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Articles

All who wander are not lost: the search for homology during homologous recombination

Jingyi Hu, J. Brooks Crickard

Biochem Soc Trans (2024) 52 (1): 367–377.

https://doi.org/10.1042/BST20230705

Published: 07 February 2024

... This is an open access article published by Portland Press Limited on behalf of the Biochemical Society and distributed under the Creative Commons Attribution License 4.0 (CC BY) . DNA repair helicases homologous recombination homology search Rad51 DNA double-strand breaks (DSBs...

View articletitled, All who wander are not lost: the search for homology during homologous recombination

Articles

Experimental systems for the analysis of mutational signatures: no ‘one-size-fits-all' solution

Dmitri Ivanov, Taejoo Hwang, Lukasz Karol Sitko, Semin Lee, Anton Gartner

Biochem Soc Trans (2023) 51 (3): 1307–1317.

https://doi.org/10.1042/BST20221482

Published: 07 June 2023

...Dmitri Ivanov; Taejoo Hwang; Lukasz Karol Sitko; Semin Lee; Anton Gartner Cells constantly accumulate mutations, which are caused by replication errors, as well as through the action of endogenous and exogenous DNA-damaging agents. Mutational patterns reflect the status of DNA repair machinery...

View articletitled, Experimental systems for the analysis of mutational signatures: no ‘one-size-fits-all' solution

Articles

Turning the Mre11/Rad50 DNA repair complex on its head: lessons from SMC protein hinges, dynamic coiled-coil movements and DNA loop-extrusion?

Ekaterina Zabolotnaya, Ioanna Mela, Robert M. Henderson, Nicholas P. Robinson

Biochem Soc Trans (2020) 48 (6): 2359–2376.

https://doi.org/10.1042/BST20170168

Published: 10 December 2020

...Ekaterina Zabolotnaya; Ioanna Mela; Robert M. Henderson; Nicholas P. Robinson The bacterial SbcC/SbcD DNA repair proteins were identified over a quarter of a century ago. Following the subsequent identification of the homologous Mre11/Rad50 complex in the eukaryotes and archaea, it has become clear...

View articletitled, Turning the Mre11/Rad50 DNA repair complex on its head: lessons from SMC protein hinges, dynamic coiled-coil movements and DNA loop-extrusion?

Articles

How do cells sense DNA lesions?

Chiara Vittoria Colombo, Marco Gnugnoli, Elisa Gobbini, Maria Pia Longhese

Biochem Soc Trans (2020) 48 (2): 677–691.

https://doi.org/10.1042/BST20191118

Published: 27 March 2020

..., DNA repair and cell cycle transitions. The importance of the DDR is highlighted by the fact that DDR inactivation is commonly found in cancer and causes many different human diseases. The protein kinases ATM and ATR, as well as their budding yeast orthologs Tel1 and Mec1, act as master regulators...

View articletitled, How do cells sense DNA lesions?

Articles

Structural mechanism of DNA-end synapsis in the non-homologous end joining pathway for repairing double-strand breaks: bridge over troubled ends

In Collection

Awards

Qian Wu

Biochem Soc Trans (2019) 47 (6): 1609–1619.

https://doi.org/10.1042/BST20180518

Published: 12 December 2019

... was the recipient of the Biochemical Society's Early Career Research Award for Signalling in 2019. 22 10 2019 25 11 2019 27 11 2019 © 2019 The Author(s). Published by Portland Press Limited on behalf of the Biochemical Society 2019 DNA damage DNA repair DNA-end synapsis double...

View articletitled, Structural mechanism of DNA-end synapsis in the non-homologous end joining pathway for repairing double-strand breaks: bridge over troubled ends

Articles

PARP inhibitors for anticancer therapy

Nicola Curtin

Biochem Soc Trans (2014) 42 (1): 82–88.

https://doi.org/10.1042/BST20130187

Published: 23 January 2014

...Nicola Curtin PARP-1 [poly(ADP-ribose) polymerase-1], which plays a key role in DNA repair, was discovered 50 years ago. PARPi (PARP inhibitors), originally made to probe the function of the enzyme, inhibit DNA repair and increase the potency of anticancer cytotoxic agents. PARPi of increasing...

