Functional association of Gdown1 with RNA polymerase II poised on human genes

Most human genes have RNA polymerase II (RNAP II) molecules poised in promoter proximal regions regardless of expression levels. We present evidence that Gdown1, a substoichiometric RNAP II subunit shown previously to render RNAP II responsive to mediator, is involved in this process. Using a defined system Gdown1 specifically blocked the positive function of TFIIF, inhibited the termination activity of TTF2, and influenced NELF and DSIF function. In the absence of P‐TEFb, Gdown1 led to the production of stably paused polymerases in the presence of nuclear extract. These polymerases retained sensitivity to the transcript cleavage factor TFIIS and in vitro this factor helps keep engaged polymerases close to the promoter. To analyze the function of Gdown1 in vivo, RNAP II ChIP‐chip and ChIP‐seq were used to demonstrate that Gdown1 co‐maps with promoter proximally paused polymerases across the human genome. Our results strongly implicate Gdown1 in generating stably poised polymerases that are still responsive to P‐TEFb. This work was supported by NIH grants GM35500 and AI074392 to D.H.P. and NHGRI grant HG002668‐05 to R.A.Y.