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

Life ◽  
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.

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

1991 ◽  
Vol 219 (3) ◽  
pp. 415-428 ◽  
Author(s):  
Alain Jacquier ◽  
Nathalie Jacquesson-Breuleux
Keyword(s):  
Splice Site ◽  
Site Selection ◽  
Group Ii Intron ◽  
Splice Site Selection ◽  
Group Ii

scholarly journals The role of exon sequences in splice site selection.

1993 ◽  
Vol 7 (3) ◽  
pp. 407-418 ◽  
Author(s):  
A Watakabe ◽  
K Tanaka ◽  
Y Shimura
Keyword(s):  
Splice Site ◽  
Site Selection ◽  
Splice Site Selection

scholarly journals Role of the 3′ Splice Site in U12-Dependent Intron Splicing

2001 ◽  
Vol 21 (6) ◽  
pp. 1942-1952 ◽  
Author(s):  
Rosemary C. Dietrich ◽  
Marian J. Peris ◽  
Andrew S. Seyboldt ◽  
Richard A. Padgett
Keyword(s):  
Splice Site ◽  
Site Selection ◽  
Intron Splicing ◽  
Splice Sites ◽  
Splice Site Selection ◽  
Branch Site ◽  
Site Function

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.

The role of nucleotide sequences in splice site selection in eukaryotic pre-messenger RNA

Nature ◽  
1986 ◽  
Vol 324 (6094) ◽  
pp. 280-282 ◽  
Author(s):  
L. P. Eperon ◽  
J. P. Estibeiro ◽  
I. C. Eperon
Keyword(s):  
Splice Site ◽  
Site Selection ◽  
Messenger Rna ◽  
Nucleotide Sequences ◽  
Splice Site Selection

scholarly journals Role of the Modular Domains of SR Proteins in Subnuclear Localization and Alternative Splicing Specificity

1997 ◽  
Vol 138 (2) ◽  
pp. 225-238 ◽  
Author(s):  
Javier F. Cáceres ◽  
Tom Misteli ◽  
Gavin R. Screaton ◽  
David L. Spector ◽  
Adrian R. Krainer
Keyword(s):  
Alternative Splicing ◽  
Splice Site ◽  
Site Selection ◽  
Cellular Localization ◽  
Sr Proteins ◽  
Dependent Manner ◽  
Splice Site Selection ◽  
Subnuclear Localization

SR proteins are required for constitutive pre-mRNA splicing and also regulate alternative splice site selection in a concentration-dependent manner. They have a modular structure that consists of one or two RNA-recognition motifs (RRMs) and a COOH-terminal arginine/serine-rich domain (RS domain). We have analyzed the role of the individual domains of these closely related proteins in cellular distribution, subnuclear localization, and regulation of alternative splicing in vivo. We observed striking differences in the localization signals present in several human SR proteins. In contrast to earlier studies of RS domains in the Drosophila suppressor-of-white-apricot (SWAP) and Transformer (Tra) alternative splicing factors, we found that the RS domain of SF2/ASF is neither necessary nor sufficient for targeting to the nuclear speckles. Although this RS domain is a nuclear localization signal, subnuclear targeting to the speckles requires at least two of the three constituent domains of SF2/ASF, which contain additive and redundant signals. In contrast, in two SR proteins that have a single RRM (SC35 and SRp20), the RS domain is both necessary and sufficient as a targeting signal to the speckles. We also show that RRM2 of SF2/ASF plays an important role in alternative splicing specificity: deletion of this domain results in a protein that, although active in alternative splicing, has altered specificity in 5′ splice site selection. These results demonstrate the modularity of SR proteins and the importance of individual domains for their cellular localization and alternative splicing function in vivo.

SR protein kinases: the splice of life

1999 ◽  
Vol 77 (4) ◽  
pp. 293-298 ◽  
Author(s):  
David F Stojdl ◽  
John C Bell
Keyword(s):  
Alternative Splicing ◽  
Splice Site ◽  
Site Selection ◽  
Developmental Process ◽  
Messenger Rnas ◽  
Splice Site Selection ◽  
Sr Protein ◽  
Specific Alternative ◽  
Mature Mrnas

The eukaryotic genome codes for most of its proteins though discontinuous coding sequences called exons, which are separated by noncoding sequences known as introns. Following transcription of a gene, these exons must be spliced precisely, removing the intervening introns, to form meaningful mature messenger RNAs (mRNA) that are transported to the cytoplasm and translated by the ribosomal machinery. To add yet another level of complexity, a process known as alternative splicing exists, whereby a single pre-mRNA can give rise to two or more mature mRNAs depending on the combination of exons spliced together. Alternative splicing of pre-mRNAs is emerging as an important mechanism for gene regulation in many organisms. The classic example of splicing as a regulator of genetic information during a developmental process is sex determination in Drosophila. The now well-characterized cascade of sex-specific alternative splicing events demonstrates nicely how the control of splice site selection during pre-mRNA processing can have a profound effect on the development of an organism. The factors involved in pre-mRNA splicing and alternative splice site selection have been the subject of active study in recent years. Emerging from these studies is a picture of regulation based on protein-protein, protein-RNA, and RNA-RNA interactions. How the interaction of the various splicing constituents is controlled, however, is still poorly understood. One of the mechanisms of regulation that has received attention recently is that of posttranslational phosphorylation. In the following article, we cite the evidence for a role of phosphorylation in constitutive and alternative splicing and discuss some of the recent information on the biochemistry and biology of the enzymes involved.Key words: phosphorylation, splicing, spliceosome, Clk kinases, SR proteins.

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