View articletitled, PARP inhibitors for anticancer therapy

Articles

Regulation of chromosome dynamics by Hsk1/Cdc7 kinase

Seiji Matsumoto, Hisao Masai

Biochem Soc Trans (2013) 41 (6): 1712–1719.

https://doi.org/10.1042/BST20130217

Published: 20 November 2013

... for the replicative helicase. Recent studies, however, indicate more diverse roles for Hsk1/Cdc7 in regulation of various chromosome dynamics, including initiation of meiotic recombination, meiotic chromosome segregation, DNA repair, replication checkpoints, centromeric heterochromatin formation and so forth. Hsk1...

View articletitled, Regulation of chromosome dynamics by Hsk1/Cdc7 kinase

Articles

CHD4 in the DNA-damage response and cell cycle progression: not so NuRDy now

Aoife O’Shaughnessy, Brian Hendrich

Biochem Soc Trans (2013) 41 (3): 777–782.

https://doi.org/10.1042/BST20130027

Published: 23 May 2013

.../licenses/by/3.0/ ) which permits unrestricted use, distribution and reproduction in any medium, provided the original work is properly cited. cell cycle chromatin chromodomain helicase DNA-binding 4 (CHD4) DNA damage DNA repair nucleosome remodelling and deacetylation (NuRD) The CHD3...

View articletitled, CHD4 in the DNA-damage response and cell cycle progression: not so NuRDy now

Articles

From Beads on a String to the Pearls of Regulation: the Structure and Dynamics of Chromatin

Richard P. Bowater, Ian C. Wood, Ben F. Luisi

Biochem Soc Trans (2012) 40 (2): 331–334.

https://doi.org/10.1042/BST20120011

Published: 21 March 2012

... correspondence should be addressed (email [email protected] ). 13 1 2012 © The Authors Journal compilation © 2012 Biochemical Society 2012 chromatin structure DNA repair nucleosome positioning nucleosome structure protein–DNA interaction Eukaryotic chromatin has been the subject...

View articletitled, From Beads on a String to the Pearls of Regulation: the Structure and Dynamics of Chromatin

Articles

DNA-damage accumulation and replicative arrest in Hutchinson–Gilford progeria syndrome

Phillip R. Musich, Yue Zou

Biochem Soc Trans (2011) 39 (6): 1764–1769.

https://doi.org/10.1042/BST20110687

Published: 21 November 2011

... proteins to the formed DSBs for repair. DNA repair genome instability Hutchinson–Gilford progeria syndrome (HGPS) lamin A premature aging xeroderma pigmentosum group A (XPA) The aging process represents progressive cellular changes which culminate in death due to accumulated...

View articletitled, DNA-damage accumulation and replicative arrest in Hutchinson–Gilford progeria syndrome

Articles

Superfamily I helicases as modular components of DNA-processing machines

Mark S. Dillingham

Biochem Soc Trans (2011) 39 (2): 413–423.

https://doi.org/10.1042/BST0390413

Published: 22 March 2011

... with partner proteins to participate in specific cellular functions. 1 email [email protected] 7 1 2011 © The Authors Journal compilation © 2011 Biochemical Society 2011 DNA recombination DNA repair PcrA superfamily I helicase UvrD It seems that the in vivo...

View articletitled, Superfamily I helicases as modular components of DNA-processing machines

Articles

Winged helix domains with unknown function in Hel308 and related helicases

Isabel L. Woodman, Edward L. Bolt

Biochem Soc Trans (2011) 39 (1): 140–144.

https://doi.org/10.1042/BST0390140

Published: 19 January 2011

... correspondence should be addressed (email [email protected] ). 29 8 2010 © The Authors Journal compilation © 2011 Biochemical Society 2011 Brr2 DNA repair Hel308 Mtr4 Prp43p A recent review covered the discovery of hel308 from genetic analysis of its involvement in DNA...

