scholarly journals Protein 4.1R Exon 16 3′ Splice Site Activation Requires Coordination among TIA1, Pcbp1, and RBM39 during Terminal Erythropoiesis

2017 ◽  
Vol 37 (9) ◽  
Author(s):  
Shu-Ching Huang ◽  
Henry S. Zhang ◽  
Brian Yu ◽  
Ellen McMahon ◽  
Dan T. Nguyen ◽  
...  
Keyword(s):  
Branch Point ◽  
Splice Site ◽  
Erythroid Differentiation ◽  
Actin Binding ◽  
Exon Definition ◽  
U2 Snrnp ◽  
Two Factors ◽  
Internal Exon ◽  
Protein 4.1R ◽  
The Impact

ABSTRACT Exon 16 of protein 4.1R encodes a spectrin/actin-binding peptide critical for erythrocyte membrane stability. Its expression during erythroid differentiation is regulated by alternative pre-mRNA splicing. A UUUUCCCCCC motif situated between the branch point and the 3′ splice site is crucial for inclusion. We show that the UUUU region and the last three C residues in this motif are necessary for the binding of splicing factors TIA1 and Pcbp1 and that these proteins appear to act in a collaborative manner to enhance exon 16 inclusion. This element also activates an internal exon when placed in a corresponding intronic position in a heterologous reporter. The impact of these two factors is further enhanced by high levels of RBM39, whose expression rises during erythroid differentiation as exon 16 inclusion increases. TIA1 and Pcbp1 associate in a complex containing RBM39, which interacts with U2AF65 and SF3b155 and promotes U2 snRNP recruitment to the branch point. Our results provide a mechanism for exon 16 3′ splice site activation in which a coordinated effort among TIA1, Pcbp1, and RBM39 stabilizes or increases U2 snRNP recruitment, enhances spliceosome A complex formation, and facilitates exon definition through RBM39-mediated splicing regulation.

scholarly journals Spliceosome Assembly Pathways for Different Types of Alternative Splicing Converge during Commitment to Splice Site Pairing in the A Complex

2008 ◽  
Vol 29 (4) ◽  
pp. 1072-1082 ◽  
Author(s):  
Matthew V. Kotlajich ◽  
Tara L. Crabb ◽  
Klemens J. Hertel
Keyword(s):  
Alternative Splicing ◽  
Branch Point ◽  
Splice Site ◽  
Atp Hydrolysis ◽  
Splice Sites ◽  
Mrna Isoforms ◽  
Exon Definition ◽  
U2 Snrnp ◽  
Kinetic Trap ◽  
Site Recognition

ABSTRACT Differential splice site pairing establishes alternative splicing patterns resulting in the generation of multiple mRNA isoforms. This process is carried out by the spliceosome, which is activated by a series of sequential structural rearrangements of its five core snRNPs. To determine when splice sites become functionally paired, we carried out a series of kinetic trap experiments using pre-mRNAs that undergo alternative 5′ splice site selection or alternative exon inclusion. We show that commitment to splice site pairing in both cases occurs in the A complex, which is characterized by the ATP-dependent association of the U2 snRNP with the branch point. Interestingly, the timing of splice site pairing is independent of the intron or exon definition modes of splice site recognition. Using the ATP analog ATPγS, we showed that ATP hydrolysis is required for splice site pairing independent from U2 snRNP binding to the pre-mRNA. These results identify the A complex as the spliceosomal assembly step dedicated to splice site pairing and suggest that ATP hydrolysis locks splice sites into a splicing pattern after stable U2 snRNP association to the branch point.

scholarly journals Regulated Fox-2 isoform expression mediates protein 4.1R splicing during erythroid differentiation

Blood ◽  
2008 ◽  
Vol 111 (1) ◽  
pp. 392-401 ◽  
Author(s):  
Guang Yang ◽  
Shu-Ching Huang ◽  
Jane Y. Wu ◽  
Edward J. Benz
Keyword(s):  
Erythroid Differentiation ◽  
Actin Binding ◽  
Dependent Manner ◽  
Specific Expression ◽  
Exon Splicing ◽  
Internal Exon ◽  
Cell Type Specific ◽  
Protein 4.1R ◽  
Dose Dependent ◽  
Splicing Enhancer

