Publications
Selected Publications
Daniel A. Bose, Greg Donahue, Danny Reinberg, Ramin Sheikhattar, Roberto Bonasio, Shelley L. Berger. Cell 168, 135–149.e22 (2017)
In our most recent paper, we showed how RNA binding to CBP could modulate CBPs enzymatic activity to control histone acetylation and gene expression. The model explains how localised transcription of eRNAs could tailor the activity of sub-populations of CBP bound at enhancers, leading to functional diversity in enhancer activity.
Organisation of an activator bound RNA polymerase holoenzyme
Daniel Bose, Tillmann Pape, Patricia C. Burrows, Mathieu Rappas, Sivaramesh Wigneshweraraj, Martin Buck, and Xiaodong Zhang. Molecular Cell, 32 (3), 337-46 (2008). PMID 18995832.
Part of a long-running collaboration with Prof. Martin Buck FRS, we used cryo-EM to describe the mechanism of the alternate sigma factor, sigma-54, in bacteria. When bound to RNA polymerase (RNAP), Sigma-54 needs to interact with a special activator protein bound at a distal enhancer-like element to initiate transcription. These activators use energy from ATP hydrolysis to re-model RNAP/sigma-54 to initiate transcription, a process that we visualised for the first time.
Nature Immersive: Starting up in science
Over the last 3.5 years, we worked with the Nature features team on an immersive article and accompanying podcast that followed our lab and Twelvetrees Lab for 3.5 years as we started our groups at The University of Sheffield. The article is wonderful, and really captures our experiences as we’ve been through the trials and tribulations of starting a lab. The feedback that we’ve had on the article has been great, and I’m glad that it has resonated with so many people.
Hot off the press!
The latest publication from our group:
Cooperation between Intrinsically Disordered Regions regulates CBP condensate behaviour.
Katie L. Gelder, Nicola A. Carruthers, Sophie S. Ball, Mark Dunning, Timothy D. Craggs, Alison E. Twelvetrees, Daniel A. Bose
Katie’s work looking at the role of individual IDRs in regulating CBP condensate behaviour. We've known for many years that CBP (and p300) form nuclear bodies. The formation of these condensates can regulate activity and transcriptional outputs. But what is the role of individual IDRs in driving these processes? Importantly, the large C-terminal tail of CBP contains two adjacent IDRs with different sequence properties and competing positive and negative effects on condensate formation. The presence of -ve IDR is required to balance the +ve IDR. This allows condensate behaviour to respond to different inputs, such as lysine acetylation in IDRs in other CBP domains. It can help to explain how transcription factors binding to different regions of CBP differentially regulate CBP activity. This was a super effort by our team. Special mention to Nicola for her work to HaloTag endogenous CBP and amazing collaborators in the Twelvetrees and Craggs lab.
Available on BioRXiv: https://www.biorxiv.org/content/10.1101/2024.06.04.597392v1
All publications
Cooper-Knock, J., Zhang, S., Kenna, K.P., Moll, T., Franklin, J.P., Allen, S., Nezhad, H.G., Iacoangeli, A., Yacovzada, N.Y., Eitan, C., et al. (2020). Rare Variant Burden Analysis within Enhancers Identifies CAV1 as an ALS Risk Gene. Cell Rep. 33, 108456.
Catizone, A.N., Uzunbas, G.K., Celadova, P., Kuang, S., Bose, D., and Sammons, M.A. (2020). Locally acting transcription factors regulate p53-dependent cis-regulatory element activity. Nucleic Acids Res. 48, 4195–4213.
Daniel A. Bose, Greg Donahue, Danny Reinberg, Ramin Sheikhattar, Roberto Bonasio, Shelley L. Berger. RNA Binding to CBP Stimulates Histone Acetylation and Transcription. Cell 168, 135–149.e22 (2017). PMID 28086087. (manuscript also available here)
(See also: Nature News and Views by Karen Adelman and Emily Egan, Nature 543, p183-185, 9 March 2017; Faculty of 1000 Biology listing.)
Sawicka M., Wanrooij P.H., Darbari V.C., Tannous E., Hailemariam S., Daniel Bose, Makarova A.V., Burgers P.M., Xiaodong Zhang. The dimeric architecture of checkpoint kinases Mec1ATR and Tel1ATM reveal a common structural organisation, J Biol Chem, 291 (26), 13436-13447 (2016), PMID 27129217.
