User:Stephen Watt

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Contact Info

Me on holiday

Education

  • 1998, BSc Biology, University of Paisley, Scotland

Research

  1. 1999-2000 Joined the Wellcome Trust Sanger Institute working in one of the human genome project sequencing teams.
  2. 2000-2003 Worked in the laboratory of Professor Mike Stratton at the WTSI searching for DNA mutations and deletions in the genomes of various cancers.
  3. 2003-2009 Worked in the laboratory of Professor Jurg Bahler at the WTSI, where we studied the transcriptional regulation of the fission yeast S.pombe using many different genomics and systems biology approaches.
  4. 2009-2013 Left the WTSI after 10 years to move across town to the lab of Dr Duncan Odom at the Cambridge Research Institute. Here we study transcriptional regulation using Illumina sequencing and evolution as our model.
  5. 2013-today Joined the laboratory of Dr Nicole Soranzo at WTSI. Using functional genomics approaches to test what affect natural variation in human DNA sequence has on transcriptional regulation and epigenetic states.

Publications

'*' co-first authors

  • Hussain S, Tuorto F, Menon S, Blanco S, Cox C, Flores JV, Watt S, Kudo NR, Lyko F, Frye M. The mouse cytosine-5 RNA methyltransferase NSun2 is a component of the chromatoid body and required for testis differentiation. Mol Cell Biol. 2013
  • Valente LP, Dehé PM, Klutstein M, Aligianni S, Watt S, Bähler J, Promisel Cooper J. Myb-domain protein Teb1 controls histone levels and centromere assembly in fission yeast. EMBO J. 2013
  • Ward MC*, Wilson MD*, Barbosa-Morais NL, Schmidt D, Stark R, Pan Q, Schwalie PC, Menon S, Lukk M, Watt S, Thybert D, Kutter C, Kirschner K, Flicek P, Blencowe BJ, Odom DT. Latent Regulatory Potential of Human-Specific Repetitive Elements. Mol Cell. 2013
  • Barbosa-Morais NL, Irimia M, Pan Q, Xiong HY, Gueroussov S, Lee LJ, Slobodeniuc V, Kutter C, Watt S, Colak R, Kim T, Misquitta-Ali CM, Wilson MD, Kim PM, Odom DT, Frey BJ, Blencowe BJ. The evolutionary landscape of alternative splicing in vertebrate species. Science. 2013
  • Kutter C*, Watt S*, Stefflova K, Wilson MD, Goncalves A, Ponting CP, Odom DT, Marques AC. Rapid Turnover of Long Noncoding RNAs and the Evolution of Gene Expression. PLoS Genet. 2012
  • Faure AJ*, Schmidt D*, Watt S , Schwalie PC, Wilson MD, Xu H, Ramsay RG, Odom DT, Flicek P. Cohesin regulates tissue-specific expression by stabilising highly occupied cis-regulatory modules. Genome Res. 2012
  • Wang Y, Kallgren SP, Reddy BD, Kuntz K, Lopez-Maury L, Thompson J, Watt S, Ma C, Hou H, Shi Y, Yates JR, Bahler J, O'Connell MJ, Jia S. Histone H3 lysine 14 acetylation is required for activation of a DNA damage checkpoint in fission yeast. J Biol Chem. 2011
  • Kutter C*, Brown GD*, Gonçalves A, Wilson MD, Watt S, Brazma A, White RJ, Odom DT. Pol III binding in six mammals shows conservation among amino acid isotypes despite divergence among tRNA genes. Nat Genet. 2011
  • Wilhelm BT, Marguerat S, Aligianni S, Codlin S, Watt S, Bahler J. Differential patterns of intronic and exonic DNA regions with respect to RNA polymerase II occupancy, nucleosome density and H3K36me3 marking in fission yeast. Genome Biol. 2011
