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首页> 外文期刊>Mobile DNA >Nested plant LTR retrotransposons target specific regions of other elements, while all LTR retrotransposons often target palindromes and nucleosome-occupied regions: in silico study
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Nested plant LTR retrotransposons target specific regions of other elements, while all LTR retrotransposons often target palindromes and nucleosome-occupied regions: in silico study

机译：嵌套植物LTR回收器瞄准其他元素的特定区域，而所有LTR回收扬声器经常瞄准回文和核心占用的地区：在Silico研究中

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摘要

Nesting is common in LTR retrotransposons, especially in large genomes containing a high number of elements. We analyzed 12 plant genomes and obtained 1491 pairs of nested and original (pre-existing) LTR retrotransposons. We systematically analyzed mutual nesting of individual LTR retrotransposons and found that certain families, more often belonging to the Ty3/gypsy than Ty1/copia superfamilies, showed a higher nesting frequency as well as a higher preference for older copies of the same family (“autoinsertions”). Nested LTR retrotransposons were preferentially located in the 3’UTR of other LTR retrotransposons, while coding and regulatory regions (LTRs) are not commonly targeted. Insertions displayed a weak preference for palindromes and were associated with a strong positional pattern of higher predicted nucleosome occupancy. Deviation from randomness in target site choice was also found in 13,983 non-nested plant LTR retrotransposons. We reveal that nesting of LTR retrotransposons is not random. Integration is correlated with sequence composition, secondary structure and the chromatin environment. Insertion into retrotransposon positions with a low negative impact on family fitness supports the concept of the genome being viewed as an ecosystem of various elements.
机译：嵌套在LTR回收分子中常见，特别是在含有大量元素的大基因组中。我们分析了12种植物基因组，并获得了1491对嵌套和原始（预先存在的）LTR回收碳膜。我们系统地分析了单个LTR回收扫描群体的相互嵌套，发现某些家庭更常见于TY3 /吉普赛人而不是TY1 / Copia Superfamilies，呈现出更高的嵌套频率，以及对同一家族的旧副本更高的偏好（“自动化“）。嵌套的LTR回收器优先位于其他LTR回收器的3'UTR中，同时编码和监管区域（LTRS）不一定是目标。插入呈现出对回文的弱偏好，并且与更高的预测核心占用的强大位置模式相关。在13,983个非嵌套植物LTR回收分子中还发现了从目标站点选择中的随机性偏差。我们揭示了LTR回收转换的嵌套不是随机的。整合与序列组成，二次结构和染色质环境相关。在对家庭健身产生低负面影响的转回转换位置支持基因组被视为各种元素的生态系统的概念。

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