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Using genome-wide data to model signalling-responsive gene regulatory networks

Principal Supervisor: Professor Constanze Bonifer, Institute of Cancer and Genomic Sciences

Co-supervisor: Professor James Bentley Brown, School of Biosciences

PhD project title: Using genome-wide data to model signalling-responsive gene regulatory networks

University of Registration: University of Birmingham


Project outline:

Haematopoietic stem cells (HSCs) ensure lifelong mature blood cell production in the adult organism but the entire pool of adult HSCs is established during embryonic development. The haematopoietic system develops in successive steps, a first wave of primitive precursors emerges around E7.5 within the blood islands of yolk sac, followed by a second wave of definitive erythro-myeloid progenitors by E8.5. The emergence of HSCs occurs only by E10.5 within the major arteries of the embryo proper, where cells of a specialized endothelium, the hemogenic endothelium (HE), undergo endothelial-to-haematopoietic transition (EHT) in which endothelial identity is lost and haematopoietic fate is acquired. Blood cell specification can be faithfully recapitulated by the differentiation of embryonic stem cells (ESCs) in vitro. The differentiation of blood cells from pluripotent stem cells, which can be generated either directly from blastocyst (i.e. ESCs) or via reprogramming (i.e. iPSCs) route therefore has the potential to be of major importance for regenerative medicine. We and others have been using the ESC model system to investigate the molecular requirements for blood cell specification. Each developmental transition is regulated by an orchestrated interplay of stage-specific transcription factors which are connected to common and distinct target genes within a dynamic transcriptional network that regulates the transition from one cellular differentiation state to another (Obier and Bonifer, 2016; Obier et al., 2016; Goode et al., 2016).

However, while the roles of transcriptional regulators of haematopoietic differentiation are beginning to be understood, it is still less clear how outside signals direct their activity and how this leads to developmental-stage specific gene expression and shifts in the gene regulatory network. The reason for this is the fact that signalling pathways consist of a myriad of different components operating in a cell type-specific fashion and displaying multiple types of cross-talk making this process difficult to study. The transmission of signals into the nucleus involves surface molecules such as receptor kinases and at the receiving end in the nucleus inducible transcription factors. Such factors bind to their cognate cis-regulatory elements and alter gene expression in a signalling dependent way. By identifying and studying the function of such sequences and the factors binding to them we can obtain a first insight into which signalling pathways are involved and how signal transduction processes are coordinated at the genomic level. We will also be able to investigate, how such factors integrate into the wider gene regulatory network that is driven by cell fate deciding factors, and how they interact with the chromatin landscape and modify gene expression. The final aim of this work is to generate data and develop methodologies that allow one to build models that predict the behaviour of gene regulatory networks and of the components within such networks. The development of such methodology is of the essence if we want to direct cell fates for biotechnology and regenerative medicine approaches.



  • Dynamic Gene Regulatory Networks Drive Hematopoietic Specification and Differentiation. Goode DK, Obier N, Vijayabaskar MS, Lie-A-Ling M, Lilly AJ, Hannah R, Lichtinger M, Batta K, Florkowska M, Patel R, Challinor M, Wallace K, Gilmour J, Assi SA, Cauchy P, Hoogenkamp M, Westhead DR, Lacaud G, Kouskoff V, Gƶttgens B, Bonifer C. Dev Cell. 2016 Mar 7;36(5):572-87.

  • Cooperative binding of AP-1 and TEAD4 modulates the balance between vascular smooth muscle and hemogenic cell fate. Obier N, Cauchy P, Assi SA, Gilmour J, Lie-A-Ling M, Lichtinger M, Hoogenkamp M, Noailles L, Cockerill PN, Lacaud G, Kouskoff V, Bonifer C. Development. 2016 Dec 1;143(23):4324-4340.

  • Chromatin programming by developmentally regulated transcription factors: lessons from the study of haematopoietic stem cell specification and differentiation. Obier N, Bonifer C. FEBS Lett. 2016 Aug 6. doi: 10.1002/1873-3468.12343.

BBSRC Strategic Research Priority: Molecules, Cells and Systems

Techniques that will be undertaken during the project:

In this project we will use a novel bottom-up approach to study the function of signalling-responsive transcription factors in blood cell development. The student will learn how to grow and differentiate embryonic stem cells. S/He will use ChIP-Sequencing, ATAC-Seq and RNA-Seq to examine where signalling responsive factors bind and how binding impacts on gene expression. S/He will use genome editing to integrate dominant negative version of such factors into the genome. We will measure the impact of the introduction of these factors on blood cell development, gene expression and the epigenome, using genome-wide approaches. We will use sophisticated bioinformatics methodology and mathematical modelling to analyse such big data and build predictive models that allow to (i) predict how cis-regulatory elements in the genome respond to signalling events, (ii) use such models to predict the response to perturbations.

Contact: Professor Constanze Bonifer, Institute of Cancer and Genomic Sciences