TY - JOUR
T1 - Nucleolar RNA polymerase II drives ribosome biogenesis
AU - Abraham, Karan J.
AU - Khosraviani, Negin
AU - Chan, Janet N.Y.
AU - Gorthi, Aparna
AU - Samman, Anas
AU - Zhao, Dorothy Y.
AU - Wang, Miling
AU - Bokros, Michael
AU - Vidya, Elva
AU - Ostrowski, Lauren A.
AU - Oshidari, Roxanne
AU - Pietrobon, Violena
AU - Patel, Parasvi S.
AU - Algouneh, Arash
AU - Singhania, Rajat
AU - Liu, Yupeng
AU - Yerlici, V. Talya
AU - De Carvalho, Daniel D.
AU - Ohh, Michael
AU - Dickson, Brendan C.
AU - Hakem, Razq
AU - Greenblatt, Jack F.
AU - Lee, Stephen
AU - Bishop, Alexander J.R.
AU - Mekhail, Karim
N1 - Funding Information:
Acknowledgements We thank D. Durocher and H. O. Lee for critical reading of the manuscript; A. F. Palazzo for technical assistance with phase-contrast microscopy; R. Kandel for technical tumour imaging; and F. Chédin for technical assistance with DRIP. K.J.A. is funded by a Canadian Institutes of Health Research (CIHR) Vanier Doctoral Scholarship, Ruggles Innovation Award, and Adel S. Sedra Award. N.K. is supported by a CIHR Scholarship. L.A.O. is funded by an Ontario Graduate Scholarship (OGS). R.O. is funded by a Natural Sciences and Engineering Research Council (NSERC) Doctoral Scholarship. This work was also supported by funds from the National Institutes of Health (NIH; grants K22ES012264, 1R01CA152063, 1R01CA241554), a Voelcker Fund Young Investigator Award and the Cancer Prevention and Research Institute of Texas (CPRIT; grant RP150445) to A.J.R.B.; by CPRIT (grant RP101491), a National Cancer Institute (NCI) T32 postdoctoral training grant (T32CA148724) and a National Center for Advancing Translational Sciences (NCATS) TL1 grant (TL1TR002647) to A.G.; and NCI funding (P30CA054174) to the sequencing facility. Funds were also provided to S.L. from the National Institute of General Medical Sciences (R01GM115342) and the NCI (R01CA200676) of the NIH, and the Sylvester Comprehensive Cancer Center. This work was mainly supported by grants to K.M. from the CIHR (388041, 399687), the Canada Research Chairs Program (CRC; 950-230661), and the Ontario Ministry of Research and Innovation (MRI-ERA; ER13-09-111).
Publisher Copyright:
© 2020, The Author(s), under exclusive licence to Springer Nature Limited.
PY - 2020/9/10
Y1 - 2020/9/10
N2 - Proteins are manufactured by ribosomes—macromolecular complexes of protein and RNA molecules that are assembled within major nuclear compartments called nucleoli1,2. Existing models suggest that RNA polymerases I and III (Pol I and Pol III) are the only enzymes that directly mediate the expression of the ribosomal RNA (rRNA) components of ribosomes. Here we show, however, that RNA polymerase II (Pol II) inside human nucleoli operates near genes encoding rRNAs to drive their expression. Pol II, assisted by the neurodegeneration-associated enzyme senataxin, generates a shield comprising triplex nucleic acid structures known as R-loops at intergenic spacers flanking nucleolar rRNA genes. The shield prevents Pol I from producing sense intergenic noncoding RNAs (sincRNAs) that can disrupt nucleolar organization and rRNA expression. These disruptive sincRNAs can be unleashed by Pol II inhibition, senataxin loss, Ewing sarcoma or locus-associated R-loop repression through an experimental system involving the proteins RNaseH1, eGFP and dCas9 (which we refer to as ‘red laser’). We reveal a nucleolar Pol-II-dependent mechanism that drives ribosome biogenesis, identify disease-associated disruption of nucleoli by noncoding RNAs, and establish locus-targeted R-loop modulation. Our findings revise theories of labour division between the major RNA polymerases, and identify nucleolar Pol II as a major factor in protein synthesis and nuclear organization, with potential implications for health and disease.
AB - Proteins are manufactured by ribosomes—macromolecular complexes of protein and RNA molecules that are assembled within major nuclear compartments called nucleoli1,2. Existing models suggest that RNA polymerases I and III (Pol I and Pol III) are the only enzymes that directly mediate the expression of the ribosomal RNA (rRNA) components of ribosomes. Here we show, however, that RNA polymerase II (Pol II) inside human nucleoli operates near genes encoding rRNAs to drive their expression. Pol II, assisted by the neurodegeneration-associated enzyme senataxin, generates a shield comprising triplex nucleic acid structures known as R-loops at intergenic spacers flanking nucleolar rRNA genes. The shield prevents Pol I from producing sense intergenic noncoding RNAs (sincRNAs) that can disrupt nucleolar organization and rRNA expression. These disruptive sincRNAs can be unleashed by Pol II inhibition, senataxin loss, Ewing sarcoma or locus-associated R-loop repression through an experimental system involving the proteins RNaseH1, eGFP and dCas9 (which we refer to as ‘red laser’). We reveal a nucleolar Pol-II-dependent mechanism that drives ribosome biogenesis, identify disease-associated disruption of nucleoli by noncoding RNAs, and establish locus-targeted R-loop modulation. Our findings revise theories of labour division between the major RNA polymerases, and identify nucleolar Pol II as a major factor in protein synthesis and nuclear organization, with potential implications for health and disease.
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U2 - 10.1038/s41586-020-2497-0
DO - 10.1038/s41586-020-2497-0
M3 - Article
C2 - 32669707
AN - SCOPUS:85087854396
VL - 585
SP - 298
EP - 302
JO - Nature
JF - Nature
SN - 0028-0836
IS - 7824
ER -