rRNA Pseudouridylation Defects Affect Ribosomal Ligand Binding and Translational Fidelity from Yeast to Human Cells

Jack, Karen D.; Bellodi, Cristian; Landry, Dori M.; Niederer, Rachel O.; Meškauskas, Arturas; Musalgaonkar, Sharmishtha; Kopmar, Noam E; Krasnykh, Olya; Dean, Alison; Thompson, Sunnie R.; Ruggero, Davide; Dinman, Jonathan D.

doi:10.1016/j.molcel.2011.09.017

Cited by 261 publications

(298 citation statements)

References 48 publications

(63 reference statements)

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“…As 3-methylation of uridine inhibits its H/ACA snoRNA-guided isomerization to psesudouridine, 22 the observed decrease in the CU/U ratio in FTO-deficient mice is in line with the increased 3meU/U ratio. Pseudouridine has recently been reported to affect translation efficiency, 30 and ribosomal activity has been linked to obesity. 31 Another interesting study has demonstrated that pseudouridylation of the spliceosomal small nuclear RNA U2 is affected by nutrition.…”

Section: Discussionmentioning

confidence: 99%

FTO levels affect RNA modification and the transcriptome

et al. 2012

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A block of single-nucleotide polymorphisms within intron 1 of the FTO (fat mass and obesity associated) gene is associated with variation in body weight. Previous works suggest that increased expression of FTO, which encodes a 2-oxoglutaratedependent nucleic acid demethylase, leads to increased body weight, although the underlying mechanism has remained unclear. To elucidate the function of FTO, we examined the consequences of altered FTO levels in cultured cells and murine brain. Here we show that a knockdown of FTO in HEK293 cells affects the transcripts levels of genes involved in the response to starvation, whereas overexpression of FTO affects the transcript levels of genes related to RNA processing and metabolism. Subcellular localization of FTO further strengthens the latter notion. Using immunocytochemistry and confocal laser scanning microscopy, we detected FTO in nuclear speckles and -to a lesser and varying extent -in the nucleoplasm and nucleoli of HEK293, HeLa and MCF-7 cells. Moreover, RNA modification analyses revealed that loss of Fto affects the 3-methyluridine/ uridine and pseudouridine/uridine ratios in total brain RNA. We conclude that altered levels of FTO have multiple and diverse consequences on RNA modifications and the transcriptome. Keywords: FTO; RNA modifications; nuclear speckles; transcriptome INTRODUCTION Genome-wide association studies have revealed a strong association between a block of single-nucleotide polymorphisms (SNPs) in intron 1 of the fat mass and obesity-associated (FTO) gene, body mass index and other obesity-related traits in children and adults of different populations. 1-3 Stratigopoulos et al 4 have suggested that one of the SNPs (rs8050136) affects binding of the transcriptional regulator CUX1. By studying allelic expression levels in heterozygous individuals, we have found that the risk allele of the FTO gene makes more transcripts and have proposed that increased expression of the FTO gene leads to increased body weight. 5 This hypothesis is supported by the clinical findings in rare patients and in mouse models with an FTO/Fto mutation. Homozygous loss-of-function of FTO was reported to cause severe growth retardation and multiple malformations, 6 whereas a duplication of FTO was found to be associated with morbid obesity. 7 Fto-knockout mice 8 and mice with a missense mutation in exon 6 9 showed leanness, postnatal growth retardation and a higher metabolic rate. Mice with one or two additional copies of Fto had a gene-dosage-dependent increase in body weight. 10 FTO is a member of non-heme Fe(II)-and a-ketoglutaratedependent oxygenase superfamily and is found in vertebrates and green algea, but not in invertebrate animals, fungi and green plants. 11 By in vitro studies, FTO was shown to function as a demethylase with a strong preference for 3meU and 3meT in single-stranded RNA and DNA, respectively. 12,13 Han et al 14 have provided structural evidence for understanding the substrate specificity of FTO and have suggested

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Section: Discussionmentioning

confidence: 99%

FTO levels affect RNA modification and the transcriptome

et al. 2012

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“…Additionally, misdirection of modification is deleterious (Liu et al 2008). Modifications are important for optimal ribosome function, however, because ribosomes that lack them demonstrate reduced translation efficiency (Baxter-Roshek et al 2007;Liang et al 2007Liang et al , 2009bJack et al 2011).…”

Section: Pre-rrna Processing Can Occur Cotranscriptionallymentioning

confidence: 99%

Ribosome Biogenesis in the YeastSaccharomyces cerevisiae

2013

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Ribosomes are highly conserved ribonucleoprotein nanomachines that translate information in the genome to create the proteome in all cells. In yeast these complex particles contain four RNAs (.5400 nucleotides) and 79 different proteins. During the past 25 years, studies in yeast have led the way to understanding how these molecules are assembled into ribosomes in vivo. Assembly begins with transcription of ribosomal RNA in the nucleolus, where the RNA then undergoes complex pathways of folding, coupled with nucleotide modification, removal of spacer sequences, and binding to ribosomal proteins. More than 200 assembly factors and 76 small nucleolar RNAs transiently associate with assembling ribosomes, to enable their accurate and efficient construction. Following export of preribosomes from the nucleus to the cytoplasm, they undergo final stages of maturation before entering the pool of functioning ribosomes. Elaborate mechanisms exist to monitor the formation of correct structural and functional neighborhoods within ribosomes and to destroy preribosomes that fail to assemble properly. Studies of yeast ribosome biogenesis provide useful models for ribosomopathies, diseases in humans that result from failure to properly assemble ribosomes. TABLE OF CONTENTS Abstract 643Introduction 644

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“…It is tempting to speculate, if 4sU treatment also reduces translational fidelity of ribosomes, as reported for ribosomes lacking pseudouridine synthase dyskerin. 24 It also remains to be established, whether other uridine analogs, such as 5-BrU or 5-eU impact on rRNA metabolism.…”

Section: Su and 5-fu Inhibit Ribosome Biogenesis Differentlymentioning

confidence: 99%