  • Hansen KR, Hazan I, Shanker S, Watt S, Verhein-Hansen J, Bähler J, Martienssen RA, Partridge JF, Cohen A, Thon G. H3K9me-Independent Gene Silencing in Fission Yeast Heterochromatin by Clr5 and Histone Deacetylases. PLoS Genet 2011
  • Zaratiegui M, Vaughn MW, Irvine DV, Goto D, Watt S, Bähler J, Arcangioli B, Martienssen RA. CENP-B preserves genome integrity at replication forks paused by retrotransposon LTR. Nature. 2011
  • Zhurinsky J, Leonhard K, Watt S, Marguerat S, Bähler J, Nurse P. A coordinated global control over cellular transcription. Curr Biol. 2010
  • Kiang L*, Heichinger C*, Watt S, Bähler J, Nurse P. Specific replication origins promote DNA amplification in fission yeast. J Cell Sci. 2010
  • Wen WL, Stevenson AL, Wang CY, Chen HJ, Kearsey SE, Norbury CJ, Watt S, Bähler J, Wang SW. Vgl1, a multi-KH domain protein, is a novel component of the fission yeast stress granules required for cell survival under thermal stress. Nucleic Acids Res. 2010
  • Schmidt D*, Wilson MD*, Ballester B*, Schwalie PC, Brown GD, Marshall A, Kutter C, Watt S, Martinez-Jimenez CP, Mackay S, Talianidis I, Flicek P, Odom DT. Five-Vertebrate ChIP-seq Reveals the Evolutionary Dynamics of Transcription Factor Binding. Science. 2010
  • Kim HS, Vanoosthuyse V, Fillingham J, Roguev A, Watt S, Kislinger T, Treyer A, Carpenter LR, Bennett CS, Emili A, Greenblatt JF, Hardwick KG, Krogan NJ, Bähler J, Keogh MC. An acetylated form of histone H2A.Z regulates chromosome architecture in Schizosaccharomyces pombe. Nat Struct Mol Biol 2009
  • Kiang L*, Heichinger C*, Watt S, Bähler J, Nurse P. Cyclin-dependent kinase inhibits reinitiation of a normal S-phase program during G2 in fission yeast. Mol Cell Biol. 2009
  • Anders A, Watt S, Bähler J, Sawin KE. Improved tools for efficient mapping of fission yeast genes: identification of microtubule nucleation modifier mod22-1 as an allele of chromatin- remodelling factor gene swr1. Yeast. 2008
  • Wilhelm BT*, Marguerat S*, Watt S, Schubert F, Wood V, Goodhead I, Penkett CJ, Rogers J, Bähler J. Dynamic repertoire of a eukaryotic transcriptome surveyed at single-nucleotide resolution. Nature. 2008
  • Udagawa T, Nemoto N, Wilkinson CR, Narashimhan J, Jiang L, Watt S, Zook A, Jones N, Wek RC, Bähler J, Asano K. Int6/eIF3e promotes general translation and Atf1 abundance to modulate Sty1 map kinase-dependent stress response in fission yeast. J Biol Chem. 2008
  • Ludin K, Mata J, Watt S, Lehmann E, Bähler J, Kohli J. Sites of strong Rec12/Spo11 binding in the fission yeast genome are associated with meiotic recombination and with centromeres. Chromosoma. 2008
  • Reiter W, Watt S, Dawson K, Lawrence CL, Bähler J, Jones N, Wilkinson CR. Fission yeast map kinase Sty1 is recruited to stress-induced genes. J Biol Chem. 2008
  • Mercier A, Watt S, Bähler J, Labbé S. Key function for the CCAAT-binding factor Php4 to regulate gene expression in response to iron deficiency in fission yeast. Eukaryot Cell. 2008
  • Dainty SJ, Kennedy CA, Watt S, Bähler J, Whitehall SK. The Response of Schizosaccharomyces pombe to Zinc Deficiency. Eukaryot Cell. 2008
