scholarly journals An RNA Switch of a Large Exon of Ninein Is Regulated by the Neural Stem Cell Specific-RNA Binding Protein, Qki5

2019 ◽  
Vol 20 (5) ◽  
pp. 1010 ◽  
Author(s):  
Yoshika Hayakawa-Yano ◽  
Masato Yano
Keyword(s):  
Alternative Splicing ◽  
High Throughput Sequencing ◽  
Rna Binding ◽  
Binding Protein ◽  
Rna Binding Protein ◽  
Neural Progenitor Cell ◽  
Conditional Knockout ◽  
Splicing Factors ◽  
Axon Development ◽  
Rna Switch

A set of tissue-specific splicing factors are thought to govern alternative splicing events during neural progenitor cell (NPC)-to-neuron transition by regulating neuron-specific exons. Here, we propose one such factor, RNA-binding protein Quaking 5 (Qki5), which is specifically expressed in the early embryonic neural stem cells. We performed mRNA-SEQ (Sequence) analysis using mRNAs obtained by developing cerebral cortices in Qk (Quaking) conditional knockout (cKO) mice. As expected, we found a large number of alternative splicing changes between control and conditional knockouts relative to changes in transcript levels. DAVID (The Database for Annotation, Visualization and Integrated Discovery) and Metascape analyses suggested that the affected spliced genes are involved in axon development and microtubule-based processes. Among these, the mRNA coding for the Ninein protein is listed as one of Qki protein-dependent alternative splicing targets. Interestingly, this exon encodes a very long polypeptide (2121 nt), and has been previously defined as a dynamic RNA switch during the NPC-to-neuron transition. Additionally, we validated that the regulation of this large exon is consistent with the Qki5-dependent alternative exon inclusion mode suggested by our previous Qki5 HITS-CLIP (high throughput sequencing-cross linking immunoprecipitation) analysis. Taken together, these data suggest that Qki5 is an important factor for alternative splicing in the NPC-to-neuron transition.

scholarly journals The RNA-binding protein Sam68 modulates the alternative splicing of Bcl-x

2007 ◽  
Vol 176 (7) ◽  
pp. 929-939 ◽  
Author(s):  
Maria Paola Paronetto ◽  
Tilman Achsel ◽  
Autumn Massiello ◽  
Charles E. Chalfant ◽  
Claudio Sette
Keyword(s):  
Alternative Splicing ◽  
Tyrosine Phosphorylation ◽  
Rna Binding ◽  
Binding Protein ◽  
Rna Binding Protein ◽  
Live Cells ◽  
Hnrnp A1 ◽  
Splice Site Selection ◽  
Subnuclear Localization ◽  
Mrna Targets

The RNA-binding protein Sam68 is involved in apoptosis, but its cellular mRNA targets and its mechanism of action remain unknown. We demonstrate that Sam68 binds the mRNA for Bcl-x and affects its alternative splicing. Depletion of Sam68 by RNA interference caused accumulation of antiapoptotic Bcl-x(L), whereas its up-regulation increased the levels of proapoptotic Bcl-x(s). Tyrosine phosphorylation of Sam68 by Fyn inverted this effect and favored the Bcl-x(L) splice site selection. A point mutation in the RNA-binding domain of Sam68 influenced its splicing activity and subnuclear localization. Moreover, coexpression of ASF/SF2 with Sam68, or fusion with an RS domain, counteracted Sam68 splicing activity toward Bcl-x. Finally, Sam68 interacted with heterogenous nuclear RNP (hnRNP) A1, and depletion of hnRNP A1 or mutations that impair this interaction attenuated Bcl-x(s) splicing. Our results indicate that Sam68 plays a role in the regulation of Bcl-x alternative splicing and that tyrosine phosphorylation of Sam68 by Src-like kinases can switch its role from proapoptotic to antiapoptotic in live cells.

scholarly journals rMAPS2: an update of the RNA map analysis and plotting server for alternative splicing regulation

