Molecular interactions are the underlying basis of all processes that are executed in an organism, and their complete mapping would be a great aid in understanding and interpreting both normal and disease functioning. Transcriptional regulatory interactions are of particular interest as they are critical in the proper spatial and temporal regulation of genes. This proposal aims to develop several novel and complementary computational methods for predicting transcription factor interactions and specificities, and for uncovering their conservation and variation across organisms. Taken together, these methods will vastly expand our knowledge of eukaryotic regulatory networks and their underlying principles. We will devise a combined constrained optimization and statistical approach to predict the DNA-binding specificities of multidomain C2H2 zinc finger proteins;these proteins comprise the largest class of transcription factors in eukaryotic genomes. We will also establish a novel comparative sequence framework for determining binding specificity variation amongst homologous transcription factors, as network divergence underlies much of the observed phenotypic and functional diversity between and within organisms;this framework will be applied to explore the extent to which changes in transcription factors can affect regulatory network variation across organisms. Finally, we will develop a cross-genomic framework for predicting genomic binding sites for transcription factors with known specificities, along with analysis techniques for inferring interactions amongst these transcription factors across organisms. The DNA-binding specificities for an increasing number of transcription factors are being determined, and this large-scale data presents new opportunities to map transcription factor binding sites and to uncover transcription factor- transcription factor interactions across organisms;these interactions are an important component of regulatory networks and their variation plays a key role in network divergence. Successful completion of these aims will result in computational methods that will significantly increase the rate with which transcriptional networks are characterized and will reveal fundamental aspects of their functioning and evolution. All developed software will be made publicly available.

Public Health Relevance

Cellular networks underlie all processes that are executed in an organism, and their complete mapping would aid in understanding both normal and disease functioning. The proposed research will yield software for uncovering and characterizing protein interactions and specificities. These computational tools will help to place proteins, including those important for disease, within the broader context of their cellular pathways, thereby expanding our understanding of diseases and providing an important avenue for uncovering putative drug targets.

Agency
National Institute of Health (NIH)
Institute
National Institute of General Medical Sciences (NIGMS)
Type
Research Project (R01)
Project #
5R01GM076275-08
Application #
8634108
Study Section
Biodata Management and Analysis Study Section (BDMA)
Program Officer
Wu, Mary Ann
Project Start
2006-02-18
Project End
2016-03-31
Budget Start
2014-04-01
Budget End
2015-03-31
Support Year
8
Fiscal Year
2014
Total Cost
$307,890
Indirect Cost
$115,390
Name
Princeton University
Department
None
Type
Organized Research Units
DUNS #
002484665
City
Princeton
State
NJ
Country
United States
Zip Code
08544
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) molBLOCKS: decomposing small molecule sets and uncovering enriched fragments. Bioinformatics 30:2081-3
Jiang, Peng; Singh, Mona (2014) CCAT: Combinatorial Code Analysis Tool for transcriptional regulation. Nucleic Acids Res 42:2833-47
Ghersi, Dario; Singh, Mona (2014) Interaction-based discovery of functionally important genes in cancers. Nucleic Acids Res 42:e18
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
Jiang, Peng; Singh, Mona; Coller, Hilary A (2013) Computational assessment of the cooperativity between RNA binding proteins and MicroRNAs in Transcript Decay. PLoS Comput Biol 9:e1003075
Song, Jimin; Singh, Mona (2013) From hub proteins to hub modules: the relationship between essentiality and centrality in the yeast interactome at different scales of organization. PLoS Comput Biol 9:e1002910
Berger, Bonnie; Peng, Jian; Singh, Mona (2013) Computational solutions for omics data. Nat Rev Genet 14:333-46
Ghersi, Dario; Singh, Mona (2013) Disentangling function from topology to infer the network properties of disease genes. BMC Syst Biol 7:5
Pritykin, Yuri; Singh, Mona (2013) Simple topological features reflect dynamics and modularity in protein interaction networks. PLoS Comput Biol 9:e1003243

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