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    Nicholas R Rhind PhD

    TitleAssociate Professor
    InstitutionUniversity of Massachusetts Medical School
    DepartmentBiochemistry and Molecular Pharmacology
    AddressUniversity of Massachusetts Medical School
    364 Plantation Street, LRB
    Worcester MA 01605
    Phone508-856-8316
      Other Positions
      InstitutionUMMS - School of Medicine
      DepartmentCell and Developmental Biology

      InstitutionUMMS - Graduate School of Biomedical Sciences
      DepartmentBiochemistry and Molecular Pharmacology

      InstitutionUMMS - Graduate School of Biomedical Sciences
      DepartmentBioinformatics and Computational Biology

      InstitutionUMMS - Graduate School of Biomedical Sciences
      DepartmentCell Biology

      InstitutionUMMS - Graduate School of Biomedical Sciences
      DepartmentInterdisciplinary Graduate Program

      InstitutionUMMS - Graduate School of Biomedical Sciences
      DepartmentMD/PhD Program

      InstitutionUMMS - Programs, Centers and Institutes
      DepartmentBioinformatics and Integrative Biology

        Overview 
        Narrative

        Academic Background

        Nick Rhind received his Ph.D. from the Department of Molecular and Cell Biology at U.C. Berkeley in 1995, where he studied worm sex determination with Barbara Meyer. He was a Leukemia and Lymphoma Society post-doctoral fellow with Paul Russell at the Scripps Research Institute from 1996 to 2001.

        Regulation of DNA Replication

        Photo: Nick Rhind

        Amajor current interest of my lab is how replication is regulated during S phase. We are interested both in how normal S phase is organized to insure efficient replication of the entire genome, and how cells respond to DNA damage during S phase to coordinate replication and repair.

        Most of the work in my lab focuses on the fission yeast Schizosaccharomyces pombe (Figure 1). Fission yeast is a great organism for studying replication because it has a simple, well-understood cell cycle and is amenable to genetic, molecular and biochemical approaches. It has the added attraction that the mechanisms of cell cycle and checkpoint control in fission yeast are very similar to those used by human cells. In fact, much of what is known about human cell cycle and checkpoints was first discovered in yeast. My lab is currently pursuing two general areas of the regulation of replication.

        Regulation of Origin Firing Kinetics

        Eukaryotic genomes replicate in defined patterns, with some parts of the genome replicating early in S phase and other parts replicating later. Replication timing correlates with transcription, chromatin modification, sub-nuclear localization and genome evolution, suggesting an intimate association between replication timing and other important aspects of chromosome metabolism. However, the mechanism of replication timing is currently unknown.

        We developed an computational approach to extract replication kinetics from genome-wide replication timecourses (Figure 2). Our results support a model where earlier-firing origins have more MCM complexes loaded and a more-accessible chromatin environment (Figure 3). The MCM complex is the replicative helicase; its loading is what establishes sites as potential replication origins. We propose that the timing of origin firing is regulated in by the number of MCM complexes loaded at an origin. Thus, for the first time, our model suggests a detailed, testable, biochemically plausible mechanism for the regulation of replication timing in eukaryotes. ChIP-seq validation of our model confirms that early firing origins have more MCM loaded. We are currently exploring how MCM loading is regulated at different origins.

        Checkpoint Regulation of Replication

        Checkpoints are mechanisms that cells use to deal with problems during the cell cycle, such as DNA damage, replication errors and misattachment of chromosomes to the mitotic spindle. By actively responding to these problems, cells can fix most of them. In contrast, cells that lack proper checkpoints are very sensitive to DNA damage and show increased rates of mutation and other chromosomal abnormalities. Loss of checkpoints is an important step in the development of cancer.

        The S-phase DNA damage checkpoint slows the rate of replication in response to DNA damage. The simple model is that this checkpoint prevents damaged DNA from being replicated before it is repaired. However, the checkpoint is clearly more subtle than that. Recent results from yeast and human cells suggest that this checkpoint coordinates recombinational repair and replication during S-phase. In particular, we have established an epistatic pathway of recombinational-repair proteins that regulate replication-fork progress in response to DNA damage. We think this pathway regulates a choice the fork makes when it encounters damage: it can replicate quickly in an error-prone manner or, via a checkpoint-dependant mechanism, it can use recombinational strand switching to replicate the damaged template accurately, but slowly (Figure 4). Furthermore, via phospho-proteomics, we have identified candidate checkpoint targets, which maybe responsible for making this decision.

