Arid1a

ChIP assay was performed according to the protocol developed by Upstate Biotechnology. Protein G beads were pre-blocked and conjugated with 2 μg antibodies at 4 °C overnight. The next day, the cells were cross-linked by 1% formaldehyde, lysed, and sonicated with Bioruptor^TM UCD-200 in sequence, of which 1.25% cell lysate from each sample were saved as WCE DNA and stored at −20 °C. The lysate was incubated with the antibody-bound beads on the rotator at 4 °C overnight. The beads next were adequately washed for seven times with RIPA buffer avoiding the false-positive fragments residual. Finally, both beads and frozen WCE input DNA were reversely cross-linked and purified using PCR Purification Kit (Qiagen) after RNase A and Proteinase K treatment. The antibodies for ChIP assays were ARID1A (Cell Signaling Technology, 12354S), BRG1 (Santa Cruz Biotechnology, sc-17796), CTCF (Cell Signaling Technology, 3418S), RAD21 (Abcam, ab992), H3K4me1 (Abcam, ab8895), H3K27ac (Abcam, ab4729), H3K9me3 (Abcam, ab8898) and H3K27me3 (Abcam, ab108245). The ChIP libraries for Illumina sequencing were constructed using NEBNext ChIP-Seq Library Prep Master Mix and sequenced on Illumina HiSeq-2500 instrument. The primers information for ChIP-QPCR assays were listed in Table S1.4.

Pancreas tissue was snap frozen in liquid nitrogen was lysed on ice with RIPA buffer containing HALT Protease and Phosphatase inhibitor cocktail. Primary antibody incubation was performed overnight at 4°C in Tris-buffered saline containing 5% milk and 0.05% Tween-20. The following antibodies were used: GFP (Cell Signaling Technology 2956), Arid1a (Cell Signaling Technology 12354), Cpa1 (R and D AF2765), Amylase (Sigma A8273) and Actin-HRP (Sigma A3854). Blots were developed with SuperSignal West Femto substrate (ThermoFisher).

Chromatin immunoprecipitation (ChIP) was performed on cells crosslinked with 1% formaldehyde for 5 minutes at 37°C, quenched with 2 mol/L glycine and washed with PBS, and then sonicated in a Covaris E220 sonicator to generate 300–600 bp DNA fragments. Immunoprecipitation was performed using a control IgG (Santa Cruz Biotechnology) and antibodies against MUC1-C (Cell Signaling Technology, catalog no. 16564, RRID:AB_2798765), JUN (Abcam, catalog no. ab32137, RRID:AB_731608), ARID1A (Cell Signaling Technology, catalog no. 12354, RRID: AB_263710), PBRM1 (Cell Signaling Technology, catalog no. E6N2K), EP300 (Cell Signaling Technology, catalog no. D2X6N), H3K27ac (Abcam, catalog no. ab4729, RRID:AB_2118291), H3K4me1 (Abcam, catalog no. ab8895, RRID:AB_306847), and H3K4me3 (Abcam, catalog no. ab8580; RRID:AB_306649). Precipitated DNAs were detected by PCR using primers listed in Supplementary Table S3. Quantitation was performed on immunoprecipitated DNA using SYBR-green and the CFX384 Real-Time PCR Machine (Bio-Rad). Data are reported as fold enrichment relative to IgG (8 (link)).

POU2F3 (#36135), H3K27ac (#8173), H3K4me1 (#5326), H3K4me3 (#9751), H3K27me3 (#9733), Histone H3 (#4499), Cleaved-PARP (#5625), Cleaved Caspase 3 (#9664), SUZ12 (#3737), EZH2 (#5246), BRG1 (#49360), BRM (#11966), ARID1A (#12354), BAF57 (#11956), BAF155 (#11956), BAF60A (#35070), BAF47 (#91735), and PTEN (#9188) antibodies were purchased from Cell Signaling. Tubulin antibody (E7) was purchased from the Developmental Studies Hybridoma Bank. HSP90 (sc-7947) antibody was purchased from Santa Cruz. BRG1 (ab110641) and EZH2 (ab191250) antibodies were purchased from Abcam, and were used for ChIP-seq. The POU2AF2 (C11orf53) antibody was produced in rabbits at Pocono Rabbit Farm And Laboratory Inc. by using full-length POU2AF2 recombinant protein as antigen. For all of the western blot experiments, the antibody dilution is 1: 2k. For immunoprecipitation (IP) and chromatin immunoprecipitation (ChIP), 5 μg of antibody per reaction was used. The small molecule inhibitors GSK126 (S7061) and JQ1 (S7110) were purchased from Selleck Chemicals. The small molecule inhibitor BRM014 (HY-119374) was purchased from Med Chem Express.