MethNet: a robust approach to identify regulatory hubs and their distal targets in cancer [pcHiC]

We present MethNet, a pipeline that integrates large-scale DNA methylation and gene expression data across multiple cancers, to uncover novel cis regulatory elements (CREs) in a 1Mb region around every promoter in the genome. MethNet identifies highly ranked CREs, referred to as 'hubs', which contribute to the regulation of multiple genes and strongly affect patient survival. Promoter-capture Hi-C confirmed that highly ranked associations involve physical interactions between CREs and their gene targets, and CRISPRi based scRNA Perturb-seq validated the functional impact of CREs. Thus, MethNet represents a valuable resource for unraveling complex mechanisms underlying gene expression, and for prioritizing the verification of predicted non-coding disease hotspots. Overall design: Promoter Capture Hi-C data was generated in K562 and A549 cell lines using the Arima Hi-C+ kit, the Arima Promoter Capture Module, and the Arima Library Prep Module according to the Arima Genomics manufacturer's protocols. The A549 and K562 cell lines were purchased from ATCC. Two replicates of the Hi-C were performed in each cell line, and for each replicate 1 million cells were collected and double cross-linked using 3mM DSG (disuccinimidyl glutarate), followed by 1% formaldehyde. Samples were sequenced with Illumina Novaseq 6000 technology according to standard protocols with around 300 million (150bp paired-ends) reads per sample. The library preparation and sequencing were conducted by NYU Langone's Genome Technology Center.