University of Dundee

Professor Angus Lamond FRS FRSE

Nuclear structure proteomics and gene expression
Position: 
Professor of Biochemistry
Address: 
College of Life Sciences, University of Dundee, Dundee
Full Telephone: 
+44 (0) 1382 385473, int ext 85473

Research

We are studying structure/function relationships and protein dynamics in the cell nucleus, using a combination of quantitative techniques, including mass-spectrometry-based proteomics, fluorescence microscopy and deep sequencing. The importance of understanding nuclear organisation is underlined by evidence showing that multiple human diseases, including inherited genetic disorders, malignancies and viral infections, modify or disrupt subnuclear bodies.

The use of high throughput proteomics technologies provides a system-wide approach allowing us to measure cellular responses for a large number of proteins in parallel. An integral part of this work is the development of new software tools for the management analysis and visualisation of complex proteomics data sets (see http://www.peptracker.com/). One major aim of our work is to characterise the composition and function of subnuclear organelles and multiprotein complexes and to identify mechanisms regulating their assembly and turnover in human cells. Combining quantitative proteomics with quantitative fluorescence microscopy imaging, using stable cell lines expressing one or more fluorescent protein tagged reporters, provides a “Dual Strategy” for analysing dynamic properties of the cell proteome.

As a major theme of our work involves the development and application of quantitative proteomics to study cell biology we have established a website to provide detailed online information that promotes the use of these technologies (see ‘The Cell Biologists Guide to Proteomics’). We have also developed ‘The Encyclopedia of Proteome Dynamics’ (Larance et. al., MCP, 2013), an online, searchable database that provides open access to all of our large-scale proteomics data sets (see http://www.peptracker.com/encyclopediaInformation/). We are employing ‘next generation’ proteomics techniques to provide a flexible set of assay platforms for measuring ‘protein properties’,  including protein-protein interactions and multi-protein complexed subcellular protein localisation, protein dynamics and turnover and post-translational protein modifications. Most recently we have used label-free mass spectrometry-based proteomics and RNA sequencing combined with centrifugal elutriation to analayse gene expression across a minimally perturbed cell cycle in human cells.

We have extended methods we previously reported, using SILAC as an unbiased procedure to identify reliably specific protein interaction partners (Trinkle-Mulcahy et. al., 2006; 2008), to analysis facilities of PepTracker (Boulon et.al., MCP 2010). The reliable discrimination between specific and non-specific protein interaction partners is aided by reference to a database that contains the results of all previous immunoprecipitation experiments, annotated with detailed metadata. Using our customisable ‘Protein Frequency Library (PFL) viewer (seehttp://www.peptracker.com/datavisual/), we can take advantage of the fact that common contaminants and ‘sticky’ proteins are detected more frequently than specific interactors to help identify bona fide interaction partners for proteins of interest. We have also developed methods for studying protein complexes using mass spectrometry-based proteomics combined with size exclusion chromatography (SEC) (Kirkwood, et. al., MCP, 2013).

Teaching

B131006 Level 3 GRE Module

Publications

“Stable Isotope Labelling with Amino acids in Nematodes”; Larance, M., Bailly, A.P., Pourkarimi, E., Hay, R.T., Buchanan, G., Coulthurst, S., Xirodimas, D., Gartner, A. and Lamond, A.I. (2011) Nature Methods, 8, 849–851 View PDF

“A Quantitative Spatial Proteomics Analysis of Proteome Turnover in Human Cells.”; Boisvert, F-M., Ahmad, Y., Gierlinski, M., Charriere, F., Lamont, D., Scott, M.S., Barton, G.J. and Lamond, A.I. (2012) Molecular & Cellular Proteomics 11 (3) View PDF

“Systematic analysis of protein pools, isoforms and modifications affecting turnover and subcellular localisation”; Ahmad, Y., Boisvert, F-M., Lundberg, E., Uhlen, M. and Lamond, A.I. (2012) Molecular & Cellular Proteomics 11 (3)  View PDF