View articletitled, Winged helix domains with unknown function in Hel308 and related helicases

Articles

Bacterial and eukaryotic systems collide in the three Rs of Methanococcus

Richard P. Parker, Alison D. Walters, James P.J. Chong

Biochem Soc Trans (2011) 39 (1): 111–115.

https://doi.org/10.1042/BST0390111

Published: 19 January 2011

... 2010 © The Authors Journal compilation © 2011 Biochemical Society 2011 archaeon DNA repair DNA replication Methanococcales recombination The chimaeric nature of archaeal genomes has been commented on at some length. In general, the information-processing pathways...

View articletitled, Bacterial and eukaryotic systems collide in the three Rs of Methanococcus

Articles

Substrate recognition and catalysis by flap endonucleases and related enzymes

Christopher G. Tomlinson, John M. Atack, Brian Chapados, John A. Tainer, Jane A. Grasby

Biochem Soc Trans (2010) 38 (2): 433–437.

https://doi.org/10.1042/BST0380433

Published: 22 March 2010

... and related enzymes. DNA repair exonuclease-1 (EXO-1) flap endonuclease 1 (FEN-1) gap endonuclease 1 (GEN-1) metal ion xeroderma pigmentosum complementation group G (XPG) We thank Professor Jon Sayers and members of the Centre for Chemical Biology (Sheffield) and the Structural Cell Biology...

View articletitled, Substrate recognition and catalysis by flap endonucleases and related enzymes

Articles

The interaction of four-way DNA junctions with resolving enzymes

David M.J. Lilley

Biochem Soc Trans (2010) 38 (2): 399–403.

https://doi.org/10.1042/BST0380399

Published: 22 March 2010

... of these enzymes is achieved. 1 email [email protected] 15 9 2009 © The Authors Journal compilation © 2010 Biochemical Society 2010 DNA repair genetic recombination Holliday junction molecular recognition nuclease Four-way DNA (Holliday) junctions [ 1...

View articletitled, The interaction of four-way DNA junctions with resolving enzymes

Articles

Ubiquitin and SUMO signalling in DNA repair

Timothy M. Thomson, Marta Guerra-Rebollo

Biochem Soc Trans (2010) 38 (1): 116–131.

https://doi.org/10.1042/BST0380116

Published: 19 January 2010

... specifically recognizes the distortions caused by photolesions, but has limited capacity to bind to other lesions, XPC, in conjunction with HR23B and CENP2 (Rad4, Rad23 and Cdc31 respectively in Saccharomyces cerevisiae ) can recognize a wider range of duplex-destabilizing lesions. DNA damage DNA repair...

View articletitled, Ubiquitin and SUMO signalling in DNA repair

Articles

DNA Damage: from Causes to Cures

Richard P. Bowater, Rhona H. Borts, Malcolm F. White

Biochem Soc Trans (2009) 37 (3): 479–481.

https://doi.org/10.1042/BST0370479

Published: 20 May 2009

..., sometimes these processes do not function correctly, leading to genome instability. Studies of DNA repair and genome instability and their causes and cures were showcased in the 2008 Biochemical Society Annual Symposium. The present article provides a summary of the talks given and the subsequent papers...

View articletitled, DNA Damage: from Causes to Cures

Articles

The associations of sequence variants in DNA-repair and cell-cycle genes with cancer risk: genotype–phenotype correlations

Janet Hall, Virginie Marcel, Celeste Bolin, Marie Fernet, Laurence Tartier, Laurence Vaslin, Pierre Hainaut

Biochem Soc Trans (2009) 37 (3): 527–533.

https://doi.org/10.1042/BST0370527

Published: 20 May 2009

...Janet Hall; Virginie Marcel; Celeste Bolin; Marie Fernet; Laurence Tartier; Laurence Vaslin; Pierre Hainaut DNA-repair systems maintain the integrity of the human genome, and cell-cycle checkpoints are a critical component of the cellular response to DNA damage. Thus the presence of sequence...

