title: Total Binding Affinity Profiles of Regulatory Regions Predict Transcription Factor Binding and Gene Expression in Human Cells.
abstract: Transcription factors regulate gene expression by binding regulatory DNA. Understanding the rules governing such binding is an essential step in describing the network of regulatory interactions, and its pathological alterations. We show that describing regulatory regions in terms of their profile of total binding affinities for transcription factors leads to increased predictive power compared to methods based on the identification of discrete binding sites. This applies both to the prediction of transcription factor binding as revealed by ChIP-seq experiments and to the prediction of gene expression through RNA-seq. Further significant improvements in predictive power are obtained when regulatory regions are defined based on chromatin states inferred from histone modification data.
authors.affiliation: Dept. of Molecular Biotechnology and Health Sciences, University of Turin, Turin, Italy.
authors.forename: Elena
authors.initials: E
authors.lastname: Grassi
authors.affiliation: Dept. of Molecular Biotechnology and Health Sciences, University of Turin, Turin, Italy.
authors.forename: Ettore
authors.initials: E
authors.lastname: Zapparoli
authors.affiliation: Dept. of Molecular Biotechnology and Health Sciences, University of Turin, Turin, Italy.
authors.forename: Ivan
authors.initials: I
authors.lastname: Molineris
authors.affiliation: Dept. of Molecular Biotechnology and Health Sciences, University of Turin, Turin, Italy.|Center for Translational Genomics and Bioinformatics, San Raffaele Scientific Institute, Milan, Italy.
authors.forename: Paolo
authors.initials: P
authors.lastname: Provero
mesh_terms: D000465:Algorithms; D001665:Binding Sites / Q000235:genetics / Q000502:physiology; D047369:Chromatin Immunoprecipitation; D059014:High-Throughput Nucleotide Sequencing; D006801:Humans; D011485:Protein Binding / Q000235:genetics / Q000502:physiology; D012045:Regulatory Sequences, Nucleic Acid / Q000235:genetics / Q000502:physiology*; D014157:Transcription Factors / Q000235:genetics / Q000378:metabolism*
chemical_list: D014157:Transcription Factors