The frozen tissues were cut and divided into 50 mg aliquots and stored in tubes at -80°C. The frozen tissues were homogenized on ice for 15–30 seconds in 500 μL 1X PBS using a tissue grinder (ACTGene, Piscataway, NJ). Tissue homogenates or cultured cells were cross-linked to final 1% formaldehyde for 10 min and quenched with 125 mM glycine for 5 min at room temperature and washed once with TBS. The pellets were resuspended in cell lysis buffer (10 mM Tris-HCl, pH7.5, 10 mM NaCl, 0.5% NP-40) and incubated on ice for 10 min. The lysates were divided into two aliquots and washed with MNase digestion buffer (20 mM Tris-HCl, pH7.5, 15 mM NaCl, 60 mM KCl, 1 mM CaCl2). After resuspending in 500 μL MNase digestion buffer containing a proteinase inhibitor cocktails (Sigma, St. Louis, MO), the lysates were incubated in the presence of 1,000 units of MNase (NEB, Ipswich, MA, Cat.# M0247S) at 37 °C for 20 min with continuous mixing in thermal mixer (Fisher Scientific, Pittsburgh, PA). After adding the same volume of sonication buffer (100 mM Tris-HCl, pH8.1, 20 mM EDTA, 200 mM NaCl, 2% Triton X-100, 0.2% sodium deoxycholate), the lysates were sonicated for 15 min (30 sec on / 30 sec off) using Bioruptor Twin (UCD-400) (Diagenode, Inc., Denville, NJ) and centrifuged at 21,130 x g for 10 min. The cleared supernatant equivalent to 10–20 mg of tissue or 1–2x106 cells was incubated with 2 ug of rabbit polyclonal anti-H3K36me3 antibody (Active Motif, Carlsbad, CA, Cat.# 61101) or 1.5 ug of rabbit monoclonal anti-H3K36me2 antibody (Cell Signaling Technology, Danvers, MA, Cat.#2901) on rocker overnight. After adding 30 μL protein G-magnetic beads (Life technologies, Carlsbad, CA), the reactions were incubated for 3 hours. The beads were extensively washed with ChIP buffer (50 mM Tris-HCl, pH8.1, 10 mM EDTA, 100 mM NaCl, 1% Triton X-100, 0.1% sodium deoxycholate), high salt buffer (50 mM Tris-HCl, pH8.1, 10 mM EDTA, 500 mM NaCl, 1% Triton X-100, 0.1% sodium deoxycholate), LiCl2 buffer (10 mM Tris-HCl, pH8.0,0.25 M LiCl2, 0.5% NP-40, 0.5% sodium deoxycholate, 1 mM EDTA), and TE buffer. Bound chromatins were eluted and reverse-crosslinked at 65°C overnight. DNAs were purified using Min-Elute PCR purification kit (Qiagen, Valencia, CA) after the treatment of RNase A and proteinase K.For RNA-seq, total RNA was extracted using the miRNeasy Mini kit (Qiagen, Valencia, CA). ChIP-seq libraries were prepared from 10 ng ChIP and input DNA using the Ovation ultralow DR Multiplex kit (NuGEN, San Carlos, CA). The ChIP-seq libraries were sequenced to 51 base pairs from both ends on an Illumina HiSeq 2000 instrument in the Mayo Clinic Center for Individualized Medicine Medical Genomics Facility.RNA-seq libraries were prepared with ovation RNA-seq system v2 kit (NuGEN) according to the manufacture’s instruction, and were sequenced on an Illumina HiSeq 2000 instrument in the Mayo Clinic Center for Individualized Medicine Medical Genomics Facility.