RT Journal
A1 Narayanan, Ishwarya Venkata
A1 Bedi, Karan
A1 Magnuson, Brian
A1 McShane, Ariel
A1 Ashaka, Mario
A1 Paulsen, Michelle
A1 Wilson, Thomas E
A1 Ljungman, Mats
T1 Isoform- and pathway-specific regulation of post-transcriptional RNA processing in human cells
JF Genome Research 
JO Genome Research 
YR 2026 
FD March 26 
DO 10.1101/gr.280892.125 
SP gr.280892.125 
UL http://genome.cshlp.org/content/early/2026/03/26/gr.280892.125.abstract 
AB Steady-state levels of RNA transcripts are determined by their rates of synthesis and degradation. In this study, we use nascent RNA Bru-seq and BruChase-seq to investigate RNA dynamics across 16 human cell lines, as part of the ENCODE4 Deeply Profiled Cell Lines collection. Our analyses show that RNA turnover dynamics differ widely between transcripts of different genes and among different classes of RNA, but remain primarily cell-type independent. Gene set enrichment analysis (GSEA) reveals that transcripts encoding proteins belonging to the same pathway often show similar turnover dynamics. Furthermore, transcript isoforms exhibit distinct turnover profiles, suggesting that RNA turnover plays an important role in regulating mRNA isoform choice. Finally, splicing of newly synthesized transcripts appears to occur in a binary manner, largely happening either fully on both sides of 47,163 exons or not at all. These data sets generated as part of the ENCODE Project illustrate the intricate and coordinated regulation of RNA dynamics in controlling gene expression, allowing for the precise coordination of cellular functions.