The LINE‐1 paradox: Active yet immobile

LINE-1 (L1) elements represent the largest family of transposable elements in mammalian genomes, making up approximately 21% and 17% of the mouse and human genome, respectively. While most of these elements are no longer intact, a significant number with potentially functional promoters, primarily from the evolutionarily youngest families in both species, are scattered throughout the genome. These L1 elements are autonomously expressed and encode RNAs, which are however not necessarily translated into proteins, nor do the elements complete their retrotransposition cycle to generate new insertions. In this issue, the hypothesis article by Mangoni et al. refers to this as the “L1 paradox,” where an increase in L1 expression levels does not necessarily lead to a proportional increase in protein levels, or observable mobilization.[1] Several observations may help to explain in part this paradox. First, the accumulation of mutations has rendered many expressed elements noncoding, which, as a result, no longer contribute to the pool of L1-encoded proteins. Second, posttranscriptional control mechanisms from the host restrict the export and the translation of L1 RNAs, thereby contributing to their accumulation. Third, L1 RNAs tend to be short lived, retained in the nucleus, bound to chromatin, and often found in close proximity to their site of transcription. This retention may occur through interactions of L1 RNAs with chromatin or nuclear factors that have an affinity for RNAs.[2-4] Based on these observations, the authors propose an additional explanation to resolve the L1 paradox, focusing on the cooperation between L1s and their host. They hypothesize that, in specific contexts, cells can leverage the accumulation of L1 RNAs in the nucleus, using them as long noncoding RNAs (lncRNAs) with beneficial regulatory potential that promote cellular growth and proliferation, while L1 elements exploit these states to enhance their chance to mobilize during mitosis. A substantial body of evidence supports the role of L1 RNAs acting as regulatory RNAs and highlights their mitogenic potential. During early embryogenesis, increased L1 RNAs levels are essential for developmental progression and chromatin accessibility.[5] In embryonic stem cells (ESCs), they sustain proliferation and self-renewal and appear to regulate transcriptional programs, crucial for early developmental transitions across different stages, in both mouse and human cells.[3, 4] During brain development, high levels of L1 RNAs were shown to sustain cell growth of neural progenitor cells (NPCs), while preventing the activation of pathways that lead to neuronal differentiation.[2, 6] At the mechanistic level, this may occur through the association of L1 RNAs with subunits of the polycomb repressive complex 2 (PRC2), which prevents the repression of genes that support NPC proliferation.[2] Importantly, these effects are independent of L1 retrotransposition, as they remain unaffected by reverse-transcriptase inhibitors. Interestingly, these mechanisms seem to be conserved in mouse and human cells, as well as across developmental contexts, despite differences in the genomic localization of individual elements and the poor evolutionary conservation of L1 subfamily sequences in these two species. This further reinforces a regulatory role for L1 RNAs. In their hypothesis, the authors emphasize that the interaction of L1 RNAs with proteins is critical for this regulatory potential, through specific sequence modules or secondary structures. L1 RNAs can then modulate protein activity, their binding to chromatin, or act as molecular scaffolds to assemble protein complexes, in a similar fashion to functional lncRNAs. This, in turn, could influence the regulation of entire transcriptional programs that sustain proliferation and delay differentiation.[1] These regulatory mechanisms would be essential for critical stages during development, when cell-fate decisions are made, or for the maintenance of a pool of stem cells. It remains to be seen whether other adult stem cells also exhibit higher L1 expression levels. In this model, cells can however accommodate a certain level of retrotransposition, whose potential detrimental effects may be diluted in the population thanks to rapid cell divisions.[1] A key remaining question is at what point an increase in L1 expression becomes detrimental and pathological for cells. Is there a threshold of L1 non-coding RNAs that, if exceeded, triggers toxicity on its own, or is the harm primarily due to retrotransposition? In such cases, compromised genome integrity could lead to pathological conditions, including neurological disorders and cancer. However, it is still unclear whether and how L1 misregulation directly causes disease. While past research has largely focused on retrotransposition, this hypothesis article advocates for exploring whether excessive levels of L1 non-coding RNAs alone could disrupt transcriptional programs and drive disease development. This article comments on the hypothesis paper by Damiano Mangoni et al., https://doi.org/10.1002/bies.202400125 This work was supported by the Portuguese FCT-Fundação para a Ciência e a Tecnologia, I.P., CEECIND/02085/2018 and 2022.02195.PTDC, and by the International Rett Syndrome Foundation (grant #3909). The author declares no conflicts of interest.