Dr Dan Bose
School of Biosciences
Sir Henry Dale Fellow
+44 114 222 2838
Full contact details
School of Biosciences
Firth Court
Western Bank
Sheffield
S10 2TN
- Profile
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Career history
- 2019 - present: Sir Henry Dale Research Fellow, University of Sheffield, Sheffield, UK
- 2017 - 2019: Research Fellow, University of Sheffield, Sheffield, UK
- 2011 - 2016: Postdoctoral Research Associate, University of Pennsylvania, Philadelphia, USA
- 2009 - 2011: Postdoctoral Research Associate, Imperial College London, London, UK
- 2004 - 2008: PhD, Imperial College London, London, UK
- Research interests
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Only a small amount of the genome contains genes that code for proteins. In fact, much of the genome is transcribed into RNA, but the importance of these non-coding RNAs is only just becoming clear. Our research focuses on the mechanism of enhancer RNAs (eRNAs), non-protein coding RNAs transcribed from enhancers. Enhancers are non-coding genetic regulatory elements that regulate cell-type specific gene expression in metazoans; in humans, enhancers are hotspots for mutations in a number of diseases.
We look at how the unique sequence and structure of eRNAs allows them to control gene expression in enhancer-specific ways and what happens when this process goes wrong, for example in diseases such as ALS where enhancers are hotspots for mutations. We integrate multidisciplinary techniques such as cryo-EM with molecular biology and functional genomics approaches to build a picture of diverse features of eRNA function and how they interact with the epigenetic-machines that control gene expression across a variety of scales.
- Publications
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Show: Featured publications All publications
Featured publications
Journal articles
- Locally acting transcription factors regulate p53-dependent cis-regulatory element activity. Nucleic Acids Research. View this article in WRRO
- RNA Binding to CBP Stimulates Histone Acetylation and Transcription. Cell, 168(1-2), 135-149.e22. View this article in WRRO
- Interactions between the nucleosome histone core and Arp8 in the INO80 chromatin remodeling complex. Proceedings of the National Academy of Sciences, 109(51), 20883-20888.
- RNA polymerase and transcription elongation factor Spt4/5 complex structure. Proceedings of the National Academy of Sciences, 108(2), 546-550.
- Organization of an Activator-Bound RNA Polymerase Holoenzyme. Molecular Cell, 32(3), 337-346.
All publications
Journal articles
- Geometry-preserving expansion microscopy microplates enable high-fidelity nanoscale distortion mapping. Cell Reports Physical Science, 4(12). View this article in WRRO
- Enhancer RNAs step forward: new insights into enhancer function. Development, 149(16).
- Erratum: Rare variant burden analysis within enhancers identifies CAV1 as an ALS risk gene (Cell Reports (2020) 33(9), (S2211124720314455), (10.1016/j.celrep.2020.108456)). Cell Reports, 34(5).
- Locally acting transcription factors regulate p53-dependent cis-regulatory element activity. Nucleic Acids Research. View this article in WRRO
- Rare Variant Burden Analysis within Enhancers Identifies CAV1 as an ALS Risk Gene. Cell Reports, 33(9), 108456-108456.
- eRNA binding produces tailored CBP activity profiles to regulate gene expression.. RNA Biology, 14(12), 1655-1659. View this article in WRRO
- RNA Binding to CBP Stimulates Histone Acetylation and Transcription. Cell, 168(1-2), 135-149.e22. View this article in WRRO
- The Dimeric Architecture of Checkpoint Kinases Mec1ATR and Tel1ATM Reveal a Common Structural Organization. Journal of Biological Chemistry, 291, 13436-13447. View this article in WRRO
- Interactions between the nucleosome histone core and Arp8 in the INO80 chromatin remodeling complex. Proceedings of the National Academy of Sciences, 109(51), 20883-20888.
- Activity Map of theEscherichia coliRNA Polymerase Bridge Helix. Journal of Biological Chemistry, 286(16), 14469-14479.
- Electron microscopy studies on the quaternary structure of p53 reveal different binding modes for p53 tetramers in complex with DNA. Proceedings of the National Academy of Sciences, 108(2), 557-562.
- RNA polymerase and transcription elongation factor Spt4/5 complex structure. Proceedings of the National Academy of Sciences, 108(2), 546-550.
- Mechanisms for activating bacterial RNA polymerase. FEMS Microbiology Reviews, 34(5), 611-627.
- Foot-and-Mouth Disease Virus 2C Is a Hexameric AAA+ Protein with a Coordinated ATP Hydrolysis Mechanism. Journal of Biological Chemistry, 285(32), 24347-24359.
- Organization of an Activator-Bound RNA Polymerase Holoenzyme. Molecular Cell, 32(3), 337-346.
- Visualizing the organization and reorganization of transcription complexes for gene expression. Biochemical Society Transactions, 36(4), 776-779.
- Modus operandi of the bacterial RNA polymerase containing the σ54promoter-specificity factor. Molecular Microbiology, 68(3), 538-546.
- Dissecting the ATP hydrolysis pathway of bacterial enhancer-binding proteins. Biochemical Society Transactions, 36(1), 83-88.
- Bacterial enhancer-binding proteins: unlocking σ54-dependent gene transcription. Current Opinion in Structural Biology, 17(1), 110-116.
- A second paradigm for gene activation in bacteria. Biochemical Society Transactions, 34(6), 1067-1071.
- Notch signalling influences cell fate decisions and HOX gene induction in axial progenitors. Development.
- Enhancers, phase separation and the RNA polymerase II transfer model. BioEssays.
Conference proceedings papers
- THE MECHANISTIC BASIS OF nif GENE ACTIVATION. BIOLOGICAL NITROGEN FIXATION: TOWARDS POVERTY ALLEVIATION THROUGH SUSTAINABLE AGRICULTURE, Vol. 42 (pp 339-+)
Preprints
- Cooperation between Intrinsically Disordered Regions regulates CBP condensate behaviour., Cold Spring Harbor Laboratory.
- Notch signalling influences cell fate decisions and HOX gene induction in axial progenitors, Cold Spring Harbor Laboratory.
- Rare Variant Burden Analysis within Enhancers Identifies <i>CAV1</i> as a New ALS Risk Gene.
- Locally acting transcription factors are required for p53-dependent cis-regulatory element activity.
- Locally acting transcription factors regulate p53-dependent cis-regulatory element activity. Nucleic Acids Research. View this article in WRRO
- Research group
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PhD studentships
We always want to hear from students interested in our research. Funded PhD studentships will be advertised here as they become available. Well qualified and motivated graduates should contact me directly to discuss potential projects and options for funding.
Sources of PhD support:
- BBSRC White Rose Doctoral Training Program
- MRC DiMeN Doctoral Training Partnership
- Joint China Scholarship Council Postdoctoral fellowships
We welcome applications from talented scientists with diverse research backgrounds. Our multidisciplinary research means we can provide training for researchers with a strong track record who are motivated to gain experience and develop skills in different areas and techniques.
Project students and internships
Students wishing to apply for summer internships are welcome and should send a CV describing their motivations and interests.
- Teaching activities
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Level 1 Modules
- MBB162: Genetics
Level 2 Modules
- MBB265: Practical molecular bioscience
Level 3 Modules
- MBB346: Genetic pathways from zygote to organism
- MBB325: The world of RNA