        Figures

        Fission Yeast
        Figure 1.Fission Yeast
        The fission yeast Schizosaccharomyces pombeis a simple, single-cell eukaryote that has proven to be an excellent model for cell cycle and checkpoint regulation. It divides by medial fission, distinguishing it from the budding yeast Saccharomyces cerevisiae, another popular lab yeast.

        Measuring Replication Kinetics

        Figure 2. Measuring Replication Kinetics
        A) Using deep sequencing to assay the change from one copy to two copies during replication, we can create replication profiles in which each origin is a peaks. Shown is the replication profile for Chromosome 3. The blue dots represent the computer-identified location and height of the origin peaks.

        B) A expanded view of the well-studied left arm of Chromosome 3. The green bars represent confirmed origins in the region. The numbered origins were previously described. We have confirmed the activity of the two unnumbered origins by single-molecule DNA fiber origin mapping.

        C) Using replication profile timecourses, we can study replication kinetics The extent of replication is determined at timepoints throughout S phase and plotted along the chromosome; for clarity, only 4 time points are show here. Peaks in the profiles (a, b and c) correspond to origins; the slope of the curve leading away from each peak is affected by fork velocity. Fork pause site are recognized as very steep curves that are only replicated by forks coming from the other direction. The individual profiles are assembled into a kinetic profile that reveals the dynamics of replication over time. In particular, the kinetics of origin firing distinguish early efficient origins (a) from early inefficient origins (b) and late efficient origins (c).

        A Model for the Regulation of Replication Timing

        Figure 3. A Model for the Regulation of Replication Timing
        We propose that the timing of origin firing is regulated by the number of MCMs loaded. Origins at which many MCMs are loaded are more likely to fire in early S and therefore have an early average firing time; origins at which fewer MCMs are loaded are less likely to fire in early S and therefore have a later average firing time. We further propose that the number of MCMs loaded is regulated by the affinity of ORC for the origin. High-affinity origins are bound by ORC for more of G1 and thus have more MCMs loaded. Heterochromatin could provide a second layer of regulation, on top of our proposed MCM-based mechanism. Heterochromatin could delay origin firing by inhibiting any step in MCM loading or activation. However, based on our preliminary results that many MCMs are loaded at late-firing heterochromatic subtelomeric origins, we propose that heterochromatin acts mainly to inhibit MCM activation.

        A Model for Checkpoint Regulation of Replication

        Figure 4. A Model for Checkpoint Regulation of Replication
        We have identified three classes of proteins required for the S-phase DNA damage checkpoint, which we think are involved in a checkpoint-dependent choice between slow and fast replication through DNA damage. Mus81 and other fork-metabolism proteins are required for Cds1-dependent checkpoint slowing of replication forks, presumably by recombinational template switching. Rad51 and other recombination protein antagonize the Mus81-dependent pathway and allow fast replication, possibly by leading-strand repriming. Sfr1, Rqh1 and other recombination regulator inhibit the Rad51-dependent pathway and allow the Mus81-dependent pathway to function.






        Rotation Projects

        Potential Rotation Projects

        1) Coordination of replication and recombination by the S-phase DNA damage checkpoint

        The replication checkpoint coordinates replication and recombinational repair to allow for the replication of damaged templates, however the mechanism by which the checkpoint regulates recombination is unknown. We have identified a number of potential checkpoint-kinase targets by phosphoproteomics. One possible rotation project would be to create site-directed mutations that would prevent kinase regulation of one or more of the targets. These mutations could be used to validate the role of the target in the checkpoint and to test the importance of checkpoint regulation in S-phase DNA repair.

