Mutational signatures of non‐homologous and polymerase theta‐mediated end‐joining in embryonic stem cells

Schimmel, Joost; Kool, Hanneke; Schendel, Robin van; Tijsterman, Marcel

doi:10.15252/embj.201796948

Cited by 122 publications

(129 citation statements)

References 74 publications

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“…1), which utilizes the additional factors of PARP and DNA polymerase theta (Pol θ), requires microhomology that ranges between 2 and 20 bp. While NHEJ dominates DSB repair in most mammalian somatic cells, Pol θ-mediated events appear at an observable frequency in certain cell types (11), for certain repair events (12), and in some organisms (13). Greater levels of resection can further promote the non-conservative homology-directed repair pathway of single-strand annealing (SSA) that requires >25 bp of homology ( Fig.…”

Section: Overview Of Nhej In Humans and Its Relationship With Other Pmentioning

confidence: 99%

Nonhomologous DNA end-joining for repair of DNA double-strand breaks

Pannunzio

Watanabe

Lieber

2018

Journal of Biological Chemistry

405

360

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Nonhomologous DNA end joining (NHEJ) is the predominant DSB repair pathway throughout the cell cycle and accounts for nearly all DSB repair outside of the S and G2 phases. NHEJ relies on Ku to thread onto DNA termini and thereby improve the affinity of the NHEJ enzymatic components consisting of polymerases (Pol m and Pol l), a nuclease (the Artemis·DNA-PKcs complex), and a ligase (XLF·XRCC4·Lig4 complex). Each of the enzymatic components is distinctive for its versatility in acting on diverse incompatible DNA end configurations coupled with a flexibility in loading order, resulting in many possible junctional outcomes from one DSB. DNA ends can either be directly ligated or, if the ends are incompatible, processed until a ligatable configuration is achieved that is often stabilized by up to 4 bp of terminal microhomology. Processing of DNA ends results in nucleotide loss or addition, explaining why DSBs repaired by NHEJ are rarely restored to their original DNA sequence. Thus, NHEJ is a single pathway with multiple enzymes at its disposal to repair DSBs, resulting in a diversity of repair outcomes.

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Section: Overview Of Nhej In Humans and Its Relationship With Other Pmentioning

confidence: 99%

Nonhomologous DNA end-joining for repair of DNA double-strand breaks

Pannunzio

Watanabe

Lieber

2018

Journal of Biological Chemistry

405

360

View full text Add to dashboard Cite

show abstract

“…The possibility of controlling CRISPR-based gene editing accuracy by pharmacological modulation of the repair process is being intensively evaluated at present [52]. In this regard, the search for selective inhibitors against Polλ SUMOylation could also be useful in the gene editing toolkit, given that a large subset of breaks generated by CRISPR-Cas systems requires specialized DNA gap-filling activity by PolX polymerases as Polλ [53,54].…”

Section: Discussionmentioning

confidence: 99%

RanBP2-mediated SUMOylation promotes human DNA polymerase lambda nuclear localization and DNA repair

Moreno-Onate

Herrero-Ruiz

García‐Domínguez

et al. 2020

Preprint

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Cellular DNA is under constant attack by a wide variety of agents, both endogenous and exogenous. To counteract DNA damage, human cells have a large collection of DNA repair factors. Among them, DNA polymerase lambda (Polλ) stands out for its versatility, as it participates in different DNA repair and damage tolerance pathways in which gap-filling DNA synthesis is required. In this work we show that human Polλ is conjugated with Small Ubiquitin-like MOdifier (SUMO) proteins both in vitro and in vivo, with Lys27 being the main target of this covalent modification. Polλ SUMOylation takes place in the nuclear pore complex and is mediated by the E3 ligase RanBP2. This post-translational modification promotes Polλ entry into the nucleus, which is required for its recruitment to DNA lesions and stimulated by DNA damage induction. Our work represents an advance in the knowledge of molecular pathways that regulate cellular localization of human Polλ, which are essential to be able to perform its functions during repair of nuclear DNA, and that might constitute an important point for the modulation of its activity in human cells.

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“…1c, Fig. S1) [19][20][21] . Indeed, the number of uniquely marked reads in a population of mutated target sites is lower when the integration barcode is not taken into account (Fig.…”

Section: A Transcribed Multi-channel and Continuously Evolving Molementioning

confidence: 99%

Molecular recording of mammalian embryogenesis

Chan

Smith

Grosswendt

et al. 2018

Preprint

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Chan, Smith et al. 2018 Molecular recording of mammalian embryogenesis 2 Understanding the emergence of complex multicellular organisms from single totipotent cells, or ontogenesis, represents a foundational question in biology. The study of mammalian development is particularly challenging due to the difficulty of monitoring embryos in utero, the variability of progenitor field sizes, and the indeterminate relationship between the generation of uncommitted progenitors and their progression to subsequent stages. Here, we present a flexible, high information, multi-channel molecular recorder with a single cell (sc) readout and apply it as an evolving lineage tracer to define a mouse cell fate map from fertilization through gastrulation. By combining lineage information with scRNA-seq profiles, we recapitulate canonical developmental relationships between different tissue types and reveal an unexpected transcriptional convergence of endodermal cells from extra-embryonic and embryonic origins, illustrating how lineage information complements scRNA-seq to define cell types. Finally, we apply our cell fate map to estimate the number of embryonic progenitor cells and the degree of asymmetric partitioning within the pluripotent epiblast during specification. Our approach enables massively parallel, high-resolution recording of lineage and other information in mammalian systems to facilitate a quantitative framework for describing developmental processes.

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Mutational signatures of non‐homologous and polymerase theta‐mediated end‐joining in embryonic stem cells

Cited by 122 publications

References 74 publications

Nonhomologous DNA end-joining for repair of DNA double-strand breaks

Nonhomologous DNA end-joining for repair of DNA double-strand breaks

RanBP2-mediated SUMOylation promotes human DNA polymerase lambda nuclear localization and DNA repair

Molecular recording of mammalian embryogenesis

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