“Characterization of MRFAP1 Turnover and Interactions Downstream of the NEDD8 Pathway”; Larance, M., Kirkwood, K.J., Xirodimas, D.P., Lundberg, E., Uhlen, M. and Lamond, A.I. (2012) Molecular & Cellular Proteomics 11 (3) View PDF

“Advancing Cell Biology Through Proteomics in Space and Time (PROSPECTS)”; Special Issue: Prospects in Space and Time; Lamond, A.I., Uhlen, M., Horning, S., Makarov, A., Robinson, C.V., Serrano, L., Hartl, F.U., Andersen, J., Vorm, O., Baumeister, W., Linial, M., Werenskiold, A.K., Aebersold, R. and Mann, M. (2012) Mol Cell Proteomics 11; First Published on February 2012 View PDF

“Global Subcellular Characterisation of Protein Degradation using Quantitative Proteomics”; Larance, M., Ahmad, Y., Kirkwood, K.J., Ly, T. and Lamond A.I. Mol Cell Proteomics. (2013) 12(3):638-50 View PDF

“Identification and Functional Characterization of FMN2, a Regulator of the Cyclin-Dependent Kinase Inhibitor p21”; Yamada, K., Ono, M., Perkins, N.D., Rocha, S. and Lamond, A.I.  Molecular Cell. (2013) 7;49(5) View PDF

“Cleaning up the Masses: Exclusion lists to reduce contamination with HPLC-MS/MS”; Hodge, K., Have, S.T., Hutton, L. and Lamond A.I.  Journal of Proteomics. (2013) 14 View PDF

“Analysis of Human Protein Replacement Stable Cell Lines Established using snoMEN-PR Vector”; Ono, M., Yamada, K., Endo, A., Avolio, F. and Lamond, A.I. PLoS One. (2013) 8(4) View PDF

“Modulation of Higher Order Chromatin Conformation in Mammalian Cell Nuclei Can Be Mediated by Polyamines and Divalent Cations”; Visvanathan, A., Ahmed, K., Even-Faitelson, L., Lleres, D., Bazett-Jones, D.P. and Lamond, A.I.  PLoS One. (2013) 8(6) View PDF

“FMN2 is a novel regulator of the cyclin-dependent kinase inhibitor p21”; Yamada, K., Ono, M., Bensaddek, D., Lamond, A.I. and Rocha, S.  Cell Cycle. (2013) 12(15) View PDF

“PHD1 Links Cell-Cycle Progression to Oxygen Sensing through Hydroxylation of the Centrosomal Protein Cep192”; Moser, S.C., Bensaddek, D., Ortmann, B., Maure, J.F., Mudie, S., Blow, J.J., Lamond, A.I., Swedlow, J.R. and Rocha, S. Dev Cell. (2013), 26(4):381-92 View PDF

“Plant SILAC: Stable-Isotope Labelling with Amino Acids of Arabidopsis Seedlings for Quantitative Proteomics”; Lewandowska, D., Ten Have, S., Hodge, K., Tillemans, V., Lamond, A.I. and Brown, J.W. PLoS One. (2013) 8(8) View PDF

“Characterisation of Native Protein Complexes and Protein Isoform Variation using Size-Fractionation Based Quantitative Proteomics”; Kirkwood, K., Ahmad, Y., Larance, M. and Lamond, A.I.  Mol. & Cell. Proteomics. (2013) View PDF

"A role for the CB-associated SUMO isopeptidase USPL1 in RNAPII-mediated snRNA transcription"; Hutten, S., Chachami, G., Winter, U., Melchior, F. and Lamond A, I.  Journal of Cell Science (2014), Jan 10. PMID: 24413172 View PDF

"A perspective on proteomics in cell biology"; Ahmad, Y. and Lamond, A. I. Trends in Cell Biology. (2014) Vol 24, Issue 4, p257-264,doi 24284280 View PDF

"A proteomic chronology of gene expression through the cell cycle in human myeloid leukemia"; Ly T, Ahmad Y, Shlien A, Soroka D, Mills A, Emanuele MJ, Stratton MR, Lamond AI. (2014)  ELife. 2014 March 4;3 doi: 10.7554/eLife.01630.  PMID 24596151 View PDF