Over the last two decades, significant experimental efforts have determined large sets of ?reference? interactions for humans and other model organisms, along with substantial knowledge about the binding specificities of proteins, including for a large fraction of human transcription factors (TFs). The resulting data have proven to be an incredibly useful resource for understanding how cells function; nevertheless, they do not capture how molecular interactions and networks are different from the reference across individuals. Indeed, while human genomes in both healthy and disease populations are rapidly being sequenced, the corresponding individual-specific interaction networks remain largely unexamined; this represents a major gap in our knowledge, as mutations that alter molecular interactions underlie a wide range of human diseases. Further, the substantial amount of genetic variation across populations makes it infeasible in the near term to experimentally determine per-individual interaction networks. Thus our long-term goal is to develop computational methods to uncover whether and how mutations within coding and non-coding portions of the genome perturb cellular interactions and networks.
Our specific aims are: (1) We will develop computational structure-based approaches to identify and catalog, at proteome-scale, variations within proteins that are likely to impact their ability to bind with DNA, RNA, small molecules, peptides or ions, thereby providing a comprehensive resource for analyzing protein interaction variation. (2) We will develop novel structure-based and probabilistic methods to predict how DNA-binding specificities are altered when a TF is mutated; since mutated TFs have been linked to numerous diseases, this will be a great aid in understanding disease networks and pathology. (3) We will develop new methods to uncover non-coding somatic mutations that alter human regulatory networks in cancer; this is a critical step towards ultimately uncovering patient-specific cancer networks. Overall by pursuing these aims?which integrate mutational information with existing knowledge about reference interactions, interfaces and specificities?we will develop novel computational methods that will significantly advance our understanding of molecular interactions perturbed in disease and healthy contexts.
The proposed research will yield new software tools that predict whether specific genetic mutations alter molecular interactions and networks. Since many human diseases are caused by mutations that affect molecular interactions, this research will expand our understanding of the underlying basis of disease and will provide new avenues for diagnosis and treatment.
|Pritykin, Yuri; Brito, Tarcisio; Schupbach, Trudi et al. (2017) Integrative analysis unveils new functions for the Drosophila Cutoff protein in noncoding RNA biogenesis and gene regulation. RNA 23:1097-1109|
|Ochoa, Alejandro; Singh, Mona (2017) Domain prediction with probabilistic directional context. Bioinformatics 33:2471-2478|
|Ochoa, Alejandro; Storey, John D; Llinás, Manuel et al. (2015) Beyond the E-Value: Stratified Statistics for Protein Domain Prediction. PLoS Comput Biol 11:e1004509|
|Persikov, Anton V; Wetzel, Joshua L; Rowland, Elizabeth F et al. (2015) A systematic survey of the Cys2His2 zinc finger DNA-binding landscape. Nucleic Acids Res 43:1965-84|
|Pritykin, Yuri; Ghersi, Dario; Singh, Mona (2015) Genome-Wide Detection and Analysis of Multifunctional Genes. PLoS Comput Biol 11:e1004467|
|Nadimpalli, Shilpa; Persikov, Anton V; Singh, Mona (2015) Pervasive variation of transcription factor orthologs contributes to regulatory network evolution. PLoS Genet 11:e1005011|
|Persikov, Anton V; Rowland, Elizabeth F; Oakes, Benjamin L et al. (2014) Deep sequencing of large library selections allows computational discovery of diverse sets of zinc fingers that bind common targets. Nucleic Acids Res 42:1497-508|
|Persikov, Anton V; Singh, Mona (2014) De novo prediction of DNA-binding specificities for Cys2His2 zinc finger proteins. Nucleic Acids Res 42:97-108|
|Ghersi, Dario; Singh, Mona (2014) Interaction-based discovery of functionally important genes in cancers. Nucleic Acids Res 42:e18|
|Jiang, Peng; Singh, Mona (2014) CCAT: Combinatorial Code Analysis Tool for transcriptional regulation. Nucleic Acids Res 42:2833-47|
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