To understand the factor interactions of transcribing RNA polymerase II (RNApII) in vivo, chromatin immunoprecipitations were used to map the crosslinking patterns of multiple elongation and polyadenylation factors across transcribed genes. Transcription through the polyadenylation site leads to a reduction in the levels of the Ctk1 kinase and its associated phosphorylation of the RNApII C-terminal domain. One group of elongation factors (Spt4/5, Spt6/Iws1, and Spt16/Pob3), thought to mediate transcription through chromatin, shows patterns matching that of RNApII. In contrast, the Paf and TREX/THO complexes partially overlap RNApII, but do not crosslink to transcribed regions downstream of polyadenylation sites. In a complementary pattern, polyadenylation factors crosslink strongly at the 3' ends of genes. Mutation of the 3' polyadenylation sequences or the Rna14 protein causes loss of polyadenylation factor crosslinking and read-through of termination sequences. Therefore, transcription termination and polyadenylation involve transitions at the 3' end of genes that may include an exchange of elongation and polyadenylation/termination factors.