Sanchez-Luque, Francisco J; Kempen, Marie-Jeanne H C; Gerdes, Patricia; Vargas-Landin, Dulce B; Richardson, Sandra R; Troskie, Robin-Lee; Jesuadian, Samuel J; Cheetham, Seth W; Carreira, Patricia E; Salvador-Palomeque, Carmen; García-Cañadas, Marta; Muñoz-Lopez, Martin; Sanchez, Laura; Lundberg, Mischa; Macia, Angela; Heras, Sara R; Brennan, Paul M; Lister, Ryan; Garcia-Perez, Jose L; Ewing, Adam D; Faulkner, Geoffrey J
LINE-1 Evasion of Epigenetic Repression in Humans (Journal Article)
In: Molecular Cell, 0 (0), 2019, ISSN: 1097-2765.
(| | )
textlessh2textgreaterSummarytextless/h2textgreatertextlessptextgreaterEpigenetic silencing defends against LINE-1 (L1) retrotransposition in mammalian cells. However, the mechanisms that repress young L1 families and how L1 escapes to cause somatic genome mosaicism in the brain remain unclear. Here we report that a conserved Yin Yang 1 (YY1) transcription factor binding site mediates L1 promoter DNA methylation in pluripotent and differentiated cells. By analyzing 24 hippocampal neurons with three distinct single-cell genomic approaches, we characterized and validated a somatic L1 insertion bearing a 3ʹ transduction. The source (donor) L1 for this insertion was slightly 5ʹ truncated, lacked the YY1 binding site, and was highly mobile when tested textitin vitro. Locus-specific bisulfite sequencing revealed that the donor L1 and other young L1s with mutated YY1 binding sites were hypomethylated in embryonic stem cells, during neurodifferentiation, and in liver and brain tissue. These results explain how L1 can evade repression and retrotranspose in the human body.textless/ptextgreater
Nguyen, Thu H M; Carreira, Patricia E; Sanchez-Luque, Francisco J; Schauer, Stephanie N; Fagg, Allister C; Richardson, Sandra R; Davies, Claire M; Jesuadian, Samuel J; Kempen, Marie-Jeanne H C; Troskie, Robin-Lee; James, Cini; Beaven, Elizabeth A; Wallis, Tristan P; Coward, Jermaine I G; Chetty, Naven P; Crandon, Alexander J; Venter, Deon J; Armes, Jane E; Perrin, Lewis C; Hooper, John D; Ewing, Adam D; Upton, Kyle R; Faulkner, Geoffrey J
L1 Retrotransposon Heterogeneity in Ovarian Tumor Cell Evolution (Journal Article)
In: Cell Reports, 23 (13), pp. 3730–3740, 2018, ISSN: 2211-1247.
(| | )
LINE-1 (L1) retrotransposons are a source of insertional mutagenesis in tumor cells. However, the clinical significance of L1 mobilization during tumorigenesis remains unclear. Here, we applied retrotransposon capture sequencing (RC-seq) to multiple single-cell clones isolated from five ovarian cancer cell lines and HeLa cells and detected endogenous L1 retrotransposition in vitro. We then applied RC-seq to ovarian tumor and matched blood samples from 19 patients and identified 88 tumor-specific L1 insertions. In one tumor, an intronic de novo L1 insertion supplied a novel cis-enhancer to the putative chemoresistance gene STC1. Notably, the tumor subclone carrying the STC1 L1 mutation increased in prevalence after chemotherapy, further increasing STC1 expression. We also identified hypomethylated donor L1s responsible for new L1 insertions in tumors and cultivated cancer cells. These congruent in vitro and in vivo results highlight L1 insertional mutagenesis as a common component of ovarian tumorigenesis and cancer genome heterogeneity.
Richardson, Sandra R; Gerdes, Patricia; Gerhardt, Daniel J; Sanchez-Luque, Francisco J; Bodea, Gabriela-Oana; noz-Lopez, Martin Mu; Jesuadian, Samuel J; Kempen, Marie-Jeanne H C; Carreira, Patricia E; Jeddeloh, Jeffrey A; Garcia-Perez, Jose L; Jr, Haig H Kazazian; Ewing, Adam D; Faulkner, Geoffrey J
In: Genome Res., 27 (8), pp. 1395–1405, 2017.
(| | )
LINE-1 (L1) retrotransposons are a noted source of genetic
diversity and disease in mammals. To expand its genomic
footprint, L1 must mobilize in cells that will contribute
their genetic material to subsequent generations. Heritable L1
insertions may therefore arise in germ cells and in
pluripotent embryonic cells, prior to germline specification,
yet the frequency and predominant developmental timing of such
events remain unclear. Here, we applied mouse retrotransposon
capture sequencing (mRC-seq) and whole-genome sequencing (WGS)
to pedigrees of C57BL/6J animals, and uncovered an L1
insertion rate of $geq$1 event per eight births. We traced
heritable L1 insertions to pluripotent embryonic cells and,
strikingly, to early primordial germ cells (PGCs). New L1
insertions bore structural hallmarks of target-site primed
reverse transcription (TPRT) and mobilized efficiently in a
cultured cell retrotransposition assay. Together, our results
highlight the rate and evolutionary impact of heritable L1
retrotransposition and reveal retrotransposition-mediated
genomic diversification as a fundamental property of
pluripotent embryonic cells in vivo.
Kempen, Marie-Jeanne H C; Bodea, Gabriela O; Faulkner, Geoffrey J
In: Human Retrotransposons in Health and Disease, pp. 107–125, Springer, Cham, 2017.
(| | )
The neuronal genome has long been considered as a stably
persisting entity interpreted as the foundation of neurobiology.
Over the past decade, it has become increasingly clear that
mobile genetic elements, such as the retrotransposon LINE-1
(L1), are actively transcribed and transpose in the healthy
brain. L1 activity therefore provides a route to somatic genome
diversity and dynamism in neuronal populations. Here, we discuss
the discovery of L1 retrotransposition during neurogenesis, and
consider how neuronal cells regulate retrotransposition in
response to endogenous and environmental stimuli. We also bring
forward hypotheses relating to how L1 impacts normal brain
development and function, as well as how abnormal L1
mobilisation could contribute to neurological disease
susceptibility and pathophysiology.
- Click to share on Twitter (Opens in new window)
- Click to share on Facebook (Opens in new window)
- Click to share on Skype (Opens in new window)
- Click to share on Tumblr (Opens in new window)
- Click to share on Pinterest (Opens in new window)
- Click to share on Pocket (Opens in new window)
- Click to print (Opens in new window)