Genomic mapping of RNA polymerase II reveals sites of co-transcriptional regulation in human cells
Brodsky, Alexander S
Keenan, Benjamin J
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CitationBrodsky, Alexander S., Clifford A. Meyer, Ian A. Swinburne, Giles Hall, Benjamin J. Keenan, Xiaole S. Liu, Edward A. Fox, and Pamela A. Silver. 2005. Genomic mapping of RNA polymerase II reveals sites of co-transcriptional regulation in human cells. Genome Biology 6(8): R64.
AbstractBackground: 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
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.
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