Evidence for a novel overlapping coding sequence in POLG initiated at a CUG start codon
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12863_2020_Article_828.pdf
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Author(s)
Khan, Yousuf A
Jungreis, Irwin
Wright, James C
Mudge, Jonathan M
Choudhary, Jyoti S
Firth, Andrew E
Kellis, Manolis
Date Issued
March 2020
Journal
BMC Genetics
Publisher
BioMed Central
Citation
Khan, Yousuf A. et al., "Evidence for a novel overlapping coding sequence in POLG initiated at a CUG start codon." BMC Genetics 21 (March 2020): no. 25 doi. 10.1186/s12863-020-0828-7 ©2020 Authors
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Abstract
Background: POLG, located on nuclear chromosome 15, encodes the DNA polymerase γ(Pol γ). Pol γ is responsible for the replication and repair of mitochondrial DNA (mtDNA). Pol γ is the only DNA polymerase found in mitochondria for most animal cells. Mutations in POLG are the most common single-gene cause of diseases of mitochondria and have been mapped over the coding region of the POLG ORF.
Results: Using PhyloCSF to survey alternative reading frames, we found a conserved coding signature in an alternative frame in exons 2 and 3 of POLG, herein referred to as ORF-Y that arose de novo in placental mammals. Using the synplot2 program, synonymous site conservation was found among mammals in the region of the POLG ORF that is overlapped by ORF-Y. Ribosome profiling data revealed that ORF-Y is translated and that initiation likely occurs at a CUG codon. Inspection of an alignment of mammalian sequences containing ORF-Y revealed that the CUG codon has a strong initiation context and that a well-conserved predicted RNA stem-loop begins 14 nucleotides downstream. Such features are associated with enhanced initiation at near-cognate non-AUG codons. Reanalysis of the Kim et al. (2014) draft human proteome dataset yielded two unique peptides that map unambiguously to ORF-Y. An additional conserved uORF, herein referred to as ORF-Z, was also found in exon 2 of POLG. Lastly, we surveyed Clinvar variants that are synonymous with respect to the POLG ORF and found that most of these variants cause amino acid changes in ORF-Y or ORF-Z.
Conclusions: We provide evidence for a novel coding sequence, ORF-Y, that overlaps the POLG ORF. Ribosome profiling and mass spectrometry data show that ORF-Y is expressed. PhyloCSF and synplot2 analysis show that ORF-Y is subject to strong purifying selection. An abundance of disease-correlated mutations that map to exons 2 and 3 of POLG but also affect ORF-Y provides potential clinical significance to this finding. ©2020
MIT Department
Massachusetts Institute of Technology. Computer Science and Artificial Intelligence Laboratory
Broad Institute of MIT and Harvard
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DOI of Published Version
https://doi.org/10.1186/s12863-020-0828-7
