Dataset Information

Reprogramming triggers endogenous L1 and Alu retrotransposition in human induced pluripotent stem cells.

ABSTRACT: Human induced pluripotent stem cells (hiPSCs) are capable of unlimited proliferation and can differentiate in vitro to generate derivatives of the three primary germ layers. Genetic and epigenetic abnormalities have been reported by Wissing and colleagues to occur during hiPSC derivation, including mobilization of engineered LINE-1 (L1) retrotransposons. However, incidence and functional impact of endogenous retrotransposition in hiPSCs are yet to be established. Here we apply retrotransposon capture sequencing to eight hiPSC lines and three human embryonic stem cell (hESC) lines, revealing endogenous L1, Alu and SINE-VNTR-Alu (SVA) mobilization during reprogramming and pluripotent stem cell cultivation. Surprisingly, 4/7 de novo L1 insertions are full length and 6/11 retrotransposition events occurred in protein-coding genes expressed in pluripotent stem cells. We further demonstrate that an intronic L1 insertion in the CADPS2 gene is acquired during hiPSC cultivation and disrupts CADPS2 expression. These experiments elucidate endogenous retrotransposition, and its potential consequences, in hiPSCs and hESCs.

SUBMITTER: Klawitter S

PROVIDER: S-EPMC4729875 | biostudies-literature | 2016 Jan

REPOSITORIES: biostudies-literature

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Publications

Reprogramming triggers endogenous L1 and Alu retrotransposition in human induced pluripotent stem cells.

Klawitter Sabine S Fuchs Nina V NV Upton Kyle R KR Muñoz-Lopez Martin M Shukla Ruchi R Wang Jichang J Garcia-Cañadas Marta M Lopez-Ruiz Cesar C Gerhardt Daniel J DJ Sebe Attila A Grabundzija Ivana I Merkert Sylvia S Gerdes Patricia P Pulgarin J Andres JA Bock Anja A Held Ulrike U Witthuhn Anett A Haase Alexandra A Sarkadi Balázs B Löwer Johannes J Wolvetang Ernst J EJ Martin Ulrich U Ivics Zoltán Z Izsvák Zsuzsanna Z Garcia-Perez Jose L JL Faulkner Geoffrey J GJ Schumann Gerald G GG

Nature communications 20160108

Human induced pluripotent stem cells (hiPSCs) are capable of unlimited proliferation and can differentiate in vitro to generate derivatives of the three primary germ layers. Genetic and epigenetic abnormalities have been reported by Wissing and colleagues to occur during hiPSC derivation, including mobilization of engineered LINE-1 (L1) retrotransposons. However, incidence and functional impact of endogenous retrotransposition in hiPSCs are yet to be established. Here we apply retrotransposon ca ...[more]

PMID: 26743714

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Project description:BackgroundCells adapt to various chronic toxic exposures in a multitude of ways to minimize further damage and maximize their growth potential. Expression of L1 elements in the human genome can be greatly deleterious to cells, generating numerous double strand breaks (DSBs). Cells have been reported to respond to chronic DSBs by altering the repair of these breaks, including increasing the rate of homology independent DSB repair. Retrotransposition is strongly affected by proteins involved in DSB repair. Therefore, L1 expression has the potential to be a source of chronic DSBs and thus bring about the changes in cellular environment that could ultimately restrict its own retrotransposition.ResultsWe demonstrate that constitutive L1 expression leads to quicker DSB repair and decreases in the retrotransposition potential of L1 and other retrotransposons dependent on L1 expression for their mobility. This cellular adaptation results in reduced sensitivity to L1 induced toxicity. These effects can be induced by constitutive expression of the functional L1 ORF2 alone, but not by the constitutive expression of an L1 open reading frame 2 with mutations to its endonuclease and reverse transcriptase domains. This adaptation correlates with the relative activity of the L1 introduced into the cells.ConclusionsThe increased number of DSBs resulting from constitutive expression of L1 results in a more rapid rate of repair. The cellular response to this L1 expression also results in attenuation of retrotransposition and reduced sensitivity of the cells to negative consequences of L1 ORF2 expression. The influence does not appear to be through RNA interference. We believe that the increased rate of DSB repair is the most likely cause of the attenuation of retrotransposition. These alterations act as a fail safe mechanism that allows cells to escape the toxicity associated with the unchecked L1 expression. This gives cells that overexpress L1, such as tumor cells, the ability to survive the high levels of expression. However, the increased rate of break repair may come at the cost of accuracy of repair of the lesion, resulting in increased genomic instability.

Dataset Information

Reprogramming triggers endogenous L1 and Alu retrotransposition in human induced pluripotent stem cells.

Publications

Reprogramming triggers endogenous L1 and Alu retrotransposition in human induced pluripotent stem cells.

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