Role of the ubiquitin-like protein Hub1 in splice-site usage and alternative splicing

Mishra, Sudhish; Ammon, Tim; Popowicz, Grzegorz M.; Krajewski, Marcin; Nagel, Roland; Ares, Manuel; Holak, Tad A.; Jentsch, Stefan

doi:10.1038/nature10143

Cited by 89 publications

(176 citation statements)

References 44 publications

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“…However, an analysis of the 5Јss hexamer for the occurrence of consensus versus non-consensus nucleotides (log odd score analysis) suggests that a statistically significant proportion of N3 nucleotides are non-consensus in our SpPrp18-dependent intron data set (data not shown). Introns with weak/ abnormal splice sites can have greater dependence on splicing factors, as reported even in budding yeast (47,48). Also, it is suggested that the splicing apparatus is limiting, and thus different cellular transcripts encounter inherent competition for these splicing factors (49).…”

Section: Discussionmentioning

confidence: 91%

The Fission Yeast Pre-mRNA-processing Factor 18 (prp18+) Has Intron-specific Splicing Functions with Links to G1-S Cell Cycle Progression

Vijaykrishna¹,

Melangath²,

Kumar³

et al. 2016

Journal of Biological Chemistry

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Edited by Linda SpremulliThe fission yeast genome, which contains numerous short introns, is an apt model for studies on fungal splicing mechanisms and splicing by intron definition. Here we perform a domain analysis of the evolutionarily conserved Schizosaccharomyces pombe pre-mRNA-processing factor, SpPrp18. Our mutational and biophysical analyses of the C-terminal ␣-helical bundle reveal critical roles for the conserved region as well as helix five. We generate a novel conditional missense mutant, spprp18-5. To assess the role of SpPrp18, we performed global splicing analyses on cells depleted of prp18 ؉ and the conditional spprp18-5 mutant, which show widespread but intron-specific defects. In the absence of functional SpPrp18, primer extension analyses on a tfIId ؉ intron 1-containing minitranscript show accumulated pre-mRNA, whereas the lariat intron-exon 2 splicing intermediate was undetectable. These phenotypes also occurred in cells lacking both SpPrp18 and SpDbr1 (lariat debranching enzyme), a genetic background suitable for detection of lariat RNAs. These data indicate a major precatalytic splicing arrest that is corroborated by the genetic interaction between spprp18-5 and spprp2-1, a mutant in the early acting U2AF59 protein. Interestingly, SpPrp18 depletion caused cell cycle arrest before S phase. The compromised splicing of transcripts coding for G 1 -S regulators, such as Res2, a transcription factor, and Skp1, a regulated proteolysis factor, are shown. The cumulative effects of SpPrp18-dependent intron splicing partly explain the G 1 arrest upon the loss of SpPrp18. Our study using conditional depletion of spprp18 ؉ and the spprp18-5 mutant uncovers an intron-specific splicing function and early spliceosomal interactions and suggests links with cell cycle progression.Pre-mRNA splicing, a fundamental step in the processing of nascent eukaryotic RNA polymerase II transcripts, achieves precise excision of introns coupled with exon ligation to generate functional mRNAs. The spliceosome, which is composed of five U snRNPs 7 and Ͼ100 auxiliary proteins, assembles onto cis splicing signals, namely the 5Ј splice site (5Јss), the branch point nucleotide, the 3Ј splice site (3Јss), and polypyrimidine (Pyn) tracts. The spliceosomal catalytic core consists of the U2, U5, and U6 snRNPs and accessory proteins. This complex mediates the two trans-esterification reactions required for splicing to occur. First, the 5Јss is cleaved to yield the branched lariat intron-exon 2 and exon 1 intermediates, followed by the second reaction, where the 3Јss is cleaved, the exons are joined, and lariat intron is excised (1, 2).Genetic and biochemical analyses in budding yeast and biochemical studies with mammalian cell extracts have established a network of interactions among factors that act at the second step of splicing (i.e. Prp8, Prp16, Prp17, Prp18, Slu7, and Prp22) (3-8). PRP18, a non-essential budding yeast gene, encodes a U5 snRNP-associated factor. Prp18 has been analyzed extensively in budding yeast and human cell...

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Section: Discussionmentioning

confidence: 91%

The Fission Yeast Pre-mRNA-processing Factor 18 (prp18+) Has Intron-specific Splicing Functions with Links to G1-S Cell Cycle Progression

Vijaykrishna¹,

Melangath²,

Kumar³

et al. 2016

Journal of Biological Chemistry

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“…(C) Quantitative RT-PCR showing accumulation of long and short GFP transcripts in the indicated genotypes. Stably expressed At5g60390 was used for normalization (Wang et al 2014). acetylation, methylation, and phosphorylation, ubiquitination is increasingly recognized for its role in regulating the spliceosomal cycle (Bellare et al 2008;Song et al 2010;Mishra et al 2011;Korneta et al 2012;Ammon et al 2014;Chen and Moore 2014;Oka et al 2014). Notably, PRP8, which can bind ubiquitin through its conserved JAMM (JAB1/MPN/Mov34 metalloenzyme) domain, was detected as an ubiquitin conjugate in affinity-purified particles in budding yeast, suggesting a means to reversibly modulate the activity of this protein (Bellare et al 2008).…”

