The availability of (nearly) complete genome sequences for a few model organisms and for humans is expected to change the way we can formulate and address biological questions. With nearly complete sets of genes in hand, the traditional approach of studying one gene and/or one protein at-a-time can now be complemented by more global approaches that consider the proteins of a cell, a tissue or an organism, all at once. However most proteins predicted from genome sequences have not been characterized experimentally. Thus, an important challenge ahead is to develop functional genomics or proteomics strategies to accelerate the assignment of potential functions for large numbers of genes and proteins. A good model system to develop the concepts and technologies needed for functional genomics approaches is the nematode C. elegans. First because its genome is nearly completely sequenced but also because of its convenience for genetic studies and the availability of a complete cell fate map. Functional genomics is developing rapidly in C. elegans. A DNA microarray has been developed. Large-scale gene knock-out projects are underway. Systematic protein localization mapping projects have been initiated to define at what stage of development and in what cell each protein is expressed. In this context our long-term goal is to generate a comprehensive protein-protein interaction map for C. elegans. Three years ago, we decided to focus on the two-hybrid system as a first step. In our progress report we describe the results of semi-automated two-hybrid screens for 150 proteins and show that the method: i) is amenable to automation, ii) recovers approximately 50 percent of previously known interactions, and iii) provides functional annotation for large numbers of uncharacterized gene products. In addition we describe that, by July 1st 01, we should have Gateway-cloned most of the C. elegans protein-encoding full-length open reading frames (ORFs). Here we propose to generate version 1.0 of the C. elegans protein interaction map. First we will subclone most ORFs into the DNA-binding (DB) and activation domain (AD) plasmids of the two-hybrid system. Second, we will screen all pairwise combinations between the corresponding DB-X and AD-Y fusion proteins. Finally, since approximately 75,000 potential interactions are expected from this work, we will describe how we plan to deal with the challenge of using this information, making it publicly available, integrating it with other functional genomic databases, and last but not least interpreting it.

National Institute of Health (NIH)
National Human Genome Research Institute (NHGRI)
Research Project (R01)
Project #
Application #
Study Section
Genome Study Section (GNM)
Program Officer
Gatlin, Christine L
Project Start
Project End
Budget Start
Budget End
Support Year
Fiscal Year
Total Cost
Indirect Cost
Dana-Farber Cancer Institute
United States
Zip Code
Choi, Dongsic; Montermini, Laura; Kim, Dae-Kyum et al. (2018) The Impact of Oncogenic EGFRvIII on the Proteome of Extracellular Vesicles Released from Glioblastoma Cells. Mol Cell Proteomics 17:1948-1964
Díaz-Mejía, J Javier; Celaj, Albi; Mellor, Joseph C et al. (2018) Mapping DNA damage-dependent genetic interactions in yeast via party mating and barcode fusion genetics. Mol Syst Biol 14:e7985
Cenik, Can; Chua, Hon Nian; Singh, Guramrit et al. (2017) A common class of transcripts with 5'-intron depletion, distinct early coding sequence features, and N1-methyladenosine modification. RNA 23:270-283
Jo, Myungjin; Chung, Ah Young; Yachie, Nozomu et al. (2017) Yeast genetic interaction screen of human genes associated with amyotrophic lateral sclerosis: identification of MAP2K5 kinase as a potential drug target. Genome Res 27:1487-1500
Karras, Georgios I; Yi, Song; Sahni, Nidhi et al. (2017) HSP90 Shapes the Consequences of Human Genetic Variation. Cell 168:856-866.e12
Chung, Chee Yeun; Khurana, Vikram; Yi, Song et al. (2017) In Situ Peroxidase Labeling and Mass-Spectrometry Connects Alpha-Synuclein Directly to Endocytic Trafficking and mRNA Metabolism in Neurons. Cell Syst 4:242-250.e4
van Leeuwen, Jolanda; Pons, Carles; Mellor, Joseph C et al. (2016) Exploring genetic suppression interactions on a global scale. Science 354:
Vo, Tommy V; Das, Jishnu; Meyer, Michael J et al. (2016) A Proteome-wide Fission Yeast Interactome Reveals Network Evolution Principles from Yeasts to Human. Cell 164:310-323
Yang, Xinping; Coulombe-Huntington, Jasmin; Kang, Shuli et al. (2016) Widespread Expansion of Protein Interaction Capabilities by Alternative Splicing. Cell 164:805-17
Zhong, Quan; Pevzner, Samuel J; Hao, Tong et al. (2016) An inter-species protein-protein interaction network across vast evolutionary distance. Mol Syst Biol 12:865

Showing the most recent 10 out of 82 publications