Research

Research in our group explores the mechanisms of genome stability, including the biochemical mechanism repairing cross-links that form between DNA strands and the DNA polymerases that help cells tolerate DNA damage, as well as their consequences for cancer.

The panel at the right shows chromosomes from mouse skin keratinocytes, either with an intact Rev3l  (+/lox) or inactivated Rev3l (-/lox) gene. Rev3l is one of the genes necessary to defend cells against DNA crosslinks.  The Rev3l gene encodes the catalytic subunit of DNA polymerase ζ.

We are also actively defining the molecular functions of DNA polymerase θ, a polymerase that provides important genome maintenance functions during development, protects cells against extensive DNA deletions, and helps limit loss of heterozygosity. Polθ is required for theta-mediated end-joining, a type of microhomology-mediated DNA repair that often results in small indels at the repair site. This enzyme becomes essential for cell survival in cells unable to repair DNA by homologous recombination, and loss of  polymerase θ sensitizes cells to DNA double strand break-inducing agents .

DNA Polymerase theta (POLQ)

We have identified and are studying the function of  DNA processing enzymes, such as DNA polymerase theta. We were the first to clone the mammalian cDNA and subsequently found that POLQ has a role in a specific DNA double-strand break (DSB) repair mechanism, theta-mediated end-joining (TMEJ). TMEJ relies on an overlap between very short regions of identical DNA sequence, called microhomologies, on single-stranded DNA. As these microhomologies are not usually at the very ends of the single-stranded DNA, repair requires another enzymatic activity to remove the unmatched parts of the single-stranded DNA ends. Repair by polymerase theta typically results in the gain or loss of a limited number of nucleotides at the repair site. Importantly, loss of polymerase theta function can increase cell sensitivity to DNA double strand breaks and some homologous recombination (HR)-defective cancers become dependent on polymerase theta for their survival, indicating that inhibiting this enzyme may provide therapeutic benefit when combined with PARP inhibitors and/or for patients with HR-defective cancers .

Funding:
NIH grants: P01 CA193124 (through 2022) and P01 CA247773

Related Publications:

Stroik S, Carvajal-Garcia J, Gupta D, Edwards A, Luthman A, Wyatt DW, Dannenberg RL, Feng W, Kunkel TA, Gupta GP, Hedglin M, Wood R, Doublié S, Rothenberg E, Ramsden DA. Stepwise requirements for polymerases δ and θ in theta-mediated end joining. Nature. 2023 Nov;623(7988):836-841. PMID: 37968395

Wood RD, Doublié S. Genome Protection by DNA Polymerase θ. Annu Rev Genet. 2022 Nov 30;56:207-228. PMID: 36028228 (Review)

Vanson S, Li Y, Wood RD, Doublié S. Probing the structure and function of polymerase θ helicase-like domain. DNA Repair (Amst). 2022 Aug;116:103358. PMID: 35753097 (review)

Llorens-Agost M, Ensminger M, Le HP, Gawai A, Liu J, Cruz-García A, Bhetawal S, Wood RD, Heyer WD, Löbrich M. POLθ-mediated end joining is restricted by RAD52 and BRCA2 until the onset of mitosis. Nat Cell Biol. 2021 Oct;23(10):1095-1104. PMID: 34616022

Hwang T, Reh S, Dunbayev Y, Zhong Y, Takata Y, Shen J, McBride KM, Murnane JP, Bhak J, Lee S, Wood RD, Takata KI. Defining the mutation signatures of DNA polymerase θ in cancer genomes. NAR Cancer. 2020 Sep;2(3):zcaa017. PMID: 32885167

Carvajal-Garcia J, Cho JE, Carvajal-Garcia P, Feng W, Wood RD, Sekelsky J, Gupta GP, Roberts SA, Ramsden DA. Mechanistic basis for microhomology identification and genome scarring by polymerase theta. Proc Natl Acad Sci U S A. 2020 Apr 14;117(15):8476-8485. doi: 10.1073/pnas.1921791117.  PMID: 32234782

Feng W, Simpson DA, Carvajal-Garcia J, Price BA, Kumar RJ, Mose LE, Wood RD, Rashid N, Purvis JE, Parker JS, Ramsden DA, Gupta GP. Genetic determinants of cellular addiction to DNA polymerase theta. Nat Commun. 2019 Sep 19;10(1):4286. doi: 10.1038/s41467-019-12234-1. PMID: 31537809

Malaby AW, Martin SK, Wood RD, Doublié S.  Expression and Structural Analyses of Human DNA Polymerase θ (POLQ). In: Eichman B, editor. DNA Repair Enzymes: Structure, Biophysics, and Mechanism. Methods in Enzymology.  2017;592:103-121

Yousefzadeh MJ, Wyatt DW, Takata K, Mu Y, Hensley SC, Tomida J, Bylund GO, Doublié S, Johansson E, Ramsden DA, McBride KM, Wood RD. Mechanism of suppression of chromosomal instability by DNA polymerase POLQ. PLoS Genet. 2014 Oct 2;10(10):e1004654.

Biochemical Mechanisms of DNA Crosslink Repair

This area of our research examines the biochemical mechanism of repair of cross-links between DNA strands. Chemicals that produce cross-links are particularly destructive to genome function and consequently, are widely used in cancer chemotherapy.

