An ambitious EC-funded research initiative on epigenetics advancing towards systems biology

University of Cambridge, Cancer Reserach UK Cambridge Institute

Description

The Markowetz lab is looking for a postdoc with a background in molecular biology (or any other 'wet-lab' discipline) to investigate determinants of oestrogen receptor (ER) binding dynamics. The postdoc will work closely together with researchers in the Markowetz lab and Carroll lab (also CRUK CI) in an integrated experimental-computational approach.

Background: Breast cancer is the most frequently occurring cancer in women, and in ~70% of all cases the estrogen receptor (ER) drives tumor growth and cell proliferation. ER is known to associate with numerous cofactors (Hurtado et al, 2011) that function on multiple levels, including many with enzymatic activity that can modify ER and other cofactors.

The interplay between ER, its cofactors and the chromatin are highly dynamic (Zwart et al 2010). ER cycles on the chromatin when stimulated, a periodicity, which is followed by the components of the transcription complex that are subsequently recruited with their own intrinsic timing. The details of this process are unknown.

To address this problem, we propose a computationally driven experimental approach in which a mathematical model of ER signalling and binding (based on Tyson et al 2011; Xu et al 2012) guides experiments to more fully understand ER dynamics. Our quantitative model will be the first to contain all major factors determining ER binding: (i) ligand inputs like oestrogen and growth factors, (ii) upstream signalling pathways (IGF, EGF) that regulate ER and co-factor activity, (iii) (epi-)genetic determinants of ER binding (DNA methylation, histone modifications, SNPs), and finally (iv) binding behaviour of ER as output.

Approach: We will activate upstream signalling pathways with ligands and then silence individual components of the ER pathway with siRNAs. We will target ER-associated pioneer factors and co-factors, which have been shown to be critical for ER-DNA interactions and regulation of ER function. For each perturbation and at three time-points, we will measure ER binding by ChIP-seq and measure the functional impact of ER binding by RNA-seq. Additionally, we plan to use fluorescence recovery after photo-bleaching (FRAP) to assess ER mobility on a timescale of seconds. Using the same target genes, time points and ligands, we will measure histone methylation H3K4me2 by ChIP-seq. Additionally, we will measure DNA methylation by pyro-sequencing of specific enhancers and regulatory elements near important ER-regulated genes and oncogenes, which are thought to represent most ER-responsive elements.

Taken together these technologies give a comprehensive picture of ER binding dynamics. Analysing how perturbing individual components of the ER complex changes these dynamics will result in a much-refined understanding of their functions and interactions. Analysing histone and DNA methylation and their changes after perturbing the ER complex will give insights into feedback mechanisms between epigenetic marks and ER signalling.

Qualifications

The ideal candidate has a PhD in one of the biological sciences (molecular biology, biochemistry, etc), extensive wet-lab experience (ChIP-seq, RNA-seq, FRAP, RNAi), strong interdisciplinary interests and a desire to learn skills in computational data analysis and mathematical modelling. Life in the Markowetz lab is very collaborative and excellent communication and inter-personal skills are a must.

Salary

Depending on qualifications

Application details

Please apply by sending your CV and publication list together with a motivation letter to:
Florian Markowetz - This e-mail address is being protected from spambots. You need JavaScript enabled to view it

Relavant web link: http://www.markowetzlab.org