2020 ◽  
Vol 48 (W1) ◽  
pp. W300-W306 ◽  
Author(s):  
Jae Y Hwang ◽  
Sungbo Jung ◽  
Tae L Kook ◽  
Eric C Rouchka ◽  
Jinwoong Bok ◽  
...  
Keyword(s):  
Alternative Splicing ◽  
High Throughput ◽  
Splice Site ◽  
High Throughput Sequencing ◽  
Rna Binding ◽  
Rna Binding Protein ◽  
Sequencing Data ◽  
High Throughput Sequencing Data ◽  
Retained Intron ◽  
Map Analysis

Abstract The rMAPS2 (RNA Map Analysis and Plotting Server 2) web server, freely available at http://rmaps.cecsresearch.org/, has provided the high-throughput sequencing data research community with curated tools for the identification of RNA binding protein sites. rMAPS2 analyzes differential alternative splicing or CLIP peak data obtained from high-throughput sequencing data analysis tools like MISO, rMATS, Piranha, PIPE-CLIP and PARalyzer, and then, graphically displays enriched RNA-binding protein target sites. The initial release of rMAPS focused only on the most common alternative splicing event, skipped exon or exon skipping. However, there was a high demand for the analysis of other major types of alternative splicing events, especially for retained intron events since this is the most common type of alternative splicing in plants, such as Arabidopsis thaliana. Here, we expanded the implementation of rMAPS2 to facilitate analyses for all five major types of alternative splicing events: skipped exon, mutually exclusive exons, alternative 5′ splice site, alternative 3′ splice site and retained intron. In addition, by employing multi-threading, rMAPS2 has vastly improved the user experience with significant reductions in running time, ∼3.5 min for the analysis of all five major alternative splicing types at once.

scholarly journals Region-specific alternative splicing in the nervous system: Implications for regulation by the RNA-binding protein NAPOR

RNA ◽  
2002 ◽  
Vol 8 (5) ◽  
pp. 671-685 ◽  
Author(s):  
WENQING ZHANG ◽  
HAIYING LIU ◽  
KYOUNGHA HAN ◽  
PAULA J. GRABOWSKI
Keyword(s):  
Nervous System ◽  
Alternative Splicing ◽  
Rna Binding ◽  
Binding Protein ◽  
Rna Binding Protein ◽  
Specific Alternative

scholarly journals RNA binding protein 24 deletion disrupts global alternative splicing and causes dilated cardiomyopathy

2018 ◽  
Vol 10 (6) ◽  
pp. 405-416 ◽  
Author(s):  
Jing Liu ◽  
Xu Kong ◽  
Mengkai Zhang ◽  
Xiao Yang ◽  
Xiuqin Xu
Keyword(s):  
Alternative Splicing ◽  
Dilated Cardiomyopathy ◽  
Rna Binding ◽  
Binding Protein ◽  
Rna Binding Protein

scholarly journals The RNA ‐binding protein Arrest (Bruno) regulates alternative splicing to enable myofibril maturation in Drosophila flight muscle

EMBO Reports ◽  
2014 ◽  
Vol 16 (2) ◽  
pp. 178-191 ◽  
Author(s):  
Maria L Spletter ◽  
Christiane Barz ◽  
Assa Yeroslaviz ◽  
Cornelia Schönbauer ◽  
Irene R S Ferreira ◽  
...  
Keyword(s):  
Alternative Splicing ◽  
Rna Binding ◽  
Flight Muscle ◽  
Binding Protein ◽  
Rna Binding Protein

scholarly journals Integrated analysis of RNA-binding protein complexes using in vitro selection and high-throughput sequencing and sequence specificity landscapes (SEQRS)

