Branson s250 digital sonicator

Chromatin immunoprecipitation (ChIP) was performed as previously published (6) . Briefly, cells were treated with 1% formaldehyde, then 0.125 M glycine was added. The cells were collected in PBS, resuspended in lysis buffer and sonicated (BRANSON S250 digital sonicator, Branson, Danbury, CT, USA). Pre-cleared chromatin was quantified using Qubit (dsDNA BR Assay Kit, Life Technologies); 2 ug chromatin was incubated overnight at 4°C with anti-IgG (Santa Cruz Biotechnology, Dallas, TX, USA), anti-DNMT1, -DNMT3A, -DNMT3B, and anti-H3K9me3, -H3K27me3, -H3K4me3 and -H3K36me3 (all Active Motif). Ten percent of the total lysate was used for input control. DNA was extracted with the Chromatin IP DNA extraction kit (Active Motif) following the manufacturer protocol.
Immunoprecipitation products were amplified using iTAq Polymerase (Bio-Rad, Hercules, CA, USA) and specific primers (Supplementary Table 1B).

Chromatin immunoprecipitation (ChIP) assays were performed based on a modification of previously published methods from our laboratory (Babbio et al., 2012) . Briefly, cells were cross-linked by adding 1% formaldehyde to the culture medium: the cross-linking reaction was quenched by adding 0.125 M glycine and collected in PBS. Cell pellets were re-suspended in lysis buffer and sonicated 14 times for 10 seconds on ice (BRANSON S250 digital sonicator, Branson, Danbury, CT, USA). Sonicated chromatin was incubated overnight at 4 °C in dilution buffer with anti-IgG (Santa Cruz Biotechnology, Santa Cruz, CA, USA), anti-UHRF1 (IGBMC), anti-H3K9me3, anti-H3K9me2, anti-H3K27me3 and anti-H3K4me3 (Active Motif). Twenty percent of the total lysate was used for input control. DNA was extracted using phenol/chloroform/isoamyl alcohol, precipitated in ethanol and resuspended in H 2 O.