Reduced Representation Bisulfite Sequencing

RRBS assay was performed as previously described^{75 (link)}. Briefly, 20 ng of genomic DNA were digested with Msp1 restriction enzyme (NEB, R0106L), DNA fragments were end-repaired and A-Tailed using Klenow fragment (3′−5- exo-) (NEB, M0212L). The DNA fragments were then ligated to illumina adaptors (Illumina, PE-940-2001) using T4 ligase (NEB, M0202M) and then size selected using AMPure XP beads (Beckman Coulter Genomics, A63881). The samples were then subjected to two consecutive bisulfite conversions using EpiTect Bisulfite Kit (QIAGEN, 59104) and PCR using PfuTurbo Cx hotstart DNA polymerase (Agilent Technologies, 600412). The RRBS libraries were sequenced by Illumina HiSeq 2000 platform.