Open reading frame dominance indicates protein-coding potential of RNAs.

Recent studies have identified numerous RNAs with both coding and noncoding functions. However, the sequence characteristics that determine this bifunctionality remain largely unknown. In the present study, we develop and test the open reading frame (ORF) dominance score, which we define as the fraction of the longest ORF in the sum of all putative ORF lengths. This score correlates with translation efficiency in coding transcripts and with translation of noncoding RNAs. In bacteria and archaea, coding and noncoding transcripts have narrow distributions of high and low ORF dominance, respectively, whereas those of eukaryotes show relatively broader ORF dominance distributions, with considerable overlap between coding and noncoding transcripts. The extent of overlap positively and negatively correlates with the mutation rate of genomes and the effective population size of species, respectively. Tissue-specific transcripts show higher ORF dominance than ubiquitously expressed transcripts, and the majority of tissue-specific transcripts are expressed in mature testes. These data suggest that the decrease in population size and the emergence of testes in eukaryotic organisms allowed for the evolution of potentially bifunctional RNAs. © 2022 The Authors. Published under the terms of the CC BY 4.0 license.

Citation

Yusuke Suenaga, Mamoru Kato, Momoko Nagai, Kazuma Nakatani, Hiroyuki Kogashi, Miho Kobatake, Takashi Makino. Open reading frame dominance indicates protein-coding potential of RNAs. EMBO reports. 2022 Jun 07;23(6):e54321

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PMID: 35438231

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