TAD-Lactuca

TAD-Lactuca is a computational method to predict the boundaries of topologically associating domains (TADs) in the 3D structure of chromatins. The method uses contextual information from epigenetic modification signals and primary DNA sequence information to infer TAD boundaries. TAD-Lactuca is stable across different resolutions and datasets, and it achieves high accuracy, outperforming state-of-the-art methods when sequence patterns are incorporated.

The study also found that several transcription factor binding motifs and the well-known CTCF motif are significantly enriched at TAD boundaries. These findings suggest that incorporating sequence features can significantly improve the performance of TAD boundary prediction and that sequence patterns may play an essential role in chromatin folding.