Genome-wide RNA-binding analysis of the trypanosome U1 snRNP proteins U1C and U1-70K reveals cis/trans-spliceosomal network

Preußer, Christian; Roßbach, Oliver; Hung, Lee-Hsueh; Li, Dan; Bindereif, Albrecht

doi:10.1093/nar/gku286

Cited by 14 publications

(13 citation statements)

References 33 publications

(47 reference statements)

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“…A recent study from our group supports the hypothesis that cis splicing may be an evolutionary relic. 11 The findings presented here further support this provocative idea. In trypanosomes only two genes contain intron sequences and require cis splicing for proper mRNA maturation: Tb927.3.3160 and Tb927.8.1510, the latter of which codes for an ATP-dependent DEAD box helicase.…”

Section: Discussionsupporting

confidence: 80%

“…However, we recently reported that the U1 snRNP may also associate with the trans-spliceosome, indicating a physical linkage between cis-and trans-splicing. 11 Taken together this suggests that the U1 snRNP functions in both splicing and polyadenylation, likely linking both processes.…”

Section: Discussionmentioning

confidence: 90%

“…However, neither RNAi depletion of either of these two factors (this study and reference 25) nor inhibition of cis splicing result in a severe growth phenotype. 11 Nevertheless, this does not exclude that the two introns may fulfill an important, still unknown function.…”

Section: Discussionmentioning

confidence: 99%

“…10 However, recent studies support the hypothesis that in trypanosomes cis splicing might not be essential for survival, questioning whether the poly(A) polymerase from the intron-containing gene in fact represents a functional enzyme. 11 In addition, the polyadenylation signal itself is poorly defined in trypanosomes, since the two canonical cis-acting elements, AAUAAA and the U/GU-rich sequence, are not conserved. Previous studies indicated that a polypyrimidine tract upstream of a trans splice site affects polyadenylation of the upstream gene and trans splicing of the downstream gene.…”

Section: Introductionmentioning

confidence: 99%

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The polyadenylation complex ofTrypanosoma brucei:Characterization of the functional poly(A) polymerase

et al. 2016

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The generation of mature mRNA in the protozoan parasite Trypanosoma brucei requires coupled polyadenylation and trans splicing. In contrast to other eukaryotes, we still know very little on components, mechanisms, and dynamics of the 3 0 end-processing machinery in trypanosomes. To characterize the catalytic core of the polyadenylation complex in T. brucei, we first identified the poly(A) polymerase [Tb927.7.3780] as the major functional, nuclear-localized enzyme in trypanosomes. In contrast, another poly(A) polymerase, encoded by an intron-containing gene [Tb927.3.3160], localizes mainly in the cytoplasm and appears not to be functional in general 3 0 end processing of mRNAs. Based on tandemaffinity purification with tagged CPSF160 and mass spectrometry, we identified ten associated components of the trypanosome polyadenylation complex, including homologues to all four CPSF subunits, Fip1, CstF50/64, and Symplekin, as well as two hypothetical proteins. RNAi-mediated knockdown revealed that most of these factors are essential for growth and required for both in vivo polyadenylation and trans splicing, arguing for a general coupling of these two mRNA-processing reactions.

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Section: Discussionsupporting

confidence: 80%

Section: Discussionmentioning

confidence: 90%

Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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The polyadenylation complex ofTrypanosoma brucei:Characterization of the functional poly(A) polymerase

et al. 2016

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“…TT sites compare favorably to all other tested noncanonical dinucleotides (except GC). Frequently, TT sites possess an extra GT at position −1 potentially providing stabilizing effects exerted by SNRPC (Rosel et al 2011;Preußer et al 2014) and LUC7-like. Indeed, in our RNA-seq data set, 37/41 high-confidence noncanonical non-GC 5 ′ ss-in particular all TT sites-contained at least one GT dinucleotide.…”

Section: Allmentioning

confidence: 99%

Ranking noncanonical 5′ splice site usage by genome-wide RNA-seq analysis and splicing reporter assays

et al. 2018

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Most human pathogenic mutations in 5′ splice sites affect the canonical GT in positions +1 and +2, leading to noncanonical dinucleotides. On the other hand, noncanonical dinucleotides are observed under physiological conditions in ∼1% of all human 5′ss. It is therefore a challenging task to understand the pathogenic mutation mechanisms underlying the conditions under which noncanonical 5′ss are used. In this work, we systematically examined noncanonical 5′ splice site selection, both experimentally using splicing competition reporters and by analyzing a large RNA-seq data set of 54 fibroblast samples from 27 subjects containing a total of 2.4 billion gapped reads covering 269,375 exon junctions. From both approaches, we consistently derived a noncanonical 5′ss usage ranking GC > TT > AT > GA > GG > CT. In our competition splicing reporter assay, noncanonical splicing was strictly dependent on the presence of upstream or downstream splicing regulatory elements (SREs), and changes in SREs could be compensated by variation of U1 snRNA complementarity in the competing 5′ss. In particular, we could confirm splicing at different positions (i.e., −1, +1, +5) of a splice site for all noncanonical dinucleotides “weaker” than GC. In our comprehensive RNA-seq data set analysis, noncanonical 5′ss were preferentially detected in weakly used exon junctions of highly expressed genes. Among high-confidence splice sites, they were 10-fold overrepresented in clusters with a neighboring, more frequently used 5′ss. Conversely, these more frequently used neighbors contained only the dinucleotides GT, GC, and TT, in accordance with the above ranking.

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SNRPC promotes hepatocellular carcinoma cell motility by inducing epithelial‐mesenchymal transition

et al. 2021

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The therapeutic outcome of hepatocellular carcinoma (HCC) remains unsatisfactory because of poor response and acquired drug resistance. To better elucidate the molecular mechanisms of HCC, here we used three Gene Expression Omnibus datasets to identify potential oncogenes, and thereby identified small nuclear ribonucleoprotein polypeptide C (SNRPC). We report that SNRPC is highly up‐regulated in HCC tissues as determined using immunohistochemistry assays of samples from a cohort of 224 patients with HCC, and overexpression of SNRPC was correlated with multiple tumors, advanced stage, and poor outcome. Kaplan–Meier analysis confirmed that patients with high SNRPC expression exhibited shorter survival in four independent HCC cohorts (all P < 0.05). Furthermore, SNRPC mutations are significantly more frequent in HCC tissues than in normal liver tissues and are an early event in the development of HCC. Functional network analysis suggested that SNRPC is linked to the regulation of ribosome, spliceosome, and proteasome signaling. Subsequently, gain‐ and loss‐of‐function assays showed that SNRPC promotes the motility and epithelial–mesenchymal transition of HCC cells in vitro. SNRPC expression was negatively correlated with the infiltration of CD4+ T cells, macrophage cells, and neutrophil cells (all P < 0.05), as determined by analyzing the TIMER (Tumor IMmune Estimation Resource) database. In conclusion, our findings suggest that SNRPC has a potential role in epithelial–mesenchymal transition and motility in HCC.

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Genome-wide RNA-binding analysis of the trypanosome U1 snRNP proteins U1C and U1-70K reveals cis/trans-spliceosomal network

Cited by 14 publications

References 33 publications

The polyadenylation complex ofTrypanosoma brucei:Characterization of the functional poly(A) polymerase

The polyadenylation complex ofTrypanosoma brucei:Characterization of the functional poly(A) polymerase

Ranking noncanonical 5′ splice site usage by genome-wide RNA-seq analysis and splicing reporter assays

SNRPC promotes hepatocellular carcinoma cell motility by inducing epithelial‐mesenchymal transition

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