High temporal resolution RNA-seq time course data reveals widespread synchronous activation between mammalian lncRNAs and neighbouring protein-coding genes
- Author(s)
- Muskovic, W; Slavich, E; Maslen, B; Kaczorowski, DC; Cursons, J; Crampin, E; Kavallaris, M;
- Journal Title
- Genome Research
- Publication Type
- epub ahead of print
- Abstract
- The advent of massively parallel sequencing revealed extensive transcription beyond protein-coding genes, identifying tens of thousands of long noncoding RNAs (lncRNAs). Selected functional examples raised the possibility that lncRNAs, as a class, may maintain broad regulatory roles. Expression of lncRNAs is strongly linked with adjacent protein-coding gene expression, suggesting potential cis-regulatory functions. A more detailed understanding of these regulatory roles may be obtained through careful examination of the precise timing of lncRNA expression relative to adjacent protein-coding genes. Despite the diversity of reported lncRNA regulatory mechanisms, where causal cis-regulatory relationships exist, lncRNA transcription is expected to precede changes in target gene expression. Using a high temporal resolution RNA-seq time course, we profiled the expression dynamics of several thousand lncRNAs and protein-coding genes in synchronized, transitioning human cells. Our findings reveal lncRNAs are expressed synchronously with adjacent protein-coding genes. Analysis of lipopolysaccharide-activated mouse dendritic cells revealed the same temporal relationship observed in transitioning human cells. Our findings suggest broad-scale cis-regulatory roles for lncRNAs are not common. The strong association between lncRNAs and adjacent genes may instead indicate an origin as transcriptional by-products from active protein-coding gene promoters and enhancers.
- Publisher
- CSHP
- Research Division(s)
- Bioinformatics
- PubMed ID
- 35760562
- Publisher's Version
- https://doi.org/10.1101/gr.276818.122
- Open Access at Publisher's Site
https://doi.org/10.1101/gr.276818.122- Terms of Use/Rights Notice
- Refer to copyright notice on published article.
Creation Date: 2022-07-04 08:56:59
Last Modified: 2022-07-04 09:04:05