ArticleEMBO reports2022
Open reading frame dominance indicates protein-coding potential of RNAs.
Article in EMBO reports, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 6 papers.
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Who cites it
6 citing papers in PubMed, 9 citations in OpenAlex.
- Review
- Current understanding of functional peptides encoded by lncRNA in cancer.Cancer cell international · 2024Review
- Inhibition of OCT4 binding at theFrontiers in oncology · 2024Article
- Regulatory miPEP Open Reading Frames Contained in the Primary Transcripts of microRNAs.International journal of molecular sciences · 2023Review
- LncCat: An ORF attention model to identify LncRNA based on ensemble learning strategy and fused sequence information.Computational and structural biotechnology journal · 2023Article
- Open reading frame dominance indicates protein-coding potential of RNAs.EMBO reports · 2022Article
Corrections and comments
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Authors and funding
7 authors at 4 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
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.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the Socratic graph.