Regulation of RNA polymerase II processivity by Spt5 is restricted to a narrow window during elongation

Spt5 is a highly conserved RNA polymerase II (Pol II)‐associated pausing and elongation factor. However, its impact on global elongation and Pol II processivity in mammalian cells has not been clarified. Here, we show that depleting Spt5 in mouse embryonic fibroblasts (MEFs) does not cause global elongation defects or decreased elongation rates. Instead, in Spt5‐depleted cells, a fraction of Pol II molecules are dislodged during elongation, thus decreasing the number of Pol II complexes that complete the transcription cycle. Most strikingly, this decrease is restricted to a narrow window between 15 and 20 kb from the promoter, a distance which coincides with the stage where accelerating Pol II attains maximum elongation speed. Consequently, long genes show a greater dependency on Spt5 for optimal elongation efficiency and overall gene expression than short genes. We propose that an important role of Spt5 in mammalian elongation is to promote the processivity of those Pol II complexes that are transitioning toward maximum elongation speed 15–20 kb from the promoter. In contrast to the global role Spt5 plays in RNA polymerase II pausing and elongation in yeast, its depletion in mouse embryonic fibroblasts triggers dissociation of Pol II at a specific region 15–20 kb downstream from the promoter. In contrast to its global role in RNA polymerase II pausing and elongation in yeast, Spt5 depletion in mouse triggers dissociation of Pol II at a specific region 15–20 kb downstream from the promoter.