Locus-resolution analysis of L1 regulation and retrotransposition potential in mouse embryonic development Gerdes, Patricia Sánchez Luque, Francisco José The authors thank Dr. John V. Moran, Dr. Ian R. Adams and members of the Richardson and Faulkner labs for helpful advice and discussion. HeLa-JVM cells were a gift from Dr. John V. Moran. The L1SM and L1SMmut2 constructs were a gift from Dr. Jef D. Boeke, and the L1spa construct was a gift from Dr. Haig Kazazian. This research was supported by an Australian Government Research Training Program Scholarship and a Mater Research Frank Clair Scholarship awarded to P.G., a University of Queensland Research Training Program Scholarship and Commonwealth Scientific and Industrial Research Organisation Postgraduate Top-Up Scholarship awarded to M.L., the People Programme (Marie Sk & lstrok;odowska-Curie Actions) of the European Union Seventh Framework Program (FP7/2007-2013) under REA grant agreement PIOF-GA-2013-623324 awarded to F.J.S.-L. and the Australian National Health and Medical Research Council (NHMRC) and Australian Research Council (ARC) Dementia Research Development Fellowship GNT1108258 awarded to G.O.B. This study was funded by the Australian NHMRC (GNT1125645, GNT1138795, and GNT1173711 to G.J.F.; GNT1173476 to S.R.R.), The ARC (DP200102919 to G.J.F. and S.R.R.), an Australian Department of Health Medical Frontiers Future Fund (MRFF) (MRF1175457) grant awarded to A.D.E., a CSL Centenary Fellowship to G.J.F., an Advance Queensland Women's Academic Fund Maternity Funding award to S.R.R., the Mater Research Strategic Grant for Outstanding Women to S.R.R, and the Mater Foundation (Equity Trustees / AE Hingeley, QFC Thomas George and KC BM Thomson Trusts). We acknowledge the TRI flow cytometry core for technical assistance and equipment. We acknowledge QBI Advanced Microscopy Facility for technical assistance and equipment, supported by ARC LIEF grant LE130100078. Mice harbor similar to 2800 intact copies of the retrotransposon Long Interspersed Element 1 (L1). The in vivo retrotransposition capacity of an L1 copy is defined by both its sequence integrity and epigenetic status, including DNA methylation of the monomeric units constituting young mouse L1 promoters. Locus-specific L1 methylation dynamics during development may therefore elucidate and explain spatiotemporal niches of endogenous retrotransposition but remain unresolved. Here, we interrogate the retrotransposition efficiency and epigenetic fate of source (donor) L1s, identified as mobile in vivo. We show that promoter monomer loss consistently attenuates the relative retrotransposition potential of their offspring (daughter) L1 insertions. We also observe that most donor/daughter L1 pairs are efficiently methylated upon differentiation in vivo and in vitro. We use Oxford Nanopore Technologies (ONT) long-read sequencing to resolve L1 methylation genome-wide and at individual L1 loci, revealing a distinctive "smile" pattern in methylation levels across the L1 promoter region. Using Pacific Biosciences (PacBio) SMRT sequencing of L1 5 ' RACE products, we then examine DNA methylation dynamics at the mouse L1 promoter in parallel with transcription start site (TSS) distribution at locus-specific resolution. Together, our results offer a novel perspective on the interplay between epigenetic repression, L1 evolution, and genome stability. 2023-12-05T13:41:16Z 2023-12-05T13:41:16Z 2023-10-05 journal article Gerdes et al. Locus-resolution analysis of L1 regulation and retrotransposition potential in mouse embryonic development. Genome Res. 2023. 33: 1465-1481. [doi: 10.1101/gr.278003.123] https://hdl.handle.net/10481/86042 10.1101/gr.278003.123 eng http://creativecommons.org/licenses/by/4.0/ open access Atribución 4.0 Internacional Cold Spring Harbor Laboratory Press