View articletitled, The associations of sequence variants in DNA-repair and cell-cycle genes with cancer risk: genotype–phenotype correlations

Articles

Repairing DNA double-strand breaks by the prokaryotic non-homologous end-joining pathway

Nigel C. Brissett, Aidan J. Doherty

Biochem Soc Trans (2009) 37 (3): 539–545.

https://doi.org/10.1042/BST0370539

Published: 20 May 2009

... correspondence should be addressed (email [email protected] ). 11 2 2009 © The Authors Journal compilation © 2009 Biochemical Society 2009 bacterium DNA ligase DNA repair Ku non-homologous end-joining (NHEJ) polymerase DSBs (double-strand breaks) in DNA represent a lethal form...

View articletitled, Repairing DNA double-strand breaks by the prokaryotic non-homologous end-joining pathway

Articles

The DNA-damage response: new molecular insights and new approaches to cancer therapy

Stephen P. Jackson

Biochem Soc Trans (2009) 37 (3): 483–494.

https://doi.org/10.1042/BST0370483

Published: 20 May 2009

... response) [ 8 , 9 ]. As shown in Figure 1 , DSBs are first detected by ‘sensor’ proteins that then interact with further proteins to mediate DNA-repair processes. Furthermore, while repair is proceeding, the sensor/repair apparatus interacts with additional proteins to generate signalling mechanisms...

View articletitled, The DNA-damage response: new molecular insights and new approaches to cancer therapy

Articles

PCNA on the crossroad of cancer

Ivaylo Stoimenov, Thomas Helleday

Biochem Soc Trans (2009) 37 (3): 605–613.

https://doi.org/10.1042/BST0370605

Published: 20 May 2009

... be addressed (email [email protected] ). 9 12 2008 © The Authors Journal compilation © 2009 Biochemical Society 2009 cancer chromatin modification DNA repair DNA replication proliferating-cell nuclear antigen (PCNA) replication fork The accurate transmission...

View articletitled, PCNA on the crossroad of cancer

Articles

Reactions to UV damage in the model archaeon Sulfolobus solfataricus

Sabrina Fröls, Malcolm F. White, Christa Schleper

Biochem Soc Trans (2009) 37 (1): 36–41.

https://doi.org/10.1042/BST0370036

Published: 20 January 2009

...Sabrina Fröls; Malcolm F. White; Christa Schleper Mechanisms involved in DNA repair and genome maintenance are essential for all organisms on Earth and have been studied intensively in bacteria and eukaryotes. Their analysis in extremely thermophilic archaea offers the opportunity to discover...

View articletitled, Reactions to UV damage in the model archaeon Sulfolobus solfataricus

Articles

Biomarkers of oxidative damage to DNA and repair

Steffen Loft, Pernille Høgh Danielsen, Lone Mikkelsen, Lotte Risom, Lykke Forchhammer, Peter Møller

Biochem Soc Trans (2008) 36 (5): 1071–1076.

https://doi.org/10.1042/BST0361071

Published: 19 September 2008

... can be assessed in tissue extracts by measurement of the 8-oxodGMP formed from 8-oxodGTP by HPLC analysis [ 24 ]. The expression levels of mRNAs of DNA repair enzymes have also been used to estimate repair capacity and demonstrate up-regulation of, e.g., OGG1 transcription from oxidative stress [ 25...

View articletitled, Biomarkers of oxidative damage to DNA and repair

Articles

The contribution of the budding yeast histone H2A C-terminal tail to DNA-damage responses

A.L. Chambers, J.A. Downs

Biochem Soc Trans (2007) 35 (6): 1519–1524.

https://doi.org/10.1042/BST0351519

Published: 23 November 2007

... To whom correspondence should be addressed (email [email protected] ). 28 6 2007 © The Authors Journal compilation © 2007 Biochemical Society 2007 chromatin DNA damage DNA repair H2AX variant histone H2A Chromatin is the term for DNA complexed with proteins that exists...

