Identification and characterization of transposable elements inserted into the coding sequences of horse genes

Kung Ahn; Jin-Han Bae; Jeong-An Gim; Ja-Rang Lee; Yi-Deun Jung; Kyung-Do Park; Kyudong Han; Byung-Wook Cho; Heui-Soo Kim

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Identification and characterization of transposable elements inserted into the coding sequences of horse genes

机译：鉴定和鉴定插入马基因编码序列中的转座因子

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Transposable elements (TEs) are repetitive sequences dispersed throughout mammalian genomes, and they occupy important genetic positions. TEs have been shown to have both harmful and beneficial effects such as exonization, polyadenylation, and/or altering transcription rates in various vertebrate genomes. However, to the best of our knowledge, no study has yet considered the relationship between TEs and horse genes. In this study, we examined the contribution of TEs to the horse genome by collecting TEs inserted within mRNA genes. By screening the abundance, distribution, and orientation of TEs, we found that the majority of TE insertions belong to retroelements and DNA elements, most of which exist in the coding sequences of horse genes. In addition, the MIR, L1, L2, ERVL, and ERVL-MaLR subfamilies were found to be the most abundant in both non-LTR and LTR elements. Retroelements (LTRs, LINEs, and SINEs) among the TEs inserted in the coding sequences showed a preference for antisense orientation. The most pronounced imbalance in insertional orientation was observed in LINEs, which represent 40 % of all TEs in antisense orientation. Through these analyses, we identified that a total of 1310 TEs have been integrated into horse mRNA genes and small fractions of them have been exonized into coding sequences.

机译：转座因子（TEs）是分散在整个哺乳动物基因组中的重复序列，它们占据重要的遗传位置。在各种脊椎动物基因组中，TEs具有有害作用和有益作用，例如外显子化，聚腺苷酸化和/或改变转录速率。然而，据我们所知，尚无研究考虑TEs与马基因之间的关系。在这项研究中，我们通过收集在mRNA基因中插入的TE来检查TE对马基因组的贡献。通过筛选TE的丰度，分布和方向，我们发现大多数TE插入属于反转录元件和DNA元件，其中大多数存在于马基因的编码序列中。此外，发现MIR，L1，L2，ERVL和ERVL-MaLR亚家族在非LTR和LTR元素中含量最高。插入编码序列中的TE中的反义元件（LTR，LINE和SINE）显示出对反义方向的偏好。在LINEs中观察到最明显的插入方向失衡，占反义方向所有TE的40％。通过这些分析，我们确定了总共1310个TE已整合到马mRNA基因中，其中一小部分已外显子化为编码序列。

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来源
《Genes & Genomics》 |2013年第4期|483-489|共7页
作者
Kung Ahn; Jin-Han Bae; Jeong-An Gim; Ja-Rang Lee; Yi-Deun Jung; Kyung-Do Park; Kyudong Han; Byung-Wook Cho; Heui-Soo Kim;
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作者单位

Department of Biological Sciences College of Natural Sciences Pusan National University">(1);

Department of Biological Sciences College of Natural Sciences Pusan National University">(1);

Department of Biological Sciences College of Natural Sciences Pusan National University">(1);

Department of Biological Sciences College of Natural Sciences Pusan National University">(1);

Department of Biological Sciences College of Natural Sciences Pusan National University">(1);

Department of Animal Life and Environment Sciences Hankyong National University">(2);

Department of Nanobiomedical Science WCU Research Center Dankook University">(3);

Department of Animal Science College of Life Sciences Pusan National University">(4);

Department of Biological Sciences College of Natural Sciences Pusan National University">(1);

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原文格式 PDF
正文语种 eng
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关键词
Horse; Transposable elements (TEs); Retroelements; DNA elements;

机译：马;转座因子（TEs）;后置元素;DNA元素;

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专利

1. Identification and characterization of transposable elements inserted into the coding sequences of horse genes [J] . Kung Ahn, Jin-Han Bae, Jeong-An Gim, Genes and genomics . 2013,第4期

机译：鉴定和鉴定插入马基因编码序列中的转座因子
2. Characterization of three active transposable elements recently inserted in three independent DFR-A alleles and one high-copy DNA transposon isolated from the Pink allele of the ANS gene in onion (Allium cepa L.) [J] . Kim Sunggil, Park Jee Young, Yang Tae-Jin Molecular genetics and genomics: MGG . 2015,第3期

