1. 25 A +1 -1787+19 hMLH1 B Acetylated H3 Enrichment SW480 RKO Position from +1 BBII ++-- SW480 BIBI ++-- RKO C hMLH1 GAPDH Ab D Methyl-H3-K4 enrichment Position from +1 SW480 RKO SW480 BBII ++-- RKO BIBI ++-- E GAPDH hMLH1 Ab Figure 1 F Methyl-H3-K9 enrichment Position from +1 SW480 RKO GAPDH hMLH1 Ab SW480 BBII ++-- BIBI ++-- G RKO

2. 27 Figure 2 Methyl-H3-K4 enrichment BBBBIIII TSA++++---- Ab -++++--- hMLH1 GAPDH C Position from +1 D -TSA +TSA Methyl-H3-K9 enrichment Position from +1 E F hMLH1 GAPDH BBBBIIII TSA++++---- Ab-++++--- -TSA +TSA Acetylated H3 enrichment A GAPDH hMLH1 BBBBIIII TSA++++---- Ab-++++--- Position from +1 B -TSA +TSA

3. 29 Figure 3 Position from +1 -5-Aza-dC +5-Aza-dC E Methyl-H3-K9 enrichment F hMLH1 GAPDH 5-Aza-dC Ab BBII ---- + -+- BBII ++++ ++-- -5-Aza-dC +5-Aza-dC Position from +1 C Methyl-H3-K4 enrichment D GAPDH 5-Aza-dC Ab BBII ---- + -+- BBII ++++ ++-- hMLH1 B BBII ---- +-+- GAPDH 5-Aza-dC Ab BBII ++ + + ++-- Position from +1 A Acetylated H3 enrichment -5-Aza-dC +5-Aza-dC

4. 31 Figure 4

5. 33 +- RT GAPDH hMLH1 mock 5-Aza-dC +++++++------- mock 5-Aza-dC dH 2 O 12 h24 h48 h5 d B mock UMUUUUUUUUUUUMMMMMMMMMMM 5-Aza-dC mock 5-Aza-dC mock RKO SW480 PCR dH 2 O Bisulfite dH 2 O 12 h24 h48 h5 d A Figure 5

6. 53 β-Actin H3.3-HA 161718192021222324 WT 12345891011121415 β-Actin H3.3-HA B A 18 bp linker 408 bp90 bp H3.33xHA Clone 10 Clone 16 WT DAPIAnti-HAMerge C D 134116121310892 RKO 2 β-Actin H3.3-HA Figure 6

7. 55 Figure 7 B 12346 RKO 2 578910 WT β-Actin H3.3-HA 13141516171819201112 β-Actin H3.3-HA A RKO 2 12346 WT 89101112 β-Actin H3.3-HA C β-Actin H 3.3-HA RKO WT 1341118 SW480 WT SW480 clone 20 RKO Clones

8. 56 Figure 8 1341118 18 IgG RKO WT RKO Clones SW480 clone 20 SW480 WT 1341118 RKO WT RKO Clones Figure 8. H3.3-HA can be immunoprecipitated with anti-HA. Whole cell (top panel) or nuclear (bottom panel) lysates were immunoprecipitated with an anti-HA antibody. Numbers across the top indicate clone number. Whole cell lysate from RKO clone 18 was incubated with normal rabbit IgG as a negative control.

9. 58 Figure 9 B Position from +1 Methyl-H3-K4 Enrichment SW480 clone SW480 WT RKO clone RKO WT A H3.3 Enrichment Position from +1 SW480 clone SW480 WT RKO clone RKO WT