Exogenous sources of intra-stand crosslinking chemicals include mitomycin C, nitrogen mustard, cisplatin, and psoralen. Endogenous sources creating crosslinks include metabolites created by lipid peroxidation such as acrolein, crotonaldehyde, malondialdehyde and nitric oxide. These agents are widely used for the treatment of leukemia and solid tumors. Although the mechanisms mammalian cells use to repair intra-strand crosslinks are not well understood, the nucleotide excision repair (NER) pathway may be highly involved in this process. We study how NER proteins help repair DNA crosslinks.

Funding:
1P01 CA193124 NIH/NCI “Processing and Repair of DNA Crosslinks”
(Wood, PI) 02/01/2017 – 01/31/2022

Related Publications:

Wang R, Lenoir WF, Wang C, Su D, McLaughlin M, Hu Q, Shen X, Tian Y, Klages-Mundt N, Lynn E, Wood RD, Chen J, Hart T, Li L. DNA polymerase iota (ι) compensates for Fanconi anemia pathway deficiency by countering DNA replication stress. Proc Natl Acad Sci U S A. 2020 Dec 29;117(52):33436-33445. 

Manandhar M, Lowery MG, Boulware KS, Lin KH, Lu Y, Wood RD.  Transcriptional consequences of XPA disruption in human cell lines. DNA Repair (Amst). 2017 Sep;57:76-90.

DNA Polymerase zeta (REV3L & REV7)

DNA polymerase zeta (pol ζ) is exceptionally important for controlling mutagenesis and genetic instability in cells and is comprised of two proteins, REV3L and REV7. REV3L is the catalytic subunit of pol ζ, whereas REV7 (MAD2L2) is considered an accessory subunit.

We have generated mouse models with specific deficiencies in DNA polymerase zeta. These models reveal that pol ζ is critical for maintaining chromosome stability and limiting tumorigenesis.  Deletion of Rev3L in p53 mutant mice leads to increased cancer incidence and a shortened lifespan. Further, two distinct REV7-binding sites in REV3L are needed to prevent chromosome breaks and confer resistance to DNA damage.

Related Publications:

Ben Yamin B, Ahmed-Seghir S, Tomida J, Despras E, Pouvelle C, Yurchenko A, Goulas J, Corre R, Delacour Q, Droin N, Dessen P, Goidin D, Lange SS, Bhetawal S, Mitjavila-Garcia MT, Baldacci G, Nikolaev S, Cadoret JC, Wood RD, Kannouche PL. DNA polymerase zeta contributes to heterochromatin replication to prevent genome instability. EMBO J. 2021 Nov 2;40(21):e104543. PMID: 34533226

Martin SK, Tomida J, Wood RD. Disruption of DNA polymerase ζ engages an innate immune response. Cell Rep. 2021 Feb 23;34(8):108775. PMID: 33626348

Martin SK, Wood RD. DNA polymerase zeta in DNA replication and repair. Nucleic Acids Res. 2019 Sep 19;47(16):8348-8361.

Lange SS, Bhetawal S, Reh S, Powell KL, Kusewitt D, Wood RD. DNA polymerase ζ deficiency causes impaired wound healing and stress-induced skin pigmentation. Life Science Alliance. 2018 June 29; 1(3):e201800048. 

Lange SS, Tomida J, Boulware KS, Bhetawal S, Wood RD.  The Polymerase Activity of Mammalian DNA Pol ζ Is Specifically Required for Cell and Embryonic Viability. PLoS Genet. 2016 Jan 4;12(1):e1005759.

DNA Polymerase nu (POLN)

We have discovered POLN as a homologue of POLQ and are working to identify its biochemical activities. The POLN gene is predominantly expressed in
testis and encodes a protein able to displace DNA strands and bypass DNA damage.

The image shows gamma-H2AX foci (green dots), which represent sites of DNA damage, in spermatid cells lacking POLN. In this example, DNA damage was induced by x-ray irradiation

Related Publications:
Takata KI, Reh S, Yousefzadeh MJ, Zelazowski MJ, Bhetawal S, Trono D, Lowery MG, Sandoval M, Takata Y, Lu Y, Lin K, Shen J, Kusewitt DF, McBride KM, Cole F Wood RD. (2017) Analysis of DNA polymerase ν function in meiotic recombination, immunoglobulin class-switching, and DNA damage tolerance. PLoS Genet. 2017 Jun 1;13(6):e1006818.

Takata K, Tomida J, Reh S, Swanjart LM, Takata M, Jukriede NA, Wood RD. Conserved overlapping gene arrangement, restricted expression, and biochemical activities of DNA polymerase ν (POLN). .J Biol Chem. 2015 Oct 2;290(40):24278-93. PMID: 26269593 

DNA Helicase HELQ

Agents that cause interstrand DNA crosslinks (ICL) are widely used to treat cancer. Our work found that the DNA helicase HELQ helps defend human cells against ICL- inducing agents. HELQ associates with the ATR-ATRIP complex that is important for cellular response to replication stress and DNA damage. HELQ also associates with signaling and homologous recombination components such as BCDX2, a RAD51 paralog, which is sometimes altered in ovarian cancer.

In the image, the red, jagged line outlined in gray represents an interstrand crosslink. HELQ, along with ATR and RAD51 paralogs, helps cells tolerate these crosslinks.

Related Publication:
Takata K, Reh S, Tomida J, Person MD, Wood RD. . Human DNA helicase HELQ participates in DNA interstrand crosslink tolerance with ATR and RAD51 paralogs. Nat Commun. 2013;4:2338.