H3k36me3

The following antibodies were used for chromatin immunoprecipitation: (i) H3K4me1: Cell Signaling Technologies, cat #5326BF, lot #2 (quantity: 3 µg/concentration: 0.015 µg/µl); (ii) H3K4me3: Cell Signaling Technologies, cat #9751BF, lot#6 (quantity: 5 µg/concentration: 0.025 µg/µl); (iii) H3K9me3: Abcam, cat #Ab8898, lot #GR93671-1 (quantity: 3 µg/concentration: 0.015 µg/µl); (iv) H3K27me3: Cell Signaling Technologies, cat #9733S, lot #6 (quantity: 10 µg/concentration: 0.05 µg/µl); (v) H3K27ac: Diagenode, cat #pAB-196-050, lot #A1723-0041D (quantity: 6 µg/concentration: 0.03 µg/µl); (vi) H3K36me3: Active motif, cat #MABI0333, lot #12003 (quantity: 2 µg/concentration: 0.01 µg/µl). Libraries were prepared using the automated protocol for the Kapa HTP Library Preparation Kit (Illumina), and sequencing was performed using the Illumina HiSeq 2000, as per the manufacturer’s instructions, to achieve at least 30 and 60 million reads for narrow (H3K27ac and H3K4me3) and broad (H3K27me3, H3K36me3, H3K4me1, and H3K9me3) marks, respectively (Supplementary Fig. 1a).

ChIP of LMNA/C, H3K4me3, H3K4me1, H3K27ac, H3K9me3, H3K27me3 and H3K36me3 was done as described [7 (link)]. Briefly, cells were fixed with 1% formaldehyde, lysed in 50 mM Tris-HCl, pH 8, 10 mM EDTA, 1% SDS, protease inhibitors and Na-butyrate, and sonicated into ~200 bp fragments using a Picorupter (Diagenode; Seraing, Belgium). After sedimentation, the chromatin supernatant was incubated with anti-LMNA/C (Santa Cruz sc7292x), H3K27ac (Diagenode c15410174), H3K4me3 (Diagenode c15410003), H3K4me1 (Diagenode c15410037), H3K9me3 (Diagenode C15410056), H3K27me3 (Diagenode C15410069) or H3K36me3 (Diagenode C15410058) antibodies, each at 2.5 µg/10⁶ cells (histones) or at 10 µg/5 × 10⁶ cells (LMNA/C). Cross-links were reversed and DNA was purified. ChIP libraries were prepared using a Microplex kit (Diagenode) and sequenced on a Nextseq 500 or Novaseq (Illumina; San Diego, CA, USA).