Deletion of many yeast introns reveals a minority of genes that require splicing for function.

No abstract is available for this paper.

• Publication year

  2008

• Venue

  Molecular Biology of the Cell

• Publication date

  2008-05-01

• Fields of study

  Biology, Medicine

• Identifiers
  DOI 10.1091/mbc.E07-12-1254PMID 18287520PMCID PMC2366882
• External record

  Open on Semantic Scholar

• Source metadata

  Semantic Scholar, PubMed

• No claims are published for this paper.

• No concepts are published for this paper.

• Transcript Specificity in Yeast Pre-mRNA Splicing Revealed by Mutations in Core Spliceosomal Components

  2007influential reference
• High-density yeast-tiling array reveals previously undiscovered introns and extensive regulation of meiotic splicing

  2007cited by this paper
• YRA1 autoregulation requires nuclear export and cytoplasmic Edc3p-mediated degradation of its pre-mRNA.

  2007cited by this paper
• The effects of camptothecin on RNA polymerase II transcription: roles of DNA topoisomerase I.

  2007cited by this paper
• Defective splicing, disease and therapy: searching for master checkpoints in exon definition

  2006cited by this paper
• Splicing regulation in neurologic disease.

  2006cited by this paper
• Identification and evolutionary analysis of novel exons and alternative splicing events using cross-species EST-to-genome comparisons in human, mouse and rat

  2006cited by this paper
• Autoregulation of the mRNA export factor Yra1p requires inefficient splicing of its pre-mRNA.

  2006influential reference
• Introns Regulate RNA and Protein Abundance in Yeast

  2006cited by this paper
• A high-throughput method to measure the sensitivity of yeast cells to genotoxic agents in liquid cultures.

  2006cited by this paper
• Splicing in action: assessing disease causing sequence changes

  2005cited by this paper
• Species-specific variation of alternative splicing and transcriptional initiation in six eukaryotes.

  2005cited by this paper
• Methods in yeast genetics : a Cold Spring Harbor Laboratory course manual

  2005cited by this paper
• Identification of a novel box C/D snoRNA from mouse nucleolar cDNA library.

  2004cited by this paper
• CYGD: the Comprehensive Yeast Genome Database

  2004cited by this paper
• RNA regulation: a new genetics?

  2004cited by this paper
• Pre-mRNA splicing and human disease.

  2003cited by this paper
• Genome-Wide Detection of Alternative Splicing in Expressed Sequences Using Partial Order Multiple Sequence Alignment Graphs

  2003cited by this paper
• Molecular evolution of eukaryotic genomes: hemiascomycetous yeast spliceosomal introns.

  2003cited by this paper
• Sequencing and comparison of yeast species to identify genes and regulatory elements

  2003cited by this paper
• Splicing-dependent and -independent modes of assembly for intron-encoded box C/D snoRNPs in mammalian cells.

  2003cited by this paper
• Intron status and 3'-end formation control cotranscriptional export of mRNA.

  2002cited by this paper
• Expression of the essential mRNA export factor Yra1p is autoregulated by a splicing-dependent mechanism.

  2002influential reference
• Yeast RSC function is required for organization of the cellular cytoskeleton via an alternative PKC1 pathway.

  2002cited by this paper
• Transformation of yeast by lithium acetate/single-stranded carrier DNA/polyethylene glycol method.

  2002cited by this paper
• Genomewide Analysis of mRNA Processing in Yeast Using Splicing-Specific Microarrays

  2002cited by this paper
• An intron in the YRA1 gene is required to control Yra1 protein expression and mRNA export in yeast

  2002influential reference
• Saccharomyces Genome Database (SGD) provides secondary gene annotation using the Gene Ontology (GO)

  2002cited by this paper
• Initial sequencing and analysis of the human genome

  2001cited by this paper
• The sequence of the human genome (abstract only)

  2001cited by this paper
• The Yeast hnRNP-Like Proteins Yra1p and Yra2p Participate in mRNA Export through Interaction with Mex67p

  2001cited by this paper
• The Sequence of the Human Genome

  2001cited by this paper
• Position within the host intron is critical for efficient processing of box C/D snoRNAs in mammalian cells

  2001cited by this paper
• The odyssey of a regulated transcript.

  2000cited by this paper
• Test of intron predictions reveals novel splice sites, alternatively spliced mRNAs and new introns in meiotically regulated genes of yeast.

  2000cited by this paper
• Yra1p, a conserved nuclear RNA‐binding protein, interacts directly with Mex67p and is required for mRNA export

  2000cited by this paper
• Lineage-specific loss and divergence of functionally linked genes in eukaryotes.

