Joint Carnegie Mellon University-University of Pittsburgh, University of Pittsburgh Computational Biology PhD Program, University of Pittsburgh, Pittsburgh, PA, USA.
Department of Computational and Systems Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA.
Genome Biol. 2024 Jul 8;25(1):183. 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.
最近的研究揭示了在注释基因之外，数千个非规范开放阅读框（nORFs）广泛存在转录和翻译。由于 nORFs 通常较短、是新出现的，且表达水平较低，因此使用传统方法很难推断 nORFs 对细胞表型的贡献。在这里，我们开发了一种专门的共表达分析框架，该框架考虑了低表达，以研究酿酒酵母中 nORFs 的转录调控、进化和潜在的细胞作用。
我们的结果表明，nORFs 往往优先与涉及细胞运输或内稳态的基因共表达，但很少与涉及 RNA 处理的基因共表达。从机制上讲，我们发现位于保守基因下游的年轻新生 nORFs 倾向于通过转录通读利用其邻居的启动子，从而导致高共表达和高表达水平。转录搭便车也会影响位于基因上游的年轻新生 nORFs 的共表达谱，但影响较小，且对表达水平没有可检测的影响。转录搭便车影响但不决定新兴基因附近 nORFs 的转录谱。大约 40%的 nORFs 与任何基因都没有强烈的共表达，但仍受到转录调控，并且往往形成全新的转录模块。我们提供了一个网络浏览器界面（https://carvunislab.csb.pitt.edu/shiny/coexpression/），可用于高效查询、可视化和下载我们的共表达推断结果。
我们的结果表明，nORF 转录受到高度调控。我们的共表达数据集为揭示 nORFs 如何整合到细胞网络中、对细胞表型的贡献以及进化提供了前所未有的资源。
