Genomes and Genes
Affiliation: University of Cambridge
- Wilson N, Kent D, Buettner F, Shehata M, Macaulay I, Calero Nieto F, et al. Combined Single-Cell Functional and Gene Expression Analysis Resolves Heterogeneity within Stem Cell Populations. Cell Stem Cell. 2015;16:712-24 pubmed publisher..Finally, we demonstrated the broader applicability of this approach for linking key molecules with defined cellular functions in another stem cell system. ..
- Wilkinson A, Kawata V, SchÃ¼tte J, Gao X, Antoniou S, Baumann C, et al. Single-cell analyses of regulatory network perturbations using enhancer-targeting TALEs suggest novel roles for PU.1 during haematopoietic specification. Development. 2014;141:4018-30 pubmed publisher..We therefore establish TALEs as powerful new tools to study the functionality of transcriptional networks that control developmental processes such as early haematopoiesis. ..
- Gottgens B, Barton L, Grafham D, Vaudin M, Green A. Tdr2, a new zebrafish transposon of the Tc1 family. Gene. 1999;239:373-9 pubmed..Tdr2 transposons may facilitate the development of novel transposon-based tools for the genetic analysis of zebrafish. ..
- Lim C, Wang H, Woodhouse S, Piterman N, Wernisch L, Fisher J, et al. BTR: training asynchronous Boolean models using single-cell expression data. BMC Bioinformatics. 2016;17:355 pubmed publisher..Given the simplicity of Boolean models and the rapid adoption of single-cell genomics by biologists, BTR has the potential to make an impact across many fields of biomedical research. ..
- Moignard V, Gottgens B. Dissecting stem cell differentiation using single cell expression profiling. Curr Opin Cell Biol. 2016;43:78-86 pubmed publisher..Here we review the contributions of single cell biology to understanding stem cell differentiation so far, both as a new methodology for defining cell types and a tool for understanding the complexities of cellular decision-making. ..
- Basilico S, Gottgens B. Dysregulation of haematopoietic stem cell regulatory programs in acute myeloid leukaemia. J Mol Med (Berl). 2017;95:719-727 pubmed publisher..Finally, we suggest that disruption of stem cell regulatory programs is likely to play an important role in many other pathologies including ageing-associated regenerative failure. ..
- Wilkinson A, Nakauchi H, Gottgens B. Mammalian Transcription Factor Networks: Recent Advances in Interrogating Biological Complexity. Cell Syst. 2017;5:319-331 pubmed publisher..We also discuss how these emerging technologies facilitate new ways to interrogate complex TF networks, consider the current open questions in the field, and comment on potential future directions and biomedical applications. ..
- Ibarra Soria X, Jawaid W, Pijuan Sala B, Ladopoulos V, Scialdone A, Jörg D, et al. Defining murine organogenesis at single-cell resolution reveals a role for the leukotriene pathway in regulating blood progenitor formation. Nat Cell Biol. 2018;20:127-134 pubmed publisher..Thus, this comprehensive single-cell map can be exploited to reveal previously unrecognized pathways that contribute to tissue development. ..
- Gottgens B, Broccardo C, Sanchez M, Deveaux S, Murphy G, Gothert J, et al. The scl +18/19 stem cell enhancer is not required for hematopoiesis: identification of a 5' bifunctional hematopoietic-endothelial enhancer bound by Fli-1 and Elf-1. Mol Cell Biol. 2004;24:1870-83 pubmed
- Gottgens B, Nastos A, Kinston S, Piltz S, Delabesse E, Stanley M, et al. Establishing the transcriptional programme for blood: the SCL stem cell enhancer is regulated by a multiprotein complex containing Ets and GATA factors. EMBO J. 2002;21:3039-50 pubmed..Our results suggest that these transcription factors are key components of an enhanceosome responsible for activating SCL transcription and establishing the transcriptional programme required for HSC formation. ..
- Sive J, Gottgens B. Transcriptional network control of normal and leukaemic haematopoiesis. Exp Cell Res. 2014;329:255-64 pubmed publisher..We look in detail at examples of how these approaches can be used to dissect out the regulatory mechanisms controlling normal haematopoiesis, as well as the dysregulated networks associated with haematological malignancies. ..
- Landry J, Kinston S, Knezevic K, Donaldson I, Green A, Gottgens B. Fli1, Elf1, and Ets1 regulate the proximal promoter of the LMO2 gene in endothelial cells. Blood. 2005;106:2680-7 pubmed..Together, these results suggest that the conserved proximal promoter is central to LMO2 transcription in hematopoietic and endothelial cells, where it is regulated by Ets factors. ..
- Gottgens B, Barton L, Chapman M, Sinclair A, Knudsen B, Grafham D, et al. Transcriptional regulation of the stem cell leukemia gene (SCL)--comparative analysis of five vertebrate SCL loci. Genome Res. 2002;12:749-59 pubmed..Analysis of the SCL promoter/enhancer revealed five motifs, which were conserved from zebrafish to mammals, and each of which is essential for the appropriate pattern or level of SCL transcription...
- Gottgens B, Gilbert J, Barton L, Grafham D, Rogers J, Bentley D, et al. Long-range comparison of human and mouse SCL loci: localized regions of sensitivity to restriction endonucleases correspond precisely with peaks of conserved noncoding sequences. Genome Res. 2001;11:87-97 pubmed
- Mutasa Göttgens E, Joshi A, Holmes H, Hedden P, Gottgens B. A new RNASeq-based reference transcriptome for sugar beet and its application in transcriptome-scale analysis of vernalization and gibberellin responses. BMC Genomics. 2012;13:99 pubmed publisher..Transcriptome-scale identification of agronomically important traits as used in this study should be widely applicable to all crop plants where genomic resources are limiting. ..