        2) Regulation of replication timing

        Heterochromatin regulates the timing of replication origin firing, however the mechanism by which it affects origin function is unknown. We have developed a model of how origin timing is regulated in non-heterochromatic chromatin; now we want to test how heterochromatin affects this mechanism. In particular, we want to manipulate the heterochromatic context at specific loci, measure the changes in origin timing and investigate the molecular mechanisms responsible for the change. One possible rotation project would be to establish heterochromatin at a well-characterized origin, measure origin timing, which we presume will be delayed, and then test at which step origin firing is delayed.



        Bibliographic 
        selected publications
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        1. Rhind N. The three most important things about origins: location, location, location. Mol Syst Biol. 2014; 10:723.
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        2. Iyer DR, Rhind N. Checkpoint regulation of replication forks: global or local? Biochem Soc Trans. 2013 Dec 1; 41(6):1701-5.
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        3. Rhind N, Gilbert DM. DNA replication timing. Cold Spring Harb Perspect Biol. 2013 Aug; 5(8):a010132.
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        4. Rhind N, Gilbert DM. DNA Replication Timing. Cold Spring Harb Perspect Med. 2013 Jul; 3(7):1-26.
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        5. Rhind N, Russell P. Signaling pathways that regulate cell division. Cold Spring Harb Perspect Biol. 2012; 4(10).
          View in: PubMed
        6. Xu J, Yanagisawa Y, Tsankov AM, Hart C, Aoki K, Kommajosyula N, Steinmann KE, Bochicchio J, Russ C, Regev A, Rando OJ, Nusbaum C, Niki H, Milos P, Weng Z, Rhind N. Genome-wide identification and characterization of replication origins by deep sequencing. Genome Biol. 2012; 13(4):R27.
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        7. Bechhoefer J, Rhind N. Replication timing and its emergence from stochastic processes. Trends Genet. 2012 Aug; 28(8):374-81.
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        8. Tsankov A, Yanagisawa Y, Rhind N, Regev A, Rando OJ. Evolutionary divergence of intrinsic and trans-regulated nucleosome positioning sequences reveals plastic rules for chromatin organization. Genome Res. 2011 Nov; 21(11):1851-62.
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        9. Grabherr MG, Haas BJ, Yassour M, Levin JZ, Thompson DA, Amit I, Adiconis X, Fan L, Raychowdhury R, Zeng Q, Chen Z, Mauceli E, Hacohen N, Gnirke A, Rhind N, di Palma F, Birren BW, Nusbaum C, Lindblad-Toh K, Friedman N, Regev A. Full-length transcriptome assembly from RNA-Seq data without a reference genome. Nat Biotechnol. 2011 Jul; 29(7):644-52.
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        10. Rhind N, Chen Z, Yassour M, Thompson DA, Haas BJ, Habib N, Wapinski I, Roy S, Lin MF, Heiman DI, Young SK, Furuya K, Guo Y, Pidoux A, Chen HM, Robbertse B, Goldberg JM, Aoki K, Bayne EH, Berlin AM, Desjardins CA, Dobbs E, Dukaj L, Fan L, FitzGerald MG, French C, Gujja S, Hansen K, Keifenheim D, Levin JZ, Mosher RA, Müller CA, Pfiffner J, Priest M, Russ C, Smialowska A, Swoboda P, Sykes SM, Vaughn M, Vengrova S, Yoder R, Zeng Q, Allshire R, Baulcombe D, Birren BW, Brown W, Ekwall K, Kellis M, Leatherwood J, Levin H, Margalit H, Martienssen R, Nieduszynski CA, Spatafora JW, Friedman N, Dalgaard JZ, Baumann P, Niki H, Regev A, Nusbaum C. Comparative functional genomics of the fission yeasts. Science. 2011 May 20; 332(6032):930-6.
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        11. Willis N, Rhind N. Studying S-phase DNA damage checkpoints using the fission yeast Schizosaccharomyces pombe. Methods Mol Biol. 2011; 782:13-21.
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        12. Willis N, Rhind N. Studying G2 DNA damage checkpoints using the fission yeast Schizosaccharomyces pombe. Methods Mol Biol. 2011; 782:1-12.
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        13. Limbo O, Porter-Goff ME, Rhind N, Russell P. Mre11 nuclease activity and Ctp1 regulate Chk1 activation by Rad3ATR and Tel1ATM checkpoint kinases at double-strand breaks. Mol Cell Biol. 2011 Feb; 31(3):573-83.
