Honors & Awards


  • Simons Foundation Postdoctoral Fellowship, Life Sciences Research Foundation (August 2017 - August 2020)
  • Long-term Postdoctoral Fellowship (accepted as non-stipendiary), EMBO (July 2017 - June 2019)

Professional Education


  • BA, The University of Cambridge, Cambridge, Natural Sciences (2011)
  • PhD, The Francis Crick Institute, London, Cell and Molecular Biology (Supervisor: Sir Paul Nurse) (2016)

Stanford Advisors


Lab Affiliations


All Publications


  • Localized phosphorylation of RNA Polymerase II by G1 cyclin-Cdk promotes cell cycle entry bioRixv Kõivomägi, M., Swaffer, M. P., Turner, J. J., Marinov, G., Skotheim, J. M. 2021
  • Size-independent mRNA synthesis and chromatin-based partitioning mechanisms generate and maintain constant amounts of protein per cell bioRixv Swaffer, M. P., Chandler-Brown, D., Langhinrichs, M., Marinov, G., Greenleaf, W., Kundaje, A., Schmoller, K. M., Skotheim, J. M. 2020
  • Quantitative Phosphoproteomics Reveals the Signaling Dynamics of Cell-Cycle Kinases in the Fission Yeast Schizosaccharomyces pombe CELL REPORTS Swaffer, M. P., Jones, A. W., Flynn, H. R., Snijders, A. P., Nurse, P. 2018; 24 (2): 503–14

    Abstract

    Multiple protein kinases regulate cell-cycle progression, of which the cyclin-dependent kinases (CDKs) are thought to act as upstream master regulators. We have used quantitative phosphoproteomics to analyze the fission yeast cell cycle at sufficiently high temporal resolution to distinguish fine-grain differences in substrate phosphorylation dynamics on a proteome-wide scale. This dataset provides a useful resource for investigating the regulatory dynamics of cell-cycle kinases and their substrates. For example, our analysis indicates that the substrates of different mitotic kinases (CDK, NIMA-related, Polo-like, and Aurora) are phosphorylated in sequential, kinase-specific waves during mitosis. Phosphoproteomics analysis after chemical-genetic manipulation of CDK activity suggests that the timing of these waves is established by the differential dependency of the downstream kinases on upstream CDK. We have also examined the temporal organization of phosphorylation during G1/S, as well as the coordination between the NDR-related kinase Orb6, which controls polarized growth, and other cell-cycle kinases.

    View details for DOI 10.1016/j.celrep.2018.06.036

    View details for Web of Science ID 000438422700022

    View details for PubMedID 29996109

    View details for PubMedCentralID PMC6057490

  • CDK Substrate Phosphorylation and Ordering the Cell Cycle Cell Swaffer, M. P., Jones, A. W., Flynn, H. R., Snijders, A. P., Nurse, P. 2016; 167: 1750–1761
  • Substrate Phosphorylation Rates as an In Vivo Measurement of Kinase Activity. Methods in molecular biology (Clifton, N.J.) Swaffer, M. P. 2021; 2329: 19-27

    Abstract

    Measuring kinase activity in different in vivo contexts is crucial for understanding the mechanism and functions of protein kinases, such as the cyclin-dependent kinases (Cdks) and other cell cycle kinases. Here, I present the rationale and the experimental framework for an alternative approach to measure kinase activity that is based on estimating substrate phosphorylation rates in vivo. The approach presented was first developed for experiments performed to measure Cdk1 activity at different stages of the fission yeast S. pombe's cell cycle [Swaffer et al., Cell 167:1750-1761, 2016]. However, it also affords a more generalizable framework that can be adaptable to other systems and kinases, as long as specific, rapid, and reversible kinase inhibition is possible. Briefly this involves transient and reversible kinase inhibition to dephosphorylate kinase substrates in vivo, followed by quantitative measurements of phosphorylation after inhibition is removed.

    View details for DOI 10.1007/978-1-0716-1538-6_2

    View details for PubMedID 34085212

  • The Hydrophobic Patch Directs Cyclin B to Centrosomes to Promote Global CDK Phosphorylation at Mitosis CURRENT BIOLOGY Basu, S., Roberts, E. L., Jones, A. W., Swaffer, M. P., Snijders, A. P., Nurse, P. 2020; 30 (5): 883-+

    Abstract

    The cyclin-dependent kinases (CDKs) are the major cell-cycle regulators that phosphorylate hundreds of substrates, controlling the onset of S phase and M phase [1-3]. However, the patterns of substrate phosphorylation increase are not uniform, as different substrates become phosphorylated at different times as cells proceed through the cell cycle [4, 5]. In fission yeast, the correct ordering of CDK substrate phosphorylation can be established by the activity of a single mitotic cyclin-CDK complex [6, 7]. Here, we investigate the substrate-docking region, the hydrophobic patch, on the fission yeast mitotic cyclin Cdc13 as a potential mechanism to correctly order CDK substrate phosphorylation. We show that the hydrophobic patch targets Cdc13 to the yeast centrosome equivalent, the spindle pole body (SPB), and disruption of this motif prevents both centrosomal localization of Cdc13 and the onset of mitosis but does not prevent S phase. CDK phosphorylation in mitosis is compromised for approximately half of all mitotic CDK substrates, with substrates affected generally being those that require the highest levels of CDK activity to become phosphorylated and those that are located at the SPB. Our experiments suggest that the hydrophobic patch of mitotic cyclins contributes to CDK substrate selection by directing the localization of Cdc13-CDK to centrosomes and that this localization of CDK contributes to the CDK substrate phosphorylation necessary to ensure proper entry into mitosis. Finally, we show that mutation of the hydrophobic patch prevents cyclin B1 localization to centrosomes in human cells, suggesting that this mechanism of cyclin-CDK spatial regulation may be conserved across eukaryotes.

