We have investigated the coupling of different RNA processing reactions and RNA transcription in yeast. By a combination of genetic and biochemical analyses we have found that the cleavage and polyadenylation factor subunit Ysh1p has multiple functions. In addition to its role in cleavage and polyadenylation it is involved in cleavage site selection and in transcription termination of messenger RNAs and small nucleolar RNAs.

In collaboration with the laboratory of Dr. André Gerber (ETH Zürich) we have carried out a genome wide analysis of the expression of the non-canonical poly(A) polymerases  Trf4p and Trf5p, which are components of the so-called TRAMP complexes that degrade aberrant and short-lived RNAs in  the budding yeast S. cerevisiae. Trf4p and Trf5p are alternative subunits of these complexes that add short poly(A) tails to their substrate RNAs that function as landing pads for exonucleases mediating RNA decay. Applying a genome-wide approach, we found overlapping yet distinct functional specificities of TRAMP complexes, and we demonstrate strong connections between RNA quality control and other RNA-related processes such as telomer length maintenance. Moreover, it appears that the degradation of specific target RNAs is not strictly dependent on the polyadenylation activity of Trf proteins in vivo.