Splice site selection and role of the lariat in a group II intron

ABSTRACT U12-dependent introns containing alterations of the 3′ splice site AC dinucleotide or alterations in the spacing between the branch site and the 3′ splice site were examined for their effects on splice site selection in vivo and in vitro. Using an intron with a 5′ splice site AU dinucleotide, any nucleotide could serve as the 3′-terminal nucleotide, although a C residue was most active, while a U residue was least active. The penultimate A residue, by contrast, was essential for 3′ splice site function. A branch site-to-3′ splice site spacing of less than 10 or more than 20 nucleotides strongly activated alternative 3′ splice sites. A strong preference for a spacing of about 12 nucleotides was observed. The combined in vivo and in vitro results suggest that the branch site is recognized in the absence of an active 3′ splice site but that formation of the prespliceosomal complex A requires an active 3′ splice site. Furthermore, the U12-type spliceosome appears to be unable to scan for a distal 3′ splice site.

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Mechanism of 3' splice site selection by the catalytic core of the sunY intron of bacteriophage T4: the role of a novel base-pairing interaction in group I introns.

Genes & Development ◽

10.1101/gad.4.5.777 ◽

1990 ◽

Vol 4 (5) ◽

pp. 777-788 ◽

Cited By ~ 35

Author(s):

F Michel ◽

P Netter ◽

M Q Xu ◽

D A Shub

Keyword(s):

Splice Site ◽

Site Selection ◽

Bacteriophage T4 ◽

Group I Introns ◽

Pairing Interaction ◽

Splice Site Selection ◽

Catalytic Core ◽

Group I ◽

Base Pairing Interaction

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CXCR3 Expression and Genome-Wide 3′ Splice Site Selection in the TCGA Breast Cancer Cohort

Life ◽

10.3390/life11080746 ◽

2021 ◽

Vol 11 (8) ◽

pp. 746

Author(s):

Lauren A. Levesque ◽

Scott Roy ◽

Nicole Salazar

Keyword(s):

Breast Cancer ◽

Splice Site ◽

Site Selection ◽

Normal Tissue ◽

Adjacent Normal Tissue ◽

Splice Site Selection ◽

Immune Infiltration ◽

Cxcr3 Expression ◽

Genome Wide

CXCR3 is a chemokine receptor with two well-characterized isoforms that have unique, context-dependent roles: CXCR3-A and CXCR3-B, which are produced through alternative 3′ splice site selection (A3SS). RNA-seq data from The Cancer Genome Atlas (TCGA) were used to correlate CXCR3 expression with breast cancer progression. This analysis revealed significant CXCR3 expression patterns associated with survival and differential expression between the tumor and adjacent normal tissue. TCGA data were used to estimate abundance of immune cells in breast cancer, which demonstrated the association of CXCR3 with immune infiltration, particularly in the triple-negative subtype. Given the importance of A3SS in CXCR3, genome-wide analysis of A3SS events was performed to identify events that were differentially spliced between breast cancer tissue and adjacent normal tissue. A total of 481 splicing events in 424 genes were found to be differentially spliced. The parent genes of differentially spliced events were enriched in RNA processing and splicing functions, indicating an underappreciated role of A3SS in the integrated splicing network of breast cancer. These results further validated the role of CXCR3 in immune infiltration of tumors, while raising questions about the role of A3SS splicing.

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