Duncan Smith

Before dividing, a cell must rapidly and accurately replicate its entire genome. Defects in DNA replication can result in a range of defects (collectively termed ‘genome instability’), including mutation and chromosomal rearrangements; these underlie the genesis of cancer and several other human diseases.

DNA replication is intrinsically asymmetric. Only one parental strand at the replication fork can be continuously replicated: the other – the lagging strand – is discontinuously synthesized via the iterative polymerization, processing and ligation of Okazaki fragments. To fully replicate the human genome, a cell must synthesize and process around 20 million Okazaki fragments. We use a combined genetic and genomic approach to define how these intermediates are synthesized and processed in vivo.

We also use Okazaki fragments as a tool to study DNA replication dynamics in the cell.  We seek to define what determines the sites of DNA replication initiation, and how the replication machinery overcomes the various obstacles it encounters in the genome.

Finally, we are also interested in DNA damage tolerance and repair. Because ribonucleotides mis-incorporated into the genome during replication are by far the most abundant lesion in DNA, we are particularly interested in ribonucleotide excision repair.

Some examples of specific questions we are currently working on are:
• How does the eukaryotic DNA replication machinery move past (or through) obstacles?
​• What defines the sites of replication initiation and termination in human and other eukaryotic genomes?
• How do imbalanced levels of the three replicative DNA polymerases compromise genome integrity?
​• How do ribonucleotides in genomic DNA affect cellular physiology, and how are they removed?

National Institutes of Health Grant R35 GM134918
 “Dissecting the impact of RNA on DNA replication and chromatin structure”. PI: Duncan Smith. 03/2020-02/2025

Date of these PubMed search results: November 3 2023
Get the current Pubmed search results

