Dynamic regulation and requirement for ribosomal RNA transcription during mammalian development

Abstract

Ribosomal RNA (rRNA) transcription by RNA polymerase I (Pol I) is a critical rate-limiting step in ribosome biogenesis, which is essential for cell survival. Despite its global function, disruptions in ribosome biogenesis cause tissue-specific birth defects called ribosomopathies, which frequently affect craniofacial development. Here, we describe a cellular and molecular mechanism underlying the susceptibility of craniofacial development to disruptions in Pol I transcription. We show that Pol I subunits are highly expressed in the neuroepithelium and neural crest cells (NCCs), which generate most of the craniofacial skeleton. High expression of Pol I subunits sustains elevated rRNA transcription in NCC progenitors, which supports their high tissue-specific levels of protein translation, but also makes NCCs particularly sensitive to rRNA synthesis defects. Consistent with this model, NCC-specific deletion of Pol I subunits Polr1a , Polr1c , and associated factor Tcof1 in mice cell-autonomously diminishes rRNA synthesis, which leads to p53 protein accumulation, resulting in NCC apoptosis and craniofacial anomalies. Furthermore, compound mutations in Pol I subunits and associated factors specifically exacerbate the craniofacial anomalies characteristic of the ribosomopathies Treacher Collins syndrome and Acrofacial Dysostosis–Cincinnati type. Mechanistically, we demonstrate that diminished rRNA synthesis causes an imbalance between rRNA and ribosomal proteins. This leads to increased binding of ribosomal proteins Rpl5 and Rpl11 to Mdm2 and concomitantly diminished binding between Mdm2 and p53. Altogether, our results demonstrate a dynamic spatiotemporal requirement for rRNA transcription during mammalian cranial NCC development and corresponding tissue-specific threshold sensitivities to disruptions in rRNA transcription in the pathogenesis of congenital craniofacial disorders.

Nucleolin loss of function leads to aberrant Fibroblast Growth Factor signaling and craniofacial anomalies

“…This raises the question of why disruptions in these ubiquitously expressed genes, which are required in a global process, result in tissue-specific craniofacial anomalies. One hypothesis is that neural crest cells (NCCs), which are the progenitors of most of the craniofacial bone and cartilage, are more proliferative or metabolically active than non-NCCs ( Falcon et al, 2022 ). In addition, NCCs form via an epithelial-to-mesenchymal transition, which involves major cytoskeletal changes, thus requiring high levels of new protein synthesis and, accordingly, more rRNA transcription.…”

rRNA transcription is integral to liquid-liquid phase separation and maintenance of nucleolar structure

“…Mutations in Pol I subunits result in preimplantation lethality [25][26][27] . To understand the function of Pol I subunits during mouse preimplantation development, we utilized our previously generated Polr1a -/-, Polr1c -/and Polr1d -/null mouse mutants 25 together with a new Polr1b -/null mutant mouse, collectively referred to as Pol I mutants hereafter.…”

“…This interaction prevents Mdm2 binding to and ubiquitinating p53 for proteasomal degradation. Consequently, p53 accumulates resulting in apoptosis of neural crest cells, the precursors of most of the craniofacial skeleton 25 .…”

The human RNA polymerase I structure reveals an HMG-like docking domain specific to metazoans

“…However, these mechanisms have been mostly studied in lower model organisms because of experimental limitations. In higher eukaryotes, regulatory variations dependent on tissue type, developmental state, and cell-cycle stage are adding additional layers of complexity ( 3 ).…”