  2000cited by this paper
• RNA Processing in Evolution: The Logic of Soft‐Wired Genomes a

  1999cited by this paper
• Using the Saccharomyces Genome Database (SGD) for analysis of protein similarities and structure

  1999cited by this paper
• Genomic-scale quantitative analysis of yeast pre-mRNA splicing: implications for splice-site recognition.

  1999cited by this paper
• Genome-wide bioinformatic and molecular analysis of introns in Saccharomyces cerevisiae.

  1999influential reference
• RNA processing and the evolution of eukaryotes

  1999influential reference
• A handful of intron-containing genes produces the lion's share of yeast mRNA.

  1999influential reference
• The Yeast Proteome Database (YPD): a model for the organization and presentation of genome-wide functional data

  1999cited by this paper
• Depletion of yeast RNase III blocks correct U2 3′ end formation and results in polyadenylated but functional U2 snRNA

  1998cited by this paper
• Nuclear mRNA Export Requires Complex Formation between Mex67p and Mtr2p at the Nuclear Pores

  1998cited by this paper
• Processing of the Intron-Encoded U18 Small Nucleolar RNA in the Yeast Saccharomyces cerevisiaeRelies on Both Exo- and Endonucleolytic Activities

  1998cited by this paper
• I-SceI-Induced Gene Replacement at a Natural Locus in Embryonic Stem Cells

  1998cited by this paper
• Designer deletion strains derived from Saccharomyces cerevisiae S288C: A useful set of strains and plasmids for PCR‐mediated gene disruption and other applications

  1998cited by this paper
• Intronic snoRNA biosynthesis in Saccharomyces cerevisiae depends on the lariat-debranching enzyme: intron length effects and activity of a precursor snoRNA.

  1998cited by this paper
• Involvement of the RE V3 gene in the methylated base-excision repair system. Co-operation of two DNA polymerases, δ and Rev3p, in the repair of MMS-induced lesions in the DNA of Saccharomyces cerevisiae

  1997cited by this paper
• Immunosuppressant Target Protein FKBP12 Is Required for P-Glycoprotein Function in Yeast*

  1996cited by this paper
• RNase III cleaves eukaryotic preribosomal RNA at a U3 snoRNP-dependent site.

  1996cited by this paper
• A mammalian gene with introns instead of exons generating stable RNA products

  1996cited by this paper
• Nuclear mRNA accumulation causes nucleolar fragmentation in yeast mtr2 mutant.

  1994cited by this paper
• Repair of a specific double-strand break generated within a mammalian chromosome by yeast endonuclease I-SceI.

  1994cited by this paper
• Consequences of unique double-stranded breaks in yeast chromosomes: death or homozygosis

  1993influential reference
• Site-specific recombination determined by I-SceI, a mitochondrial group I intron-encoded endonuclease expressed in the yeast nucleus.

  1992cited by this paper
• Multifunctional yeast high-copy-number shuttle vectors.

  1992influential reference
• Methods in Yeast Genetics: A Laboratory Course Manual

  1990cited by this paper
• A system of shuttle vectors and yeast host strains designed for efficient manipulation of DNA in Saccharomyces cerevisiae.

  1989influential reference
• 5-Fluoroorotic acid as a selective agent in yeast molecular genetics.

  1987cited by this paper
• Transformation of intact yeast cells treated with alkali cations.

  1984cited by this paper
• Transformation of intact yeast cells treated with alkali cations

  1983cited by this paper
• Construction, replication, and chromatin structure of TRP1 RI circle, a multiple-copy synthetic plasmid derived from Saccharomyces cerevisiae chromosomal DNA

  1982cited by this paper
• Methods in yeast genetics

  1979cited by this paper
• Repair of MMS-induced DNA double-strand breaks in haploid cells of Saccharomyces cerevisiae, which requires the presence of a duplicate genome

  1979cited by this paper

• Integrative analysis of Hub1 overexpression: driving transcriptional reprogramming and alternative splicing in Saccharomyces cerevisiae

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• Dissociation of the nuclear basket triggers chromosome loss in aging yeast

  2025cites this paper
• The patterns of alternative TSS usage explain the highly heterogeneous landscape of 5′UTR lengths in eukaryotes

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• Comprehensive analysis of the role of ASC1 and APE2 introns on cellular fitness, transcription, and post‐transcriptional dynamics

  2025cites this paper
• Hierarchical metabolic engineering for rewiring cellular metabolism

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• Building synthetic chromosomes one yeast at a time: insights from Sc2.0

  2025cites this paper
• Autoregulation of RPL7B by inhibition of a structural splicing enhancer

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• Autoregulation of RPL7B by inhibition of a structural splicing enhancer

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• Cells resist starvation through a nutrient stress splice switch

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• Domain acquisition enabled functional expansion of the TFIIS transcription factor family

