TY  - JOUR
A1  - Muskovic, Walter
A1  - Slavich, Eve
A1  - Maslen, Ben
A1  - Kaczorowski, Dominik C.
A1  - Cursons, Joseph
A1  - Crampin, Edmund
A1  - Kavallaris, Maria
T1  - High temporal resolution RNA-seq time course data reveals widespread synchronous activation between mammalian lncRNAs and neighboring protein-coding genes
Y1  - 2022/08/01 
JF  - Genome Research 
JO  - Genome Research 
SP  - 1463 
EP  - 1473 
DO  - 10.1101/gr.276818.122 
VL  - 32 
IS  - 8 
UR  - http://genome.cshlp.org/content/32/8/1463.abstract 
N2  - 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. 
ER  -