A mutational analysis of the polypyrimidine tract of introns. Effects of sequence differences in pyrimidine tracts on splicing

Roscigno, R F; Weiner, Madeline; García-Blanco, Mariano A.

doi:10.1016/s0021-9258(18)82114-7

Cited by 140 publications

(31 citation statements)

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“…1 A). Differences in the sequences of PPTs of human U2 introns modulate the assembly of the spliceosome and ultimately splicing of pre-mRNAs ( Roscigno et al 1993 ). Actually, the composition of the PPT is an important factor in determining the strength of the 3′ss because it modulates the recruitment of U2AF2.…”

Section: Resultsmentioning

confidence: 99%

U2AF2 binds IL7R exon 6 ectopically and represses its inclusion

Schott

Galarza-Muñoz

Trevino

et al. 2021

RNA

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Interleukin 7 receptor α-chain is crucial for the development and maintenance of T cells and genetically associated with autoimmune disorders including multiple sclerosis (MS). Exon 6 of IL7R encodes for its transmembrane domain and regulated by alternative splicing (AS): Inclusion or skipping of IL7R exon 6 results in membrane-bound or soluble IL7R isoforms, respectively. We previously identified SNP rs6897932 in IL7R exon 6, associated with MS risk, and showed that the risk allele (C) results in increased exon skipping and elevated sIL7R. Elevated levels of sIL7R have been shown to exacerbate the disease in the experimental autoimmune encephalomyelitis mouse model of MS. Here we report two mechanisms by which IL7R exon 6 is controlled. A competition between PTBP1 and U2AF2 at the polypyrimidine tract (PPT) of intron 5, and an unexpected U2AF2-mediated assembly of splicing factors in the exon. We noted the presence of a branchpoint sequence (BPS) (TACTAAT or TACTAAC) within exon 6, which is stronger with the C allele. Importantly, the BPS is followed by a PPT and we conjectured that silencing could be mediated by binding of U2AF2 to that tract. Here, we show that evolutionary conservation of the exonic PPT correlates well with the degree of AS of exon 6 in two nonhuman primate species and that U2AF2 binding to this PPT recruits U2 snRNP components to the exon. These observations provide the first explanation for the stronger silencing of IL7R exon 6 with the disease-associated C allele at rs6897932.

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Section: Resultsmentioning

confidence: 99%

U2AF2 binds IL7R exon 6 ectopically and represses its inclusion

Schott

Galarza-Muñoz

Trevino

et al. 2021

RNA

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“…Since we had previously shown that replacement of U residues with C in intronic py tracts inhibits splicing of model pre-mRNA substrates in vitro (Roscigno et al, 1993), we posited that the C-rich py tracts in FOXP3 introns would make these inefficient and highly sensitive to DDX39B levels. To test this we made reporter constructs where FOXP3 introns interrupted a Renilla luciferase ORF, and splicing efficiency could be inferred by luciferase activity and measured directly using RT-PCR (Fig.…”

Section: Ddx39b Controls Expression Of Genes Associated With Multiple Sclerosis Riskmentioning

confidence: 99%

The RNA helicase DDX39B activates FOXP3 RNA splicing to control T regulatory cell fate

Hirano

Galarza-Muñoz

Schott

et al. 2022

Preprint

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Genes associated with increased susceptibility to multiple sclerosis (MS) have been identified, but their functions are incompletely understood. One of these genes codes for the RNA helicase DExD/H-Box Polypeptide 39B (DDX39B), which shows genetic and functional epistasis with interleukin-7 receptor-α gene (IL7R) in MS-risk. Based on evolutionary and functional arguments we postulated that DDX39B enhances immune tolerance decreasing MS risk. Consistent with such a role we show that DDX39B controls the expression of many MS susceptibility genes and important immune-related genes. Among these we identified Forkhead Box P3 (FOXP3), which codes for the master transcriptional factor in CD4+/CD25+ T regulatory cells. DDX39B knockdown led to loss of immune-regulatory and gain of immune-effector expression signatures. Splicing of FOXP3 introns, which belong to a previously unrecognized subclass of introns with C-rich polypyrimidine tracts, was exquisitely sensitive to DDX39B levels. Given the importance of FOXP3 in autoimmunity, this work cements DDX39B as an important guardian of immune tolerance.

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“…Remarkably, most of the studies addressing the requirement of Py tracts for U2AF65 binding and subsequent splicing are based on in vitro splicing reactions uncoupled from transcription and with selected pre-mRNAs. Genome-wide bioinformatics analyses have, however, revealed that a large portion of human introns contains only weak PY tracts which are not likely to represent binding sites for U2AF65 [123,138,139]. From an evolutionary perspective, the requirement on U2AF65 for efficient splicing therefore stems from the stable interaction with SF1 and U2AF35 rather than from binding to Py tracts, as is the case in S. pombe [98].…”

Section: The U2af Heterodimer: Beyond Py Tract Binding-a Physical Link Between the Branchpoint And 3 Ssmentioning

confidence: 99%

Evolution of the Early Spliceosomal Complex—From Constitutive to Regulated Splicing

Borao

Ayté

Hümmer

2021

IJMS

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Pre-mRNA splicing is a major process in the regulated expression of genes in eukaryotes, and alternative splicing is used to generate different proteins from the same coding gene. Splicing is a catalytic process that removes introns and ligates exons to create the RNA sequence that codifies the final protein. While this is achieved in an autocatalytic process in ancestral group II introns in prokaryotes, the spliceosome has evolved during eukaryogenesis to assist in this process and to finally provide the opportunity for intron-specific splicing. In the early stage of splicing, the RNA 5′ and 3′ splice sites must be brought within proximity to correctly assemble the active spliceosome and perform the excision and ligation reactions. The assembly of this first complex, termed E-complex, is currently the least understood process. We focused in this review on the formation of the E-complex and compared its composition and function in three different organisms. We highlight the common ancestral mechanisms in S. cerevisiae, S. pombe, and mammals and conclude with a unifying model for intron definition in constitutive and regulated co-transcriptional splicing.

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A mutational analysis of the polypyrimidine tract of introns. Effects of sequence differences in pyrimidine tracts on splicing

Cited by 140 publications

References 0 publications

U2AF2 binds IL7R exon 6 ectopically and represses its inclusion

U2AF2 binds IL7R exon 6 ectopically and represses its inclusion

The RNA helicase DDX39B activates FOXP3 RNA splicing to control T regulatory cell fate

Evolution of the Early Spliceosomal Complex—From Constitutive to Regulated Splicing

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