Supplementary Material for: The structures of mouse and human L1 elements reflect their insertion mechanism

L1 is an abundant, interspersed repeated DNA element of mammalian genomes. It has achieved its high copy number via retrotransposition. Like other non-LTR retrotransposons, L1 insertion into chromosomal DNA apparently occurs by target-site primed reverse transcription, or TPRT. L1 retrotransposition often generates elements with 5�� truncations that are flanked by a duplication of the genomic target site (TSD). It is typically assumed that the 5�� truncated elements are the consequence of poor processivity of the L1 reverse transcriptase. However, we find that the majority of young L1 elements from both the human and mouse genomes are truncated at sequences that can basepair with the target site. Thus, to whatever extent truncation is a consequence of poor processivity, we suggest that truncation is likely to occur when target site sequence can basepair with L1 sequence. This finding supports a model for insertion that occurs by two sequential TPRT reactions, the second of which relies upon the homology between the target site and L1. Because perfect heteroduplex formation is not required for all insertions, a dynamic relationship between the primer, template and enzyme during reverse transcription is inferred. 5�� truncation may be a successful evolutionary strategy that is exploited by L1 as a means to escape host suppression of transposition.L1是哺乳动物基因组中一类丰度极高的散在重复DNA元件，其通过反转录转座（retrotransposition）获得了庞大的拷贝数。与其他非长末端重复序列反转录转座子（non-LTR retrotransposons）类似，L1插入染色体DNA的过程显然通过靶位点引导的反转录（target-site primed reverse transcription，TPRT）完成。L1反转录转座通常会产生带有5'端截短的元件，其侧翼带有基因组靶位点的重复序列（target site duplication，TSD）。学界普遍认为，这类5'端截短的元件是L1反转录酶过程性不足的结果。然而本研究发现，人类与小鼠基因组中绝大多数年轻L1元件的截短位点，均位于可与靶位点形成碱基配对的序列区域。因此，即便截短在一定程度上源于反转录酶的过程性缺陷，我们认为截短更易发生在靶位点序列可与L1序列形成碱基配对的场景中。这一发现支持了一种通过两次连续TPRT反应实现插入的模型，其中第二次反应依赖于靶位点与L1之间的序列同源性。由于并非所有插入事件都需要完美异源双链的形成，我们可以推断反转录过程中引物、模板与酶之间存在动态相互作用。5'端截短或许是L1演化出的一种成功策略，可帮助其逃逸宿主对转座过程的抑制作用。