View articletitled, The contribution of the budding yeast histone H2A C-terminal tail to DNA-damage responses

Articles

Cellular functions of the BRCA tumour-suppressor proteins

S.J. Boulton

Biochem Soc Trans (2006) 34 (5): 633–645.

https://doi.org/10.1042/BST0340633

Published: 25 October 2006

... of the homologous recombination machinery, whereas BRCA1 is an E3 ubiquitin ligase that has an impact on DNA repair, transcriptional regulation, cell-cycle progression and meiotic sex chromosome inactivation. In this article, I will review the most recent advances and provide a perspective of potential future...

View articletitled, Cellular functions of the BRCA tumour-suppressor proteins

Articles

De-ubiquitinating enzymes: intracellular signalling and disease

J.A. Johnston, J.F. Burrows

Biochem Soc Trans (2006) 34 (5): 764–769.

https://doi.org/10.1042/BST0340764

Published: 25 October 2006

... of immune signalling and the initiation of DNA repair. In addition, we look at the evidence implicating these enzymes in the pathogenesis of diseases such as cancer and neurodegenerative diseases. 1 To whom correspondence should be addressed (email [email protected] ). 10 8 2006 ©...

View articletitled, De-ubiquitinating enzymes: intracellular signalling and disease

Articles

Helicases that interact with replication forks: new candidates from archaea

E.L. Bolt

Biochem Soc Trans (2005) 33 (6): 1471–1473.

https://doi.org/10.1042/BST0331471

Published: 26 October 2005

... blocks to the leading strand DNA polymerase ( Figure 1 B) was first proposed in mammalian cells [ 3 ] and involves the formation of a Holliday junction ‘chickenfoot’, where nascent strands anneal allowing polymerase template switching ( Figure 1 B). archaea DNA repair Hel308 helicase...

View articletitled, Helicases that interact with replication forks: new candidates from archaea

Articles

Understanding the roles of RecQ helicases in the maintenance of genome integrity and suppression of tumorigenesis

H.W. Mankouri, I.D. Hickson

Biochem Soc Trans (2004) 32 (6): 957–958.

https://doi.org/10.1042/BST0320957

Published: 26 October 2004

... cancer DNA repair helicase recombination topoisomerase The RecQ family of DNA helicases has received considerable interest due to their putative roles in suppression of cancer and premature ageing in humans [ 1 ]. Mutations in three different human RecQ helicase genes cause BS (Bloom's syndrome...

View articletitled, Understanding the roles of RecQ helicases in the maintenance of genome integrity and suppression of tumorigenesis

Articles

Poly(ADP-ribose) polymerase inhibitors as potential chemotherapeutic agents

H.E. Bryant, T. Helleday

Biochem Soc Trans (2004) 32 (6): 959–961.

https://doi.org/10.1042/BST0320959

Published: 26 October 2004

...H.E. Bryant; T. Helleday PARP [poly(ADP-ribose) polymerase] activity is up-regulated by binding to DNA strand breaks and its association with DNA repair is well documented. Many anticancer therapies work by inducing breaks in DNA, if unrepaired these can lead to cell death. As PARP promotes DNA...

View articletitled, Poly(ADP-ribose) polymerase inhibitors as potential chemotherapeutic agents

Articles

Monitoring base excision repair proteins on damaged DNA using human cell extracts

J.L. Parsons, G.L. Dianov

Biochem Soc Trans (2004) 32 (6): 962–963.

https://doi.org/10.1042/BST0320962

Published: 26 October 2004

.... Toxicology 2003 193 35 41 Using HeLa WCE and a uracil hairpin substrate, we were able to cross-link several DNA repair proteins analysed, including Pol β (DNA polymerase β), DNA ligase IIIα–XRCC1 (X-ray cross-complementing protein 1) complex and poly(ADP-ribose) polymerase-1 (PARP-1; Figure 2...

View articletitled, Monitoring base excision repair proteins on damaged DNA using human cell extracts

Articles

Genetic analysis of homologous recombination in Archaea: Haloferax volcanii as a model organism

T. Allers, H.-P. Ngo

Biochem Soc Trans (2003) 31 (3): 706–710.

https://doi.org/10.1042/bst0310706

Published: 01 June 2003

... be addressed (e-mail [email protected] ). Molecular Mechanisms and Manipulation in Archaea, a Biochemical Society-sponsored meeting held at The University of Nottingham, 30–31 January 2003 16 January 2003 © 2003 Biochemical Society 2003 Archaea DNA repair Haloferax...

