X-chromosome inactivation draws L1 mutagenesis to the human X chromosome
- Jose de los Rios Barreda
- Maria E. Ferreiro
- Natasha Jansz
- Charles C. Bell
- Juan M. Botto
- Trung V. Nguyen
- Barun Pradhan
- Minchun Chen
- Ana Colomer-Boronat
- Darwin J. Da Costa Guevara
- Diane A. Flasch
- Sabrina Gericke
- Thomas E. Wilson
- Adam D. Ewing
- Sara R. Heras
- Francisco J. Sanchez-Luque
- Ryan Lister
- John V. Moran
- Geoffrey J. Faulkner
2026-07-30
X-chromosome inactivation (XCI) enables gene dosage compensation in XX eutherians. Long interspersed element-1 (LINE-1 or L1) retrotransposons are unusually abundant on the human X chromosome and are hypothesized to facilitate XCI. Here, we used long-read DNA sequencing to conduct a haplotype-aware analysis of engineered L1 integration preferences in the PA-1 human embryonic carcinoma cell line. Crucially, clonal XCI in PA-1 cells enabled derivation of active (Xa) and inactive (Xi) X-chromosome haplotypes. L1 integration strongly favored the Xi and other genomic regions that undergo DNA replication late in S-phase. These results suggest that the X chromosome is L1 rich because of XCI and imply that L1 integration preference for the Xi in XX individuals could potentially double the frequency of X-linked pathogenic L1 mutations in their XY descendants.