A regulated splicing event in protein 4.1R pre-mRNA—the inclusion of exon 16–encoding peptides for spectrin-actin binding—occurs in late erythroid differentiation. We defined the functional significance of an intronic splicing enhancer, UGCAUG, and its cognate splicing factor, mFox2A, on exon 16 splicing during differentiation. UGCAUG displays cell-type–specific splicing regulation in a test neutral reporter and has a dose-dependent enhancing effect. Erythroid cells express 2 UGCAUG-binding mFox-2 isoforms, an erythroid differentiation–inducible mFox-2A and a commonly expressed mFox-2F. When overexpressed, both enhanced internal exon splicing in an UGCAUG-dependent manner, with mFox-2A exerting a much stronger effect than mFox-2F. A significant reciprocal increase in mFox-2A and decrease in mFox-2F occurred during erythroid differentiation and correlated with exon 16 inclusion. Furthermore, isoform-specific expression reduction reversed mFox-2A–enhancing activity, but not that of mFox-2F on exon 16 inclusion. Our results suggest that an erythroid differentiation–inducible mFox-2A isoform is a critical regulator of the differentiation-specific exon 16 splicing switch, and that its up-regulation in late erythroid differentiation is vital for exon 16 splicing.

scholarly journals A Role for SRp54 during Intron Bridging of Small Introns with Pyrimidine Tracts Upstream of the Branch Point

1998 ◽  
Vol 18 (9) ◽  
pp. 5425-5434 ◽  
Author(s):  
Catharine F. Kennedy ◽  
Angela Krämer ◽  
Susan M. Berget
Keyword(s):  
Binding Site ◽  
Branch Point ◽  
Splice Site ◽  
Early Recognition ◽  
Splicing Factor ◽  
Splicing Factors ◽  
Sr Protein ◽  
U2 Snrnp ◽  
Auxiliary Factor ◽  
Splicing Factor 1

ABSTRACT One of the earliest steps in pre-mRNA recognition involves binding of the splicing factor U2 snRNP auxiliary factor (U2AF or MUD2 inSaccharomyces cerevisiae) to the 3′ splice site region. U2AF interacts with a number of other proteins, including members of the serine/arginine (SR) family of splicing factors as well as splicing factor 1 (SF1 or branch point bridging protein in S. cerevisiae), thereby participating in bridging either exons or introns. In vertebrates, the binding site for U2AF is the pyrimidine tract located between the branch point and 3′ splice site. Many small introns, especially those in nonvertebrates, lack a classical 3′ pyrimidine tract. Here we show that a 59-nucleotide Drosophila melanogaster intron contains C-rich pyrimidine tracts between the 5′ splice site and branch point that are needed for maximal binding of both U1 snRNPs and U2 snRNPs to the 5′ and 3′ splice site, respectively, suggesting that the tracts are the binding site for an intron bridging factor. The tracts are shown to bind both U2AF and the SR protein SRp54 but not SF1. Addition of a strong 3′ pyrimidine tract downstream of the branch point increases binding of SF1, but in this context, the upstream pyrimidine tracts are inhibitory. We suggest that U2AF- and/or SRp54-mediated intron bridging may be an alternative early recognition mode to SF1-directed bridging for small introns, suggesting gene-specific early spliceosome assembly.

scholarly journals A 5′ Splice Site-Proximal Enhancer Binds SF1 and Activates Exon Bridging of a Microexon

2000 ◽  
Vol 20 (11) ◽  
pp. 3988-3995 ◽  
Author(s):  
Troy Carlo ◽  
Rebecca Sierra ◽  
Susan M. Berget
Keyword(s):  
Splice Site ◽  
Troponin T ◽  
Repeated Sequence ◽  
Single Copy ◽  
Splice Sites ◽  
Exon Definition ◽  
Internal Exon ◽  
Splicing Factor 1

ABSTRACT Internal exon size in vertebrates occurs over a narrow size range. Experimentally, exons shorter than 50 nucleotides are poorly included in mRNA unless accompanied by strengthened splice sites or accessory sequences that act as splicing enhancers, suggesting steric interference between snRNPs and other splicing factors binding simultaneously to the 3′ and 5′ splice sites of microexons. Despite these problems, very small naturally occurring exons exist. Here we studied the factors and mechanism involved in recognizing a constitutively included six-nucleotide exon from the cardiac troponin T gene. Inclusion of this exon is dependent on an enhancer located downstream of the 5′ splice site. This enhancer contains six copies of the simple sequence GGGGCUG. The enhancer activates heterologous microexons and will work when located either upstream or downstream of the target exon, suggesting an ability to bind factors that bridge splicing units. A single copy of this sequence is sufficient for in vivo exon inclusion and is the binding site for the known bridging mammalian splicing factor 1 (SF1). The enhancer and its bound SF1 act to increase recognition of the upstream exon during exon definition, such that competition of in vitro reactions with RNAs containing the GGGGCUG repeated sequence depress splicing of the upstream intron, assembly of the spliceosome on the 3′ splice site of the exon, and cross-linking of SF1. These results suggest a model in which SF1 bridges the small exon during initial assembly, thereby effectively extending the domain of the exon.

