24.04.09 Presentation at ISMB/ECCB 2009

Computational analysis about functional and non-functional transcription factor binding will be presented.

Joint work of the Workman and Beyer labs will be presented at ISMB/ECCB 2009 in Stockholm. Duygu Ucar will talk about how to distinguish functional from non-functional transcription factor binding. It turns out that about 50% of the observed binding events have no effect on the transcript levels of adjacent genes. The analysis shows that the presence or absence of specific co-factors is the major determinant of functionality.

Here is the full abstract:

Predicting Functionality of Protein-DNA Interactions by
Integrating Diverse Evidence

Chromatin immunoprecipitation (ChIP-chip) experiments enable
capturing physical interactions between regulatory proteins and DNA
in vivo. However, measurement of chromatin binding alone is not
sufficient to detect regulatory interactions. A detected binding event
may not be biologically relevant, or a known regulatory interaction
might not be observed under the growth conditions tested so-far. To
correctly identify physical interactions between TFs and genes and
to determine their regulatory implications under various experimen-
tal conditions, we integrated ChIP-chip data with motif binding sites,
nucleosome occupancy and mRNA expression datasets within a pro-
babilistic framework. This framework was specifically tailored for the
identification of functional and non-functional DNA binding events.
Using this, we estimate that only 50% of condition specific protein-
DNA binding in budding yeast is functional. We further investigated
the molecular factors determining the functionality of protein-DNA
interactions under diverse growth conditions. Our analysis suggests
that the functionality of binding is highly condition specific and highly
dependent on the presence of specific co-factors. Hence, the joint
analysis of both, functional and non-functional DNA binding may lend
important new insights into transcriptional regulation.

Link to the publication.


Go to Homepage