Eukaryotic protein-coding genes are transcribed by RNA polymerase II (RNAPII) through a cycle composed of three main phases: initiation, elongation, and termination. Recent studies using chromatin immunoprecipitation coupled to high-throughput sequencing suggest that the density of RNAPII molecules is higher at the 39-end relative to the gene body. Here we show that this view is biased due to averaging density profiles for ''metagene'' analysis. Indeed, the majority of genes exhibit little, if any, detectable accumulation of polymerases during transcription termination. Compared with genes with no enrichment, genes that accumulate RNAPII at the 39-end are shorter, more frequently contain the canonical polyadenylation [poly(A)] signal AATAAA and G-rich motifs in the downstream sequence element, and have higher levels of expression. In 1% to 4% of actively transcribing genes, the RNAPII enriched at the 39-end is phosphorylated on Ser5, and we provide evidence suggesting that these genes have their promoter and terminator regions juxtaposed. We also found a striking correlation between RNAPII accumulation and nucleosome organization, suggesting that the presence of nucleosomes after the poly(A) site induces pausing of polymerases, leading to their accumulation. Yet we further observe that nucleosome occupancy at the 39-end of genes is dynamic and correlates with RNAPII density. Taken together, our results provide novel insight to transcription termination, a fundamental process that remains one of the least understood stages of the transcription cycle.[Supplemental material is available for this article.]Eukaryotic protein-coding genes are transcribed by a molecular engine powered by RNA polymerase II (RNAPII). Transcription is a repetitive, cyclic process composed of three main phases: initiation, elongation, and termination (Fuda et al. 2009). The transcription cycle starts with RNAPII gaining access to the promoter, unwinding DNA and initiating RNA synthesis. RNAPII must then get a stable grip on both the template DNA and the growing RNA chain and proceed elongating through the entire body of the gene. Finally, the RNA is released and RNAPII can reinitiate to start a new round of transcription. In mammals, termination by RNAPII can occur anywhere from a few base pairs to several kilobases downstream from the annotated 39-end of the gene, which corresponds to the polyadenylation [poly ( the other results from a ''torpedo'' effect on RNAPII induced by rapid exonuclease degradation of the 59-uncapped RNA produced after cleavage at the poly(A) site.Transcription termination plays a vital role in cells because it controls gene expression and ensures genomic partitioning (Kuehner et al. 2011). However, termination remains one of the least understood stages of the transcription cycle. Recent studies using chromatin immunoprecipitation coupled to high-throughput sequencing (ChIP-seq) revealed higher average polymerase density downstream from the polyadenylation [poly(A)] site compared with the transcribed region (Rahl e...