Fox-2A Modulates Protein 4.1R Exon 16 5' Splice Site Activation.

Blood ◽  
2009 ◽  
Vol 114 (22) ◽  
pp. 778-778
Author(s):  
Shu-Ching Huang ◽  
Guang Yang ◽  
Jennie Park ◽  
Alexander Ou ◽  
Edward J. Benz
Keyword(s):  
Mechanical Stability ◽  
Conflicts Of Interest ◽  
Early Recognition ◽  
Erythroid Differentiation ◽  
Actin Binding ◽  
Dependent Manner ◽  
Enhancer Element ◽  
U1 Snrna ◽  
U1 Snrnp ◽  
Protein 4.1R

Abstract Abstract 778 Erythroid differentiation-induced Fox-2A is an important regulator for the differentiation-specific exon 16 splicing switch in protein 4.1R. Up-regulation of Fox-2A in late erythroid differentiation is critical for inclusion of exon 16, which encodes a portion of the spectrin/actin binding domain vital for maintaining the mechanical stability of red blood cell membranes. Fox-2A exerts its splicing enhancing activity in a motif-dependent manner, binding to UGCAUGs located downstream of exon 16. In this study, we investigated the mechanism by which Fox-2A modulates the expression of exon 16. The excision of introns and the joining of exons depends on the recognition and usage of 5' and 3' splice sites (5' ss and 3' ss, respectively) by the splicing machinery. Exon 16 possesses a relatively strong 3' ss but a weak 5' ss. Mutation of the weak 5' ss (GAGIGTTTGT) to a strong consensus 5' ss (GAGIGTAAGT) led to nearly total exon 16 inclusion. While mutations impairing Fox-2A binding drastically reduced exon 16 inclusion in the presence of the weak 5' ss, no effect on exon 16 inclusion was observed when the strong 5' ss was presented with these mutations. These results suggest that Fox-2A facilitates exon 16 splicing by supporting the weak 5' ss. Early recognition of the 5' ss involves base-pairing interaction with the 5' end of U1 snRNA and stabilization by U1 snRNP. Psoralen-mediated UV cross-linking assays revealed a reduction in U1 snRNA recruitment to the weak 5' ss when Fox-2A binding sites were impaired, suggesting that binding of Fox-2A could promote recruitment and stabilization of U1 snRNP to the weak 5' ss. In support for a role of Fox-2A in modulating the activation of the weak 5' ss by recruiting U1 snRNP, we demonstrated that Fox-2A directly interacts with U1 specific protein U1C in an RNA-independent manner. The C-terminal domain of Fox-2A is responsible for its association with U1C. These data suggest a novel mode for exon 16 5' ss activation in which the binding of Fox-2A to an intronic splicing enhancer element UGCAUG may stabilize the pre-mRNA-U1 snRNP complex through interactions with U1C. These could then result in spliceosome commitment complex formation and exon 16 inclusion. Disclosures: No relevant conflicts of interest to declare.

An erythroid differentiation–specific splicing switch in protein 4.1R mediated by the interaction of SF2/ASF with an exonic splicing enhancer

Blood ◽  
2005 ◽  
Vol 105 (5) ◽  
pp. 2146-2153 ◽  
Author(s):  
Guang Yang ◽  
Shu-Ching Huang ◽  
Jane Y. Wu ◽  
Edward J. Benz
Keyword(s):  
Erythroid Differentiation ◽  
Splicing Factor ◽  
Actin Binding ◽  
Junctional Complex ◽  
Exonic Splicing Enhancer ◽  
Differentiation Stage ◽  
Protein 4.1R ◽  
Splicing Enhancer ◽  
Mouse Erythroleukemia