View articletitled, Genetic analysis of homologous recombination in Archaea: Haloferax volcanii as a model organism

Articles

Archaeal DNA repair: paradigms and puzzles

M.F. White

Biochem Soc Trans (2003) 31 (3): 690–693.

https://doi.org/10.1042/bst0310690

Published: 01 June 2003

... extensively as simpler models of the much more complex eukaryal ones. Archaeal DNA-repair pathways are not yet well characterized, and their relationship with repair pathways in bacteria and eukarya are still open to question. There are also strong distinctions between the major subdivisions crenarchaea...

View articletitled, Archaeal DNA repair: paradigms and puzzles

Articles

Uracil recognition by archaeal family B DNA polymerases

B.A. Connolly, M.J. Fogg, G. Shuttleworth, B.T. Wilson

Biochem Soc Trans (2003) 31 (3): 699–702.

https://doi.org/10.1042/bst0310699

Published: 01 June 2003

... 2002 © 2003 Biochemical Society 2003 Archaea deoxyuridine-triphosphate pyrophosphatase DNA polymerase DNA repair uracil uracil-DNA glycosylase Abbreviations used: dUTPase, deoxyuridine-triphosphate pyrophophatase; UDGase, uracil-DNA glycosylase. Molecular Mechanisms...

View articletitled, Uracil recognition by archaeal family B DNA polymerases

Articles

The complex matter of DNA double-strand break detection

J.M. Bradbury, S.P. Jackson

Biochem Soc Trans (2003) 31 (1): 40–44.

https://doi.org/10.1042/bst0310040

Published: 01 February 2003

... Copyright 2003 Biochemical Society 2003 DNA damage sensor DNA repair Abbreviations used: ATM, ataxia telangiectasiamutated protein; ATR, ataxia telangiectasia and Rad3-related protein; ATRIP, ATR-interacting protein; DNA-PK, DNA-dependent protein kinase; DNA-PKcs, DNA-dependent protein...

View articletitled, The complex matter of DNA double-strand break detection

Articles

Detecting, signalling and repairing DNA double-strand breaks

S. P. Jackson

Biochem Soc Trans (2001) 29 (6): 655–661.

https://doi.org/10.1042/bst0290655

Published: 01 November 2001

[email protected] 9 7 2001 © 2001 Biochemical Society 2001 checkpoints DNA repair radiosensitivity ATM, ataxia telangiectasia mutated protein ATR, ataxia telangiectasia-related protein DNA-PKcs, DNA-dependent protein kinase catalytic subunit DSB, double-strand break HR, homologous...

View articletitled, Detecting, signalling and repairing DNA double-strand breaks

Articles

ATM (ataxia telangiectasia mutated): expanding roles in the DNA damage response and cellular homeostasis

Y. Shiloh

Biochem Soc Trans (2001) 29 (6): 661–666.

https://doi.org/10.1042/bst0290661

Published: 01 November 2001

...Y. Shiloh DNA damage is one of the most acute threats to cellular homeostasis and life. The cell responds to such damage by activating a vast array of responses, ranging from DNA repair to numerous signalling pathways, which temporarily slow down the cellular life cycle while the damage is being...

View articletitled, ATM (ataxia telangiectasia mutated): expanding roles in the DNA damage response and cellular homeostasis

Articles

Double-strand-break-induced homologous recombination in mammalian cells

R. D. Johnson, M. Jasin

Biochem Soc Trans (2001) 29 (2): 196–201.

https://doi.org/10.1042/bst0290196

Published: 01 May 2001

... correspondence should be addressed (e-mail [email protected] ) 3 11 2000 © 2001 Biochemical Society 2001 BRCAI DNA repair non-homologous end-joining sister chromatid tumorigenesis DSB, double-strand break HR, homologous recombination NHEJ, non-homologous end-joining...

View articletitled, Double-strand-break-induced homologous recombination in mammalian cells

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