Targeting of Aberrant mRNAs to Cytoplasmic Processing Bodies

Sheth, Ujwal; Parker, Roy

doi:10.1016/j.cell.2006.04.037

Cited by 262 publications

(313 citation statements)

References 46 publications

(60 reference statements)

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“…Loss of function of NMD factors, including UPF2 and UPF3, leads to enhanced formation of P bodies in yeast (Sheth and Parker, 2006). Thus, mutants with increased P body number could be involved in regulation of NMD in C. elegans.…”

Section: Regulation Of Nmd By a Subset Of Identified Genes That Modulmentioning

confidence: 99%

A genome-wide RNAi screen identifies genes regulating the formation of P bodies in C. elegans and their functions in NMD and RNAi

et al. 2011

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Cytoplasmic processing bodies, termed P bodies, are involved in diverse post-transcriptional processes including mRNA decay, nonsense-mediated RNA decay (NMD), RNAi, miRNA-mediated translational repression and storage of translationally silenced mRNAs. Regulation of the formation of P bodies in the context of multicellular organisms is poorly understood. Here we describe a systematic RNAi screen in C. elegans that identified 224 genes with diverse cellular functions whose inactivations result in a dramatic increase in the number of P bodies. 83 of these genes form a complex functional interaction network regulating NMD. We demonstrate that NMD interfaces with many cellular processes including translation, ubiquitin-mediated protein degradation, intracellular trafficking and cytoskeleton structure. We also uncover an extensive link between translation and RNAi, with different steps in protein synthesis appearing to have distinct effects on RNAi efficiency. Moreover, the intracellular vesicular trafficking network plays an important role in the regulation of RNAi. A subset of genes enhancing P body formation also regulate the formation of stress granules in C. elegans. Our study offers insights into the cellular mechanisms that regulate the formation of P bodies and also provides a framework for system-level understanding of NMD and RNAi in the context of the development of multicellular organisms.

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Section: Regulation Of Nmd By a Subset Of Identified Genes That Modulmentioning

confidence: 99%

A genome-wide RNAi screen identifies genes regulating the formation of P bodies in C. elegans and their functions in NMD and RNAi

et al. 2011

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“…Finally, we examined the binding of Dhh1 to a single-stranded deoxyribose nucleic acid probe. Dhh1 bound to a poly(dT 20 ) probe with high affinity (ϳ77 nM), but this is ϳ30-fold lower than the rU20 probe (Table 2). However, it is unclear if Dhh1 binds single-stranded DNA in vivo.…”

Section: Dmentioning

confidence: 99%

Intermolecular Interactions within the Abundant DEAD-box Protein Dhh1 Regulate Its Activity in Vivo

Dutta

Zheng

Jain

et al. 2011

Journal of Biological Chemistry

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Dhh1 is a highly conserved DEAD-box protein that has been implicated in many processes involved in mRNA regulation. At least some functions of Dhh1 may be carried out in cytoplasmic foci called processing bodies (P-bodies). Dhh1 was identified initially as a putative RNA helicase based solely on the presence of conserved helicase motifs found in the superfamily 2 (Sf2) of DEXD/H-box proteins. Although initial mutagenesis studies revealed that the signature DEAD-box motif is required for Dhh1 function in vivo, enzymatic (ATPase or helicase) or ATP binding activities of Dhh1 or those of any its many higher eukaryotic orthologues have not been described. Here we provide the first characterization of the biochemical activities of Dhh1. Dhh1 has weaker RNA-dependent ATPase activity than other well characterized DEAD-box helicases. We provide evidence that intermolecular interactions between the N-and C-terminal RecA-like helicase domains restrict its ATPase activity; mutation of residues mediating these interactions enhanced ATP hydrolysis. Interestingly, the interdomain interaction mutant displayed enhanced mRNA turnover, RNA binding, and recruitment into cytoplasmic foci in vivo compared with wild type Dhh1. Also, we demonstrate that the ATPase activity of Dhh1 is not required for it to be recruited into cytoplasmic foci, but it regulates its association with RNA in vivo. We hypothesize that the activity of Dhh1 is restricted by interdomain interactions, which can be regulated by cellular factors to impart stringent control over this very abundant RNA helicase.The regulation of gene expression in eukaryotes is a complex series of events that is well coordinated by different cellular machineries. Central to this process is the regulation of mRNA metabolism. It begins with transcription followed by pre-mRNA processing in the nucleus, nucleo-cytoplasmic transport, translation, and finally, the controlled degradation of mRNA.mRNA degradation is one of the important means of mRNA quality control. In eukaryotic cells two major pathways have evolved for mRNA degradation; they are non-sense-mediated decay, which is deadenylation-independent and the more ubiquitously used deadenylation-dependent pathway (1). Nonsense-mediated decay is the process of choice for quick and efficient removal of transcripts with non-sense codons, unspliced introns, or extended 3Ј-UTR (2). The deadenylationdependent pathway begins with the removal of the 3Ј-poly(A) tail by 3Ј-5Ј exonucleases Ccr4 and Pop2 or poly(A) nuclease (3-7). This is followed by removal of the 5Ј-m 7 -guanosine triphosphate cap by the Dcp2/Dcp1 decapping complex (8, 9). The binding of Dcp1/Dcp2 to the 5Ј cap and decapping are enhanced by a complex of seven Lsm (like-Sm) proteins (Lsm1 through Lsm7), Pat1, Edc3,. The final step in the pathway involves degradation of the decapped and deadenylated RNA by the 5Ј-3Ј exonuclease Xrn1 and by the exosome that acts in the 3Ј-5Ј direction (16,17). Proteins involved in mRNA turnover are localized to distinct foci in the cytoplasm call...

