Comparison of ChIP-seq data and a reference motif set for human KRAB C2H2 zinc finger proteins

Marjan Barazandeh1, Sam Lambert2, Mihai Albu1, and Timothy R. Hughes1,2,3,*

1Terrence Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, 160 College St., Toronto, ON M5S 3E1 CANADA
2Department of Molecular Genetics, Unversity of Toronto, 1 King’s College Circle, Toronto, ON M5S 1A8 CANADA
3Canadian Institutes For Advanced Research, 661 University Ave, Toronto, ON M5G 1M1 CANADA
*To whom correspondence should be addressed:; 416-946-8260

KRAB C2H2 zinc finger proteins (KZNFs) are the largest and most diverse family of human transcription factors, likely due to diversifying selection driven by novel endogenous retroelements (EREs), but the vast majority lack binding motifs or any functional data. Two recent studies analyzed a majority of the human KZNFs using either ChIP-seq ((SCHMITGES et al. 2016); 60 proteins) or ChIP-exo ((IMBEAULT et al. 2017); 221 proteins) in the same cell type (HEK293). The ChIP-exo paper did not describe binding motifs, however. Thirty-nine proteins are represented in both studies, enabling the systematic comparison of the data sets presented here. Typically, only a minority of peaks overlap, but the two studies nonetheless display significant similarity in ERE binding for 32/39, and yield highly similar DNA binding motifs for 23 and related motifs for 34 (MoSBAT similarity score > 0.5 and > 0.2, respectively). Thus, there is overall (albeit imperfect) agreement between the two studies. For the 242 proteins represented in at least one study, we selected a highest-confidence motif for each protein, utilizing several motif-derivation approaches, and evaluating motifs within and across data sets. Peaks for the majority (158) are enriched (96% with AUC > 0.6 predicting peak vs non peak) for a motif that is supported by the C2H2 “recognition code”, consistent with intrinsic sequence specificity driving DNA binding in cells. An additional 63 yield motifs enriched in peaks, but not supported by the recognition code, which could reflect indirect binding. Altogether, these analyses validate both data sets, and provide a reference motif set with associated quality metrics.