An overview of pre‐ribosomal <scp>RNA</scp> processing in eukaryotes

Henras, Anthony K.; Plisson‐Chastang, Célia; O’Donohue, Marie-Françoise; Chakraborty, Anirban; Gleizes, Pierre‐Emmanuel

doi:10.1002/wrna.1269

Cited by 500 publications

(602 citation statements)

References 179 publications

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“…A recent study revealed that RNA binding of HNRNPC is enhanced upon addition of m 6 A modifications (Liu et al 2015), and it is possible that HNRNPC interacts with rRNA in an m 6 A-dependent manner. Furthermore, HNRNPD was identified in the same study as being involved in large ribosomal subunit maturation (Henras et al 2015). This finding agrees with the strong enrichment of HNRNPD in the 28S rRNA interactome and its absence in the 18S rRNA interactome.…”

Section: Identification Of Previously Unrecognized Ribosomal Rbpssupporting

confidence: 78%

Specific RNP capture with antisense LNA/DNA mixmers

Rogell

Fischer

Rettel

et al. 2017

RNA

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RNA-binding proteins (RBPs) play essential roles in RNA biology, responding to cellular and environmental stimuli to regulate gene expression. Important advances have helped to determine the (near) complete repertoires of cellular RBPs. However, identification of RBPs associated with specific transcripts remains a challenge. Here, we describe "specific ribonucleoprotein (RNP) capture," a versatile method for the determination of the proteins bound to specific transcripts in vitro and in cellular systems. Specific RNP capture uses UV irradiation to covalently stabilize protein-RNA interactions taking place at "zero distance." Proteins bound to the target RNA are captured by hybridization with antisense locked nucleic acid (LNA)/DNA oligonucleotides covalently coupled to a magnetic resin. After stringent washing, interacting proteins are identified by quantitative mass spectrometry. Applied to in vitro extracts, specific RNP capture identifies the RBPs bound to a reporter mRNA containing the Sex-lethal (Sxl) binding motifs, revealing that the Sxl homolog sister of Sex lethal (Ssx) displays similar binding preferences. This method also revealed the repertoire of RBPs binding to 18S or 28S rRNAs in HeLa cells, including previously unknown rRNA-binding proteins.

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Section: Identification Of Previously Unrecognized Ribosomal Rbpssupporting

confidence: 78%

Specific RNP capture with antisense LNA/DNA mixmers

Rogell

Fischer

Rettel

et al. 2017

RNA

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“…Despite our detailed knowledge of the pre-rRNA processing pathway in yeast and human cells [7,63], the enzymes that cleave the pre-rRNA at sites A 0 , A 1 , and A 2 have not yet been unambiguously assigned. While all three cleavages depend on the U3 snoRNP, processing at sites A 1 and A 2 appears to be coupled and occurs independently of A 0 cleavage [7].…”

