A dynamic bulge in the U6 RNA internal stem-loop functions in spliceosome assembly and activation. (Q36148315)

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:17925343%20AND%20SRC:MED&resulttype=core&format=json

8 January 2020

title

A dynamic bulge in the U6 RNA internal stem-loop functions in spliceosome assembly and activation (English)

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8 January 2020

0 references

1

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8 January 2020

author name string

Matthew L Schwartz

series ordinal

2

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8 January 2020

Samuel E Butcher

series ordinal

3

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8 January 2020

David A Brow

series ordinal

4

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8 January 2020

language of work or name

English

0 references

publication date

9 October 2007

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8 January 2020

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8 January 2020

volume

13

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8 January 2020

issue

12

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8 January 2020

page(s)

2252-2265

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Fluorescence and solution NMR study of the active site of a 160-kDa group II intron ribozyme

8 January 2020

cites work

1 reference

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The EF-G-like GTPase Snu114p regulates spliceosome dynamics mediated by Brr2p, a DExD/H box ATPase

2 October 2017

1 reference

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Exon ligation is proofread by the DExD/H-box ATPase Prp22p

2 October 2017

1 reference

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Accumulation of unstable promoter-associated transcripts upon loss of the nuclear exosome subunit Rrp6p in Saccharomyces cerevisiae

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2080595

Structure of a self-splicing group II intron catalytic effector domain 5: parallels with spliceosomal U6 RNA

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2080595

RNA structure and RNA-protein interactions in purified yeast U6 snRNPs

2 October 2017

1 reference

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Genetic analysis reveals a role for the C terminus of the Saccharomyces cerevisiae GTPase Snu114 during spliceosome activation

2 October 2017

1 reference

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Prp8 protein: at the heart of the spliceosome

2 October 2017

1 reference

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The N- and C-terminal RNA recognition motifs of splicing factor Prp24 have distinct functions in U6 RNA binding

2 October 2017

1 reference

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Dynamics in the U6 RNA intramolecular stem-loop: a base flipping conformational change

2 October 2017

1 reference

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The Prp19p-associated complex in spliceosome activation

2 October 2017

1 reference

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New 'marker swap' plasmids for converting selectable markers on budding yeast gene disruptions and plasmids

2 October 2017

1 reference

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Characterization of the catalytic activity of U2 and U6 snRNAs

2 October 2017

1 reference

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Structural Basis for a Lethal Mutation in U6 RNA † , ‡

2 October 2017

1 reference

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Allosteric cascade of spliceosome activation

2 October 2017

1 reference

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The conserved central domain of yeast U6 snRNA: importance of U2-U6 helix Ia in spliceosome assembly

2 October 2017

1 reference

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Distinct domains of splicing factor Prp8 mediate different aspects of spliceosome activation

2 October 2017

1 reference

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A catalytically active group II intron domain 5 can function in the U12-dependent spliceosome

2 October 2017

1 reference

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Characterization of U4 and U6 interactions with the 5' splice site using a S. cerevisiae in vitro trans-splicing system

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2080595

New roles for the Snp1 and Exo84 proteins in yeast pre-mRNA splicing

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2080595

Suppressors of a cold-sensitive mutation in yeast U4 RNA define five domains in the splicing factor Prp8 that influence spliceosome activation

2 October 2017

1 reference

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A tertiary interaction that links active-site domains to the 5' splice site of a group II intron

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2080595

RNA bulges as architectural and recognition motifs

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2080595

Multiple functions of Saccharomyces cerevisiae splicing protein Prp24 in U6 RNA structural rearrangements

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2080595

Protein-RNA interactions in the U5 snRNP of Saccharomyces cerevisiae

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2080595

RNA unwinding in U4/U6 snRNPs requires ATP hydrolysis and the DEIH-box splicing factor Brr2

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2080595

Mechanical devices of the spliceosome: motors, clocks, springs, and things

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2080595

A spliceosomal recycling factor that reanneals U4 and U6 small nuclear ribonucleoprotein particles

