Massively integrated coexpression analysis reveals transcriptional regulation, evolution and cellular implications of the yeast noncanonical translatome

• Published in: Genome Biology Vol. 25; no. 1; pp. 183 - 28
• Main Authors: Rich, April, Acar, Omer, Carvunis, Anne-Ruxandra
• Format: Journal Article
• Language: English
• Published: England BioMed Central 08-07-2024; BMC
• Subjects: Cell cycle; Coexpression networks; Datasets; De novo gene birth; Evolution, Molecular; Evolutionary genetics; Gene Expression Regulation, Fungal; Gene regulation; Genes; Genomes; Homeostasis; Noncanonical ORFs; Open Reading Frames; Peptides; Phenotypes; Physiology; Protein Biosynthesis; Proteins; Ribonucleic acid; RNA; RNA processing; RNA transport; Saccharomyces cerevisiae - genetics; Saccharomyces cerevisiae - metabolism; smORFs; Sparsity; Transcription; Transcription, Genetic; Transcriptional regulation; Translatome; Yeast; smORFs; De novo gene birth; Translatome; Noncanonical ORFs; Transcriptional regulation; Coexpression networks
• ISSN: 1474-760X; 1474-7596; 1474-760X
• DOI: 10.1186/s13059-024-03287-7

Recent studies uncovered pervasive transcription and translation of thousands of noncanonical open reading frames (nORFs) outside of annotated genes. The contribution of nORFs to cellular phenotypes is difficult to infer using conventional approaches because nORFs tend to be short, of recent de novo origins, and lowly expressed. Here we develop a dedicated coexpression analysis framework that accounts for low expression to investigate the transcriptional regulation, evolution, and potential cellular roles of nORFs in Saccharomyces cerevisiae.
Our results reveal that nORFs tend to be preferentially coexpressed with genes involved in cellular transport or homeostasis but rarely with genes involved in RNA processing. Mechanistically, we discover that young de novo nORFs located downstream of conserved genes tend to leverage their neighbors' promoters through transcription readthrough, resulting in high coexpression and high expression levels. Transcriptional piggybacking also influences the coexpression profiles of young de novo nORFs located upstream of genes, but to a lesser extent and without detectable impact on expression levels. Transcriptional piggybacking influences, but does not determine, the transcription profiles of de novo nORFs emerging nearby genes. About 40% of nORFs are not strongly coexpressed with any gene but are transcriptionally regulated nonetheless and tend to form entirely new transcription modules. We offer a web browser interface ( https://carvunislab.csb.pitt.edu/shiny/coexpression/ ) to efficiently query, visualize, and download our coexpression inferences.
Our results suggest that nORF transcription is highly regulated. Our coexpression dataset serves as an unprecedented resource for unraveling how nORFs integrate into cellular networks, contribute to cellular phenotypes, and evolve.