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.

中文翻译：

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嵌套植物 LTR 反转录转座子靶向其他元素的特定区域，而所有 LTR 反转录转座子通常靶向回文和核小体占据区域：计算机研究

嵌套在 LTR 反转录转座子中很常见，尤其是在包含大量元素的大型基因组中。我们分析了 12 个植物基因组并获得了 1491 对嵌套和原始（预先存在的）LTR 反转录转座子。我们系统地分析了单个 LTR 反转录转座子的相互嵌套，发现某些家族，通常属于 Ty3/吉普赛而不是 Ty1/copia 超家族，表现出更高的嵌套频率以及对同一家族的旧副本的更高偏好（“自动插入”）。嵌套的 LTR 反转录转座子优先位于其他 LTR 反转录转座子的 3'UTR，而编码和调节区 (LTR) 通常不是目标。插入显示出对回文的弱偏好，并且与更高预测的核小体占用率的强位置模式相关。在 13,983 个非嵌套植物 LTR 反转录转座子中也发现了目标位点选择的随机性偏差。我们揭示了 LTR 反转录转座子的嵌套不是随机的。整合与序列组成、二级结构和染色质环境相关。插入对家庭适应性具有低负面影响的反转录转座子位置支持将基因组视为各种元素的生态系统的概念。