Dynamic bimodal changes in CpG and non-CpG methylation genome-wide upon CGGBP1 loss-of-function

By depleting CGGBP1 in normal human fibroblasts 1064Sk using lentiviral shmiR (non-targeting or targeting CGGBP1) and by performing genome-wide sequencing (on bisulfite converted genomic DNA from both samples) we show that both gain and loss of cytosine methylation occurs upon CGGBP1 depletion. This gain and loss of methylation is clustered, spatially overlapping at major functional genomic regions and transcends all three cytosine sequence contexts. We demonstrate that CGGBP1 regulates cytosine methylation genome-wide through cis and trans-acting mechanisms. Library preparation for sequencing has been described in PMID 25981527. Control shmiR and CGGBP1 shmiR genomic DNA (both with bisulfite conversion) used for Illumina sequencing experiments.