Coupling Between Production of Ribosomal RNA and Maturation: Just at the Beginning

Abstract

Ribosomal RNA (rRNA) production represents the most active transcription in the cell. Synthesis of the large rRNA precursors (35S/47S in yeast/human) is achieved by up to hundreds of RNA polymerase I (Pol I) enzymes simultaneously transcribing a single rRNA gene. In this review, we present recent advances in understanding the coupling between rRNA production and nascent rRNA folding. Mapping of the distribution of Pol I along ribosomal DNA at nucleotide resolution, using either native elongating transcript sequencing (NET-Seq) or crosslinking and analysis of cDNAs (CRAC), revealed frequent Pol I pausing, and CRAC results revealed a direct coupling between pausing and nascent RNA folding. High density of Pol I per gene imposes topological constraints that establish a defined pattern of polymerase distribution along the gene, with a persistent spacing between transcribing enzymes. RNA folding during transcription directly acts as an anti-pausing mechanism, implying that proper folding of the nascent rRNA favors elongation in vivo. Defects in co-transcriptional folding of rRNA are likely to induce Pol I pausing. We propose that premature termination of transcription, at defined positions, can control rRNA production in vivo.

Ribosomal RNA synthesis by RNA polymerase I is regulated by premature termination of transcription

“…The structures of Pol I initiation complex (Pre-Initiation Complex and Initially Transcribing Complex) are now available (Engel et al, 2018). Although Pol I transcription is well known to be regulatable at the initiation level (Blattner et al, 2011; Sadian et al, 2019; Schneider et al, 2007), rRNA synthesis and pre-rRNA processing are, at least partially, controlled during the elongation phase of Pol I transcription (Azouzi et al, 2021; Schneider et al, 2007). A statistical view of Pol I pausing within rDNA was obtained using high-throughput methods such as Net-Seq or CRAC (Clarke et al, 2018; Turowski et al, 2020a).…”