Spliceosome-mediated decay (SMD) regulates expression of nonintronic genes in budding yeast. (Q42650602)

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23 February 2020

title

Spliceosome-mediated decay (SMD) regulates expression of nonintronic genes in budding yeast (English)

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23 February 2020

0 references

3

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23 February 2020

Sander Granneman

6

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23 February 2020

Sneha Shah

4

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23 February 2020

Cornelia Kilchert

5

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23 February 2020

Lidia Vasiljeva

7

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23 February 2020

author name string

Adam Volanakis

1

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23 February 2020

Monica Passoni

2

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23 February 2020

publication date

1 September 2013

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23 February 2020

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23 February 2020

volume

27

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23 February 2020

issue

18

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23 February 2020

page(s)

2025-2038

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Intronic sequence elements impede exon ligation and trigger a discard pathway that yields functional telomerase RNA in fission yeast

23 February 2020

cites work

1 reference

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Interplay between BDF1 and BDF2 and their roles in regulating the yeast salt stress response

27 May 2018

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Extensive degradation of RNA precursors by the exosome in wild-type cells

27 May 2018

1 reference

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Transcription-associated quality control of mRNP.

27 May 2018

1 reference

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Dissecting DNA damage response pathways by analysing protein localization and abundance changes during DNA replication stress

27 May 2018

1 reference

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RNA degradation in Saccharomyces cerevisae

27 May 2018

1 reference

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Sequential RNA degradation pathways provide a fail-safe mechanism to limit the accumulation of unspliced transcripts in Saccharomyces cerevisiae

27 May 2018

1 reference

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Global analysis of mRNA decay intermediates in Saccharomyces cerevisiae

27 May 2018

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A quantitative, high-throughput reverse genetic screen reveals novel connections between Pre-mRNA splicing and 5' and 3' end transcript determinants

27 May 2018

1 reference

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Telomerase RNA biogenesis involves sequential binding by Sm and Lsm complexes

27 May 2018

1 reference

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Design principles of interconnections between chromatin and pre-mRNA splicing

27 May 2018

1 reference

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TopHat-Fusion: an algorithm for discovery of novel fusion transcripts

27 May 2018

1 reference

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Pause locally, splice globally

27 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3792478

Spliceosome Structure and Function

27 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3792478

Comprehensive phenotypic analysis of single-gene deletion and overexpression strains of Saccharomyces cerevisiae

27 May 2018

1 reference

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A comprehensive genomic binding map of gene and chromatin regulatory proteins in Saccharomyces

27 May 2018

1 reference

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Proofreading and spellchecking: a two-tier strategy for pre-mRNA splicing quality control

27 May 2018

1 reference

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A meiotic gene regulatory cascade driven by alternative fates for newly synthesized transcripts

27 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3792478

Spliceosome discards intermediates via the DEAH box ATPase Prp43p

27 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3792478

The spliceosome: design principles of a dynamic RNP machine

27 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3792478

Pre-mRNA processing reaches back to transcription and ahead to translation

27 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3792478

A complex gene regulatory mechanism that operates at the nexus of multiple RNA processing decisions

27 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3792478

Widespread impact of nonsense-mediated mRNA decay on the yeast intronome

27 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3792478

Degradation of histone mRNA requires oligouridylation followed by decapping and simultaneous degradation of the mRNA both 5' to 3' and 3' to 5'

27 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3792478

Rapid, transcript-specific changes in splicing in response to environmental stress

27 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3792478

Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project

27 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3792478

NuA4-directed chromatin transactions throughout the Saccharomyces cerevisiae genome

27 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3792478

Ultraconserved elements are associated with homeostatic control of splicing regulators by alternative splicing and nonsense-mediated decay

27 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3792478

Genome-wide identification of spliced introns using a tiling microarray

27 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3792478

A genome-wide analysis indicates that yeast pre-mRNA splicing is predominantly posttranscriptional

27 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3792478

Contribution of Trf4/5 and the nuclear exosome to genome stability through regulation of histone mRNA levels in Saccharomyces cerevisiae

27 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3792478

RNA-quality control by the exosome

27 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3792478

Nrd1 interacts with the nuclear exosome for 3' processing of RNA polymerase II transcripts

27 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3792478

Lsm proteins and RNA processing

27 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3792478

Transitions in RNA polymerase II elongation complexes at the 3' ends of genes

27 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3792478

Cotranscriptional recruitment of the U1 snRNP to intron-containing genes in yeast

27 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3792478

Different sensitivities of bromodomain factors 1 and 2 to histone H4 acetylation

27 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3792478

Remodeling of yeast genome expression in response to environmental changes

27 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3792478

Identification of a regulated pathway for nuclear pre-mRNA turnover.

27 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3792478

The splicing factor, Prp40, binds the phosphorylated carboxyl-terminal domain of RNA polymerase II.

27 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3792478

Bromodomain factor 1 corresponds to a missing piece of yeast TFIID.

27 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3792478

Saccharomyces cerevisiae telomerase is an Sm small nuclear ribonucleoprotein particle

27 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3792478

Transcriptional termination signals for RNA polymerase II in fission yeast

27 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3792478

The role of branchpoint-3' splice site spacing and interaction between intron terminal nucleotides in 3' splice site selection in Saccharomyces cerevisiae

27 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3792478

Identification of novel genes required for yeast pre-mRNA splicing by means of cold-sensitive mutations

27 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3792478

The yeast BDF1 gene encodes a transcription factor involved in the expression of a broad class of genes including snRNAs.

27 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3792478

Bdf1, a yeast chromosomal protein required for sporulation

27 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3792478

Characterization and functional ordering of Slu7p and Prp17p during the second step of pre-mRNA splicing in yeast

27 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3792478

Characterization of an SNR gene locus in Saccharomyces cerevisiae that specifies both dispensible and essential small nuclear RNAs

27 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3792478

Deciphering 3'ss selection in the yeast genome reveals an RNA thermosensor that mediates alternative splicing

27 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3792478

Spliceosomal cleavage generates the 3' end of telomerase RNA.

16 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3792478

Unproductive splicing of SR genes associated with highly conserved and ultraconserved DNA elements

16 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3792478

Using chromatin immunoprecipitation to map cotranscriptional mRNA processing in Saccharomyces cerevisiae.

16 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3792478

Autoregulation of polypyrimidine tract binding protein by alternative splicing leading to nonsense-mediated decay

16 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3792478

Cytoplasmic degradation of splice-defective pre-mRNAs and intermediates

16 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3792478

A biochemical function for the Sm complex.

16 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3792478

16 August 2018

Pseudogenes in yeast?

1 reference

12 December 2020

Differential recruitment of the splicing machinery during transcription predicts genome-wide patterns of mRNA splicing

1 reference

12 December 2020

Genetic and comparative transcriptome analysis of bromodomain factor 1 in the salt stress response of Saccharomyces cerevisiae

1 reference

12 December 2020

The splicing factor Prp17 interacts with the U2, U5 and U6 snRNPs and associates with the spliceosome pre- and post-catalysis

1 reference

12 December 2020

Identifiers

DOI

10.1101/GAD.221960.113

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:24065768%20AND%20SRC:MED&resulttype=core&format=json

23 February 2020

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:24065768%20AND%20SRC:MED&resulttype=core&format=json

23 February 2020

PubMed publication ID

24065768

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:24065768%20AND%20SRC:MED&resulttype=core&format=json