Binding of PurH to a Muscle-specific Splicing Enhancer Functionally Correlates with Exon Inclusion in Vivo

Ryan, Kathryn J.; Charlet-B., Nicolas; Cooper, Thomas A.

doi:10.1074/jbc.m909977199

Cited by 6 publications

(7 citation statements)

References 43 publications

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“…This system depends on strong constitutive splicing signals consisting of a branchpoint, polypyrimidine tract and exon bridging interactions (Simpson et al ., 2000, 2002). It therefore differs from most metazoan mini‐exon systems, which depend on specific splicing enhancer or silencer sequences, which are recognised by general or gene‐specific trans ‐acting proteins to regulate mini‐exon inclusion or skipping (Modafferi and Black, 1999; Ryan et al ., 2000). The sensitivity of this mini‐exon system to alterations in these splicing parameters has allowed dissection of both the branchpoint and polypyrimidine tract sequences (Simpson et al ., 2002).…”

Section: Discussionmentioning

confidence: 99%

Dual functionality of a plant U‐rich intronic sequence element

Simpson¹,

Jennings²,

Clark³

et al. 2003

The Plant Journal

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SummaryIn potato invertase genes, the constitutively included, 9-nucleotide (nt)-long mini-exon requires a strong branchpoint and U-rich polypyrimidine tract for inclusion. The strength of these splicing signals was demonstrated by greatly enhanced splicing of a poorly spliced intron and by their ability to support splicing of an arti®cial mini-exon, following their introduction. Plant introns also require a second splicing signal, UA-rich intronic elements, for ef®cient intron splicing. Mutation of the branchpoint caused loss of mini-exon inclusion without loss of splicing enhancement, showing that the same U-rich sequence can function as either a polypyrimidine tract or a UA-rich intronic element. The distinction between the splicing signals depended on intron context (the presence or absence of an upstream, adjacent and functional branchpoint), and on the sequence context of the U-rich elements. Polypyrimidine tracts tolerated C residues while UA-rich intronic elements tolerated As. Thus, in plant introns, U-rich splicing elements can have dual roles as either a general plant U-rich splicing signal or a polypyrimidine tract. Finally, overexpression of two different U-rich binding proteins enhanced intron recognition signi®cantly. These results highlight the importance of co-operation between splicing signals, the importance of other nucleotides within U-rich elements for optimal binding of competing splicing factors and effects on splicing ef®ciency of U-rich binding proteins.

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Section: Discussionmentioning

confidence: 99%

Dual functionality of a plant U‐rich intronic sequence element

Simpson¹,

Jennings²,

Clark³

et al. 2003

The Plant Journal

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“…A number of other protein families that consist of one or more RNA recognition motifs (RRM) (27) and confer tighter RNA-binding specificity have become visible as splicing regulators, e.g., PurH (39), Sam68 (35), TIA-1 (10), SAP155 (28), and Fox-2 (54). Some are composed of arginine-aspartic acid (RD), arginine-glutamic acid (RE), arginine-glycine-rich motifs, and/or other domains (19,44,50) that can mediate interactions between protein and RNA or protein molecules.…”

