Jonathan Chubb Research Group

1995, BA, Cambridge University
2000, PhD, University College London
Jonathan Chubb
Tel: +44 (0)207 679 7271
Awards: 
Wellcome Trust Senior Fellowship
Previous Posts: 
2000-03: Post-doctoral fellow, MRC Human Genetics Unit, Edinburgh
2003-05: Post-doctoral fellow, Albert-Einstein College of Medicine, New York
2005-11: Principal Investigator, College of Life Sciences, University of Dundee

Imaging transcriptional dynamics

Despite the generation of transcriptional differences between nearby related cells being the basis of most differentiation and disease, our standard measures of RNA synthesis do not register the origins of these differences. Although useful for a preliminary rough sorting of genes to context, the widespread techniques of Northern blotting, microarrays, RT-PCR and RNA-Seq measure bulk RNA levels from homogenous population extracts. These approaches lose dynamic information from individual cells, and give the impression transcription is a continuous smooth process. The reality is that transcription is irregular, with strong variable duration periods of activity, interspersed by variable duration periods of inactivity (see movie sequences). Averaged over millions of cells, this appears continuous. But at the individual cell level, there is considerable variability, and for most genes, very little activity at any one time.  Transcription of genes, the process which transforms the stable code written in DNA into the mobile RNA message can occur in "bursts" or"pulses" (see movie sequence). These phenomena have recently come to light with the advent of new technologies, to detect RNA in single cells, allowing precise measurements of RNA number, or RNA emergence at a gene.  We would like to understand the mechanistic basis of pulsing, and how it is responsive to signals, developmental and chromatin context. And we are testing the implications of noisy transcription on the generation of diversity between cells in developmental and clinical contexts.

Lab Members: 
Danielle Cannon
Agnès Miermont
Publications
Jump to: 2014 | 2013 | 2012 | 2011 | 2010 | 2009 | 2008 | 2007 | 2006 | 2004 | 2003 | 2002 | 2001 | 2000
Number of items: 25.

2014

Pisani, F; Livermore, T; Rose, G; Chubb, JR; Gaspari, M; Saiardi, A; (2014) Analysis of Dictyostelium discoideum Inositol Pyrophosphate Metabolism by Gel Electrophoresis. PLoS One , 9 (1) , Article e85533 . 10.1371/journal.pone.0085533. Green and gold open access
file

2013

Chubb, JR; Stevense, M; Cannon, D; Muramoto, T; Corrigan, AM; (2013) Imaging nascent RNA dynamics in dictyostelium. Methods Mol Biol , 1042 101 - 113. 10.1007/978-1-62703-526-2_8.

Corrigan, AM; Chubb, JR; (2013) Regulation of Transcriptional Bursting by a Naturally Oscillating Signal. Curr Biol 10.1016/j.cub.2013.12.011.

2012

Hsu, DW; Chubb, JR; Muramoto, T; Pears, CJ; Mahadevan, LC; (2012) Dynamic acetylation of lysine-4-trimethylated histone H3 and H3 variant biology in a simple multicellular eukaryote. Nucleic Acids Research , 40 7247 - 7256.

Muramoto, T; Cannon, D; Gierlinski, M; Corrigan, A; Barton, GJ; Chubb, JR; (2012) Live imaging of nascent RNA dynamics reveals distinct types of transcriptional pulse regulation. Proc Natl Acad Sci U S A , 109 (19) 7350 - 7355. 10.1073/pnas.1117603109.

2011

Cannon, D; Chubb, JR; (2011) Pol II caught speeding by single gene imaging. EMBO Rep , 12 (12) 1208 - 1210. 10.1038/embor.2011.217.

Stevense, M; Chubb, JR; Muramoto, T; (2011) Nuclear organization and transcriptional dynamics in Dictyostelium. Dev Growth Differ , 53 (4) 576 - 586. 10.1111/j.1440-169X.2011.01271.x.

2010

Chubb, JR; Liverpool, TB; (2010) Bursts and pulses: insights from single cell studies into transcriptional mechanisms. Curr Opin Genet Dev , 20 (5) 478 - 484. 10.1016/j.gde.2010.06.009.

