The Steve Jackson Laboratory Website
Transformative discoveries in genome and cellular integrity

Publications

Predicting the mutations generated by repair of Cas9-induced double-strand breaks.

Allen F, Crepaldi L, Alsinet C, Strong AJ, Kleshchevnikov V, De Angeli P, Páleníková P, Khodak A, Kiselev V, Kosicki M, Bassett AR, Harding H, Galanty Y, Muñoz-Martínez F, Metzakopian E, Jackson SP, Parts L. (2018)

Nature Biotechnology Nov 27 [Epub ahead of print]

The DNA mutation produced by cellular repair of a CRISPR-Cas9-generated double-strand break determines its phenotypic effect. It is known that the mutational outcomes are not random, but depend on DNA sequence at the targeted location. Here we systematically study the influence of flanking DNA sequence on repair outcome by measuring the edits generated by >40,000 guide RNAs (gRNAs) in synthetic constructs.

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Kate Dry
Phosphorylation of Histone H4T80 Triggers DNA Damage Checkpoint Recovery.

Millan-Zambrano G, Santos-Rosa H, Puddu F, Robson SC, Jackson SP, Kouzarides T. (2018)

Molecular Cell 72(4):625-635.

In response to genotoxic stress, cells activate a signaling cascade known as the DNA damage checkpoint (DDC) that leads to a temporary cell cycle arrest and activation of DNA repair mechanisms. Because persistent DDC activation compromises cell viability, this process must be tightly regulated. However, despite its importance, the mechanisms regulating DDC recovery are not completely understood. Here, we identify a DNA-damage-regulated histone modification in Saccharomyces cerevisiae, phosphorylation of H4 threonine 80 (H4T80ph), and show that it triggers checkpoint inactivation.

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Kate Dry
Shieldin complex promotes DNA end-joining and counters homologous recombination in BRCA1-null cells

Dev H, Chiang TW, Lescale C, de Krijger I, Martin AG, Pilger D, Coates J, Sczaniecka-Clift M, Wei W, Ostermaier M, Herzog M, Lam J, Shea A, Demir M, Qian Wu Q, Yang F, Fu B, Lai Z, Balmus G, Belotserkovskaya R, Serra V, O’Connor MJ, runa A, Beli P, Pellegrini L, Caldas C, Deriano L, Jacobs JJL, Galanty Y and Jackson SP. (2018)

Nature Cell Biology 20, 954-965

BRCA1 deficiencies cause breast, ovarian, prostate and other cancers, and render tumours hypersensitive to poly(ADP-ribose) polymerase (PARP) inhibitors. To understand the resistance mechanisms, we conducted whole-genome CRISPR–Cas9 synthetic-viability/resistance screens in BRCA1-deficient breast cancer cells treated with PARP inhibitors. We identified two previously uncharacterized proteins, C20orf196 and FAM35A, whose inactivation confers strong PARP-inhibitor resistance.

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Kate Dry
Inhibition of the acetyltransferase NAT10 normalizes progeric and aging cells by rebalancing the Transportin-1 nuclear import pathway

Larrieu D, Viré E, Robson S, Breusegem SY, Kouzarides T, Jackson SP. (2018)

Science Signaling 11, eaar5401

Cells from patients with Hutchinson-Gilford progeria syndrome (HGPS) have defects in nuclear architecture and function that lead to premature cellular senescence, aging, and early death. Larrieu et al. (see the Focus by Wilson) found that inhibition or depletion of the acetyltransferase NAT10 rescued many of the phenotypes of HGPS patient cells by destabilizing microtubules, which reversed the abnormal cytoplasmic accumulation of the nuclear importer Transportin-1 (TNPO1). This restored proper assembly of the nuclear pore complex, import of nuclear proteins, chromatin organization, and gene expression patterns.

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Kate Dry
Map of synthetic rescue interactions for the Fanconi anemia DNA repair pathway identifies USP48

Velimezi G, Robinson-Garcia L, Muñoz-Martínez F, Wiegant WW, Ferreira da Silva J, Owusu M, Moder M, Wiedner M, Rosenthal SB, Fisch KM, Moffat J, Menche J, Van Attikum H, Jackson SP and Loizou JI. (2018)

Nature Communications 9, Article number 2280

Defects in DNA repair can cause various genetic diseases with severe pathological phenotypes. Fanconi anemia (FA) is a rare disease characterized by bone marrow failure, developmental abnormalities, and increased cancer risk that is caused by defective repair of DNA interstrand crosslinks (ICLs). Here, we identify the deubiquitylating enzyme USP48 as synthetic viable for FA-gene deficiencies by performing genome-wide loss-of-function screens across a panel of human haploid isogenic FA-defective cells (FANCA, FANCC, FANCG, FANCI, FANCD2).

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Kate Dry
ATM orchestrates the DNA-damage response to counter toxic non-homologous end-joining at broken replication forks

Balmus G, Pilger D, Coates J, Demir M, Sczaniecka-Clift M, Barros A, Woods M, Fu B,Yang F, Chen E, Ostermaier M, Stankovic T, Ponstingl H, Herzog M, Yusa K, Munoz-Martinez F, Durant ST, Galanty Y, Beli P, Adams DJ, Bradley A, Metzakopian E, Forment JV, Jackson SP. (2018).


BioRxiv
Mutations in the ATM tumor suppressor confer hypersensitivity to DNA-damaging agents. To explore genetic resistance mechanisms, we performed genome-wide CRISPR-Cas9 screens in cells treated with the DNA topoisomerase poison topotecan. Thus, we establish that loss of terminal components of the non-homologous end-joining (NHEJ) machinery or the BRCA1-A complex specifically confers topotecan resistance to ATM-deficient cells.

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Kate Dry
Validating the concept of mutational signatures with isogenic cell models

Zou X, Owusu M, Harris R, Jackson SP, Loizou JI, Nik-Zainal S. (2018)

Nature Communications 9(1):1744.
The diversity of somatic mutations in human cancers can be decomposed into individual mutational signatures, patterns of mutagenesis that arise because of DNA damage and DNA repair processes that have occurred in cells as they evolved towards malignancy. Correlations between mutational signatures and environmental exposures, enzymatic activities and genetic defects have been described, but human cancers are not ideal experimental systems—the exposures to different mutational processes in a patient’s lifetime are uncontrolled and any relationships observed can only be described as an association.

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Kate Dry
Targeting of NAT10 enhances healthspan in a mouse model of human accelerated aging syndrome

Balmus G, Larrieu D, Barros AC, Collins C, Abrudan M, Demir M, Geisler NJ, Lelliott CJ, White JK, Karp NA, Atkinson J, Kirton A, Jacobsen M, Clift D, Rodriguez R, Sanger Mouse Genetics Project, Adams DJ, Jackson SP. (2018)

Nature Communications 9, Article number 1700

Hutchinson-Gilford Progeria Syndrome (HGPS) is a rare, but devastating genetic disease characterized by segmental premature aging, with cardiovascular disease being the main cause of death. Cells from HGPS patients accumulate progerin, a permanently farnesylated, toxic form of Lamin A, disrupting the nuclear shape and chromatin organization, leading to DNA-damage accumulation and senescence.

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Kate Dry