  • Watt S, Mata J, López-Maury L, Marguerat S, Burns G, Bähler J. urg1:A Uracil-Regulatable Promoter System for Fission Yeast with Short Induction and Repression Times. PLoS ONE. 2008
  • Wang SW, Stevenson AL, Kearsey SE, Watt S, Bähler J. Global role for polyadenylation-assisted nuclear RNA degradation in post-transcriptional gene silencing. Mol Cell Biol. 2008
  • Chen D, Wilkinson CR, Watt S, Penkett CJ, Toone WM, Jones N, Bähler J. Multiple Pathways Differentially Regulate Global Oxidative Stress Responses in Fission Yeast. Mol Biol Cell. 2008
  • Miklos I, Szilagyi Z, Watt S, Zilahi E, Batta G, Antunovics Z, Enczi K, Bahler J, Sipiczki M. Genomic expression patterns in cell separation mutants of Schizosaccharomyces pombe defective in the genes sep10 ( + ) and sep15 ( + ) coding for the Mediator subunits Med31 and Med8. Mol Genet Genomics. 2008
  • Lackner DH, Beilharz TH, Marguerat S, Mata J, Watt S, Schubert F, Preiss T, Bahler J. A Network of Multiple Regulatory Layers Shapes Gene Expression in Fission Yeast. Mol Cell. 2007
  • Rodriguez-Gabriel MA, Watt S, Bahler J, Russell P. upf1, an RNA helicase required for nonsense-mediated mRNA decay, modulates the transcriptional response to oxidative stress in fission yeast. Mol Cell Biol. 2006
  • Sharma N, Marguerat S, Mehta S, Watt S, Bahler J. The fission yeast Rpb4 subunit of RNA polymerase II plays a specialized role in cell separation. Mol Genet Genomics. 2006
  • Martin V, Rodriguez-Gabriel MA, McDonald WH, Watt S, Yates JR 3rd, Bahler J, Russell P. Cip1 and Cip2 are novel RNA-Recognition-Motif proteins that counteract Csx1 function during oxidative stress. Mol Biol Cell. 2006
  • Lee KM, Miklos I, Du H, Watt S, Szilagyi Z, Saiz JE, Madabhushi R, Penkett CJ, Sipiczki M, Bahler J, Fisher RP. Impairment of the TFIIH-associated CDK-activating kinase selectively affects cell cycle-regulated gene expression in fission yeast. Mol Biol Cell. 2005
  • Cox C, Bignell G, Greenman C, Stabenau A, Warren W, Stephens P, Davies H, Watt S, Teague J, Edkins S, Birney E, Easton DF, Wooster R, Futreal PA, Stratton MR. A survey of homozygous deletions in human cancer genomes. Proc Natl Acad Sci U S A. 2005
  • Bignell GR, Huang J, Greshock J, Watt S, Butler A, West S, Grigorova M, Jones KW, Wei W, Stratton MR, Futreal PA, Weber B, Shapero MH, Wooster R. High-resolution analysis of DNA copy number using oligonucleotide microarrays. Genome Res. 2004
  • Davies H, Bignell GR, Cox C, Stephens P, Edkins S, Clegg S, Teague J, Woffendin H, Garnett MJ, Bottomley W, Davis N, Dicks E, Ewing R, Floyd Y, Gray K, Hall S, Hawes R, Hughes J, Kosmidou V, Menzies A, Mould C, Parker A, Stevens C, Watt S, Hooper S, Wilson R, Jayatilake H, Gusterson BA, Cooper C, Shipley J, Hargrave D, Pritchard-Jones K, Maitland N, Chenevix-Trench G, Riggins GJ, Bigner DD, Palmieri G, Cossu A, Flanagan A, Nicholson A, Ho JW, Leung SY, Yuen ST, Weber BL, Seigler HF, Darrow TL, Paterson H, Marais R, Marshall CJ, Wooster R, Stratton MR, Futreal PA. Mutations of the BRAF gene in human cancer. Nature. 2002

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