BACKGROUND L1Md retrotransposons are the most abundant and active transposable elements in the mouse genome. The promoters of many L1Md retrotransposons are composed of tandem repeats called monomers. The number of monomers varies between retrotransposon copies, thus making it difficult to annotate L1Md promoters. Duplication of monomers contributes to the maintenance of L1Md promoters during truncation-prone retrotranspositions, but the associated mechanism remains unclear. Since the current classification of monomers is based on limited data, a comprehensive monomer annotation is needed for supporting functional studies of L1Md promoters genome-wide. RESULTS We developed a pipeline for de novo monomer detection and classification. Identified monomers are further classified into subtypes based on their sequence profiles. We applied this pipeline to genome assemblies of various rodent species. A major monomer subtype of the lab mouse was also found in other Mus species, implying that such subtype has emerged in the common ancestor of involved species. We also characterized the positioning pattern of monomer subtypes within individual promoters. Our analyses indicate that the subtype composition of an L1Md promoter can be used to infer its transcriptional activity during male germ cell development. CONCLUSIONS We identified subtypes for all monomer types using comprehensive data, greatly expanding the spectrum of monomer variants. The analysis of monomer subtype positioning provides evidence supporting both previously proposed models of L1Md promoter expansion. The transcription silencing of L1Md promoters differs between promoter types, which supports a model involving distinct suppressive pathways rather than a universal mechanism for retrotransposon repression in gametogenesis.

中文翻译：

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L1Md逆转录转座子启动子的亚型分类和功能注释。


背景L1Md逆转录转座子是小鼠基因组中最丰富和最活跃的转座元件。许多 L1Md 逆转录转座子的启动子由称为单体的串联重复序列组成。逆转录转座子拷贝之间的单体数量不同，因此很难注释 L1Md 启动子。单体的复制有助于在易截断的逆转录转座过程中维持 L1Md 启动子，但相关机制仍不清楚。由于目前单体的分类基于有限的数据，因此需要全面的单体注释来支持 L1Md 启动子全基因组的功能研究。结果我们开发了一条用于从头单体检测和分类的管道。已识别的单体根据其序列概况进一步分为亚型。我们将该流程应用于各种啮齿动物物种的基因组组装。在其他鼠属物种中也发现了实验室小鼠的主要单体亚型，这意味着这种亚型已经出现在相关物种的共同祖先中。我们还描述了单个启动子内单体亚型的定位模式。我们的分析表明，L1Md 启动子的亚型组成可用于推断其在雄性生殖细胞发育过程中的转录活性。结论我们使用综合数据确定了所有单体类型的亚型，极大地扩展了单体变体的范围。单体亚型定位的分析提供了支持先前提出的 L1Md 启动子扩展模型的证据。 L1Md 启动子的转录沉默在启动子类型之间有所不同，这支持了涉及不同抑制途径的模型，而不是配子发生中逆转录转座子抑制的通用机制。