This web page was produced as an assignment for Genetics 564, an undergraduate capstone course at UW-Madison.
What is Gene Ontology?
Gene ontology is essentially a "gene dictionary". It is a major bioinformatics initiative to unify the representation of gene and gene product attributes across all species. The ontology covers three domains: Cellular Component, Molecular Function, and Biological Process [1].
Cellular Component
The parts of a cell or its extracellular environment. A cellular component may be an anatomical structure such as the rough endoplasmic reticulum or nucleus. It could also be a gene product group such as a ribosome, proteasome or a protein dimer.
Molecular Function
The elemental activities of a gene product at the molecular level, such as binding or catalysis. The general rule is that a process must have more than one distinct steps. Examples of broad biological process terms are cellular physiological process or signal transduction.
Biological Process
Operations or sets of molecular events with a defined beginning and end, pertinent to the functioning of integrated living units: cells, tissues, organs, and organisms.
The parts of a cell or its extracellular environment. A cellular component may be an anatomical structure such as the rough endoplasmic reticulum or nucleus. It could also be a gene product group such as a ribosome, proteasome or a protein dimer.
Molecular Function
The elemental activities of a gene product at the molecular level, such as binding or catalysis. The general rule is that a process must have more than one distinct steps. Examples of broad biological process terms are cellular physiological process or signal transduction.
Biological Process
Operations or sets of molecular events with a defined beginning and end, pertinent to the functioning of integrated living units: cells, tissues, organs, and organisms.
GO Terms of NRXN3
Cellular ComponentNeurexin (NRXN) including NRXN3 is a presynaptic protein located mostly on the presynaptic membrane and contains a single transmembrane domain [2]. In a chemical synapse, the presynaptic membrane is the cell membrane of an axon terminal that faces the receiving cell. The postsynaptic membrane is separated from the presynaptic membrane by the synaptic cleft [3].
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Molecular FunctionNRXN3 encodes neurexins (family of proteins) that function in the vertebrate nervous system as cell adhesion molecules and receptors [4]. The extracellular domain interacts with proteins in the synaptic cleft, most notably neuroligins which are also cell adhesion molecules located on the postsynaptic membrane of a neuron [5]. More specifically, neurexins bind to neuroligins, resulting in a connection between the two neurons.
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Biological ProcessNeurexins are involved in the process of synapse formation or synaptogenesis. When neurexins and neuroligins "shake hands," it results in the connection between the two neurons and the production of a synapse [6]. The function of the synapse is to transfer electrical activity (information) from one neuron to another [7].
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Conclusion
Gene ontology is crucial in understanding the role NRXN3 plays in alcohol dependence disorder. Being able to understand where it is located and what processes it is involved in will shed more light on how exactly the gene carries out these functions in the body. Thus, we can begin to understand how the gene is regulated and how mutations in the gene are reflected through behavioral phenotypes.
References
[1] Gene Ontology. (n.d.). An Introduction to the Gene Ontology. <ftp://ftp.geneontology.org/go/www/GO.doc.shtml>
[2] Gene Family: Neurexins (NRXN). (n.d.). Retrieved from https://www.genenames.org/cgi-bin/genefamilies/set/1582
[3] European Bioinformatics InstituteProtein Information ResourceSIB Swiss Institute of Bioinformatics. (n.d.). European Bioinformatics Institute. Retrieved from https://www.uniprot.org/locations/SL-0222
[4] NRXN3/Neurexin 3. (n.d.). Retrieved from https://www.sinobiological.com/NRXN3-Neurexin-3-a-488
[5] Chen, F., Venugopal, V., Murray, B., & Rudenko, G. (2011). The Structure of Neurexin 1α Reveals Features Promoting a Role as Synaptic Organizer. Structure, 19(6), 779-789. doi:10.1016/j.str.2011.03.012
[6] Scheiffele, P., Fan, J., Choih, J., Fetter, R., & Serafini, T. (2000). Neuroligin Expressed in Nonneuronal Cells Triggers Presynaptic Development in Contacting Axons. Cell, 101(6).
[7] 5.2 Synapses. (n.d.). Retrieved from http://www.bem.fi/book/05/05.htm
Images
Header: https://www.computecanada.ca/wp-content/uploads/2015/02/ROLAND-SANTOS-1075x605.jpg
Figure 1: https://ars.els-cdn.com/content/image/1-s2.0-S0028390811000359-gr1.jpg
Figure 2: http://www.jneurosci.org/content/jneuro/24/42/9244/F1.large.jpg
Figure 3: https://www.neuroskills.com/images/synaptogenesis.jpg
[1] Gene Ontology. (n.d.). An Introduction to the Gene Ontology. <ftp://ftp.geneontology.org/go/www/GO.doc.shtml>
[2] Gene Family: Neurexins (NRXN). (n.d.). Retrieved from https://www.genenames.org/cgi-bin/genefamilies/set/1582
[3] European Bioinformatics InstituteProtein Information ResourceSIB Swiss Institute of Bioinformatics. (n.d.). European Bioinformatics Institute. Retrieved from https://www.uniprot.org/locations/SL-0222
[4] NRXN3/Neurexin 3. (n.d.). Retrieved from https://www.sinobiological.com/NRXN3-Neurexin-3-a-488
[5] Chen, F., Venugopal, V., Murray, B., & Rudenko, G. (2011). The Structure of Neurexin 1α Reveals Features Promoting a Role as Synaptic Organizer. Structure, 19(6), 779-789. doi:10.1016/j.str.2011.03.012
[6] Scheiffele, P., Fan, J., Choih, J., Fetter, R., & Serafini, T. (2000). Neuroligin Expressed in Nonneuronal Cells Triggers Presynaptic Development in Contacting Axons. Cell, 101(6).
[7] 5.2 Synapses. (n.d.). Retrieved from http://www.bem.fi/book/05/05.htm
Images
Header: https://www.computecanada.ca/wp-content/uploads/2015/02/ROLAND-SANTOS-1075x605.jpg
Figure 1: https://ars.els-cdn.com/content/image/1-s2.0-S0028390811000359-gr1.jpg
Figure 2: http://www.jneurosci.org/content/jneuro/24/42/9244/F1.large.jpg
Figure 3: https://www.neuroskills.com/images/synaptogenesis.jpg