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.
Highlights
Specialty section: This article was submitted to Protein and RNA Networks, a section of the journal Frontiers in Molecular Biosciences
These transcribed regions are separated by intergenic spacers (IGSs): IGS1 starts at the transcription termination site of the 35S gene and ends at the 5S Ribosomal RNA (rRNA) gene terminator and IGS2 corresponds to the region between the 5S rRNA gene promoter and the promoter of the 35S gene (Nomura, 2001)
The mechanism leading to this increased rRNA production is not well understood. We proposed that this mutation alleviates an intrinsic repressive element of the polymerase, leading to increased processivity during elongation, i.e. the ability of polymerase I (Pol I) to carry out continuous RNA synthesis on the DNA template without premature termination
Summary
Specialty section: This article was submitted to Protein and RNA Networks, a section of the journal Frontiers in Molecular Biosciences. In an rpa49 deletion strain, Rrn3 is recruited less efficiently at the promoter and fails to dissociate from elongating polymerases following transcription initiation (Beckouet et al, 2008).
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