Genome-wide Analysis Reveals SR Protein Cooperation and Competition in Regulated Splicing

Pandit, Shatakshi; Zhou, Yu; Shiue, Lily; Coutinho-Mansfield, Gabriela; Li, Hairi; Qiu, Jinsong; Huang, Jinfeng; Yeo, G; Ares, Manuel; Fu, Xiang‐Dong

doi:10.1016/j.molcel.2013.03.001

Cited by 270 publications

(325 citation statements)

References 55 publications

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“…However, their mode of action appears to be more diverse than anticipated, with a variety of possible mechanisms influencing splice-site selection. Recent genome-wide analysis performed in mammalian cells confirmed the idea that SR proteins can either promote or inhibit exon inclusion depending on their position on pre-mRNAs (57). Their binding to intronic sequences was reported primarily to promote exon skipping (58), but the effect of their interaction with exonic sequences seems to be more complex.…”

Section: Discussionmentioning

confidence: 97%

“…We still need to understand the link between SRSF1 pseudo-RRM and the spliceosome machinery, but our data indicate that this domain can be crucial and even sufficient to regulate these types of splicing events. Finally, the activity of pseudo-RRMs in splicing is likely to be influenced by multiple additional parameters, including formation of RNA secondary structures or competition with other proteins targeting overlapping binding sites (57,58), which may limit the accessibility to these domains of 5′-AGGA-3′ motifs that are not involved in splicing regulation.…”

Section: Discussionmentioning

confidence: 99%

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Isolated pseudo–RNA-recognition motifs of SR proteins can regulate splicing using a noncanonical mode of RNA recognition

Cléry

Sinha

Anczuków

et al. 2013

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

115

166

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Serine/arginine (SR) proteins, one of the major families of alternativesplicing regulators in Eukarya, have two types of RNA-recognition motifs (RRMs): a canonical RRM and a pseudo-RRM. Although pseudo-RRMs are crucial for activity of SR proteins, their mode of action was unknown. By solving the structure of the human SRSF1 pseudo-RRM bound to RNA, we discovered a very unusual and sequence-specific RNA-binding mode that is centered on one α-helix and does not involve the β-sheet surface, which typically mediates RNA binding by RRMs. Remarkably, this mode of binding is conserved in all pseudo-RRMs tested. Furthermore, the isolated pseudo-RRM is sufficient to regulate splicing of about half of the SRSF1 target genes tested, and the bound α-helix is a pivotal element for this function. Our results strongly suggest that SR proteins with a pseudo-RRM frequently regulate splicing by competing with, rather than recruiting, spliceosome components, using solely this unusual RRM.NMR | protein-RNA complex | splicing factor S erine/arginine (SR) proteins are highly conserved in Eukarya and are key regulators of gene expression. These proteins are required for pre-mRNA splicing, regulate alternative splicing events, and play crucial roles in genomic stability, mRNA transcription, nuclear export, nonsense-mediated mRNA decay, and translation (1-5). Several studies have revealed links between these proteins and diseases (6), making the proteins potential therapeutic targets (7). For the last two decades, SR proteins have been studied intensively as regulators of alternative splicing, a mechanism used to modulate the expression of more than 95% of human genes (8, 9). Importantly, it is estimated that 15-50% of human disease-causing mutations affect splicing (10). Alternative splicing consists of the alternative selection of splice sites present within pre-mRNA, leading to different versions of mature mRNAs from a single gene (11). As a result, in some cases, proteins with opposite functions can be generated. In the context of cancer, alternative splicing can generate pro-or antiapoptotic isoforms (12). As an example, alternatively spliced variants of FAS/CD95 can be generated by inclusion or skipping of exon 6, depending on competition between antagonistic splicing factors (13-16). In the absence of Fas exon 6, the apoptotic receptor lacks the transmembrane domain and becomes soluble and antiapoptotic (17).Each SR protein has a modular structure with one or two RNA-recognition motifs (RRMs) at its N-terminal part, followed by a C-terminal arginine-serine-rich (RS) domain containing multiple RS dipeptide repeats. In many cases, SR proteins have been shown to interact with purine-rich exonic splicing enhancers (ESEs) and to promote inclusion of the targeted exon in mRNAs (18). Two main models have been proposed to explain the mode of action of ESE-bound SR proteins in splicing regulation. In the recruitment model SR proteins recruit U1-70K and/or U2AF35 to 5′ and 3′ splice sites, respectively, to promote spliceosome assembly (4)....

