scholarly journals Mer1p is a modular splicing factor whose function depends on the conserved U2 snRNP protein Snu17p

2004 ◽  
Vol 32 (3) ◽  
pp. 1242-1250 ◽  
Author(s):  
M. Spingola
Keyword(s):  
Splicing Factor ◽  
U2 Snrnp ◽  
Snrnp Protein

scholarly journals SPF45/RBM17-dependent, but not U2AF-dependent, splicing in a distinct subset of human short introns

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Kazuhiro Fukumura ◽  
Rei Yoshimoto ◽  
Luca Sperotto ◽  
Hyun-Seo Kang ◽  
Tetsuro Hirose ◽  
...  
Keyword(s):  
Transcriptome Sequencing ◽  
Splicing Factor ◽  
Nuclear Proteins ◽  
Distinct Subset ◽  
U2 Snrnp ◽  
Whole Transcriptome Sequencing ◽  
Snrnp Protein ◽  
Constitutive Splicing ◽  
Splicing Regulator ◽  
Whole Transcriptome

AbstractHuman pre-mRNA introns vary in size from under fifty to over a million nucleotides. We searched for essential factors involved in the splicing of human short introns by screening siRNAs against 154 human nuclear proteins. The splicing activity was assayed with a model HNRNPH1 pre-mRNA containing short 56-nucleotide intron. We identify a known alternative splicing regulator SPF45 (RBM17) as a constitutive splicing factor that is required to splice out this 56-nt intron. Whole-transcriptome sequencing of SPF45-deficient cells reveals that SPF45 is essential in the efficient splicing of many short introns. To initiate the spliceosome assembly on a short intron with the truncated poly-pyrimidine tract, the U2AF-homology motif (UHM) of SPF45 competes out that of U2AF65 (U2AF2) for binding to the UHM-ligand motif (ULM) of the U2 snRNP protein SF3b155 (SF3B1). We propose that splicing in a distinct subset of human short introns depends on SPF45 but not U2AF heterodimer.

scholarly journals SPF45/RBM17-dependent, but not U2AF-dependent, splicing in human short introns

2019 ◽  
Author(s):  
Kazuhiro Fukumura ◽  
Rei Yoshimoto ◽  
Luca Sperotto ◽  
Hyun-Seo Kang ◽  
Tetsuro Hirose ◽  
...  
Keyword(s):  
Transcriptome Sequencing ◽  
Splicing Factor ◽  
Nuclear Proteins ◽  
Distinct Subset ◽  
U2 Snrnp ◽  
Whole Transcriptome Sequencing ◽  
Snrnp Protein ◽  
Splicing Regulator ◽  
Biochemical Analyses ◽  
Whole Transcriptome

Human pre-mRNA introns vary in size from under fifty to over a million nucleotides. We searched for essential factors specifically involved in the splicing of human short introns by screening siRNAs against 154 human nuclear proteins for activity on a model short 56-nucleotide intron-containing HNRNPH1 pre-mRNA. We identified a known alternative splicing regulator SPF45 (RBM17) as a general splicing factor that is essential to splice out this 56-nt intron. Whole-transcriptome sequencing of SPF45-deficient cells revealed that SPF45 is specifically required for the efficient splicing of many short introns. Our crosslinking and biochemical analyses demonstrate that SPF45 specifically replaces the U2AF heterodimer on the truncated poly-pyrimidine tracts in these short intron. To initiate splicing, the U2AF-homology motif (UHM) of the replaced SPF45 interacts with the UHM-ligand motif (ULM) of the U2 snRNP protein SF3b155 (SF3B1). We propose that splicing in a distinct subset of human short introns depends on SPF45 but not U2AF heterodimer.

scholarly journals SPF45/RBM17-dependent, but not U2AF-dependent, splicing in human short introns

2020 ◽  
Author(s):  
Kazuhiro Fukumura ◽  
Rei Yoshimoto ◽  
Luca Sperotto ◽  
Hyun-Seo Kang ◽  
Tetsuro Hirose ◽  
...  
Keyword(s):  
Transcriptome Sequencing ◽  
Splicing Factor ◽  
Nuclear Proteins ◽  
Distinct Subset ◽  
U2 Snrnp ◽  
Whole Transcriptome Sequencing ◽  
Snrnp Protein ◽  
Splicing Regulator ◽  
Biochemical Analyses ◽  
Whole Transcriptome

Abstract Human pre-mRNA introns vary in size from under fifty to over a million nucleotides. We searched for essential factors specifically involved in the splicing of human short introns by screening siRNAs against 154 human nuclear proteins for activity on a model short 56-nucleotide intron-containing HNRNPH1 pre-mRNA. We identified a known alternative splicing regulator SPF45 (RBM17) as a general splicing factor that is essential to splice out this 56-nt intron. Whole-transcriptome sequencing of SPF45-deficient cells revealed that SPF45 is specifically required for the efficient splicing of many short introns. Our crosslinking and biochemical analyses demonstrate that SPF45 specifically replaces the U2AF heterodimer on the truncated poly-pyrimidine tracts in these short intron. To initiate splicing, the U2AF-homology motif (UHM) of the replaced SPF45 interacts with the UHM-ligand motif (ULM) of the U2 snRNP protein SF3b155 (SF3B1). We propose that splicing in a distinct subset of human short introns depends on SPF45 but not U2AF heterodimer.