  2025cites this paper
• Taxonomy of introns and the evolution of minor introns

  2024cites this paper
• The de novo design and synthesis of yeast chromosome XIII facilitates investigations on aging

  2024cites this paper
• Defenders of the Transcriptome: Guard Protein-Mediated mRNA Quality Control in Saccharomyces cerevisiae

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• Mechanisms and regulation of spliceosome-mediated pre-mRNA splicing in Saccharomyces cerevisiae

  2024cites this paper
• Horizontal transmission of functionally diverse transposons is a major source of new introns

  2024cites this paper
• Impact of random 50-base sequences inserted into an intron on splicing in Saccharomyces cerevisiae

  2023cites this paper
• Investigation of Genome Biology by Synthetic Genome Engineering

  2023cites this paper
• A novel approach to analyze the association characteristics between post-spliced introns and their corresponding mRNA

  2023cites this paper
• MAE-seq refines regulatory elements across the genome

  2023cites this paper
• Impact on splicing in Saccharomyces cerevisiae of random 50-base sequences inserted into an intron

  2023cites this paper
• The Y-ome Conundrum: Insights into Uncharacterized Genes and Approaches for Functional Annotation

  2023cites this paper
• Introns: the “dark matter” of the eukaryotic genome

  2023cites this paper
• Non-Mammalian Eukaryotic Expression Systems Yeast and Fungi in the Production of Biologics

  2022cites this paper
• Proximity to the Promoter and Terminator Regions Regulates the Transcription Enhancement Potential of an Intron

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• Ribosome proteins—Their balanced production

  2021cites this paper
• Post-Transcriptional Control of Mating-Type Gene Expression during Gametogenesis in Saccharomyces cerevisiae

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• Analysis of Fungal Genomes Reveals Commonalities of Intron Gain or Loss and Functions in Intron-Poor Species

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• Pseudouridine-mediated stop codon readthrough in S. cerevisiae is sequence context–independent

  2020cites this paper
• Control of ribosomal protein synthesis by Microprocessor complex

  2020cites this paper
• Opportunities and challenges in phenotypic screening for neurodegenerative disease research.

  2020cites this paper
• Origin, conservation, and loss of alternative splicing events that diversify the proteome in Saccharomycotina budding yeasts

  2020cites this paper
• Probing eukaryotic genome functions with synthetic chromosomes.

  2020cites this paper
• Global transcriptomics reveals specialized roles for splicing regulatory proteins in the macrophage innate immune response

  2020cites this paper
• DANGO: Predicting higher-order genetic interactions

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• C. briggsae genome annotation and comparative analysis with C. elegans using RNA-Seq data

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• Differential activation mechanisms of two isoforms of Gcr1 transcription factor generated from spliced and un-spliced transcripts in Saccharomyces cerevisiae

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• Synthetic yeast genomes for studying chromosomal features

  2020cites this paper
• Regulation of ribosomal protein genes: An ordered anarchy

  2020cites this paper
• Analysis of fungal genomes reveals commonalities of intron loss/gain and functions in intron-poor species

  2020influential citation
• Brain cell somatic gene recombination and its phylogenetic foundations

  2020cites this paper
• Selective defects in gene expression control genome instability in yeast splicing mutants

  2019cites this paper
• Introns: Good Day Junk Is Bad Day Treasure.

  2019cites this paper
• Introns are mediators of cell response to starvation

  2019cites this paper
• Intron RNA sequences help yeast cells to survive starvation

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• QTL analysis of natural Saccharomyces cerevisiae isolates reveals unique alleles involved in lignocellulosic inhibitor tolerance.

  2019cites this paper
• Differential expression of duplicated ribosomal protein genes modifies ribosome composition in response to stress

  2019cites this paper
• 5′ untranslated regions: the next regulatory sequence in yeast synthetic biology

  2019cites this paper
• Promoter-dependent nuclear RNA degradation ensures cell cycle-specific gene expression

  2019cites this paper
• Rapidly evolving protointrons in Saccharomyces genomes revealed by a hungry spliceosome

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• Splicing and Alternative Splicing Impact on Gene Design

  2018cites this paper
• Computational analysis of high-replicate RNA-seq data in Saccharomyces cerevisiae : searching for new genomic features

  2018cites this paper
• Impact phénotypique des réarrangements chromosomiques et évolution des génomes de levures

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• Novel Intronic RNA Structures Contribute to Maintenance of Phenotype in Saccharomyces cerevisiae

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• Rubbish DNA: The Functionless Fraction of the Human Genome

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  2015cites this paper
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  2014cites this paper
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• COMPUTATIONAL METHODS IN PROTEIN STRUCTURE, EVOLUTION AND NETWORKS.

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  2013cites this paper
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  2013cites this paper
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  2013cites this paper