机译：从洋葱中ANS基因的粉红等位基因中分离出的三个独立的DFR-A等位基因和一个高拷贝DNA转座子中最近插入的三个活性转座子的特性
3. Characterization of transcriptional activation and inserted-into-gene preference of various transposable elements in the Brassica species [J] . Gao Caihua, Xiao Meili, Jiang Lingyan, Molecular biology reports . 2012,第7期

机译：芸苔属物种中各种转座元件的转录激活和插入基因偏好的表征
4. Sequences Which Are Period Invariant Under Rearrangement Of The Elements: Relations To Generalized Hadamard Codes [C] . Charlie H. Cooke 7th World Multiconference on Systemics, Cybernetics and Informatics(SCI 2003) vol.3: Communication, Network and Control Systems, Technologies and Applications . 2003

机译：在元素重排下周期不变的序列：与广义Hadamard码的关系
5. Characterization of minimal sequence requirements for piggyBac transposable element and construction of a new generation of piggyBac transformation vectors. [D] . Li, Xu. 2000

机译：用于piggyBac转座元件的最小序列要求的表征和新一代piggyBac转化载体的构建。
6. Widespread Exonization of Transposable Elements in Human Coding Sequences is Associated with Epigenetic Regulation of Transcription [O] . Ahsan Huda, Pierre R Bushel -1

机译：转座因子在人类编码序列中的广泛外显子化与转录的表观遗传调控有关。
7. Figure 4: (A) One conserved sequence, which occurs 79 times in 46,264 binding site peaks from the ChIP-seq data-set. The mutation profile of this conserved sequence is illustrated, where ’_ ’ indicates this base is unchanged; DEL indicates this base is lost; INS X indicates a new base X is inserted in front of this base. (B) Several repeated elements patterns are listed. (C) In the first column, the top five DNA motifs, mined by meme-chip tools (Machanick Bailey, 2011) are illustrated. The resemblant conserved sequences, found by the CFSP algorithm are listed in the second column. In the third column, the position-specific scoring matrices, which are transformed from mutational information are listed. The similarity between meme motif and resemblant conserved sequence with PSSM format was calculated via a stamp motif comparison tool (Mahony Benos, 2007). The E-values for the similarity of those pairs is displayed in the fourth column. (D) One motif is selected in each group clustered by gkmsvm descriptors, and the corresponding motif found by the CFSP algorithm is listed below. (E) There are additional datasets (File No: ENCFF100GRL, ENCFF616IRT, ENCFF870CER, Target: SREBF1) collected from https://www.encodeproject.org. The top two motifs are selected in each file using meme tools, and the corresponding motifs found by our algorithm are listed below. [O] . -1

机译：图4：（a）一种保守序列，其发生在芯片-SEQ数据集中的46,264个结合位点峰值中的79倍。说明了这种保守序列的突变分布，其中'_'表示该碱度不变; del表示此基础丢失; INS X表示新的基础X插入此基础前面。（b）列出了几种重复的元素模式。（c）在第一栏中，示出了由MEME芯片工具（Machanick＆Bailey，2011）开采的前五个DNA主题。由CFSP算法发现的相应保守序列列于第二列中。在第三列中，列出了从突变信息转换的特定位置的评分矩阵。 MEME主题与PSSM格式的相似性与PSSM格式之间的相似性通过邮票图章比较工具（Mahony＆Benos，2007）计算。这些对相似性的电子值显示在第四列中。（d）在由GKMSVM描述符聚集的每个组中选择了一个图案，下面列出了CFSP算法的相应主题。（e）从https://www.encodeproject.org收集的，有附加数据集（文件no：cernff100grl，cenf616irl，conf8.20cer，target：srebf1）。使用MEME工具在每个文件中选择前两个图案，并且我们的算法发现的相应主题如下所示。
8. Identification and Functional Characterization of Somatic Mutations in Human MicroRNAs and their Responsive Elements in Target Genes in Ovarian Tumor Tissues [R] . Zhao, H. 2009

机译：人类微小RNa中体细胞突变的鉴定和功能表征及其在卵巢肿瘤组织靶基因中的反应元件

Identification and characterization of transposable elements inserted into the coding sequences of horse genes

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