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Gottlieb B, Beitel LK, Trifiro M. Changing genetic paradigms: creating next-generation genetic databases as tools to understand the emerging complexities of genotype/phenotype relationships. Hum Genomics 2014; 8:9. [PMID: 24885908 PMCID: PMC4040485 DOI: 10.1186/1479-7364-8-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2014] [Accepted: 04/25/2014] [Indexed: 12/18/2022] Open
Abstract
Understanding genotype/phenotype relationships has become more complicated as increasing amounts of inter- and intra-tissue genetic heterogeneity have been revealed through next-generation sequencing and evidence showing that factors such as epigenetic modifications, non-coding RNAs and RNA editing can play an important role in determining phenotype. Such findings have challenged a number of classic genetic assumptions including (i) analysis of genomic sequence obtained from blood is an accurate reflection of the genotype responsible for phenotype expression in an individual; (ii) that significant genetic alterations will be found only in diseased individuals, in germline tissues in inherited diseases, or in specific diseased tissues in somatic diseases such as cancer; and (iii) that mutation rates in putative disease-associated genes solely determine disease phenotypes. With the breakdown of our traditional understanding of genotype to phenotype relationships, it is becoming increasingly apparent that new analytical tools will be required to determine the relationship between genotype and phenotypic expression. To this end, we are proposing that next-generation genetic database (NGDB) platforms be created that include new bioinformatics tools based on algorithms that can evaluate genetic heterogeneity, as well as powerful systems biology analysis tools to actively process and evaluate the vast amounts of both genomic and genomic-modifying information required to reveal the true relationships between genotype and phenotype.
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Affiliation(s)
- Bruce Gottlieb
- Lady Davis Institute for Medical Research, 3755 Côte Ste Catherine Road, Montreal, QC H3T 1E2, Canada
- Segal Cancer Centre, Jewish General Hospital, 3755 Côte Ste Catherine Road, Montreal, QC H3T 1E2, Canada
- Department of Human Genetics, McGill University, Montreal, QC, Canada
| | - Lenore K Beitel
- Lady Davis Institute for Medical Research, 3755 Côte Ste Catherine Road, Montreal, QC H3T 1E2, Canada
- Department of Human Genetics, McGill University, Montreal, QC, Canada
- Department of Medicine, McGill University, Montreal, QC, Canada
| | - Mark Trifiro
- Lady Davis Institute for Medical Research, 3755 Côte Ste Catherine Road, Montreal, QC H3T 1E2, Canada
- Segal Cancer Centre, Jewish General Hospital, 3755 Côte Ste Catherine Road, Montreal, QC H3T 1E2, Canada
- Department of Human Genetics, McGill University, Montreal, QC, Canada
- Department of Medicine, McGill University, Montreal, QC, Canada
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Bailer SM, Lieber D. A high-throughput yeast two-hybrid protocol to determine virus-host protein interactions. Methods Mol Biol 2014; 1064:1-15. [PMID: 23996246 PMCID: PMC7122120 DOI: 10.1007/978-1-62703-601-6_1] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
The yeast two-hybrid (Y2H) system is a powerful method to identify and analyze binary protein interactions. In the field of virology, the Y2H system has significantly increased our knowledge of structure and function of viral proteins by systematically assessing intraviral protein interactions. Several comprehensive approaches to determine virus-host interactions have provided insight into viral strategies to manipulate the host for efficient replication and to escape host-derived countermeasures. To expand our knowledge of intraviral and virus-host protein interactions, we here present a Y2H protocol that is well suited for high-throughput screening. Yeast mating followed by liquid handling in a 96-well format as well as fluorescent readout of the reporter system provides a highly standardized and fully automated screening situation. The protocol can either be applied to screen complex host cDNA libraries or protein pairs arrayed for cross-testing. The ease of use, the cost-effectiveness as well as the robotic handling allows for extensive and multiple rounds of screening providing high coverage of protein-protein interactions. Thus, this protocol represents an improved "deep" screening method for high-throughput Y2H assays.
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Affiliation(s)
- Susanne M. Bailer
- University of Stuttgart Institute of Interfacial Process, Stuttgart, Germany
| | - Diana Lieber
- Ulm University Medical Center Institute of Virology, Ulm, Germany
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Bello AM, Wei L, Majchrzak-Kita B, Salum N, Purohit MK, Fish EN, Kotra LP. Small molecule mimetics of an interferon-α receptor interacting domain. Bioorg Med Chem 2014; 22:978-85. [DOI: 10.1016/j.bmc.2013.12.049] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2013] [Revised: 12/12/2013] [Accepted: 12/21/2013] [Indexed: 10/25/2022]
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