@article{Muskovic01082022,
author = {Muskovic, Walter and Slavich, Eve and Maslen, Ben and Kaczorowski, Dominik C. and Cursons, Joseph and Crampin, Edmund and Kavallaris, Maria}, 
title = {High temporal resolution RNA-seq time course data reveals widespread synchronous activation between mammalian lncRNAs and neighboring protein-coding genes},
volume = {32}, 
number = {8}, 
pages = {1463-1473}, 
year = {2022}, 
doi = {10.1101/gr.276818.122}, 
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.}, 
URL = {http://genome.cshlp.org/content/32/8/1463.abstract}, 
eprint = {http://genome.cshlp.org/content/32/8/1463.full.pdf+html}, 
journal = {Genome Research} 
}