    View details for DOI 10.1016/j.cub.2019.12.053

    View details for Web of Science ID 000518561000029

    View details for PubMedID 32084401

    View details for PubMedCentralID PMC7063568

  • Long-range single-molecule mapping of chromatin accessibility in eukaryotes. Nature methods Shipony, Z., Marinov, G. K., Swaffer, M. P., Sinnott-Armstrong, N. A., Skotheim, J. M., Kundaje, A., Greenleaf, W. J. 2020

    Abstract

    Mapping open chromatin regions has emerged as a widely used tool for identifying active regulatory elements in eukaryotes. However, existing approaches, limited by reliance on DNA fragmentation and short-read sequencing, cannot provide information about large-scale chromatin states or reveal coordination between the states of distal regulatory elements. We have developed a method for profiling the accessibility of individual chromatin fibers, a single-molecule long-read accessible chromatin mapping sequencing assay (SMAC-seq), enabling the simultaneous, high-resolution, single-molecule assessment of chromatin states at multikilobase length scales. Our strategy is based on combining the preferential methylation of open chromatin regions by DNA methyltransferases with low sequence specificity, in this case EcoGII, an N6-methyladenosine (m6A) methyltransferase, and the ability of nanopore sequencing to directly read DNA modifications. We demonstrate that aggregate SMAC-seq signals match bulk-level accessibility measurements, observe single-molecule nucleosome and transcription factor protection footprints, and quantify the correlation between chromatin states of distal genomic elements.

    View details for DOI 10.1038/s41592-019-0730-2

    View details for PubMedID 32042188

  • Science during lockdown - from virtual seminars to sustainable online communities. Journal of cell science Bottanelli, F. n., Cadot, B. n., Campelo, F. n., Curran, S. n., Davidson, P. M., Dey, G. n., Raote, I. n., Straube, A. n., Swaffer, M. P. 2020; 133 (15)

    Abstract

    The COVID-19 pandemic has disrupted traditional modes of scientific communication. In-person conferences and seminars have been cancelled and most scientists around the world have been confined to their homes. Although challenging, this situation has presented an opportunity to adopt new ways to communicate science and build scientific relationships within a digital environment, thereby reducing the environmental impact and increasing the inclusivity of scientific events. As a group of researchers who have recently created online seminar series for our respective research communities, we have come together to share our experiences and insights. Only a few weeks into this process, and often learning 'on the job', we have collectively encountered different problems and solutions. Here, we share our advice on formats and tools, security concerns, spreading the word to your community and creating a diverse, inclusive and collegial space online. We hope our experience will help others launch their own online initiatives, helping to shape the future of scientific communication as we move past the current crisis.

    View details for DOI 10.1242/jcs.249607

    View details for PubMedID 32801132

  • An Imaging Flow Cytometry-based approach to analyse the fission yeast cell cycle in fixed cells METHODS Patterson, J. O., Swaffer, M., Filby, A. 2015; 82: 74–84

    Abstract

    Fission yeast (Schizosaccharomyces pombe) is an excellent model organism for studying eukaryotic cell division because many of the underlying principles and key regulators of cell cycle biology are conserved from yeast to humans. As such it can be employed as tool for understanding complex human diseases that arise from dis-regulation in cell cycle controls, including cancers. Conventional Flow Cytometry (CFC) is a high-throughput, multi-parameter, fluorescence-based single cell analysis technology. It is widely used for studying the mammalian cell cycle both in the context of the normal and disease states by measuring changes in DNA content during the transition through G1, S and G2/M using fluorescent DNA-binding dyes. Unfortunately analysis of the fission yeast cell cycle by CFC is not straightforward because, unlike mammalian cells, cytokinesis occurs after S-phase meaning that bi-nucleated G1 cells have the same DNA content as mono-nucleated G2 cells and cannot be distinguished using total integrated fluorescence (pulse area). It has been elegantly shown that the width of the DNA pulse can be used to distinguish G2 cells with a single 2C foci versus G1 cells with two 1C foci, however the accuracy of this measurement is dependent on the orientation of the cell as it traverses the laser beam. To this end we sought to improve the accuracy of the fission yeast cell cycle analysis and have developed an Imaging Flow Cytometry (IFC)-based method that is able to preserve the high throughput, objective analysis afforded by CFC in combination with the spatial and morphometric information provide by microscopy. We have been able to derive an analysis framework for subdividing the yeast cell cycle that is based on intensiometric and morphometric measurements and is thus robust against orientation-based miss-classification. In addition we can employ image-based metrics to define populations of septated/bi-nucleated cells and measure cellular dimensions. To our knowledge, this is the first use of IFC to study fission yeast and we are confident that this will provide a springboard for further IFC-based analysis across all aspects of fission yeast biology.

    View details for DOI 10.1016/j.ymeth.2015.04.026

    View details for Web of Science ID 000356910700010

    View details for PubMedID 25952947

  • What determines cell size? BMC BIOLOGY Marshall, W. F., Young, K. D., Swaffer, M., Wood, E., Nurse, P., Kimura, A., Frankel, J., Wallingford, J., Walbot, V., Qu, X., Roeder, A. H. 2012; 10

    View details for DOI 10.1186/1741-7007-10-101

    View details for Web of Science ID 000312301200001

    View details for PubMedID 23241366

    View details for PubMedCentralID PMC3522064