mentioning

confidence: 99%

Novel Splicing Factor RBM25 Modulates Bcl-x Pre-mRNA 5′ Splice Site Selection

Zhou

Cho

et al. 2008

Molecular and Cellular Biology

111

109

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RBM25 has been shown to associate with splicing cofactors SRm160/300 and assembled splicing complexes, but little is known about its splicing regulation. Here, we characterize the functional role of RBM25 in alternative pre-mRNA splicing. Increased RBM25 expression correlated with increased apoptosis and specifically affected the expression of Bcl-x isoforms. RBM25 stimulated proapoptotic Bcl-x S 5 splice site (5 ss) selection in a dose-dependent manner, whereas its depletion caused the accumulation of antiapoptotic Bcl-x L . Furthermore, RBM25 specifically bound to Bcl-x RNA through a CGGGCA sequence located within exon 2. Mutation in this element abolished the ability of RBM25 to enhance Bcl-x S 5 ss selection, leading to decreased Bcl-x S isoform expression. Binding of RBM25 was shown to promote the recruitment of the U1 small nuclear ribonucleoprotein particle (snRNP) to the weak 5 ss; however, it was not required when a strong consensus 5 ss was present. In support of a role for RBM25 in modulating the selection of a 5 ss, we demonstrated that RBM25 associated selectively with the human homolog of yeast U1 snRNP-associated factor hLuc7A. These data suggest a novel mode for Bcl-x S 5 ss activation in which binding of RBM25 with exonic element CGGGCA may stabilize the pre-mRNA-U1 snRNP through interactions with hLuc7A.Alternative splicing is a regulatory mechanism that allows eukaryotes to generate numerous protein isoforms, often with diverse biological functions, from a single gene (2,26,49). Pre-mRNA splicing takes place within the spliceosome, which is assembled stepwise by the addition of small nuclear ribonucleoprotein particles (snRNP) and numerous accessory nonsnRNP splicing factors (23, 31). The excision of introns and the joining of exons depend on the recognition and usage of 5Ј splice sites (5Ј ss) and 3Ј ss by the splicing machinery (21, 33). The commitment complex forms when the 5Ј ss is recognized by U1 snRNA base pairing and stabilized by U1 snRNP while the 3Ј ss is recognized by the U2 auxiliary factor (U2AF) through U2 snRNA base pairing with the branch point. Subsequently, the U4/5/6 tri-snRNP is incorporated into the complex and the U1 snRNA base paired at the 5Ј ss is replaced by U6 snRNA. These processes result in a fully assembled spliceosome that supports a series of rearrangements via RNA-RNA and RNA-protein interactions and activates the catalytic steps of cleavage, exon joining, and intron release (2, 26).However, the splice site signals that define the 5Ј ss and 3Ј ss are often degenerate. How and when they are used are believed to be modulated by a combinational interplay of positive (splicing enhancers) and negative (splicing silencers) cis elements and trans-acting factors (2, 26), forming the basis of alternative splicing. The splicing regulatory (SR) proteins (18, 41) and the heterogeneous nuclear ribonucleoproteins (hnRNPs) (11,46) bind with specificity to pre-mRNA (20).The SR proteins generally bind to enhancer elements through the RNA-binding domain and activate splicing at...

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“…The first eukaryote PURH cloned is from an avian hepatic cDNA library (Aimi et al, 1990). Recombinant human PURH protein directly binds to muscle specific splicing enhancer 3 (MSE3) RNA and PURH is the primary determinant that is responsible for the sequencespecific binding activity of this complex (Ryan et al, 2000). These observations strongly suggest that PURH performs a second function as a component of a complex that regulates MSE3-dependent exon inclusion (Ryan et al, 2000).…”

Section: Discussionmentioning

confidence: 99%

The Expression of Genes Related to Egg Production in the Liver of Taiwan Country Chickens

Ding¹,

Ko²,

Ou³

et al. 2008

Asian Australas. J. Anim. Sci

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The purpose of this study was to detect expression of genes related to egg production in Taiwan Country chickens by suppression subtractive hybridization. Liver samples of mRNA extraction from two Taiwan Country chicken strains (L2 and B), originated from the same population but with very distinct egg production rates after long-term selection for egg and meat production respectively. Two-way subtraction was performed. The hepatic cDNA from the low egg production chickens (B) was subtracted from the hepatic cDNA from the high egg production strain (L2). The reversed subtraction (L2 from B) was also performed. The resulting differentially expressed gene fragments were cloned and sequenced. We sequenced 288 clones from the forward subtraction and 96 clones from the reverse subtraction. These genes were subjected to further screening to confirm the differential expression between the two genetic breeds of chickens. The apolipoprotein B (apoB) was expressed to a greater extent in the liver of the L2 than in the B line chickens. The 5-aminoimidazole-4-carboxamide ribonucleotide formyltransferase/IMP cyclohydrolase (PURH) was expressed to a greater extent in the liver of the B than in the L2 strain chickens. We demonstrated that both apoB and PURH were more highly expressed in the liver than that in other tissues (muscle, ovary, and oviduct) in laying Taiwan Country chickens. Taken together, these data suggest that after the selection for egg production, expression of apoB and PURH genes were also changed. Whether the changed expression of these genes is directly related to egg production is not known, but these two genes may be useful markers for egg laying performance in Taiwan Country chickens.

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Binding of PurH to a Muscle-specific Splicing Enhancer Functionally Correlates with Exon Inclusion in Vivo

Cited by 6 publications

References 43 publications

Dual functionality of a plant U‐rich intronic sequence element

Dual functionality of a plant U‐rich intronic sequence element

Novel Splicing Factor RBM25 Modulates Bcl-x Pre-mRNA 5′ Splice Site Selection

The Expression of Genes Related to Egg Production in the Liver of Taiwan Country Chickens

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