Methods ◽  
2017 ◽  
Vol 118-119 ◽  
pp. 171-181 ◽  
Author(s):  
Tzu-Fang Lou ◽  
Chase A. Weidmann ◽  
Jordan Killingsworth ◽  
Traci M. Tanaka Hall ◽  
Aaron C. Goldstrohm ◽  
...  
Keyword(s):  
High Throughput ◽  
High Throughput Sequencing ◽  
In Vitro Selection ◽  
Rna Binding ◽  
Protein Complexes ◽  
Binding Protein ◽  
Rna Binding Protein ◽  
Integrated Analysis ◽  
Sequence Specificity

scholarly journals The RNA-binding protein Rbfox2: an essential regulator of EMT-driven alternative splicing and a mediator of cellular invasion

Oncogene ◽  
2013 ◽  
Vol 33 (9) ◽  
pp. 1082-1092 ◽  
Author(s):  
C Braeutigam ◽  
L Rago ◽  
A Rolke ◽  
L Waldmeier ◽  
G Christofori ◽  
...  
Keyword(s):  
Alternative Splicing ◽  
Rna Binding ◽  
Binding Protein ◽  
Rna Binding Protein ◽  
Cellular Invasion

scholarly journals Targeting of RBM10 to S1-1 Nuclear Bodies: Targeting Sequences and its Biological Significance

2019 ◽  
Author(s):  
Ling-Yu Wang ◽  
Sheng-Jun Xiao ◽  
Hiroyuki Kunimoto ◽  
Kazuaki Tokunaga ◽  
Hirotada Kojima ◽  
...  
Keyword(s):  
Alternative Splicing ◽  
Transcriptional Activity ◽  
Rna Binding ◽  
Binding Protein ◽  
Rna Binding Protein ◽  
Biological Significance ◽  
Nuclear Bodies ◽  
Transient Component ◽  
Cellular Transcription ◽  
Splicing Machinery

AbstractRBM10 is an RNA-binding protein that regulates alternative splicing (AS). This protein localizes to the extra-nucleolar nucleoplasm and S1-1 nuclear bodies (NBs). We investigated the biological significance of RBM10 localization to S1-1 NBs, which is poorly understood. Our analyses revealed that RBM10 possesses two S1-1 NB-targeting sequences (NBTSs), one in the KEKE motif region and another in the C2H2 Zn finger (ZnF). These NBTSs acted synergistically and were sufficient for localization of RBM10 to S1-1 NBs. Furthermore, the C2H2 ZnF not only acted as an NBTS, but was also essential for regulation of AS by RBM10. RBM10 did not participate in S1-1 NB formation. We confirmed the previous finding that localization of RBM10 to S1-1 NBs increases as cellular transcriptional activity decreases and vice versa. These results indicate that RBM10 is a transient component of S1-1 NBs and is sequestered in these structures via its NBTSs when cellular transcription decreases. We propose that the NB-targeting activity of the C2H2 ZnF is induced when it is not bound to pre-mRNA or the splicing machinery complex under conditions of reduced transcription.

scholarly journals RNA-binding protein Ptbp1 regulates alternative splicing and transcriptome in spermatogonia and maintains spermatogenesis in concert with Nanos3

2020 ◽  
Vol 66 (5) ◽  
pp. 459-467
Author(s):  
Manami SENOO ◽  
Hiroshi HOZOJI ◽  
Yu ISHIKAWA-YAMAUCHI ◽  
Takashi TAKIJIRI ◽  
Sho OHTA ◽  
...  
Keyword(s):  
Alternative Splicing ◽  
Rna Binding ◽  
Binding Protein ◽  
Rna Binding Protein

scholarly journals Hypothermia induces changes in the alternative splicing pattern of cold-inducible RNA-binding protein transcripts in a non-hibernator, the mouse

2019 ◽  
Vol 40 (4) ◽  
pp. 153-161 ◽  
Author(s):  
Yuuki HORII ◽  
Takahiko SHIINA ◽  
Saki UEHARA ◽  
Kanako NOMURA ◽  
Hiroki SHIMAOKA ◽  
...  
Keyword(s):  
Alternative Splicing ◽  
Rna Binding ◽  
Binding Protein ◽  
Rna Binding Protein ◽  
Splicing Pattern
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