Tracking pre-mRNA maturation across subcellular compartments identifies developmental gene regulation through intron retention and nuclear anchoring

Abstract

To globally assess the distribution and processing of gene transcripts across subcellular compartments, we developed extensive RNA-seq datasets of both polyA+ and total RNA from chromatin, nucleoplasm and cytoplasm of mouse ESC, neuronal progenitors, and neurons. We identified protein-coding genes whose polyadenylated transcripts were more abundant in chromatin than cytoplasm. We defined introns exhibiting cotranscriptional splicing, complete intron retention in cytoplasmic RNA, and many introns retained in nucleoplasmic and chromatin RNA but absent from cytoplasmic RNA, including new introns controlled during neuronal development. In particular, we found that polyadenylated Gabbr1 transcripts are expressed in mESC but remain sequestered on chromatin until neuronal differentiation when they are processed and released to the cytoplasm. This developmental regulation of splicing and chromatin association demonstrates that the abundance of polyadenylated RNA is not always an indicator of functional gene expression. Our datasets provide a rich resource for analyzing many other aspects of mRNA maturation.

Type I and II PRMTs inversely regulate post-transcriptional intron detention through Sm and CHTOP methylation

“…We next sought to identify the factors responsible for mediating the post-transcriptional consequences of PRMT inhibition. Previous reports have highlighted that delayed cotranscriptional splicing leads to chromatin retention of poly(A) transcripts (Brody et al 2011;Pandya-Jones et al 2013;Yeom et al 2021). Therefore, we analyzed differences in proteins bound to chromatin-associated poly(A) RNA.…”

Cue-specific remodeling of the neuronal transcriptome through intron retention programs

“…To test this hypothesis, we examined whether the nuclear IRs harbor specific sequence properties. Nuclear retained introns exhibit weak 5' and 3' splice sites compared to canonically spliced introns -a general property of IRs (Boutz et al, 2015;Braunschweig et al, 2014;Mauger et al, 2016;Ullrich and Guigó, 2020;Yeom et al, 2021). However, the splice site strength of stable nuclear retained introns is indistinguishable from the one of cytosolic retained introns (Figure 1E and F).…”

“…Furthermore, active nuclear retention of mRNAs is emerging as a novel form of posttranscriptional gene regulation. Notably, nuclear retention of RNAs can be regulated through long-lasting processes such as neuronal differentiation (Yeom et al, 2021). Also, candidate gene approaches in several systems revealed that some stored and nuclear transcripts can be released into the cytosol upon acute signals, thereby rapidly increasing mRNAs' availability for translation (Boutz et al, 2015;Mauger et al, 2016;Naro et al, 2017;Ninomiya et al, 2011;Prasanth et al, 2005).…”

“…Intron retention rates have been reported to be regulated over days of neuronal differentiation (Braunschweig et al, 2014;Yap et al, 2012;Yeom et al, 2021) or in mature neurons in response to elevation of neuronal network activity (Mauger et al, 2016). Mature neurons exhibit specific forms of plasticity in response to specific plasticity cues.…”

“…In line with this, we shed light on the extensive export of transcripts that undergo splicing completion in response to neuronal stimulation (Figure 4). Other studies also revealed a link between IRs and the nucleo-cytosolic localization of their host transcripts (Boutz et al, 2015;Mauger et al, 2016;Naro et al, 2017;Ninomiya et al, 2011;Yeom et al, 2021). Though, in most of the cases, it was unclear i) whether existing transcripts repurposed their fate and localization through splicing completion or ii) whether co-transcriptional production of spliced isoforms is required for their cytosolic expression.…”