Abstract Protein 4.1R is a vital component of the red blood cell membrane cytoskeleton. Promotion of cytoskeletal junctional complex stability requires an erythroid differentiation stage–specific splicing switch promoting inclusion of exon 16 within the spectrin/actin binding domain. We showed earlier that an intricate combination of positive and negative RNA elements controls exon 16 splicing. In this report, we further identified 3 putative exonic splicing enhancers within exon 16 and investigated the function of the sequence CAGACAT in the regulation of exon 16 splicing. Mutation of these sequences leads to increased exclusion of exon 16 in both in vivo and in vitro splicing assays, indicating that CAGACAT is a functional exonic splicing enhancer. UV cross-linking further detects an approximately 33-kDa protein that specifically binds to the CAGACAT-containing transcript. An anti-SF2/ASF antibody specifically immunoprecipitates the approximately 33-kDa protein. Furthermore, SF2/ASF stimulates exon 16 inclusion in both in vitro complementation assays and minigene-transfected mouse erythroleukemia cells (MELCs). Finally, SF2/ASF expression is up-regulated and correlates with exon 16 inclusion in differentiated MELCs. These results suggest that increased splicing factor 2/alternative splicing factor (SF2/ASF) expression in differentiated mouse erythroleukemia mediates a differentiation stage–specific exon 16 splicing switch through its interaction with the exonic splicing enhancer.

A Novel Splicing Factor RBM-9 Regulates Protein 4.1R Exon 16 Splicing.

Blood ◽  
2005 ◽  
Vol 106 (11) ◽  
pp. 805-805 ◽  
Author(s):  
Guang Yang ◽  
Shu-Ching Huang ◽  
Edward J. Benz
Keyword(s):  
Mutational Analysis ◽  
Erythroid Differentiation ◽  
Splicing Factor ◽  
Actin Binding ◽  
Dependent Manner ◽  
Mobility Shift ◽  
Red Cell Membrane ◽  
Protein 4.1R ◽  
Dose Dependent ◽  
Splicing Enhancer

Abstract Protein 4.1R (4.1R), a vital component of the red cell membrane cytoskeleton, stabilizes the spectrin-actin lattice and attaches it to embedded membrane proteins. A regulated splicing event, the inclusion of exon 16 that encodes for peptides critical for spectrin/actin binding, occurs during late erythroid differentiation. We showed earlier that an intricate combination of enhancer and silencer elements direct exon 16 splicing. Regulated expression of splicing factors, SF2/ASF and hnRNP A/B, has also been implicated in mediating exon 16 splicing. In this study, we attempted to characterize the mechanism involved in exon 16 splicing through UGCAUG, an intronic splicing enhancer present in three copies in the intron downstream of exon 16. We first used a wild-type minigene construct consisting of exons 13, 16, 17 and their respective flanking introns that mimics endogenous exon 16 splicing during the induced differentiation of mouse erythroleukemia cells (MELC). Mutational analysis showed a dose-dependent effect of UGCAUG on exon 16 splicing: the presence of all three copies had the most effect. These results were recapitulated with an internal chimeric exon in a test neutral reporter system “DUP4-1”, suggesting that the enhancing effect could be attributed directly to UGCAUG. Furthermore, we identified a novel splicing factor, RBM-9, from MELC that enhanced the internal exon splicing in an UGCAUG-dependent manner in both the exon 16 minigene and DUP4-1 reporter systems. Our characterization of RBM-9 revealed that diverse isoforms of RBM-9 are generated by the utilization of alternative translation initiation sites and tissue-specific alternative splicing; different isoforms from various tissues exhibited differential exon 16 splicing enhancing activities. MELC-RBM-9 enhanced exon 16 splicing the most among all RBM-9 isoforms tested. Inhibition of RBM-9 expression by RBM-9-shRNA reversed its enhancing activity on exon 16 inclusion in MELC. RBM-9-shRNA also reduced exon 16 splicing in a dose-dependent manner in HeLa cells. Furthermore, purified RBM-9 specifically binds to the UGCAUG sequence in a gel-mobility shift assay. Finally, expression of RBM-9 is upregulated and correlates with exon 16 inclusion during MELC differentiation. These results suggest that a novel splicing factor, RBM-9, enhances erythroid differentiation stage-specific exon 16 splicing by interacting with the splicing enhancer UGCAUG.

scholarly journals Identification and characterization by antisense oligonucleotides of exon and intron sequences required for splicing.

