Aroul Selvam1, Thomas Down2, Tim Hubbard
1asr25@cam.ac.uk, The Wellcome Trust Sanger Institute; 2td2@sanger.ac.uk, The Wellcome Trust Sanger Institute

The role of polyA signals (AATAAA) and poly(A) site in eukaryotic RNA polymerase II (polII) transcription termination was well known. However, it is becoming clear now that transcription does not stop at the poly(A) site but extends downstream for up to 2 kb. The extended mRNA then undergoes a co-transcriptional cleavage at a separate termination region before cleavage at poly(A) site and polymerase release (Dye and Proudfoot, 2001). To search for a common signal in this downstream region we took 200 bp upstream and 2000 bp downstream of poly(A) site for 422 annotated genes from human chromosome 22 (Collins, et. al., 2003). Initial attempts showed no significant base composition changes or hairpin structural motifs. However, by using the Eponine classifier (Down and Hubbard, 2002), a motif based sequence analysis package, we got models with consistent downstream signals. The models comprise a GC-rich motif and non-poly(T) motif, along with previously known poly(A) signal and GT motif, spread along the downstream region. These signals are thought to have a potential role in the polII transcription termination process by taking part in the co-transcriptional cleavage activity and subsequent polymerase release.