Duncan Smith

Assistant Professor of Biology

Education

Areas of Research/Interest

Mechanisms and regulation of DNA replication; epigenetics; RNA processing

Research

Broadly, we are interested in the mechanism and consequences of asymmetric DNA replication

As a consequence of the antiparallel arrangement of the two strands of the double helix and the 5'-3' polarity of DNA polymerases, 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 generation, processing and ligation of Okazaki fragments to generate an intact daughter strand. In each S-phase, mammalian cells generate around 20 million Okazaki fragments: we are interested in the molecular mechanisms underlying this remarkable process, as well as the various potential consequences of the asymmetric mechanism by which DNA is replicated.

Fig. 1

Lagging-strand synthesis requires a coordinated sequence of several enzymatic activities (Fig. 1). Each Okazaki fragment is (i) initiated by Pol alpha/primase and (ii) subsequently extended by DNA polymerase delta (Pol delta); the 5’ end of the preceding fragment is (iii) displaced by ongoing Pol delta synthesis and degraded by one of several nucleases; finally, (iv) DNA ligase joins the fragment to the nascent daughter strand. My lab is working on several broad questions related to the regulation and coordination of lagging-strand synthesis, which we investigate using a combined genetic, biochemical and genomic approach, generally in the model yeast S. cerevisiae but with occasional forays into more exotic territory.

Things we're currently working on and/or interested in include:

  • What mediates the transitions between sequential enzymatic steps in Okazaki fragment synthesis?
  • What are the specialized in vivo roles of partially redundant enzymes in Okazaki fragment synthesis, and how are these activities regulated?
  • What can Okazaki fragment distributions tell us about global replication dynamics, both under normal conditions and in response to perturbations?
  • What are the consequences of altered polymerase dynamics for the replication of un-damaged and damaged templates?
  • Why do all eukaryotes maintain separate leading- and lagging-strand polymerases?
  • Does the asymmetric mechanism of replication help to seed epigenetic differences between daughter cells?

Fellowships/Honors

Publications

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

Detection and Sequencing of Okazaki Fragments in S. cerevisiae.
Methods Mol Biol (2015) PMC4860728 free full-text archive
Smith DJ, Yadav T, Whitehouse I

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

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

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

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

Intrinsic coupling of lagging-strand synthesis to chromatin assembly.
Nature (2012 Mar 14) PMC3490407 free full-text archive
Smith DJ, Whitehouse I

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

A critical assessment of the utility of protein-free splicing systems.
RNA (2009 Jan) PMC2612767 free full-text archive
Smith DJ, Konarska MM

Identification and characterization of a short 2'-3' bond-forming ribozyme.
RNA (2009 Jan) PMC2612773 free full-text archive
Smith DJ, Konarska MM

Mechanistic insights from reversible splicing catalysis.
RNA (2008 Oct) PMC2553733 free full-text archive
Smith DJ, Konarska MM

"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

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

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