TI - Genomic mapping of RNA polymerase II reveals sites of co-transcriptional regulation in human cells . AB - Background Transcription by RNA polymerase II is regulated at many steps including initiation , promoter release , elongation and termination . Accumulation of RNA polymerase II at particular locations across genes can be indicative of sites of regulation . RNA polymerase II is thought to accumulate at the promoter and at sites of co-transcriptional alternative splicing where the rate of RNA synthesis slows . Results To further understand transcriptional regulation at a global level , we determined the distribution of RNA polymerase II within regions of the human genome designated by the ENCODE project . HypoPHOSphorylated RNA polymerase II localizes almost exclusively to 5' ends of genes . On the other hand , localization of total RNA polymerase II reveals a variety of distinct landscapes across many genes with 74% of the observed enriched locations at exons . RNA polymerase II accumulates at many annotated constitutively spliced exons , but is biased for alternatively spliced exons . Finally , RNA polymerase II is also observed at locations not in gene regions . Conclusion Localizing RNA polymerase II across many millions of base pairs in the human genome identifies novel sites of transcription and provides insights into the regulation of transcription elongation . These data indicate that RNA polymerase II accumulates most often at exons during transcription . Thus , a major factor of transcription elongation control in mammalian cells is the coordination of transcription and pre-mRNA processing to define exons .