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        14. Yang SC, Rhind N, Bechhoefer J. Modeling genome-wide replication kinetics reveals a mechanism for regulation of replication timing. Mol Syst Biol. 2010 Aug 24; 6:404.
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        15. Willis N, Rhind N. The fission yeast Rad32(Mre11)-Rad50-Nbs1 complex acts both upstream and downstream of checkpoint signaling in the S-phase DNA damage checkpoint. Genetics. 2010 Apr; 184(4):887-97.
          View in: PubMed
        16. Rhind N, Yang SC, Bechhoefer J. Reconciling stochastic origin firing with defined replication timing. Chromosome Res. 2010 Jan; 18(1):35-43.
          View in: PubMed
        17. Dutta C, Rhind N. The role of specific checkpoint-induced S-phase transcripts in resistance to replicative stress. PLoS One. 2009; 4(9):e6944.
          View in: PubMed
        18. Willis N, Rhind N. Regulation of DNA replication by the S-phase DNA damage checkpoint. Cell Div. 2009; 4:13.
          View in: PubMed
        19. Rhind N. Changing of the guard: how ATM hands off DNA double-strand break signaling to ATR. Mol Cell. 2009 Mar 27; 33(6):672-4.
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        20. Porter-Goff ME, Rhind N. The role of MRN in the S-phase DNA damage checkpoint is independent of its Ctp1-dependent roles in double-strand break repair and checkpoint signaling. Mol Biol Cell. 2009 Apr; 20(7):2096-107.
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        21. Rhind N. Incorporation of thymidine analogs for studying replication kinetics in fission yeast. Methods Mol Biol. 2009; 521:509-15.
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        22. Willis N, Rhind N. Mus81, Rhp51(Rad51), and Rqh1 form an epistatic pathway required for the S-phase DNA damage checkpoint. Mol Biol Cell. 2009 Feb; 20(3):819-33.
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        23. Patel PK, Kommajosyula N, Rosebrock A, Bensimon A, Leatherwood J, Bechhoefer J, Rhind N. The Hsk1(Cdc7) replication kinase regulates origin efficiency. Mol Biol Cell. 2008 Dec; 19(12):5550-8.
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        24. Rhind N. An intrinsic checkpoint model for regulation of replication origins. Cell Cycle. 2008 Sep 1; 7(17):2619-20.
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        25. Dutta C, Patel PK, Rosebrock A, Oliva A, Leatherwood J, Rhind N. The DNA replication checkpoint directly regulates MBF-dependent G1/S transcription. Mol Cell Biol. 2008 Oct; 28(19):5977-85.
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        26. Rhind N. DNA replication timing: random thoughts about origin firing. Nat Cell Biol. 2006 Dec; 8(12):1313-6.
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        27. Kommajosyula N, Rhind N. Cdc2 tyrosine phosphorylation is not required for the S-phase DNA damage checkpoint in fission yeast. Cell Cycle. 2006 Nov 1; 5(21):2495-500.
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        28. Forsburg SL, Rhind N. Basic methods for fission yeast. Yeast. 2006 Feb; 23(3):173-83.
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        29. Patel PK, Arcangioli B, Baker SP, Bensimon A, Rhind N. DNA replication origins fire stochastically in fission yeast. Mol Biol Cell. 2006 Jan; 17(1):308-16.
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        30. Sigova A, Rhind N, Zamore PD. A single Argonaute protein mediates both transcriptional and posttranscriptional silencing in Schizosaccharomyces pombe. Genes Dev. 2004 Oct 1; 18(19):2359-67.
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        31. Sivakumar S, Porter-Goff M, Patel PK, Benoit K, Rhind N. In vivo labeling of fission yeast DNA with thymidine and thymidine analogs. Methods. 2004 Jul; 33(3):213-9.
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        32. Chahwan C, Nakamura TM, Sivakumar S, Russell P, Rhind N. The fission yeast Rad32 (Mre11)-Rad50-Nbs1 complex is required for the S-phase DNA damage checkpoint. Mol Cell Biol. 2003 Sep; 23(18):6564-73.
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