Nuclear export dynamics of RNA–protein complexes

Grünwald, David; Singer, Robert H.; Rout, Michael P.

doi:10.1038/nature10318

Cited by 164 publications

(159 citation statements)

References 100 publications

(194 reference statements)

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“…This is somewhat surprising, since both splicing and polyadenylation are known to strongly stimulate nuclear export in protein-coding transcripts (27,28). Thus, the nuclear localization of fully processed lncRNAs points to the presence of additional, hithertounknown subcellular localization mechanisms and, potentially, novel RNA motifs that govern the functionally required nuclear retention or import of these transcripts.…”

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confidence: 98%

“…Further, the nuclear localization of these RNAs likely plays a crucial functional role by preventing them from interacting with the translation machinery and coding for potentially harmful short peptides. Studies on subcellular localization of RNAs have mostly focused on the nuclear export of protein-coding RNAs, in which 5= capping, splicing, and deposition of the exon junction complex and polyadenylation play the major roles, although the involvement of some RNA sequence motifs has also been documented (27)(28)(29)(30)(31). In intronless RNAs, polyadenylation seems to play the dominant role in export of RNAs to the cytoplasm (32)(33)(34)(35).…”

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confidence: 99%

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A Novel RNA Motif Mediates the Strict Nuclear Localization of a Long Noncoding RNA

Zhang

Gunawardane

Niazi

et al. 2014

Molecular and Cellular Biology

141

113

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The ubiquitous presence of long noncoding RNAs (lncRNAs) in eukaryotes points to the importance of understanding how their sequences impact function. As many lncRNAs regulate nuclear events and thus must localize to nuclei, we analyzed the sequence requirements for nuclear localization in an intergenic lncRNA named BORG (BMP2-OP1-responsive gene), which is both spliced and polyadenylated but is strictly localized in nuclei. Subcellular localization of BORG was not dependent on the context or level of its expression or decay but rather depended on the sequence of the mature, spliced transcript. Mutational analyses indicated that nuclear localization of BORG was mediated through a novel RNA motif consisting of the pentamer sequence AGCCC with sequence restrictions at positions ؊8 (T or A) and ؊3 (G or C) relative to the first nucleotide of the pentamer. Mutation of the motif to a scrambled sequence resulted in complete loss of nuclear localization, while addition of even a single copy of the motif to a cytoplasmically localized RNA was sufficient to impart nuclear localization. Further, the presence of this motif in other cellular RNAs showed a direct correlation with nuclear localization, suggesting that the motif may act as a general nuclear localization signal for cellular RNAs.

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confidence: 98%

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confidence: 99%

A Novel RNA Motif Mediates the Strict Nuclear Localization of a Long Noncoding RNA

Zhang

Gunawardane

Niazi

et al. 2014

Molecular and Cellular Biology

141

113

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“…A key question is how TFs transport rapidly through the FG repeats, with measured dwell times of approximately milliseconds (21,22), while interacting sufficiently strongly with the FG repeats to maintain a high level of transport selectivity. Several proposed models of NPC transport differ significantly with regard to assumptions about the structure and dynamics of the FG repeats, their interactions with each other and with TFs, and their structural changes during these interactions (1,3,15,(23)(24)(25)(26)(27)(28).…”

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confidence: 99%

Slide-and-exchange mechanism for rapid and selective transport through the nuclear pore complex

