The LINE-1 regulatory network: genome-wide impact of recent transposable elements on mammalian genic activity – ImpacTE

To this end, the ImpacTE project has combined recent technological advances, such as in-cell and in vivo (epi)genome modifications, genetic screening and chromatin capture by CRISPR, ultra-long-read sequencing, and retrotransposon mapping, while taking advantage of the recognized expertise of both partners in transposon biology and bioinformatics analysis, mouse genetics and epigenetics.

The ImpacTE project has revealed that the impact of L1 retrotransposons is strongly influenced by their own transcriptional regulation. This regulation, which involves the binding of transcription factors or repressive complexes as well as epigenetic modifications, largely determines the influence that these transposable elements exert on genes located in the vicinity of their integration site. Thus, we have shown that the epigenetic status of an L1 can frequently spread to its nearby genomic region, and that in the absence of DNA methylation, L1s can be bound by specific transcription factors that alter the transcriptional control of nearby genes, leading to the formation of chimeric transcripts between the L1 and the neighboring gene. Moreover, the ImpacTE project has revealed new repressors of L1s for which the mechanism of action is currently under investigation.

In conclusion, the ImpacTE project has enabled the identification of insertions that alter gene expression in a cell type-specific manner through the formation of chimeric transcripts, as well as the cellular pathways involved in the control of these new transcripts. Notably, some of these transcripts have been described by others as a source of tumor neoantigens that can stimulate the anti-tumor immune response and could therefore be used in the future as a basis for anti-tumor vaccines. L1s also appear to be strongly stimulated in certain autoimmune diseases such as lupus. Understanding the regulatory mechanisms of these antigens could therefore improve the efficacy of anti-tumor vaccines or, conversely, reduce the immune response in patients affected by autoimmune pathologies. Finally, this work will help in the future to rationally predict the impact of thousands of retrotransposon copies identified in the context of genomic medicine and to expand our understanding of their role in the evolution of gene regulatory networks and new protein functions in mammals.

Billon V, Cristofari G. Nascent RNA m6A methylation at the heart of the gene- retrotransposon conflict. Cell Res. 2021 Jun 9.

Lanciano S, Cristofari G. Measuring and interpreting transposable element expression. Nat Rev Genet. 2020 Dec;21(12):721-736.

Repetitive DNA sequences account for almost half of the human and mouse genomes. Most of them are degenerated remnants of ancient mobile genetic elements. However, a subset of evolutionary recent transposable elements, particularly those belonging to the LINE-1 (L1) retrotransposon family, actively contribute to the plasticity of modern mammalian genomes and to the diversity of individual genomes. Their insertions into new genomic locations convey multiple cis-acting DNA regulatory elements, and can attract and even drive the evolution of chromatin factors and other host proteins. Because the vast majority of these potentially active L1s map outside of exons, predicting their impact on gene expression, transcript structure and function remains challenging. Considering the growing number of evidences that link L1 elements to the regulation of normal developmental processes but also to the etiology of diseases, understanding how L1s influence gene activity genome-wide represents a timely and relevant endeavor.

Here, we propose to test to which extent the youngest L1 retrotransposon families, L1-HS and L1-A, found in humans and mice, respectively, can influence gene expression at the genome-wide level. More specifically, the ImpacTE proposal will explore the impact of their 1) sequence, 2) transcription, and 3) chromatin states on gene regulation. This will be achieved at the global level rather than at individual loci, by combining recent technological developments, such as CRISPR-mediated (epi)genome engineering in cellula and in vivo, genetic screens and chromatin capture, ultra long-read sequencing, and retrotransposon mapping, while capitalizing on the expertise of the two scientific partners in the biology and bioinformatic analysis of transposons, mouse genetics and epigenetics. This proposal has the potential to reveal L1 insertions that alter gene expression in a cell-type- or tissue-specific manner and by which mechanisms they do so. Moreover, by relying on two mammalian representatives, mouse and human, and by including information from the cellular to the organismal level, we will gain complementary insights into the universal principles and specificities of the impact of L1s on mammalian genome regulation. Ultimately, our work will establish a rational basis for predicting the potential impact of thousands of retrotransposon copies identified in sequencing projects, as well as broaden our understanding of their role in the evolution of regulatory networks and novel protein functions in mammals.