Matheshwaran Saravanan*, Jochen Wuerges*, Daniel Bose*, Elizabeth A. McCormack, Nicola J. Cook, Xiaodong Zhang and Dale B. Wigley. Functional role for an Arp8 dimer within the INO80 Chromatin Remodelling Complex, PNAS, 109 (51), 20883-8 (2012), PMID 23213201.
Milija Jovanovic, Patricia C. Burrows, Daniel Bose, Beatriz Cámara, Simone Wiesler, Xiaodong Zhang, Sivaramesh Wigneshweraraj, Robert O J Weinzierl, Martin Buck. Activity map of the Escherichia coli RNA polymerase bridge helix, J Biol Chem, 286 (16) 14469-79 (2011), PMID 21357417.
Brianna J. Klein*, Daniel Bose*, Kevin J. Baker, Zahirah M. Yusoff, Xiaodong Zhang, and Katsuhiko S. Murakami.
Structure of the cellular RNA polymerase and transcription elongation complex, Proc Natl Acad Sci USA, 108 (2), 546-50 (2011). PMID 21187417.
Trevor R. Sweeney, Valentina Cisnetto, Daniel Bose, Matthew Bailey, Jon R. Wilson, Xiaodong Zhang, Graham J. Belsham and Stephen Curry. Foot-and-mouth disease virus 2C is a hexameric AAA+ protein with a coordinated ATP hydrolysis mechanism. J Biol Chem, 285 (32), 24347-59 (2010). PMID 20507978
Daniel Bose, Tillmann Pape, Patricia C. Burrows, Mathieu Rappas, Sivaramesh Wigneshweraraj, Martin Buck, and Xiaodong Zhang. Organisation of an activator bound RNA polymerase holoenzyme, Molecular Cell, 32 (3), 337-46 (2008). PMID 18995832.
(See also: Cover illustration; Research Highlight, Nature Reviews Microbiology 7, 3 January 2009; Faculty of 1000 Biology listing.)
*Authors contributed equally to the work.
Reviews
Harrison, L. J. & Bose, D. Enhancer RNAs step forward: new insights into enhancer function. Development 149, (2022).
Bose, D.A., and Berger, S.L. eRNA binding produces tailored CBP activity profiles to regulate gene expression. RNA Biol 00–00, 1-5. (2017), PMID 28891741
Tamaswati Ghosh, Daniel Bose and Xiaodong Zhang. Mechanisms for activating bacterial RNA polymerase, FEMS microbiology reviews 34 (5), 611-27 (2010), PMID 20629756.
Patricia C. Burrows, Sivaramesh Wigneshweraraj, Daniel Bose, Nicolas Joly, Jorg Schumacher, Mathieu Rappas, Tillmann Pape, Peter Stockley, Xiaodong Zhang and Martin Buck. Visualizing the organization and reorganization of transcription complexes for gene expression. Biochem Soc Trans. 36, 776-9 (2008). PMID 18631157.
Daniel Bose, Nicolas Joly, Tillmann Pape, Mathieu Rappas, Jorg Schumacher, Martin Buck, and Xiaodong Zhang. Dissecting the ATP hydrolysis pathway of bacterial enhancer binding proteins. Biochem Soc Trans. (36), 83-8 (2008). PMID 18208391.
Sivaramesh Wigneshweraraj, Daniel Bose, Patricia C. Burrows, Nicolas Joly, Schumacher, Mathieu Rappas, Tillmann Pape, Xiaodong Zhang, Peter Stockley, Konstantin Severinov, Martin Buck. Modus Operandi of a unique bacterial RNA polymerase class. Molecular Microbiology. 68 (3), 538-46 (2008). PMID 18331472.
Mathieu Rappas, Daniel Bose and Xiaodong Zhang. Bacterial Enhancer-Binding Proteins: unlocking 54 dependent gene transcription. Curr Opinion Struct Biol. 7, 110-6 (2007). PMID 17157497.
Martin Buck, Daniel Bose, Patricia C. Burrows, Wendy Cannon, Nicolas Joly, Tillmann Pape, Mathieu Rappas, Jorg Schumacher, Sivaramesh Wigneshweraraj, Xiaodong Zhang. A second paradigm for gene activation in bacteria. Biochem Soc Trans. 34, 1067-71 (2006). PMID 17073752.