Suppressors of a Cold-Sensitive Mutation in Yeast U4 RNA Define Five Domains in the Splicing Factor Prp8 That Influence Spliceosome Activation

Genetics ◽  
2000 ◽  
Vol 155 (4) ◽  
pp. 1667-1682 ◽  
Author(s):  
Andreas N Kuhn ◽  
David A Brow
Keyword(s):  
Large Scale ◽  
Splicing Factor ◽  
Cold Sensitivity ◽  
Splicing Factors ◽  
Loss Of Function ◽  
U1 Snrnp ◽  
Snrnp Protein ◽  
Cold Sensitive ◽  
Spliceosome Activation ◽  
U4 Rna

AbstractThe highly conserved splicing factor Prp8 has been implicated in multiple stages of the splicing reaction. However, assignment of a specific function to any part of the 280-kD U5 snRNP protein has been difficult, in part because Prp8 lacks recognizable functional or structural motifs. We have used a large-scale screen for Saccharomyces cerevisiae PRP8 alleles that suppress the cold sensitivity caused by U4-cs1, a mutant U4 RNA that blocks U4/U6 unwinding, to identify with high resolution five distinct regions of PRP8 involved in the control of spliceosome activation. Genetic interactions between two of these regions reveal a potential long-range intramolecular fold. Identification of a yeast two-hybrid interaction, together with previously reported results, implicates two other regions in direct and indirect contacts to the U1 snRNP. In contrast to the suppressor mutations in PRP8, loss-of-function mutations in the genes for two other splicing factors implicated in U4/U6 unwinding, Prp44 (Brr2/Rss1/Slt22/Snu246) and Prp24, show synthetic enhancement with U4-cs1. On the basis of these results we propose a model in which allosteric changes in Prp8 initiate spliceosome activation by (1) disrupting contacts between the U1 snRNP and the U4/U6-U5 tri-snRNP and (2) orchestrating the activities of Prp44 and Prp24.

scholarly journals Demonstration of a dynamic, transcription-dependent organization of pre-mRNA splicing factors in polytene nuclei.

1996 ◽  
Vol 133 (5) ◽  
pp. 929-941 ◽  
Author(s):  
G Baurén ◽  
W Q Jiang ◽  
K Bernholm ◽  
F Gu ◽  
L Wieslander
Keyword(s):  
Mrna Splicing ◽  
Splicing Factor ◽  
Splicing Factors ◽  
Chironomus Tentans ◽  
Transcription Inhibition ◽  
Physiological Conditions ◽  
Active Gene ◽  
U2 Snrnp ◽  
Tight Linkage ◽  
Polytene Nuclei

We describe the dynamic organization of pre-mRNA splicing factors in the intact polytene nuclei of the dipteran Chironomus tentans. The snRNPs and an SR non-snRNP splicing factor are present in excess, mainly distributed throughout the interchromatin. Approximately 10% of the U2 snRNP and an SR non-snRNP splicing factor are associated with the chromosomes, highly enriched in active gene loci where they are bound to RNA. We demonstrate that the splicing factors are specifically recruited to a defined gene upon induction of transcription during physiological conditions. Concomitantly, the splicing factors leave gene loci in which transcription is turned off. We also demonstrated that upon general transcription inhibition, the splicing factors redistribute from active gene loci to the interchromatin. Our findings demonstrate the dynamic intranuclear organization of splicing factors and a tight linkage between transcription and the intranuclear organization of the splicing machinery.

scholarly journals Interactions of the Yeast SF3b Splicing Factor

2005 ◽  
Vol 25 (24) ◽  
pp. 10745-10754 ◽  
Author(s):  
Qiang Wang ◽  
Jin He ◽  
Bert Lynn ◽  
Brian C. Rymond
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Amino Acids ◽  
Binding Protein ◽  
Splicing Factor ◽  
Splicing Factors ◽  
Genetic Studies ◽  
U2 Snrnp ◽  
Two Hybrid

ABSTRACT The U2 snRNP promotes prespliceosome assembly through interactions that minimally involve the branchpoint binding protein, Mud2p, and the pre-mRNA. We previously showed that seven proteins copurify with the yeast (Saccharomyces cerevisiae) SF3b U2 subcomplex that associates with the pre-mRNA branchpoint region: Rse1p, Hsh155p, Hsh49p, Cus1p, and Rds3p and unidentified subunits p10 and p17. Here proteomic and genetic studies identify Rcp10p as p10 and show that it contributes to SF3b stability and is necessary for normal cellular Cus1p accumulation and for U2 snRNP recruitment in splicing. Remarkably, only the final 53 amino acids of Rcp10p are essential. p17 is shown to be composed of two accessory splicing factors, Bud31p and Ist3p, the latter of which independently associates with the RES complex implicated in the nuclear pre-mRNA retention. A directed two-hybrid screen reveals a network of prospective interactions that includes previously unreported intra-SF3b contacts and SF3b interactions with the RES subunit Bud13p, the Prp5p DExD/H-box protein, Mud2p, and the late-acting nineteen complex. These data establish the concordance of yeast and mammalian SF3b complexes, implicate accessory splicing factors in U2 snRNP function, and support SF3b contribution from early pre-mRNP recognition to late steps in splicing.

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