1. 3box PSE -55 DSE -220+1 +350 U2 -800-500 +700 +150 -15-200 +215 % of input PTF 4563 Figure S1. High resolution chromatin immunoprecipitation of PTF on U2 snRNA genes. qRT-PCR of ChIP analysis of the U2 gene using anti-PTF antibodies and the primers noted on the diagram of the U2 genes shown above.

2. % of input Histone H4 Histone H2A Histone H2B RNU2 locus -actin gene Histone H4 Histone H2A Histone H2B % of input Figure S2. All four histones have the same pattern of depletion on the U2 and the -actin genes. qRT-PCR of ChIP analysis of the U2 and -actin genes using antibodies against the histones noted.

3. % of input - -amanitin + -amanitin % of input Histone H3RNA pol II RNU2 locus Figure S3. Nucleosomal depletion on U2 genes is transcription-independent. qRT-PCR of ChIP analysis of the U2 gene using antibodies against H3 and pol II, with or without treatment of the cells with -amanitin.

4. 3box PSE -55 DSE -220 +1 +215 CT-rich +600 U2 +850+1500+2100+300+500+700 78 transcription % of input NELF-E Histone H3 CTCF Figure S4. Fine mapping of NELF and CTCF on the RNU2 locus. qRT-PCR of ChIP analysis of the RNU2 locus, using antibodies against H3, NELF-E and CTCF using the primers noted on the diagram of the RNU2 locus above.

5. RNU2 locus -actin gene 3box PSE -55 DSE -220 +1 +215 CT-rich +600 U2 4a 456 3 Ser5 relative to Pol II Ser7 relative to Pol II -800 Figure S5. Distribution of Ser5 and Ser7 phosphorylation on the RNU2 locus and the -actin gene. qRT-PCR of ChIP analysis using antibodies against phospho-Ser5 and phospho-Ser7, relative to the Pol II signal. The additional primer, 4a, is noted on the diagram of the RNU2 locus above. All other primers are as shown in Figure 1.

6. Spt16 level (% input) Pol II level (% input) Spt16 Pol II Spt16 Pol II RNU2 locus -actin gene Figure S6. FACT is associated with both snRNA and protein-coding genes. qRT-PCR of ChIP analysis of the U2 and -actin genes, using antibodies against the Spt16 subunit of FACT. The pol II level is indicated by a dotted line. Ac-H4 (related to H4) RNU2 locus -actin gene H4 level (% input) AcH4/H4 H4 Figure S7. H4 acetylation across the RNU2 locus and -actin gene. qRT-PCR of ChIP analysis of the U2 and -actin genes using antibodies against H4 and acetyl H4 (Ac-H4). The H4 level is indicated by a dotted line and the Ac-H4 level is shown relative to total H4.

7. H3-K36M 3 (related to H3) RNU2 locus -actin gene +DRB DRB - +DRB DRB - H3-K36M 3 (related to H3) Figure S8. H3-K36 trimethylation is DRB-sensitive. qRT-PCR of ChIP analysis of the U2 and -actin genes using antibodies against trimethyl H3-K36 (H3-K36M3) with or without treatment of the cells with DRB. H3-K9M 3 (related to H3) RNU2 locus -actin gene H3 level (% input) H3-K9M 3 /H3 H3 H3-K9M 3 (related to H3) Figure S9. H3-K9 trimethylation across the RNU2 locus and -actin gene. qRT-PCR of ChIP analysis of the U2 and -actin genes using antibodies against trimethyl H3-K9 (H3-K9M3). The H3 level is indicated by a dotted line and the H3-K9M3 level is shown relative to total H3.

8. RNU2 locus -actin gene GAPDH gene -actin gene 1 -2780/-2600-609/-479-119/+30-102/+71 2 -2000/-1819-169/-10+258/+407+246/+415 3 -919/-739+222/+361+658/+817+666/+895 4 -40/+35+742/+911+1018/+1167+989/+1122 5 +270/+460+1112/+1242+1328/+1501+1656/+1789 6 +651/+820+1382/+1511+3333/+3507+2550/+2664 7 +1422/+1560+2540/+2671 8 +2022/+2202+3541/+3682 Figure S10. Regions analysed by qRT-PCR after chromatin immunoprecipitation. Regions amplified by each pair of primers on the RNU2 locus, the -actin, GAPDH and -actin genes are indicated relative to the transcription start site.