Section: Discussionmentioning

confidence: 99%

An Rtf2 Domain-Containing Protein Influences Pre-mRNA Splicing and Is Essential for Embryonic Development in Arabidopsis thaliana

et al. 2015

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Alternative splicing is prevalent in plants, but little is known about its regulation in the context of developmental and signaling pathways. We describe here a new factor that influences pre-messengerRNA (mRNA) splicing and is essential for embryonic development in Arabidopsis thaliana. This factor was retrieved in a genetic screen that identified mutants impaired in expression of an alternatively spliced GFP reporter gene. In addition to the known spliceosomal component PRP8, the screen recovered Arabidopsis RTF2 (AtRTF2), a previously uncharacterized, evolutionarily conserved protein containing a replication termination factor 2 (Rtf2) domain. A homozygous null mutation in AtRTF2 is embryo lethal, indicating that AtRTF2 is an essential protein. Quantitative RT-PCR demonstrated that impaired expression of GFP in atrtf2 and prp8 mutants is due to inefficient splicing of the GFP pre-mRNA. A genome-wide analysis using RNA sequencing indicated that 13-16% of total introns are retained to a significant degree in atrtf2 mutants. Considering these results and previous suggestions that Rtf2 represents an ubiquitin-related domain, we discuss the possible role of AtRTF2 in ubiquitin-based regulation of pre-mRNA splicing.KEYWORDS alternative splicing; C2HC2 zinc finger; intron retention; Rtf2 domain; ubiquitin ligase I T is increasingly recognized that cotranscriptional and posttranscriptional gene regulation is comparable to transcriptional regulation in intricacy and importance. Pre-mRNA splicing is a cotranscriptional process and a major determinant of transcript abundance and complexity (Reddy et al. 2013). Constitutive splicing refers to the use of only one set of splice sites to generate a single mature mRNA. By contrast, alternative splicing occurs when variable splice sites are selected, leading to the generation of more than one processed RNA product from a single pre-messenger RNA (mRNA). An individual gene can thus potentially encode multiple proteins, leading to a substantial increase in proteomic diversity (Chen and Manley 2009;Syed et al. 2012;Reddy et al. 2013).Recent work has established that alternative splicing is common in plants, affecting 60% of intron-containing genes . Alternative splicing has important roles in plant growth, development, abiotic stress tolerance, circadian rhythms, and pathogen defense (Staiger and Brown 2013). The most common outcome of alternative splicing in plants is intron retention Lan et al. 2013), which occurs when an intron fails to be spliced out of the premRNA. Retained introns frequently contain premature termination codons (PTCs) that can channel the transcript into the nonsense-mediated decay (NMD) pathway. Intron retention provides a means for "transcriptome tuning" (Braunschweig et al. 2014) and contributes to the post-transcriptional regulation of gene expression by reducing levels of inappropriately expressed transcripts Ge and Porse 2013).Alternative splicing is subject to elaborate regulation that relies on general and specific trans-acting factors as ...

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“…The ubiquitin-proteasome pathway is the key mechanism for proteolysis that has been implicated in protein folding, cell cycle progression, and apoptosis (17). This complex and tightly controlled pathway has the capacity to precisely regulate the timing of protein degradation during the cell cycle or after exposure to specific external stimuli and is implicated in epigenetic regulation (18), including histone methylation (19). Spliceosome, splicing factors, and DNA methylation.…”

Section: Critical Metabolic Network In Apis Are Enriched In Methylatedmentioning

confidence: 99%

DNA methylation dynamics, metabolic fluxes, gene splicing, and alternative phenotypes in honey bees

Fôret

Kucharski

Pellegrini

et al. 2012

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

306

317

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In honey bees (Apis mellifera), the development of a larva into either a queen or worker depends on differential feeding with royal jelly and involves epigenomic modifications by DNA methyltransferases. To understand the role of DNA methylation in this process we sequenced the larval methylomes in both queens and workers. We show that the number of differentially methylated genes (DMGs) in larval head is significantly increased relative to adult brain (2,399 vs. 560) with more than 80% of DMGs up-methylated in worker larvae. Several highly conserved metabolic and signaling pathways are enriched in methylated genes, underscoring the connection between dietary intake and metabolic flux. This includes genes related to juvenile hormone and insulin, two hormones shown previously to regulate caste determination. We also tie methylation data to expressional profiling and describe a distinct role for one of the DMGs encoding anaplastic lymphoma kinase (ALK), an important regulator of metabolism. We show that alk is not only differentially methylated and alternatively spliced in Apis, but also seems to be regulated by a cis-acting, anti-sense nonprotein-coding transcript. The unusually complex regulation of ALK in Apis suggests that this protein could represent a previously unknown node in a process that activates downstream signaling according to a nutritional context. The correlation between methylation and alternative splicing of alk is consistent with the recently described mechanism involving RNA polymerase II pausing. Our study offers insights into diet-controlled development in Apis.polyphenism | ubiquitin | spliceosome

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Role of the ubiquitin-like protein Hub1 in splice-site usage and alternative splicing

Cited by 89 publications

References 44 publications

The Fission Yeast Pre-mRNA-processing Factor 18 (prp18+) Has Intron-specific Splicing Functions with Links to G1-S Cell Cycle Progression

The Fission Yeast Pre-mRNA-processing Factor 18 (prp18+) Has Intron-specific Splicing Functions with Links to G1-S Cell Cycle Progression

An Rtf2 Domain-Containing Protein Influences Pre-mRNA Splicing and Is Essential for Embryonic Development in Arabidopsis thaliana

DNA methylation dynamics, metabolic fluxes, gene splicing, and alternative phenotypes in honey bees

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