Interpreting regulatory mechanisms of Hippo signaling through a deep learning sequence model.
Journal:
Cell genomics
PMID:
40174587
Abstract
Signaling pathway components are well studied, but how they mediate cell-type-specific transcription responses is an unresolved problem. Using the Hippo pathway in mouse trophoblast stem cells as a model, we show that the DNA binding of signaling effectors is driven by cell-type-specific sequence rules that can be learned genome wide by deep learning models. Through model interpretation and experimental validation, we show that motifs for the cell-type-specific transcription factor TFAP2C enhance TEAD4/YAP1 binding in a nucleosome-range and distance-dependent manner, driving synergistic enhancer activation. We also discovered that Tead double motifs are widespread, highly active canonical response elements. Molecular dynamics simulations suggest that TEAD4 binds them cooperatively through surprisingly labile protein-protein interactions that depend on the DNA template. These results show that the response to signaling pathways is encoded in the cis-regulatory sequences and that interpreting the rules reveals insights into the mechanisms by which signaling effectors influence cell-type-specific enhancer activity.
Authors
Keywords
Adaptor Proteins, Signal Transducing
Animals
Deep Learning
DNA-Binding Proteins
Enhancer Elements, Genetic
Hippo Signaling Pathway
Mice
Molecular Dynamics Simulation
Muscle Proteins
Phosphoproteins
Protein Binding
Protein Serine-Threonine Kinases
Signal Transduction
TEA Domain Transcription Factors
Transcription Factors
Trophoblasts
YAP-Signaling Proteins