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Proc Natl Acad Sci U S A. 2016 May 24;113(21):E2889-98. doi: 10.1073/pnas.1601722113. Epub 2016 May 9.

Achieving diverse and monoallelic olfactory receptor selection through dual-objective optimization design.

Author information

1
Department of Computational and Systems Biology, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15260;
2
Genetics, Bioinformatics, and Computational Biology Program, Virginia Polytechnic Institute and State University, Blacksburg, VA 24060;
3
The TECBio Research Experiences for Undergraduates Program, University of Pittsburgh, Pittsburgh, PA 15260.
4
Department of Computational and Systems Biology, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15260; xing1@pitt.edu.

Abstract

Multiple-objective optimization is common in biological systems. In the mammalian olfactory system, each sensory neuron stochastically expresses only one out of up to thousands of olfactory receptor (OR) gene alleles; at the organism level, the types of expressed ORs need to be maximized. Existing models focus only on monoallele activation, and cannot explain recent observations in mutants, especially the reduced global diversity of expressed ORs in G9a/GLP knockouts. In this work we integrated existing information on OR expression, and constructed a comprehensive model that has all its components based on physical interactions. Analyzing the model reveals an evolutionarily optimized three-layer regulation mechanism, which includes zonal segregation, epigenetic barrier crossing coupled to a negative feedback loop that mechanistically differs from previous theoretical proposals, and a previously unidentified enhancer competition step. This model not only recapitulates monoallelic OR expression, but also elucidates how the olfactory system maximizes and maintains the diversity of OR expression, and has multiple predictions validated by existing experimental results. Through making an analogy to a physical system with thermally activated barrier crossing and comparative reverse engineering analyses, the study reveals that the olfactory receptor selection system is optimally designed, and particularly underscores cooperativity and synergy as a general design principle for multiobjective optimization in biology.

KEYWORDS:

barrier crossing; cooperativity; dual-objective optimization; enhancer competition; epigenetics

PMID:
27162367
PMCID:
PMC4889386
DOI:
10.1073/pnas.1601722113
[Indexed for MEDLINE]
Free PMC Article

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