1994 ◽  
Vol 14 (11) ◽  
pp. 7445-7454 ◽  
Author(s):  
Z Dominski ◽  
R Kole
Keyword(s):  
Branch Point ◽  
Splice Site ◽  
Consensus Sequence ◽  
Aberrant Splice ◽  
Splice Sites ◽  
Branch Point Sequence ◽  
Splice Site Sequence ◽  
Internal Exon ◽  
Cryptic Splice Sites

Certain thalassemic human beta-globin pre-mRNAs carry mutations that generate aberrant splice sites and/or activate cryptic splice sites, providing a convenient and clinically relevant system to study splice site selection. Antisense 2'-O-methyl oligoribonucleotides were used to block a number of sequences in these pre-mRNAs and were tested for their ability to inhibit splicing in vitro or to affect the ratio between aberrantly and correctly spliced products. By this approach, it was found that (i) up to 19 nucleotides upstream from the branch point adenosine are involved in proper recognition and functioning of the branch point sequence; (ii) whereas at least 25 nucleotides of exon sequences at both 3' and 5' ends are required for splicing, this requirement does not extend past the 5' splice site sequence of the intron; and (iii) improving the 5' splice site of the internal exon to match the consensus sequence strongly decreases the accessibility of the upstream 3' splice site to antisense 2'-O-methyl oligoribonucleotides. This result most likely reflects changes in the strength of interactions near the 3' splice site in response to improvement of the 5' splice site and further supports the existence of communication between these sites across the exon.

scholarly journals Identification and characterization by antisense oligonucleotides of exon and intron sequences required for splicing

1994 ◽  
Vol 14 (11) ◽  
pp. 7445-7454
Author(s):  
Z Dominski ◽  
R Kole
Keyword(s):  
Branch Point ◽  
Splice Site ◽  
Consensus Sequence ◽  
Aberrant Splice ◽  
Splice Sites ◽  
Branch Point Sequence ◽  
Splice Site Sequence ◽  
Internal Exon ◽  
Cryptic Splice Sites

Certain thalassemic human beta-globin pre-mRNAs carry mutations that generate aberrant splice sites and/or activate cryptic splice sites, providing a convenient and clinically relevant system to study splice site selection. Antisense 2'-O-methyl oligoribonucleotides were used to block a number of sequences in these pre-mRNAs and were tested for their ability to inhibit splicing in vitro or to affect the ratio between aberrantly and correctly spliced products. By this approach, it was found that (i) up to 19 nucleotides upstream from the branch point adenosine are involved in proper recognition and functioning of the branch point sequence; (ii) whereas at least 25 nucleotides of exon sequences at both 3' and 5' ends are required for splicing, this requirement does not extend past the 5' splice site sequence of the intron; and (iii) improving the 5' splice site of the internal exon to match the consensus sequence strongly decreases the accessibility of the upstream 3' splice site to antisense 2'-O-methyl oligoribonucleotides. This result most likely reflects changes in the strength of interactions near the 3' splice site in response to improvement of the 5' splice site and further supports the existence of communication between these sites across the exon.

Alternative splicing of protein 4.1R exon 16: ordered excision of flanking introns ensures proper splice site choice

Blood ◽  
2000 ◽  
Vol 95 (2) ◽  
pp. 692-699 ◽  
Author(s):  
Sherry L. Gee ◽  
Kazuko Aoyagi ◽  
Robert Lersch ◽  
Victor Hou ◽  
Michael Wu ◽  
...  
Keyword(s):  
Alternative Splicing ◽  
Splice Site ◽  
Messenger Rna ◽  
Spatial Organization ◽  
Regulatory Elements ◽  
Binding Domain ◽  
Alternative Exon ◽  
Actin Binding ◽  
Actin Binding Domain ◽  
Protein 4.1R

Alternative splicing plays a major role in regulating tissue-specific expression of cytoskeletal protein 4.1R isoforms. In particular, expression of the protein's functionally critical spectrin-actin binding domain, essential for maintenance of red cell membrane mechanical properties, is governed by a developmentally regulated splicing switch involving alternative exon 16. Using a model 3-exon 4.1R pre–messenger RNA (pre-mRNA), we explored the sequence requirements for excision of the introns flanking exon 16. These studies revealed that splicing of this alternative exon occurs preferentially in an ordered fashion. The first step is excision of the downstream intron to join exons 16 and 17, followed by excision of the upstream intron. Constructs designed to test the converse pathway were spliced less efficiently and with less fidelity, in part due to activation of a cryptic 5′ splice site in exon 16. This downstream-first model for ordered splicing is consistent with the hypothesis that regulated alternative splicing requires cooperation between multiple exonic and/or intronic regulatory elements whose spatial organization is critical for recruitment of appropriate splicing factors. Our results predict that exon 16 splicing is regulated at the first step—excision of the downstream intron—and that cells unable to catalyze this step will exhibit exon 16 skipping. In cells that include exon 16, adherence to an ordered pathway is important for efficient and accurate production of mature 4.1R mRNA encoding an intact spectrin-actin binding domain.

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