Modelling the transcriptional response to ER signalling in breast cancer cells

Add to your list(s) Download to your calendar using vCal

• Magnus Rattray (Manchester)
• Monday 06 October 2014, 16:00-17:00
• CRUK CI Lecture Theatre.

If you have a question about this talk, please contact Florian Markowetz.

We are developing computational models of transcription and its regulation from high-throughput time course data. I will discuss two models: (1) We model RNA polymerase (pol-II) dynamics using data from pol-II ChIP-Seq time course datasets (wa Maina et al. 2014). Our model is used to estimate the elongation speed and promoter activation kinetics for early targets of ER-alpha in MCF7 cells. By clustering the promoter activation profiles we can associate differences in the kinetics with transcription factor binding, e.g. the earliest clusters are all associated with nearby FOXA1 binding. (2) We model the relationship between pol-II dynamics and mRNA production by combining 3’ pol-II ChIP-Seq data with RNA -Seq data. We find that 11% of genes where we can fit our model exhibit surprisingly long production delays which appear to be associated with splicing. Although transcription delays are longer than splicing delays for most genes, there are a significant set where splicing is the rate-limiting step. We use a Bayesian non-parametric approach to model temporal profiles such as the pol-II activation which allows us to limit the number of free parameters in our model and to capture the uncertainty in our inferences.

C. wa Maina, A. Honkela, F. Matarese, K. Grote, H. Stunnenberg, G. Reid, N. Lawrence and M. Rattray. “Inference of RNA Polymerase II Transcription Dynamics from Chromatin Immunoprecipitation Time Course Data.” PLoS computational biology 10, no. 5 (2014): e1003598.

This talk is part of the Seminars on Quantitative Biology @ CRUK Cambridge Institute series.

This talk is included in these lists:

• All CMS Events
• All Talks (aka the CURE list)
• Biology
• CCC talks for website
• CRUK CI Lecture Theatre
• CRUK CI Seminars
• CamBridgeSens
• Cambridge Centre for Data-Driven Discovery (C2D3)
• Cambridge talks
• Chris Davis' list
• Computational and Systems Biology
• Graduate-Seminars
• Interested Talks
• Liam
• Life Science Interface Seminars
• Life Sciences
• Life Sciences
• ME Seminar
• PMRFPS's
• School of Physical Sciences
• Seminars on Quantitative Biology @ CRUK Cambridge Institute
• Trust & Technology Initiative - interesting events
• bld31
• custom
• my_list
• ndk22's list
• ob366-ai4er
• other talks
• rp587
• se393's list
• sfm36

Note that ex-directory lists are not shown.