Evidence for a novel overlapping coding sequence in POLG initiated at a CUG start codon

Area of Science:

• Genomics
• Molecular Biology
• Evolutionary Biology

Background:

• The POLG gene encodes DNA polymerase gamma (Pol γ), crucial for mitochondrial DNA replication and repair.
• Mutations in POLG are a leading genetic cause of mitochondrial diseases.
• Pol γ is the primary DNA polymerase in mitochondria for most animal cells.

Purpose of the Study:

• To investigate novel coding sequences within the POLG gene.
• To determine the evolutionary conservation and expression of alternative reading frames in POLG.
• To assess the clinical relevance of newly identified coding sequences in POLG.

Main Methods:

• PhyloCSF analysis to detect conserved alternative reading frames.
• Synplot2 program to assess synonymous site conservation.
• Ribosome profiling to identify translated sequences.
• Mass spectrometry to confirm peptide mapping.
• Clinvar variant analysis.

Main Results:

• A novel conserved coding sequence, ORF-Y, was identified in an alternative reading frame within POLG exons 2 and 3, originating in placental mammals.
• Ribosome profiling and mass spectrometry confirmed the translation and expression of ORF-Y.
• ORF-Y is under strong purifying selection, indicating functional importance.
• A second conserved upstream open reading frame, ORF-Z, was found in POLG exon 2.
• Many disease-associated variants in POLG cause amino acid changes in ORF-Y or ORF-Z.

Conclusions:

• Evidence supports the existence and expression of a novel coding sequence, ORF-Y, overlapping the POLG gene.
• PhyloCSF and synplot2 analyses demonstrate strong purifying selection on ORF-Y.
• Disease-correlated mutations affecting ORF-Y highlight its potential clinical significance in mitochondrial disorders.