Evidence for a novel overlapping coding sequence in POLG initiated at a CUG start codon
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 c...
| Main Authors: | , , , , , , |
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| Format: | Article |
| Language: | English |
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BioMed Central
2020
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| Online Access: | https://hdl.handle.net/1721.1/126141 |
| _version_ | 1811068618751868928 |
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| author | Khan, Yousuf A Jungreis, Irwin Wright, James C Mudge, Jonathan M Choudhary, Jyoti S Firth, Andrew E Kellis, Manolis |
| author2 | Massachusetts Institute of Technology. Computer Science and Artificial Intelligence Laboratory |
| author_facet | Massachusetts Institute of Technology. Computer Science and Artificial Intelligence Laboratory Khan, Yousuf A Jungreis, Irwin Wright, James C Mudge, Jonathan M Choudhary, Jyoti S Firth, Andrew E Kellis, Manolis |
| author_sort | Khan, Yousuf A |
| collection | MIT |
| description | 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 |
| first_indexed | 2024-09-23T07:58:38Z |
| format | Article |
| id | mit-1721.1/126141 |
| institution | Massachusetts Institute of Technology |
| language | English |
| last_indexed | 2024-09-23T07:58:38Z |
| publishDate | 2020 |
| publisher | BioMed Central |
| record_format | dspace |
| spelling | mit-1721.1/1261412022-09-23T10:03:08Z Evidence for a novel overlapping coding sequence in POLG initiated at a CUG start codon Khan, Yousuf A Jungreis, Irwin Wright, James C Mudge, Jonathan M Choudhary, Jyoti S Firth, Andrew E Kellis, Manolis Massachusetts Institute of Technology. Computer Science and Artificial Intelligence Laboratory Broad Institute of MIT and Harvard 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 National Human Genome Research Institute of the NIH (Award no. U41HG007234) R01 HG004037 Wellcome Trust (grant 106207) 2020-07-10T20:28:44Z 2020-07-10T20:28:44Z 2020-03 2019-11 2020-06-26T11:02:48Z Article http://purl.org/eprint/type/JournalArticle 1471-2156 https://hdl.handle.net/1721.1/126141 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 PUBLISHER_CC en https://dx.doi.org/10.1186/s12863-020-0828-7 BMC Genetics Creative Commons Attribution https://creativecommons.org/licenses/by/4.0/ The Author(s). application/pdf BioMed Central BioMed Central |
| spellingShingle | Khan, Yousuf A Jungreis, Irwin Wright, James C Mudge, Jonathan M Choudhary, Jyoti S Firth, Andrew E Kellis, Manolis Evidence for a novel overlapping coding sequence in POLG initiated at a CUG start codon |
| title | Evidence for a novel overlapping coding sequence in POLG initiated at a CUG start codon |
| title_full | Evidence for a novel overlapping coding sequence in POLG initiated at a CUG start codon |
| title_fullStr | Evidence for a novel overlapping coding sequence in POLG initiated at a CUG start codon |
| title_full_unstemmed | Evidence for a novel overlapping coding sequence in POLG initiated at a CUG start codon |
| title_short | Evidence for a novel overlapping coding sequence in POLG initiated at a CUG start codon |
| title_sort | evidence for a novel overlapping coding sequence in polg initiated at a cug start codon |
| url | https://hdl.handle.net/1721.1/126141 |
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