Organ-, sex-, and age-dependent patterns of endogenous LINE-1 mRNA expression at a single locus resolution

Expression of full-length LINE-1 mRNA, the first step in the L1 copy-and-paste amplification cycle, is a prerequisite for L1-associated genomic instability resulting from DNA damage and insertional mutagenesis. We used our stringent bioinformatics method to parse L1 mRNA transcripts and measure the level of full-length L1 mRNA expressed in mouse and rat organs at a locus-specific resolution. We find that expression of L1 loci in rodents exhibits striking organ specificity with less than 0.8% of loci shared between different organs of the same organism. This organ specificity in L1 mRNA expression is preserved in male and female mice and across different age groups. Unexpectedly, we discovered notable differences in L1 mRNA expression between sexes with only 5% of expressed L1 loci shared between male and female mice. Moreover, we report that the levels of total L1 mRNA expression and the number and spectrum of expressed L1 loci fluctuate with age as independent variables, demonstrating different patterns in different organs and sexes. Overall, our comparisons between organs and sexes and across ages ranging from 2 to 22 months establish previously unforeseen dynamic changes in L1 mRNA expression in vivo. These milestone findings establish a previously lacking atlas of endogenous L1 mRNA expression across a broad range of biological variables that will guide future studies addressing the understanding of mechanisms that govern expression of a limited number of L1 loci in any given organ and the impact of environmental and genetic perturbations on L1 mRNA expression and its involvement in disease initiation and progression. RNA Sequencing of multiple organs from 12 male mice, 9 female mice, and 3 rats. Mouse samples are from ages ranging 2-22 months. Testes, brains, and livers were collected from 6 mice: 3 at 7.6 months old (mo) and 3 at 12.8 mo. Lungs were collected from 5 mice: 2 at 7.6 mo and 3 at 12.8 mo. Only testes and livers were collected from 6 additional mice: 2 at 1.9 mo, 1 at 3.6 mo, and 3 at 22.3 mo. Brains, lungs, and ovaries were collected from 9 mice: 2 at 2.2 mo, 1 at 3.2 mo, 2 at 8 mo, 1 at 8.6 mo, 1 at 8.7 mo, and 2 at 16.5 mo. Uteri were collected from 6 mice: 1 at 2.2 mo, 1 at 8 mo, 1 at 8.6 mo, 1 at 8.7 mo, and 2 at 16.5- mo Testes, brains, livers, and lungs were collected from 3 rats, all 4.8 mo. The .fastq files contain RNA-sequencing of the whole cytoplasm. The .txt files contain analysis of the LINE-1 retrotransposon which has ~3,000 full length copies scattered throughout the mouse genome.全长长散在核元件1（LINE-1）信使RNA（mRNA）的表达，作为L1拷贝-粘贴扩增循环的首要步骤，是由DNA损伤与插入突变所引发的L1相关基因组不稳定性的必要前提。本研究采用严谨的生物信息学方法解析L1 mRNA转录本，并以位点特异性分辨率检测小鼠与大鼠器官中全长L1 mRNA的表达水平。本研究发现，啮齿类动物体内L1位点的表达呈现出显著的器官特异性，同一生物体不同器官间仅存在不足0.8%的共有L1表达位点。L1 mRNA表达的这种器官特异性在雌雄小鼠以及不同年龄组中均保持稳定。出乎意料的是，本研究还发现雌雄小鼠间L1 mRNA表达存在显著差异，二者仅存在5%的共有表达L1位点。此外，本研究表明，总L1 mRNA表达水平以及表达L1位点的数量与谱型作为独立变量随年龄发生波动，且在不同器官与性别间呈现出各异的变化模式。综上，本研究通过对不同器官、性别以及2至22月龄跨度内的年龄梯度进行比较，揭示了体内L1 mRNA表达此前未被发现的动态变化特征。这些里程碑式的研究成果构建了此前缺失的、覆盖多类生物学变量的内源性L1 mRNA表达图谱，将为后续研究提供指导——包括解析特定器官内有限数量L1位点的表达调控机制，以及环境与遗传扰动对L1 mRNA表达的影响，及其在疾病发生与进展中的作用。本数据集包含12只雄性小鼠、9只雌性小鼠与3只大鼠的多器官RNA测序数据。小鼠样本的采集年龄跨度为2至22月龄。其中，从6只小鼠中采集了睾丸、大脑与肝脏样本：3只为7.6月龄，另外3只为12.8月龄；从5只小鼠中采集了肺组织样本：2只为7.6月龄，3只为12.8月龄；额外6只小鼠仅采集了睾丸与肝脏样本：2只为1.9月龄，1只为3.6月龄，3只为22.3月龄；从9只小鼠中采集了大脑、肺与卵巢样本：2只为2.2月龄，1只为3.2月龄，2只为8月龄，1只为8.6月龄，1只为8.7月龄，2只为16.5月龄；从6只小鼠中采集了子宫样本：1只为2.2月龄，1只为8月龄，1只为8.6月龄，1只为8.7月龄，2只为16.5月龄；从3只均为4.8月龄的大鼠中采集了睾丸、大脑、肝脏与肺组织样本。本数据集的.fastq格式文件包含全细胞质RNA测序数据；.txt格式文件则包含针对LINE-1逆转录转座子的分析结果——小鼠基因组中约散布有3000个全长LINE-1拷贝。