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“…31, 32 and references therein]. Although the association of the group II intron-related RNAs with Dcp2 and Pab1 needs to be interpreted with caution, this association may be reflective of translational repression or sequestration of group II intron-related RNAs in ribonucleoprotein (RNP) granules, particularly PBs and SGs, which communicate NMD (33,34) and inhibit mRNA translation (13). It remains to be determined if targeting to these particles may result from mRNA-pre-mRNA interactions, or if mRNA-premRNA interactions could result from in situ splicing in PBs and/ or SGs.…”

Section: Rna Miscompartmentalization As a Roadblock To Gene Expressionmentioning

confidence: 99%

RNA–RNA interactions and pre-mRNA mislocalization as drivers of group II intron loss from nuclear genomes

Dong

Piazza

et al. 2014

Proc. Natl. Acad. Sci. U.S.A.

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Group II introns are commonly believed to be the progenitors of spliceosomal introns, but they are notably absent from nuclear genomes. Barriers to group II intron function in nuclear genomes therefore beg examination. A previous study showed that nuclear expression of a group II intron in yeast results in nonsensemediated decay and translational repression of mRNA, and that these roadblocks to expression are group II intron-specific. To determine the molecular basis for repression of gene expression, we investigated cellular dynamics of processed group II intron RNAs, from transcription to cellular localization. Our data show pre-mRNA mislocalization to the cytoplasm, where the RNAs are targeted to foci. Furthermore, tenacious mRNA-pre-mRNA interactions, based on intron-exon binding sequences, result in reduced abundance of spliced mRNAs. Nuclear retention of pre-mRNA prevents this interaction and relieves these expression blocks. In addition to providing a mechanistic rationale for group II intronspecific repression, our data support the hypothesis that RNA silencing of the host gene contributed to expulsion of group II introns from nuclear genomes and drove the evolution of spliceosomal introns.intron-mediated nuclear gene silencing | spliceosomal intron evolution G roup II introns that reside in genomes of bacteria, archaea, and eukaryotic organelles are ribozymes that self-splice from pre-mRNA transcripts independent of protein catalysis (1-3). Group II introns are also mobile retroelements that integrate into DNAs via an RNA intermediate (2, 3). Group II intron splicing is usually facilitated in vivo by an intron-encoded protein that acts as a maturase to help form the required secondary and tertiary structures (3). The intron RNA-protein complex is also required for group II intron retromobility. Both splicing and mobility of group II introns require interactions between exon-binding sequences (EBSs) within the intron and intron-binding sequences (IBSs) in the flanking exons of RNA or DNA targets (2, 3).The chemical steps of group II intron splicing are identical to those of nuclear spliceosomal introns (4, 5). There are also similarities of RNA sequences at the splice sites and of RNA structures within the ribozyme and the spliceosome (6-9). Because of these parallels, the catalytic group II introns are believed to be the progenitors of spliceosomal introns (6, 10, 11). It is widely speculated that group II introns entered the eukaryotic lineage with the mitochondrial endosymbiosis, invaded the nucleus, and evolved from RNA catalysts into efficient spliceosomedependent introns. However, group II introns are strikingly absent from modern nuclear genomes (1), which are replete with spliceosomal introns. It is still elusive how the ancestral group II introns might have evolved into spliceosomal introns or how they were expunged from nuclear genomes.As an initial effort to answer these questions, we had probed the fate of group II introns introduced into RNA polymerase II transcripts in Saccharomyces cerevis...

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Targeting of Aberrant mRNAs to Cytoplasmic Processing Bodies

Cited by 262 publications

References 46 publications

A genome-wide RNAi screen identifies genes regulating the formation of P bodies in C. elegans and their functions in NMD and RNAi

A genome-wide RNAi screen identifies genes regulating the formation of P bodies in C. elegans and their functions in NMD and RNAi

Intermolecular Interactions within the Abundant DEAD-box Protein Dhh1 Regulate Its Activity in Vivo

RNA–RNA interactions and pre-mRNA mislocalization as drivers of group II intron loss from nuclear genomes

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