Section: Dismantling Of the 90s Preribosome Releases An Early Pre-40smentioning

confidence: 99%

A Puzzle of Life: Crafting Ribosomal Subunits

Kressler

Hurt

Baßler

2017

Trends in Biochemical Sciences

163

127

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The biogenesis of eukaryotic ribosomes is a complicated process during which the transcription, modification, folding, and processing of the rRNA is coupled with the ordered assembly of $80 ribosomal proteins (r-proteins). Ribosome synthesis is catalyzed and coordinated by more than 200 biogenesis factors as the preribosomal subunits acquire maturity on their path from the nucleolus to the cytoplasm. Several biogenesis factors also interconnect the progression of ribosome assembly with quality control of important domains, ensuring that only functional subunits engage in translation. With the recent visualization of several assembly intermediates by cryoelectron microscopy (cryo-EM), a structural view of ribosome assembly begins to emerge. In this review we integrate these first structural insights into an updated overview of the consecutive ribosome assembly steps. Synopsis of Eukaryotic Ribosome AssemblyRibosomes are the molecular machines that translate the genetic information from the intermediary mRNA templates into proteins [1]. Eukaryotic 80S ribosomes comprise two unequal subunits that contain four different rRNAs and around 80 r-proteins ( Figure 1). The small 40S subunit (SSU) comprises the 18S rRNA and 33 r-proteins (referred to as RPS or S). The large 60S subunit (LSU) comprises the 25S/28S, 5.8S, and 5S rRNA and, in most eukaryotic species, 47 r-proteins (RPL or L); a notable exception is budding yeasts, which lack eL28The act of building a ribosome begins in the nucleolus, where the ribosomal DNA (rDNA) is transcribed into a long pre-rRNA precursor (35S pre-rRNA in yeast) and involves the ordered assembly of the r-proteins with the pre-rRNA, which is concomitantly processed into the mature rRNA species [5][6][7][8] (Figure 1 and Box 1). These assembly and processing events are tightly coupled and occur within preribosomal particles (see Glossary) that travel, as maturation progresses, from the nucleus across nuclear pore complexes (NPCs) to the cytoplasm, where they are ultimately converted into translation-competent ribosomal subunits [5,[9][10][11][12][13] (Figure 2, Key Figure). Given the gargantuan complexity of this process, it is unsurprising that the assembly of eukaryotic ribosomes strictly requires the assistance of a plethora (>200) of mostly essential ribosome biogenesis factors, which are also called trans-acting or assembly factors [5,14,15].Our current knowledge has been mainly obtained by studying ribosome biogenesis in the yeast Saccharomyces cerevisiae. Research conducted in the 1970s defined the r-protein composition of ribosomes, revealed the major pre-rRNA processing intermediates, and uncovered the existence of the 90S, 43S, and 66S preribosomal particles. The following 25 years witnessed the identification of numerous biogenesis factors and attributed functional roles TrendsCryoelectron microscopy analyses of the 90S preribosome show that the biogenesis factors create a casting mold that encloses the nascent pre-40S subunit.Structures of nuclear pre-60S particles reveal that a...

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“…Since the mid-1960s the nucleolus has been known as the site of ribosomal RNA (rRNA) transcription, processing and ribosomal assembly, and the different substructures within the nucleolus likely mediate distinct stages of the ribosome assembly process (Pederson 2011;Hernandez-Verdun et al 2010). Several decades of research by many groups have made great strides towards elucidating the complicated succession of processing steps required to assemble nascent rRNA into functional ribosomes, as well as the identifying the ~80 ribosomal proteins (RPs) and >300 ribosomal maturation factors that are required to accomplish them (Henras et al 2014;Venema and Tollervey, 1999;Woolford and Baserga 2013).…”

Section: Introductionmentioning

confidence: 99%

“…The production of ribosomal RNA occupies >50% of all eukaryotic transcription and represents the major source of cellular energy consumption, as well as being tightly coordinated with cell growth and division (Henras et al 2014). As a result, any defect in ribosome biogenesis must be rapidly communicated to the cell's proliferative machinery to prevent division of cells with insufficient translational capacity; similarly, inhibition of ribosome synthesis in response to DNA damage or other stresses is essential to prevent cellular energy depletion and/or production of aberrant ribosomes from damaged rDNA (James et al 2014;Tsai and Pederson 2014).…”

Section: Introductionmentioning

confidence: 99%

Nucleolin and nucleophosmin: nucleolar proteins with multiple functions in DNA repair

Scott

Oeffinger

2016

Biochem. Cell Biol.

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The nucleolus represents a highly multifunctional intranuclear organelle in which, in addition to the canonical ribosome assembly, numerous processes such as transcription, DNA repair and replication, the cell cycle and apoptosis are coordinated. The nucleolus is further a key hub in the sensing of cellular stress and undergoes major structural and compositional changes in response to cellular perturbations.Numerous nucleolar proteins have been identified that, upon nucleolar stress sensing, deploy additional, non-ribosomal roles in the regulation of varied cell processes including cell cycle arrest, arrest of DNA replication, induction of DNA repair, and apoptosis, among others. The highly abundant proteins nucleophosmin (NPM1) and nucleolin (NCL) are two such factors that transit to the nucleoplasm in response to stress, and participate directly in the repair of numerous different DNA damages. This review discusses the contributions made by NCL and/or NPM1 to the different DNA repair pathways employed by mammalian cells to repair DNA insults, and examines the implications of such activities for the regulation, pathogenesis and therapeutic targeting of NPM1 and NCL.

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An overview of pre‐ribosomal RNA processing in eukaryotes

Cited by 500 publications

References 179 publications

Specific RNP capture with antisense LNA/DNA mixmers

Specific RNP capture with antisense LNA/DNA mixmers

A Puzzle of Life: Crafting Ribosomal Subunits

Nucleolin and nucleophosmin: nucleolar proteins with multiple functions in DNA repair

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