News feed

Junior Group Leader Fellowship from the Lundbeck foundation!

Wed, 7 Dec 2011 15:03:14 +0100

We received a large grant of 10 million DKK from The Lundbeck foundation! Press release in Danish here. The grant has two main themes: Fundamental core promoter biology and alternative promoter usage in disease, using both experimental and computational methods.

Predicting RNA Polymerase II dynamics

Thu, 3 Nov 2011 09:56:35 +0100

Yun Chen, Mette Jörgensen, Raivo Kolde and coworkers have showed the feasibility of predicting recruitment, elongation of stalling of RNA polymerase II, using machine learning methods. The study also showed that a distinct set of epigenetic signals are necessary for recruitment of RNAPII, but not elongation. The report was published in BMC Genomics (open access).

Japan travel grant

Wed, 2 Nov 2011 15:43:25 +0100

Mette Boyd, postdoc in the group, received a grant from Japan Society for the Promotion of Science to make a short stay at RIKEN, Japan to learn experimental techniques.

Culture Night Copenhagen

Tue, 18 Oct 2011 12:12:02 +0200

The group had a very popular display at the Botanical Garden at the yearly Copenhagen Culture Night. The theme was gene regulation and DNA, with activities from extracting DNA from kiwi fruit, look at cells in microscope, looking at molecular visualizations and try out some protein structure manipulation in the computer. More photos here.
Thanks to everyone that participated or helped out on the way.

Review in Trends in Genetics

Wed, 21 Sep 2011 15:34:56 +0200

Eivind Valen and Albin Sandelin published a review in the highly respected journal Trends in Genetics. The review tries to describe the various types of signals that are important for transcription initiation - from sequence elements to chromatin marks. The article can be downloaded here.

Abstract is below:

Genomic and chromatin signals underlying transcription start-site selection

A central question in cellular biology is how the cell regulates transcription and discerns when and where to initiate it. Locating transcription start sites (TSSs), the signals that specify them, and ultimately elucidating the mechanisms of regulated initiation has therefore been a recurrent theme. In recent years substantial progress has been made towards this goal, spurred by the possibility of applying genome-wide, sequencing-based analysis. We now have a large collection of high-resolution datasets identifying locations of TSSs, protein–DNA interactions, and chromatin features over whole genomes; the field is now faced with the daunting challenge of translating these descriptive maps into quantitative and predictive models describing the underlying biology. We review here the genomic and chromatin features that underlie TSS selection and usage, focusing on the differences between the major classes of core promoters.