Large-scale remodeling of a repressed exon ribonucleoprotein to an exon definition complex active for splicing

Wongpalee, Somsakul Pop; Vashisht, Ajay A.; Sharma, Shalini; Chui, Darryl; Wohlschlegel, James A.; Black, Douglas L.

doi:10.7554/elife.19743

Cited by 19 publications

(25 citation statements)

References 115 publications

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“…This model contrasts with a previous proposal for sequential, intron-definitiontype interactions in the recognition of microexons (Sterner and Berget, 1993) and is also different from a more recent model invoking exon-enhancer-dependent interactions in the context of the extensively studied neuronal (N1) microexon of the Src gene (Wongpalee et al, 2016). This microexon is repressed in non-neural cells by Ptbp1-dependent interactions (Sharma et al, 2005), yet its mechanism of activation in neural cells has largely remained unclear (Wongpalee et al, 2016). We observe that knockdown of Srrm4, Srsf11, and Rnps1 all result in increased skipping of the N1 microexon ( Figure S4B).…”

Section: Discussioncontrasting

confidence: 89%

“…In this model, the bi-partite ISE bound by Srsf11, Rnps1, and Srrm4 obviates the requirement for an exonic splicing enhancer (ESE) and thus enables the recognition of exons that are too short to harbor these elements or else may be subject to protein coding constraints that preclude the positioning of ESEs within exons. This model contrasts with a previous proposal for sequential, intron-definitiontype interactions in the recognition of microexons (Sterner and Berget, 1993) and is also different from a more recent model invoking exon-enhancer-dependent interactions in the context of the extensively studied neuronal (N1) microexon of the Src gene (Wongpalee et al, 2016). This microexon is repressed in non-neural cells by Ptbp1-dependent interactions (Sharma et al, 2005), yet its mechanism of activation in neural cells has largely remained unclear (Wongpalee et al, 2016).…”

Section: Discussionmentioning

confidence: 59%

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Genome-wide CRISPR-Cas9 Interrogation of Splicing Networks Reveals a Mechanism for Recognition of Autism-Misregulated Neuronal Microexons

Gonatopoulos-Pournatzis

et al. 2018

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Graphical Abstract Highlights d Genome-wide CRISPR-Cas9 screens for detection of alternative splicing regulators d Identification of 200 regulators of neuronal microexons often disrupted in autism d Diverse regulators include chromatin, protein turnover and RNA processing factors d A mechanism for the definition of neuronal microexons SUMMARYAlternative splicing is crucial for diverse cellular, developmental, and pathological processes. However, the full networks of factors that control individual splicing events are not known. Here, we describe a CRISPR-based strategy for the genome-wide elucidation of pathways that control splicing and apply it to microexons with important functions in nervous system development and that are commonly misregulated in autism. Approximately 200 genes associated with functionally diverse regulatory layers and enriched in genetic links to autism control neuronal microexons. Remarkably, the widely expressed RNA binding proteins Srsf11 and Rnps1 directly, preferentially, and frequently co-activate these microexons. These factors form critical interactions with the neuronal splicing regulator Srrm4 and a bi-partite intronic splicing enhancer element to promote spliceosome formation. Our study thus presents a versatile system for the identification of entire splicing regulatory pathways and further reveals a common mechanism for the definition of neuronal microexons that is disrupted in autism.

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Section: Discussioncontrasting

confidence: 89%

Section: Discussionmentioning

confidence: 59%

Genome-wide CRISPR-Cas9 Interrogation of Splicing Networks Reveals a Mechanism for Recognition of Autism-Misregulated Neuronal Microexons

Gonatopoulos-Pournatzis

et al. 2018

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“…PTBP1 is known to interact with hnRNP K (29), which binds directly to the viral M mRNA, as we previously reported (9). Since U1A binds U1 snRNA, which interacts with the 5′ splice site of pre-mRNAs to mediate the first steps of splicing (22), and PTBP1 represses the early stages of splicing (37), the NS1-BP BACK domain and hnRNP K likely interact with the PTBP1 complex to mediate or regulate the early stages of splicing. Furthermore, the Kelch domain of NS1-BP binds the Pol II CTD that interacts with the virus polymerase (33,34).…”

Section: Discussionmentioning

confidence: 70%

Structural–functional interactions of NS1-BP protein with the splicing and mRNA export machineries for viral and host gene expression

Zhang

Shang

Padavannil

et al. 2018

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

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The influenza virulence factor NS1 protein interacts with the cellular NS1-BP protein to promote splicing and nuclear export of the viral M mRNAs. The viral M1 mRNA encodes the M1 matrix protein and is alternatively spliced into the M2 mRNA, which is translated into the M2 ion channel. These proteins have key functions in viral trafficking and budding. To uncover the NS1-BP structural and functional activities in splicing and nuclear export, we performed proteomics analysis of nuclear NS1-BP binding partners and showed its interaction with constituents of the splicing and mRNA export machineries. NS1-BP BTB domains form dimers in the crystal. Full-length NS1-BP is a dimer in solution and forms at least a dimer in cells. Mutations suggest that dimerization is important for splicing. The central BACK domain of NS1-BP interacts directly with splicing factors such as hnRNP K and PTBP1 and with the viral NS1 protein. The BACK domain is also the site for interactions with mRNA export factor Aly/REF and is required for viral M mRNA nuclear export. The crystal structure of the C-terminal Kelch domain shows that it forms a β-propeller fold, which is required for the splicing function of NS1-BP. This domain interacts with the polymerase II C-terminal domain and SART1, which are involved in recruitment of splicing factors and spliceosome assembly, respectively. NS1-BP functions are not only critical for processing a subset of viral mRNAs but also impact levels and nuclear export of a subset of cellular mRNAs encoding factors involved in metastasis and immunity.

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“…4h, Supplementary Fig. 7, and Supplementary Dataset 2) 7,17 . The effect of C3 peptide requires SF1 ( Supplementary Fig.…”

Section: Resultsmentioning

confidence: 99%

A novel protein domain in an ancestral splicing factor drove the evolution of neural microexons

et al. 2019

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Large-scale remodeling of a repressed exon ribonucleoprotein to an exon definition complex active for splicing

Cited by 19 publications

References 115 publications

Genome-wide CRISPR-Cas9 Interrogation of Splicing Networks Reveals a Mechanism for Recognition of Autism-Misregulated Neuronal Microexons

Genome-wide CRISPR-Cas9 Interrogation of Splicing Networks Reveals a Mechanism for Recognition of Autism-Misregulated Neuronal Microexons

Structural–functional interactions of NS1-BP protein with the splicing and mRNA export machineries for viral and host gene expression

A novel protein domain in an ancestral splicing factor drove the evolution of neural microexons

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