1. Transcription-Replication Conflicts as a Source of Genome Instability.
   Annu Rev Genet. (2023 Aug 8) PMID: 37552891
   Goehring L, Huang TT, Smith DJ
2. A novel single alpha-helix DNA-binding domain in CAF-1 promotes gene silencing and DNA damage survival through tetrasome-length DNA selectivity and spacer function.
   Elife (2023 Jul 11) PMID: 37432722
   Rosas R, Aguilar RR, Arslanovic N, Seck A, Smith DJ, Tyler JK, Churchill MEA.
3. USP1-trapping lesions as a source of DNA replication stress and genomic instability.
   Nat Commun (2022 Apr 1) PMID: 35365626
   Coleman KE, Yin Y, Lui SKL, Keegan S, Fenyo D, Smith DJ, Rothenberg E, Huang TT.
4. Post-replicative nick translation occurs on the lagging strand during prolonged depletion of DNA ligase I in Saccharomyces cerevisiae.
   G3 (Bethesda) (2021 Aug 7) PMID: 34849819
   Koussa NC, Smith DJ
5. Limiting DNA polymerase delta alters replication dynamics and leads to a dependence on checkpoint activation and recombination-mediated DNA repair.
   PLoS Genet (2021 Jan 25) PMID: 33493195
   Koussa NC, Smith DJ
6. Monitoring genome-wide replication fork directionality by Okazaki fragment sequencing in mammalian cells.
   Nature Protocols (2021 Feb 16) PMID: 33442052
   Kit Leng Lui S, Keegan S, Tonzi P, Kahli M, Chen YH, Chalhoub N, Coleman KE, Fenyo D, Smith DJ, Huang TT.
7. Hold on Tight: Lagging-Strand DNA Polymerases Synthesize Multiple Okazaki Fragments without Letting Go.
   Mol Cell (2020 Oct 1) PMID: 33007257
   Kellner V, Smith DJ
8. Separable, Ctf4-mediated recruitment of DNA Polymerase α for initiation of DNA synthesis at replication origins and lagging-strand priming during replication elongation.
   PLoS Genet (2020 May 7) PMID: 32379761
   Porcella SY, Koussa NC, Tang CP, Kramer DN, Srivastava P, Smith DJ.
9. Determinants of Replication-Fork Pausing at tRNA Genes in Saccharomyces cerevisiae.
   Genetics (2020 Feb 18) PMID: 32071194
   Yeung R, Smith DJ
10. Transcription shapes DNA replication initiation and termination in human cells.
    Nat Struct Mol Biol (2019 Jan) PMC6320713 free full-text archive
    Chen YH, Keegan S, Kahli M, Tonzi P, Fenyo D, Huang TT, Smith DJ
11. Rotational and translational positions determine the structural and dynamic impact of a single ribonucleotide incorporated in the nucleosome.
    DNA Repair (Amst) (2019 Jan) PMC6376976 free full-text archive
    Fu I, Smith DJ, Broyde S
12. Processing of eukaryotic Okazaki fragments by redundant nucleases can be uncoupled from ongoing DNA replication in vivo.
    Nucleic Acids Res (2019 Feb 28) PMC6393292 free full-text archive
    Kahli M, Osmundson JS, Yeung R, Smith DJ
13. Pif1-family helicases cooperatively suppress widespread replication-fork arrest at tRNA genes.
    Nat Struct Mol Biol (2017 Feb) PMC5296403 free full-text archive
    Osmundson JS, Kumar J, Yeung R, Smith DJ
14. Detection and Sequencing of Okazaki Fragments in S. cerevisiae.
    Methods Mol Biol (2015) PMC4860728 free full-text archive
    Smith DJ, Yadav T, Whitehouse I
15. Tracking replication enzymology in vivo by genome-wide mapping of ribonucleotide incorporation.
    Nat Struct Mol Biol (2015 Mar) PMC4351163 free full-text archive
    Clausen AR, Lujan SA, Burkholder AB, Orebaugh CD, Williams JS, Clausen MF, Malc EP, Mieczkowski PA, Fargo DC, Smith DJ, Kunkel TA
16. Quantitative, genome-wide analysis of eukaryotic replication initiation and termination.
    Mol Cell (2013 Apr 11) PMC3628276 free full-text archive
    McGuffee SR, Smith DJ, Whitehouse I
17. Chromatin dynamics at the replication fork: there's more to life than histones.
    Curr Opin Genet Dev (2013 Apr) PMC3657310 free full-text archive
    Whitehouse I, Smith DJ
18. An Eco1-independent sister chromatid cohesion establishment pathway in S. cerevisiae.
    Chromosoma (2013 Mar) PMC3608886 free full-text archive
    Borges V, Smith DJ, Whitehouse I, Uhlmann F
19. Intrinsic coupling of lagging-strand synthesis to chromatin assembly.
    Nature (2012 Mar 14) PMC3490407 free full-text archive
    Smith DJ, Whitehouse I
20. Insights into branch nucleophile positioning and activation from an orthogonal pre-mRNA splicing system in yeast.
    Mol Cell (2009 May 15) PMC2730498 free full-text archive
    Smith DJ, Konarska MM, Query CC
21. A critical assessment of the utility of protein-free splicing systems.
    RNA (2009 Jan) PMC2612767 free full-text archive
    Smith DJ, Konarska MM
22. Identification and characterization of a short 2'-3' bond-forming ribozyme.
    RNA (2009 Jan) PMC2612773 free full-text archive
    Smith DJ, Konarska MM
23. Mechanistic insights from reversible splicing catalysis.
    RNA (2008 Oct) PMC2553733 free full-text archive
    Smith DJ, Konarska MM
24. "Nought may endure but mutability": spliceosome dynamics and the regulation of splicing.
    Mol Cell (2008 Jun 20) PMC2610350 free full-text archive
    Smith DJ, Query CC, Konarska MM
25. trans-splicing to spliceosomal U2 snRNA suggests disruption of branch site-U2 pairing during pre-mRNA splicing.
    Mol Cell (2007 Jun 22) PMC1973159 free full-text archive
    Smith DJ, Query CC, Konarska MM
26. Circulating levels of MCP-1 and eotaxin are not associated with presence of atherosclerosis or previous myocardial infarction.
    Atherosclerosis (2005 Dec) PMID: 15894320
    Mosedale DE, Smith DJ, Aitken S, Schofield PM, Clarke SC, McNab D, Goddard H, Gale CR, Martyn CN, Bethell HW, Barnard C, Hayns S, Nugent C, Panicker A, Grainger DJ