High temporal resolution RNA-seq time course data reveals widespread synchronous activation between mammalian lncRNAs and neighboring protein-coding genes

Walter Muskovic; Eve Slavich; Ben Maslen; Dominik C Kaczorowski; Joseph Cursons; Edmund Crampin; Maria Kavallaris

doi:10.1101/gr.276818.122

High temporal resolution RNA-seq time course data reveals widespread synchronous activation between mammalian lncRNAs and neighboring protein-coding genes

Genome Res. 2022 Jun 27;32(8):1463-1473. doi: 10.1101/gr.276818.122. Online ahead of print.

Authors

Walter Muskovic^{1

2

3}, Eve Slavich⁴, Ben Maslen⁴, Dominik C Kaczorowski⁵, Joseph Cursons^{6

7}, Edmund Crampin^{8

9}, Maria Kavallaris^{1

2

3}

Affiliations

¹ Children's Cancer Institute, Lowy Cancer Research Centre, University of New South Wales, Sydney, New South Wales 2052, Australia.
² ARC Centre of Excellence in Convergent Bio-Nano Science and Technology, Australian Centre for NanoMedicine, University of New South Wales Australia, Sydney, New South Wales 2052, Australia.
³ School of Clinical Medicine, University of New South Wales Medicine and Health, University of New South Wales Sydney, Sydney, New South Wales 2052, Australia.
⁴ Stats Central, Mark Wainwright Analytical Centre, University of New South Wales, Sydney, New South Wales 2052, Australia.
⁵ Garvan Institute of Medical Research, Sydney, New South Wales 2010, Australia.
⁶ The Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria 3800, Australia.
⁷ Bioinformatics Division, The Walter and Eliza Hall Institute of Medical Research and Department of Medical Biology and Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Parkville, Victoria 3052, Australia.
⁸ Systems Biology Laboratory, School of Mathematics and Statistics and Department of Biomedical Engineering, University of Melbourne, Victoria 3010, Australia.
⁹ ARC Centre of Excellence in Convergent Bio-Nano Science and Technology, Melbourne School of Engineering, University of Melbourne, Parkville, Victoria 3010, Australia.

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 that 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.