Transcribed Tc1-like transposons in salmonid fish.
Transcribed Tc1-like transposons in salmonid fish.
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DOI：
10.1186/1471-2164-6-107
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发表时间：
2005-08-12
期刊：
影响因子：
4.4
通讯作者：
Mölsä H
中科院分区：
文献类型：
--
作者：
Krasnov A;Koskinen H;Afanasyev S;Mölsä H
可移动的遗传元件构成了脊椎动物基因组的很大一部分。这些基因被认为是有害的，在脊椎动物中，它们通常是不活跃的。对鲑鱼文库的高通量测序发现了大量的转座子，这些转座子在翻译失活的情况下仍能转录。本文就这些基因的结构和潜在作用作一综述。对EST的搜索表明，鲑鱼中转录转座子的比例(即占所有独特的cdna序列的0.5%)是其他脊椎动物的2.4-32倍，其中68%属于DNA转座子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，远缘关系基因反复转位到鱼类基因组中。克隆了两个新的DNA转座子的多个拷贝。这些拷贝的差异相对较小(11.4%和1.9%)。后者基因在虹鲑鱼组织中高水平转录，并存在于许多系统发育遥远的鱼类物种的基因组中。对同义和非同义差异的比较显示，年轻的基因中存在分歧进化的残余，而较老的基因以中性模式进化。从一个1.2MB的基因组DNA片段中，鲑鱼基因组包含大约105个类似Tc1的序列，其中大部分没有转录。我们的微阵列研究表明，虹鱼转座子的转录可以被外界刺激激活，如毒性、应激和细菌抗原。Tc1类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)。鲑鱼基因组中含有大量转录的可移动遗传元件。基因组内的分化或中性进化和横向传播可以解释Tc1样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中，它们的转录在对急性条件的反应中得到增强。
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 105 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.
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影响因子：
10.7
作者：
Lampe, DJ;Witherspoon, DJ;Robertson, HM
通讯作者：
Robertson, HM
影响因子：
4.7
作者：
Jensen, I;Larsen, R;Robertsen, B
通讯作者：
Robertsen, B
影响因子：
14.9
作者：
Aljanabi, SM;Martinez, I
通讯作者：
Martinez, I
影响因子：
14.9
作者：
Mulder, NJ;Apweiler, R;Zdobnov, EM
通讯作者：
Zdobnov, EM
DOI：
10.1016/j.bbrc.2004.06.024
发表时间：
2004-07-30
影响因子：
3.1
作者：
Koskinen, H;Pehkonen, P;Oikari, A
通讯作者：
Oikari, A