Prediction of YY1 loop anchor based on multi-omics features

[Display omitted] •A LightGBM model is proposed for YY1-loop anchor prediction.•The genomic and epigenomic signals are extracted as input features.•Both sequence context and epigenetic modifications can affect the formation of YY1-loop anchors. The three-dimensional structure of chromatin is crucial for the regulation of gene expression. YY1 promotes enhancer-promoter interactions in a manner analogous to CTCF-mediated chromatin interactions. However, little is known about which YY1 binding sites can form loop anchors. In this study, the LightGBM model was used to predict YY1-loop anchors by integrating multi-omics data. Due to the large imbalance in the number of positive and negative samples, we use AUPRC to reflect the quality of the classifier. The results show that the LightGBM model exhibits strong predictive performance (AUPRC≥0.93). To verify the robustness of the model, the dataset was divided into training and test sets at a 4:1 ratio. The results show that the model performs well for YY1-loop anchor prediction on both the training and independent test sets. Additionally, we ranked the importance of the features and found that the formation of YY1-loop anchors is primarily influenced by the co-binding of transcription factors CTCF, SMC3, and RAD21, as well as histone modifications and sequence context.