Muller, I; Boyle, S; Singer, RH; Bickmore, WA; Chubb, JR; (2010) Stable morphology, but dynamic internal reorganisation, of interphase human chromosomes in living cells. PLoS One , 5 (7) , Article e11460 . 10.1371/journal.pone.0011560. Green and gold open access
file

Muramoto, T; Muller, I; Thomas, G; Melvin, A; Chubb, JR; (2010) Methylation of H3K4 is required for inheritance of active transcriptional states. Current Biology , 20 (5) 397 - 406.

Stevense, M; Muramoto, T; Muller, I; Chubb, JR; (2010) Digital nature of the immediate-early transcriptional response. Development , 137 579 - 584.

2009

Chubb, JR; (2009) Gene activation at the edge of the nucleus. EMBO J , 28 (15) 2145 - 2146. 10.1038/emboj.2009.148.

2008

Finlan, LE; Sproul, D; Thomson, I; Boyle, S; Kerr, E; Perry, P; ... Bickmore, WA; + view all (2008) Recruitment to the nuclear periphery can alter expression of genes in human cells. PLoS Genetics , 4 (3) , Article e1000039 . 10.1371/journal.pgen.1000039. Green and gold open access
file

Muramoto, T; Chubb, JR; (2008) Live imaging of the Dictyostelium cell cycle reveals widespread S phase during development, a G2 bias in spore differentiation and a premitotic checkpoint. Development , 135 1647 - 1657.

2007

Levsky, JM; Shenoy, SM; Chubb, JR; Hall, CB; Capodieci, P; Singer, RH; (2007) The spatial order of transcription in mammalian cells. J Cell Biochem , 102 (3) 609 - 617. 10.1002/jcb.21495.

2006

Chubb, JR; Bloomfield, G; Xu, Q; Kaller, M; Ivens, A; Skelton, J; ... Singer, RH; + view all (2006) Developmental timing in Dictyostelium is regulated by the Set1 histone methyltransferase. Dev Biol , 292 (2) 519 - 532. 10.1016/j.ydbio.2005.12.054.

Chubb, JR; Trcek, T; Shenoy, SM; Singer, RH; (2006) Transcriptional pulsing of a developmental gene. Curr Biol , 16 (10) 1018 - 1025. 10.1016/j.cub.2006.03.092.

2004

Thomson, I; Gilchrist, S; Bickmore, WA; Chubb, JR; (2004) The radial positioning of chromatin is not inherited through mitosis but is established de novo in early G1. Curr Biol , 14 (2) 166 - 172.

2003

Bickmore, WA; Chubb, JR; (2003) Chromosome position: Now, where was I? CURRENT BIOLOGY , 13 (9) R357 - R359. 10.1016/S0960-9822(03)00276-8.

Bickmore, WA; Chubb, JR; (2003) Dispatch. Chromosome position: now, where was I? Curr Biol , 13 (9) R357 - R359.

Chubb, JR; Bickmore, WA; (2003) Considering nuclear compartmentalization in the light of nuclear dynamics. Cell , 112 (4) 403 - 406.

2002

Chubb, JR; Boyle, S; Perry, P; Bickmore, WA; (2002) Chromatin motion is constrained by association with nuclear compartments in human cells. Curr Biol , 12 (6) 439 - 445.

2001

Chubb, JR; Insall, RH; (2001) Dictyostelium: an ideal organism for genetic dissection of Ras signalling networks. Biochim Biophys Acta , 1525 (3) 262 - 271.

2000

Chubb, JR; Wilkins, A; Thomas, GM; Insall, RH; (2000) The Dictyostelium RasS protein is required for macropinocytosis, phagocytosis and the control of cell movement. J CELL SCI , 113 (4) 709 - 719.

Wilkins, A; Chubb, JR; Insall, RH; (2000) A novel Dictyostelium RasGEF is required for normal endocytosis, cell motility and multicellular development. Curr Biol , 10 (22) 1427 - 1437.

This list was generated on Sun Jul 27 22:50:59 2014 BST.