Table I Comparison of peptide data quality for RNA polymerase II subunits

All known RNA polymerase II subunits (Pol2A–Pol2L) except Pol2F were identified and quantified in the SILAC co-IP using GFP-Pol2C as bait. They all show high sequence coverage and a large number of peptides identified and quantified, underlining the quality of the data. The bait protein, GFP-Pol2C, is bold. log2(H/M) ratios of all subunits are normalized in the table so that log2(H/M) of Pol2C is 0. Subunits are listed above the bait protein when their interaction with the bait was increased upon α-amanitin treatment (log2(H/M) versus 2C > 0), whereas subunits are listed below when their interaction with the bait protein was decreased upon α-amanitin treatment (log2(H/M) versus 2C < 0). Interactions are considered significantly affected when log2(H/M) versus 2C > 1 or log2(H/M) versus 2C < −1 (equivalent to a change in value of 2-fold or greater).

Gene namesAccession numbersNo. of unique peptidesSequence coverageNo. of peptides quantifiedSILAC M/L ratiolog2(H/M) vs. 2C(H/M) S.D.
POLR2JIPI00003310.2, IPI00873238.1, IPI00291359.3, IPI00884938.1, IPI00878433.1, IPI00553186.2, IPI00744926.1, IPI00472231.7, IPI00556199.1, IPI00016841.3, IPI00748167.1, IPI00879159.1, IPI00880135.1457.52121.20.3515.5
POLR2BIPI00027808.1, IPI00873948.2, IPI00894355.1, IPI00894141.1, IPI00418797.4, IPI00026445.3, IPI00184886.3, IPI00894524.1, IPI00894248.18162.127221.50.3516.6
POLR2AIPI00031627.3, IPI00385524.1, IPI00419565.3, IPI00383337.1, IPI00784155.111661.421522.2−0.9736.1
POLR2HIPI00003309.4, IPI00791019.1, IPI00790361.1, IPI00791273.18581229.9−1.1531.5