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Section: Discussionmentioning

confidence: 97%

Section: Discussionmentioning

confidence: 99%

Isolated pseudo–RNA-recognition motifs of SR proteins can regulate splicing using a noncanonical mode of RNA recognition

Cléry

Sinha

Anczuków

et al. 2013

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

115

166

View full text Add to dashboard Cite

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“…Each of HA-tagged pcDNA3.0-SRSFs or empty vector controls was transiently transfected into 293T cells, and ultraviolet cross-linking was performed at 400 mJ cm À 2 with a Stratalinker ultraviolet crosslinker (Stratagene). Immunoprecipitation was done with anti-HA antibody (Abcam ab9110, 5 mg per reaction) 41 -coupled protein A/G magnetic beads (50 ml per reaction) by using Magna RIP kit (Millipore). RNA was extracted from the immunoprecipitate and cDNA was synthesized with random primers.…”

Section: Methodsmentioning

confidence: 99%

BCLAF1 and its splicing regulator SRSF10 regulate the tumorigenic potential of colon cancer cells

et al. 2014

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Bcl-2-associated transcription factor 1 (BCLAF1) is known to be involved in multiple biological processes. Although several splice variants of BCLAF1 have been identified, little is known about how BCLAF1 splicing is regulated or the contribution of alternative splicing to its developmental functions. Here we find that inclusion of alternative exon5a was significantly increased in colorectal cancer (CRC) samples. Knockdown of the BCLAF1 protein isoform resulting from exon5a inclusion inhibited growth and that its overexpression increased tumorigenic potential. We also found that the splicing factor SRSF10 stimulates inclusion of exon5a and has growth-inducing activity. Importantly, the upregulation of SRSF10 expression observed in clinical CRC samples parallels the increased inclusion of BCLAF1 exon5a, both of which are associated with higher tumour grade. These findings identify SRSF10 as a key regulator of BCLAF1 pre-mRNA splicing and the maintenance of oncogenic features in human colon cancer cells.

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“…13,23 TCR stimulation results in actin polymerization. 24 For full activation, however, T cells also require ‘outside-in’ costimulation, which leads to significant rearrangement of the actin cytoskeleton and promotes accumulation of receptors and raft membrane microdomains at the interface between T cells and APCs.…”

Section: Discussionmentioning

confidence: 99%

Actin stabilizer TAGLN2 potentiates adoptive T cell therapy by boosting the inside-out costimulation via lymphocyte function-associated antigen-1

et al. 2018

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Correct temporal and spatial control of actin dynamics is essential for the cytotoxic T cell effector function against tumor cells. However, little is known whether actin engineering in tumor-targeted T cells can enhance their antitumor responses, thereby potentiating the adoptive T cell therapy. Here, we report that TAGLN2, a 22-KDa actin-stabilizing protein which is physically associated with lymphocyte function-associated antigen-1 (LFA-1), potentiates the OTI TCR CD8+ T cells to kill the intercellular adhesion molecule-1 (ICAM-1)-positive/OVA-presenting E0771 cells, but not ICAM-1-negative OVA-B16F10 cells, suggesting an ‘inside-out’ activation of LFA-1, which causes more efficient immunological synapse formation between T cells and tumor cells. Notably, recombinant TAGLN2 fused with the protein transduction domain (TG2P) overcame the disadvantages of viral gene delivery, leading to a significant reduction in tumor growth in mice. TG2P also potentiated the CD19-targeted, chimeric antigen receptor (CAR)-modified T cells to kill Raji B-lymphoma cells. Our findings indicate that activating the TAGLN2–actin–LFA-1 axis is an effective strategy to potentiate the adoptive T-cell immunotherapy.

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Genome-wide Analysis Reveals SR Protein Cooperation and Competition in Regulated Splicing

Cited by 270 publications

References 55 publications

Isolated pseudo–RNA-recognition motifs of SR proteins can regulate splicing using a noncanonical mode of RNA recognition

Isolated pseudo–RNA-recognition motifs of SR proteins can regulate splicing using a noncanonical mode of RNA recognition

BCLAF1 and its splicing regulator SRSF10 regulate the tumorigenic potential of colon cancer cells

Actin stabilizer TAGLN2 potentiates adoptive T cell therapy by boosting the inside-out costimulation via lymphocyte function-associated antigen-1

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