-synonymous divergence revealed remnants of divergent evolution in the younger gene, while the older gene evolved in a neutral mode. From a 1.2 MB fragment of genomic DNA, the salmonid genome contains approximately 10(5) Tc1-like sequences, the major fraction of which is not transcribed. Our microarray studies showed that transcription of rainbow trout transposons is activated by external stimuli, such as toxicity, stress and bacterial antigens. The expression profiles of Tc1-like transposons gave a strong correlation (r2 = 0.63-0.88) with a group of genes implicated in defense response, signal transduction and regulation of transcription.
Salmonid genomes contain a large quantity of transcribed mobile genetic elements. Divergent or neutral evolution within genomes and lateral transmission can account for the diversity and sustained persistence of Tc1-like transposons in lower vertebrates. A small part of transposons remain transcribed and their transcription is enhanced by responses to acute conditions.
可移动遗传元件在脊椎动物基因组中占很大比例。这些基因被认为是有害的，在脊椎动物中通常处于不活跃状态。鲑科鱼类cDNA文库的高通量测序揭示了大量转座子，尽管翻译失活，但它们仍在转录。本文报道了这些基因的结构和潜在作用。
对EST的搜索显示，鲑科鱼类中转录的转座子比例（即所有独特cDNA序列的0.5%）比其他脊椎动物物种高2.4至32倍，其中68%的基因属于DNA转座子的Tc1家族。对阅读框的系统发育分析表明，在漫长的进化时间间隔内，远缘相关基因反复转座到鱼类基因组中。克隆了两个新DNA转座子的几个拷贝。这些拷贝显示出相对较小的差异（11.4%和1.9%）。后一个基因在虹鳟鱼组织中高水平转录，并且存在于许多系统发育关系较远的鱼类物种的基因组中。同义与非同义差异的比较揭示了较年轻基因中分歧进化的残余，而较老的基因以中性模式进化。从1.2MB的基因组DNA片段来看，鲑科鱼类基因组包含约10^5个类似Tc1的序列，其中大部分不转录。我们的微阵列研究表明，虹鳟鱼转座子的转录受到外部刺激的激活，如毒性、应激和细菌抗原。类似Tc1的转座子的表达谱与一组参与防御反应、信号转导和转录调控的基因具有很强的相关性（r2 = 0.63 - 0.88）。
鲑科鱼类基因组包含大量转录的可移动遗传元件。基因组内的分歧或中性进化以及横向传播可以解释类似Tc1的转座子在低等脊椎动物中的多样性和持续存在。一小部分转座子仍在转录，并且它们的转录通过对急性条件的反应而增强。
