This web page was produced as an assignment for Genetics 564, an undergraduate capstone course at UW-Madison.
What is gene ontology?
Gene ontology (GO) refers to a classification initiative that seek seeks to provide a shared vocabulary for genes and better classify their importance [1]. Gene ontologies are important because the help scientists understand the full picture of what a gene does within an organism Gene ontologies will contain things like the descriptions of a gene, the functions of gene, and the location of gene products, and this information is classified into three separate ontologies:
Biological ProcessThis ontology will contain holistic information about what processes a gene is involved in including subcellular events up to tissue and organism level processes [2]. For example, what pathways is CNBP implicated in to cause muscle wasting? |
Molecular FunctionThis ontology provides information about the gene or gene products function at a molecular level [2]. For example, what binding interactions are the zinc-finger domains of CNBP taking part in? |
Cellular ComponentThis ontology provides information about the location of a gene product and where it is found throughout the cell [2]. For example, does CNBP localize to ribosomes to promote translation of specific mRNAs? |
What is are the GO terms of the CNBP gene?
Two common gene ontology databases used by scientists are GO and AMIGO. When searching for the CNBP gene in these databases, no results with a specific gene ontology tag were returned. This is likely due to the fact that the functions of CNBP gene and resulting CNBP protein are relatively unknown. When searching on the Cancer Genome Anatomy Project database, however, the following gene ontology terms were returned:
Biological Process
Cholesterol biosynthetic process Regulation of cell proliferation Regulation of transcription/translation |
Molecular Function
Metal/zinc ion binding Nucleic acid binding Single-stranded RNA binding Single-stranded DNA binding |
Cellular Component
Cytosol Endoplasmic reticulum Nucleus |
More detailed information regarding these general GO components and how various processes go awry in the disease state can be seen below. Information was pulled from the Human Protein Atlas and PubMed.
Cellular Component
The CNBP protein is a protein that is primary localized to the cytosol, a water-based gel matrix in which organelles are housed, and in the nucleus, the portion of the cell that houses DNA (Figures 1 & 2). CNBP is also heavily expressed in skeletal muscle tissue, which makes sense since its deregulation in the cell contributes to the detrimental muscle phenotypes observed in myotonic dystrophy type 2 (Figure 3).
Molecular Function
Below is an image from a 2017 review paper on the molecular mechanisms of DM2 showing that untranslated, CNBP pre-mRNA with tetranucleotide repeats in the first intron creates pre-mRNA foci that sequester MBNL proteins. MBNL proteins are critical for regulating the splicing of other genes that are critical to muscle function, thus illustrating the effects of toxic CNBP pre-mRNA on various cellular processes. In addition, CNBP protein levels are subsequently decreased, thus leading to dysregulation of its molecular functions like RNA binding [3].
Biological Process
The exact biological processes CNBP protein is in involved remains relatively ambiguous, but a recent 2017 paper by Benhalevy et al. found that CNBP can act as a cytoplasmic RNA-binding protein that binds guanine rich elements of ~4000 target mRNAs to promote translation (Figure 5). In doing so, CNBP is believed to resolve secondary guanine-guanine interactions that may occur in target mRNAs and promote their translation. The zinc-finger domains of CNBP are likely to play a role in these interactions, but the exact target mRNAs and overall biological processes that are affected from low CNBP levels in the disease state are unknown [4].
References
- Gene ontology. (n.d.). Retrieved March 15, 2018, from https://www.nature.com/subjects/gene-ontology
- What is GO? (2018, March 12). Retrieved March 16, 2018, from https://www.ebi.ac.uk/training/online/course/goa-and-quickgo-quick-tour/what-go
- Meola, G., & Cardani, R. (2017). Myotonic dystrophy type 2 and modifier genes: An update on clinical and pathomolecular aspects. Neurological Sciences, 38(4), 535-546. doi:10.1007/s10072-016-2805-5
- Benhalevy, D., Gupta, S. K., Danan, C. H., Ghosal, S., Sun, H., Kazemier, H. G., . . . Juranek, S. A. (2017). The Human CCHC-type Zinc Finger Nucleic Acid-Binding Protein Binds G-Rich Elements in Target mRNA Coding Sequences and Promotes Translation. Cell Reports, 18(12), 2979-2990. doi:10.1016/j.celrep.2017.02.080
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