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2080595

Cross-intron bridging interactions in the yeast commitment complex are conserved in mammals

2 October 2017

1 reference

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The human U6 snRNA intramolecular helix: structural constraints and lack of sequence specificity

2 October 2017

1 reference

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A stem/loop in U6 RNA defines a conformational switch required for pre-mRNA splicing

2 October 2017

1 reference

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A rapid assay for quantitative detection of specific RNAs

2 October 2017

1 reference

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Evidence for a Prp24 binding site in U6 snRNA and in a putative intermediate in the annealing of U6 and U4 snRNAs

2 October 2017

1 reference

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Lethal mutations in a yeast U6 RNA gene B block promoter element identify essential contacts with transcription factor-IIIC.

2 October 2017

1 reference

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Specificity of Prp24 binding to RNA: a role for Prp24 in the dynamic interaction of U4 and U6 snRNAs

2 October 2017

1 reference

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A ten-minute DNA preparation from yeast efficiently releases autonomous plasmids for transformation of Escherichia coli

2 October 2017

1 reference

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Yeast mRNA splicing in vitro

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2080595

Spliceosome assembly in yeast

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2080595

Multiple roles for U6 snRNA in the splicing pathway

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2080595

A cold-sensitive mRNA splicing mutant is a member of the RNA helicase gene family

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2080595

Suppressors of a U4 snRNA mutation define a novel U6 snRNP protein with RNA-binding motifs

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2080595

A rapid method for localized mutagenesis of yeast genes

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2080595

Evidence for a base-pairing interaction between U6 small nuclear RNA and 5' splice site during the splicing reaction in yeast

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2080595

Dynamics and metal ion binding in the U6 RNA intramolecular stem-loop as analyzed by NMR.

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2080595

The ribosomal translocase homologue Snu114p is involved in unwinding U4/U6 RNA during activation of the spliceosome

2 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2080595

Functional contacts with a range of splicing proteins suggest a central role for Brr2p in the dynamic control of the order of events in spliceosomes of Saccharomyces cerevisiae

2 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2080595

An RNA switch at the 5' splice site requires ATP and the DEAD box protein Prp28p

2 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2080595

Mutations of the two-nucleotide bulge of D5 of a group II intron block splicing in vitro and in vivo: phenotypes and suppressor mutations

2 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2080595

Interactions of the yeast U6 RNA with the pre-mRNA branch site

2 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2080595

An element in human U6 RNA destabilizes the U4/U6 spliceosomal RNA complex

2 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2080595

Base-pairing interactions involving the 5' and 3'-terminal nucleotides of group II self-splicing introns

2 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2080595

Proximity of conserved U6 and U2 snRNA elements to the 5' splice site region in activated spliceosomes

2 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2080595

Mutagenesis Suggests Several Roles of Snu114p in Pre-mRNA Splicing

23 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2080595

AA.AG@helix.ends: A:A and A:G base-pairs at the ends of 16 S and 23 S rRNA helices

23 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2080595

Metal-ion coordination by U6 small nuclear RNA contributes to catalysis in the spliceosome.

23 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2080595

A spontaneous duplication in U6 spliceosomal RNA uncouples the early and late functions of the ACAGA element in vivo.

23 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2080595

A novel role for a U5 snRNP protein in 3' splice site selection.

23 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2080595

U2–U6 RNA folding reveals a group II intron-like domain and a four-helix junction

23 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2080595

Conformational changes of U6 RNA during the spliceosome cycle: an intramolecular helix is essential both for initiating the U4-U6 interaction and for the first step of slicing

5 December 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/17925343

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Splicing factor Prp8 governs U4/U6 RNA unwinding during activation of the spliceosome

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/17925343

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

A yeast spliceosome assay

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/17925343

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1261/RNA.699907

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:17925343%20AND%20SRC:MED&resulttype=core&format=json

8 January 2020

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:17925343%20AND%20SRC:MED&resulttype=core&format=json

8 January 2020

PubMed publication ID

17925343

1 reference