Proteome analysis of a CTR9 deficient yeast strain suggests that Ctr9 has function(s) independent of the Paf1 complex

The Ctr9 protein is a member of the Paf1 complex implicated in multiple functions: transcription initiation and elongation by RNA pol II, RNA processing and histone modifications. It has also been described as a triple-helical DNA binding protein. Loss of Ctr9 results in severe phenotypes similar to the loss of Paf1p, a Paf1 complex subunit. However, the exact role of Ctr9 is not entirely established. To study the biological role of the protein Ctr9 in yeast, we used 2-D gel electrophoresis and characterized proteome alterations in a ctr9Δ mutant strain. Here we present results suggesting that Ctr9 has function distinct from its established role in the Paf1 complex. This role could be linked to its ability to bind to DNA complex structures as triplexes that may have function in regulation of gene expression.

► Ctr9 is a yeast nuclear protein member of the Paf1 complex.
► The proteome of ctr9Δ and paf1Δ was analyzed.
► Ctr9 has distinct functions from its role in the Paf1 complex.
► Ctr9 binds to triple-helical DNA structures.
► Alterations in ctr9Δ are not directly correlated to unusual DNA structures.