Raveh

Karp

Sparks

et al. 2016

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

131

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Nucleocytoplasmic transport is mediated by the interaction of transport factors (TFs) with disordered phenylalanine-glycine (FG) repeats that fill the central channel of the nuclear pore complex (NPC). However, the mechanism by which TFs rapidly diffuse through multiple FG repeats without compromising NPC selectivity is not yet fully understood. In this study, we build on our recent NMR investigations showing that FG repeats are highly dynamic, flexible, and rapidly exchanging among TF interaction sites. We use unbiased long timescale all-atom simulations on the Anton supercomputer, combined with extensive enhanced sampling simulations and NMR experiments, to characterize the thermodynamic and kinetic properties of FG repeats and their interaction with a model transport factor. Both the simulations and experimental data indicate that FG repeats are highly dynamic random coils, lack intrachain interactions, and exhibit significant entropically driven resistance to spatial confinement. We show that the FG motifs reversibly slide in and out of multiple TF interaction sites, transitioning rapidly between a strongly interacting state and a weakly interacting state, rather than undergoing a much slower transition between strongly interacting and completely noninteracting (unbound) states. In the weakly interacting state, FG motifs can be more easily displaced by other competing FG motifs, providing a simple mechanism for rapid exchange of TF/FG motif contacts during transport. This slide-and-exchange mechanism highlights the direct role of the disorder within FG repeats in nucleocytoplasmic transport, and resolves the apparent conflict between the selectivity and speed of transport.nuclear pore | molecular dynamics | nucleoporins | transport factors | NMR T he nuclear pore complex (NPC) regulates macromolecular transport between the nucleus and the cytoplasm in all eukaryotic cells (1, 2). The NPC allows for passive diffusion of small molecules including sugars, ions, and water, while simultaneously imposing size-dependent exclusion of macromolecules without nuclear transport factor (TF) binding sites, generating unique nuclear and cytoplasmic compartments (3, 4). Larger macromolecules can bypass the selectivity barrier of the NPC by interacting with TFs that shuttle cargo through the central channel of the pore. In pathological conditions, including many cancers and viral infections, the NPC is hijacked and used to transport undesired particles, or it is modified to attenuate the cellular responses to disease onset (5, 6).TFs traverse the NPC by selective and reversible association with disordered phenylalanine-glycine (FG) repeat domains of the FG nucleoporin proteins (FG Nups), which line the surface of the NPC (7-14). Each FG repeat domain consists of 5-50 FG repeats. In turn, each FG repeat consists of a single FG motif of various sequence flavors, such as the FSFG and GLFG motifs, and 10-30 spacer residues that separate consecutive FG motifs (15, 16). The spacer residues are strongly hydrophilic (17) and rich ...

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“…Until recently, it was thought that all mRNA export occurred one molecule at a time through the nuclear pore complex (NPC) (Grü nwald et al, 2011;Kö hler and Hurt, 2007). However, we recently uncovered a mechanism by which large ribonucleoprotein (megaRNP) granules exit the nucleus via nuclear envelope (NE) budding , a mechanism previously shown to be utilized for the nuclear export of large herpes-type viral capsids (Maric et al, 2011;Mettenleiter et al, 2006).…”

Section: Introductionmentioning

confidence: 99%

A Novel Locomotion-based Validation Assay for Candidate Drugs Using Drosophila DYT1 Disease Model

Ito¹

2013

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Public reporting burden for this collection of information is estimated to average 1 hour per response, including the time for reviewing instructions, searching existing data sources, gathering and maintaining the data needed, and completing and reviewing this collection of information. Send comments regarding this burden estimate or any other aspect of this collection of information, including suggestions for reducing this burden to Department of Defense, Washington Headquarters Services, Directorate for Information PERFORMING ORGANIZATION NAME(S) AND ADDRESS(ES) AND ADDRESS(ES) PERFORMING ORGANIZATION REPORT NUMBERMassachusetts General Hospital Charlestown, Massachusetts 02129 SPONSORING / MONITORING AGENCY NAME(S) AND ADDRESS(ES) 10. SPONSOR/MONITOR'S ACRONYM(S) U.S. Army Medical Research and Materiel Command Fort Detrick, Maryland 21702-5012 SPONSOR/MONITOR'S REPORT NUMBER(S) DISTRIBUTION / AVAILABILITY STATEMENTApproved for Public Release; Distribution Unlimited SUPPLEMENTARY NOTES ABSTRACTWe have established fly lines expressing a mutant form of human torsinA (torsinAΔE) in fly brains. We have shown that (1) human torsinAΔE protein is expressed in fly brains; (2) expression of human torsinAΔE dominantly suppresses larval locomotion and GTPC cyclrohydolase protein levels; (3) supplementation of dopamine can partially rescue the locomotion defects of Drosophila larvae caused by the expression of human torsinAΔE. These results demonstrated that human torsinA can cause locomotion defects and reduction of GTP cyclohydrolase proteins very similar to the phenotypes in dtorsin-null larval brains. These results suggested that we can study the molecular defects of human torsinAΔE using our fly model system. We have submitted a manuscript describing our results. We have conducted preliminary RNAi screen to identify modifiers of dtorsin-null locomotion defect phenotype. Our preliminary results suggest that (1) dopamine signaling pathway; (2) RNP transport pathway; (3) axon guidance pathway; and (4) other early-onset dystonia genes as candidates for modifiers. These RNAi screen will be very useful for identifying potential therapeutic targets of early-onset dystonia patients.

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Nuclear export dynamics of RNA–protein complexes

Cited by 164 publications

References 100 publications

A Novel RNA Motif Mediates the Strict Nuclear Localization of a Long Noncoding RNA

A Novel RNA Motif Mediates the Strict Nuclear Localization of a Long Noncoding RNA

Slide-and-exchange mechanism for rapid and selective transport through the nuclear pore complex

A Novel Locomotion-based Validation Assay for Candidate Drugs Using Drosophila DYT1 Disease Model

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