Identification of the RNA polymerase I-RNA interactome

Nucleic Acids Research
David PiñeiroAnne E Willis

Abstract

Ribosome biogenesis is a complex process orchestrated by a host of ribosome assembly factors. Although it is known that many of the proteins involved in this process have RNA binding activity, the full repertoire of proteins that interact with the precursor ribosomal RNA is currently unknown. To gain a greater understanding of the extent to which RNA-protein interactions have the potential to control ribosome biogenesis, we used RNA affinity isolation coupled with proteomics to measure the changes in RNA-protein interactions that occur when rRNA transcription is blocked. Our analysis identified 211 out of 457 nuclear RNA binding proteins with a >3-fold decrease in RNA-protein interaction after inhibition of RNA polymerase I (RNAPI). We have designated these 211 RNA binding proteins as the RNAPI RNA interactome. As expected, the RNAPI RNA interactome is highly enriched for nucleolar proteins and proteins associated with ribosome biogenesis. Selected proteins from the interactome were shown to be nucleolar in location and to have RNA binding activity that was dependent on RNAPI activity. Furthermore, our data show that two proteins, which are required for rRNA maturation, AATF and NGDN, and which form part of the RNA interactome,...Continue Reading

Citations

Feb 6, 2020·The Biochemical Journal·Jana AlexandrovaAnne E Willis
May 19, 2020·Nucleic Acids Research·Cristina SorinoSimona Iezzi
Dec 5, 2018·Chromosome Research : an International Journal on the Molecular, Supramolecular and Evolutionary Aspects of Chromosome Biology·Farah Bughio, Keith A Maggert
Aug 1, 2019·Scientific Reports·Rainer W J KaiserFrancesca Fabretti
Jun 27, 2020·Frontiers in Oncology·Rainer W J KaiserRoman-Ulrich Müller
May 1, 2021·International Journal of Molecular Sciences·Anthony J Hayes, James Melrose

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Methods Mentioned

BETA
immunoprecipitation
immunoprecipitations
RIP
Cross-linking RIP
cross-linking immunoprecipitation
cross-linked immunoprecipitations

Software Mentioned

NOPdb
ImageJ
mygene
Bioconductor
goseq
ClusterProfiler
R

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