Abstract
The rate of RNA polymerase II (RNAPII) elongation has an important role in the control of alternative splicing (AS); however, the in vivo consequences of an altered elongation rate are unknown. Here, we generated mouse embryonic stem cells (ESCs) knocked in for a slow elongating form of RNAPII. We show that a reduced transcriptional elongation rate results in early embryonic lethality in mice. Focusing on neuronal differentiation as a model, we observed that slow elongation impairs development of the neural lineage from ESCs, which is accompanied by changes in AS and in gene expression along this pathway. In particular, we found a crucial role for RNAPII elongation rate in transcription and splicing of long neuronal genes involved in synapse signaling. The impact of the kinetic coupling of RNAPII elongation rate with AS is greater in ESC‐differentiated neurons than in pluripotent cells. Our results demonstrate the requirement for an appropriate transcriptional elongation rate to ensure proper gene expression and to regulate AS during development.
Highlights
Alternative splicing (AS) is a highly regulated process that generates RNA diversity and is a major contributor to protein isoform diversity
Generation of a slow RNA Polymerase II (RNAPII) knock-in mutant mouse ES cells To address the consequences of an altered transcriptional elongation rate for gene expression and for the kinetic control of AS, we set out to generate an in vivo model of a slow RNAPII by introducing a heterozygous or homozygous R749H mutation into the endogenous Polr2a in mouse embryonic stem cells (ESCs)
A slow elongation rate causes early embryonic lethality We observed that a slow RNAPII mutant caused embryonic lethality even in heterozygosity (Fig 2)
Summary
Alternative splicing (AS) is a highly regulated process that generates RNA diversity and is a major contributor to protein isoform diversity. The co-transcriptional nature of pre-mRNA splicing led to the suggestion that the rate of transcription elongation acts to control AS in mammalian cells (Beyer & Osheim, 1988; Roberts et al, 1998; Pandya-Jones & Black, 2009). The elongation control of transcription can be highly regulated and have a profound effect on gene expression. Following transcription initiation, the transition of RNAPII from a paused to a productive elongation stage constitutes a major ratelimiting step in the transcription of approximately 40% of mRNA-encoding genes (Min et al, 2011; Vos et al, 2018a, 2018b). Transcription elongation is variable, as synthesis rates can differ between genes by several-fold and these variations in elongation rates could be associated with different gene features and epigenetic modifications
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