Promoter Capture and Hi-C Sequencing

Promoter Capture was performed as previously described [21 (link)–23 (link)]. Briefly, Biotinylated 120-mer RNA baits were designed to target both ends of HindIII restriction fragments overlapping the Ensembl promoters of protein-coding and noncoding transcripts and UCEs as described in detail in [22 (link)]. Promoter Capture was carried out using in nucleus Hi-C libraries derived from three biological replicates at ZT0 0, 6, 12, and 18 with the SureSelect target enrichment system and the biotinylated RNA bait library according to the manufacturer’s instructions (Agilent Technologies). After library enrichment, a post-capture PCR amplification step was carried out using the PE PCR 1.0 and PE PCR 2.0 primers (Illumina) with 4–6 PCR amplification cycles as required. In nucleus Hi-C and CHi-C libraries were sequenced on the Illumina HiSeq 2000 platform.