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Regulation of splicing factors by alternative splicing and NMD is conserved between kingdoms yet evolutionarily flexible.

Lareau LF, Brenner SE - Mol. Biol. Evol. (2015)

Bottom Line: Ultraconserved elements, unusually long regions of perfect sequence identity, are found in genes encoding numerous RNA-binding proteins including arginine-serine rich (SR) splicing factors.We demonstrate that unproductive splicing of the splicing factor SRSF5 (SRp40) is conserved among all animals and even observed in fungi; this is a rare example of alternative splicing conserved between kingdoms, yet its effect is to trigger mRNA degradation.SR genes have consistently employed unproductive splicing, and while it is exceptionally conserved in some of these genes, turnover in specific events among paralogs shows flexible means to the same regulatory end.

View Article: PubMed Central - PubMed

Affiliation: Departments of Molecular and Cell Biology and Plant and Microbial Biology, University of California, Berkeley Department of Biochemistry, Stanford University School of Medicine.

No MeSH data available.


Related in: MedlinePlus

Conservation of SRSF4, SRSF5, and SRSF6 was assessed using data from vertebrate PhyloP conservation scores and whole-genome alignment tracks in the UCSC human genome browser (Pollard et al. 2010; Fujita et al. 2011). Regions of human/mouse 100% identity in alternative exons are marked with red bars. Vertebrate alignments are from MultiZ alignment of 46 vertebrates against human genome version hg19 and sea urchin alignment is from Strongylocentrotus purpuratus (September 2006 [Baylor 2.1/strPur2]) net alignment against human genome version hg18. The alternative exons of (A) SRSF5 and (B) SRSF6 have detectable similarity in all vertebrates and SRSF5 also has detectable homology in sea urchin. (C) Intron 1 of SRSF4, including three cassette exons, has no detectable similarity outside of mammals.
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msv002-F4: Conservation of SRSF4, SRSF5, and SRSF6 was assessed using data from vertebrate PhyloP conservation scores and whole-genome alignment tracks in the UCSC human genome browser (Pollard et al. 2010; Fujita et al. 2011). Regions of human/mouse 100% identity in alternative exons are marked with red bars. Vertebrate alignments are from MultiZ alignment of 46 vertebrates against human genome version hg19 and sea urchin alignment is from Strongylocentrotus purpuratus (September 2006 [Baylor 2.1/strPur2]) net alignment against human genome version hg18. The alternative exons of (A) SRSF5 and (B) SRSF6 have detectable similarity in all vertebrates and SRSF5 also has detectable homology in sea urchin. (C) Intron 1 of SRSF4, including three cassette exons, has no detectable similarity outside of mammals.

Mentions: The second-intron cassette exon is ultraconserved in SRSF6 but less conserved in SRSF4, suggesting relaxed selective pressure in SRSF4 (fig. 4), and the exon appears in ESTs from fewer species. After the second duplication and slight divergence of SRSF4, the cassette exon may have been lost in SRSF4 in many vertebrate lineages, or it may be spliced at low levels that are less likely to be detected.Fig. 4.


Regulation of splicing factors by alternative splicing and NMD is conserved between kingdoms yet evolutionarily flexible.

Lareau LF, Brenner SE - Mol. Biol. Evol. (2015)

Conservation of SRSF4, SRSF5, and SRSF6 was assessed using data from vertebrate PhyloP conservation scores and whole-genome alignment tracks in the UCSC human genome browser (Pollard et al. 2010; Fujita et al. 2011). Regions of human/mouse 100% identity in alternative exons are marked with red bars. Vertebrate alignments are from MultiZ alignment of 46 vertebrates against human genome version hg19 and sea urchin alignment is from Strongylocentrotus purpuratus (September 2006 [Baylor 2.1/strPur2]) net alignment against human genome version hg18. The alternative exons of (A) SRSF5 and (B) SRSF6 have detectable similarity in all vertebrates and SRSF5 also has detectable homology in sea urchin. (C) Intron 1 of SRSF4, including three cassette exons, has no detectable similarity outside of mammals.
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Related In: Results  -  Collection

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getmorefigures.php?uid=PMC4379411&req=5

msv002-F4: Conservation of SRSF4, SRSF5, and SRSF6 was assessed using data from vertebrate PhyloP conservation scores and whole-genome alignment tracks in the UCSC human genome browser (Pollard et al. 2010; Fujita et al. 2011). Regions of human/mouse 100% identity in alternative exons are marked with red bars. Vertebrate alignments are from MultiZ alignment of 46 vertebrates against human genome version hg19 and sea urchin alignment is from Strongylocentrotus purpuratus (September 2006 [Baylor 2.1/strPur2]) net alignment against human genome version hg18. The alternative exons of (A) SRSF5 and (B) SRSF6 have detectable similarity in all vertebrates and SRSF5 also has detectable homology in sea urchin. (C) Intron 1 of SRSF4, including three cassette exons, has no detectable similarity outside of mammals.
Mentions: The second-intron cassette exon is ultraconserved in SRSF6 but less conserved in SRSF4, suggesting relaxed selective pressure in SRSF4 (fig. 4), and the exon appears in ESTs from fewer species. After the second duplication and slight divergence of SRSF4, the cassette exon may have been lost in SRSF4 in many vertebrate lineages, or it may be spliced at low levels that are less likely to be detected.Fig. 4.

Bottom Line: Ultraconserved elements, unusually long regions of perfect sequence identity, are found in genes encoding numerous RNA-binding proteins including arginine-serine rich (SR) splicing factors.We demonstrate that unproductive splicing of the splicing factor SRSF5 (SRp40) is conserved among all animals and even observed in fungi; this is a rare example of alternative splicing conserved between kingdoms, yet its effect is to trigger mRNA degradation.SR genes have consistently employed unproductive splicing, and while it is exceptionally conserved in some of these genes, turnover in specific events among paralogs shows flexible means to the same regulatory end.

View Article: PubMed Central - PubMed

Affiliation: Departments of Molecular and Cell Biology and Plant and Microbial Biology, University of California, Berkeley Department of Biochemistry, Stanford University School of Medicine.

No MeSH data available.


Related in: MedlinePlus