Physiological state co-regulates thousands of mammalian mRNA splicing events at tandem splice sites and alternative exons

Abstract

Thousands of tandem alternative splice sites (TASS) give rise to mRNA insertion/deletion variants with small size differences. Recent work has concentrated on the question of biological relevance in general, and the physiological regulation of TASS in particular. We have quantitatively studied 11 representative TASS cases in comparison to one mutually exclusive exon case and two cassette exons (CEs) using a panel of human and mouse tissues, as well as cultured cell lines. Tissues show small but significant differences in TASS isoform ratios, with a variance 4- to 20-fold lower than seen for CEs. Remarkably, in cultured cells, all studied alternative splicing (AS) cases showed a cell-density-dependent shift of isoform ratios with similar time series profiles. A respective genome-wide co-regulation of TASS splicing was shown by next-generation mRNA sequencing data. Moreover, data from human and mouse organs indicate that this co-regulation of TASS occurs in vivo, with brain showing the strongest difference to other organs. Together, the results indicate a physiological AS regulation mechanism that functions almost independently from the splice site context and sequence.

It's a bit over, is that ok? The subtle surplus from tandem alternative splicing

“…6 Together, three studies provided highresolution evidence that 3 0 TASS isoform ratios differ across different mammalian tissues. 6,34,38 Even though Tsai and Lin concluded that NAGNAG isoform ratios are "almost constant among tissues," their presented results do nicely fit other reports which diagnose cross-tissue differences. 34,38 Also the results from RNA-seq data support the tissue-dependent differences, with somewhat less resolution on individual TASS cases but clearly higher genome-wide coverage.…”

“…6,34,38 Even though Tsai and Lin concluded that NAGNAG isoform ratios are "almost constant among tissues," their presented results do nicely fit other reports which diagnose cross-tissue differences. 34,38 Also the results from RNA-seq data support the tissue-dependent differences, with somewhat less resolution on individual TASS cases but clearly higher genome-wide coverage. 6 Next, concerning the extent of crosstissue variation in isoform ratios, two studies are very close in their conclusion that the isoform ratios are "almost constant" or "very small" compared to tissue-specific splicing of cassette exons.…”

“…Another study from our group analyzed 11 cases of 5 0 and 3 0 TASS in multiple human and mouse tissues and found a median cross-tissue variation of TASS isoform ratio with §2.5%. 34 The tissue-associated variation was statistically significant in 90% of the cases, but the variation level was low in comparison to cassette and mutally exclusive exons which showed a 7-fold higher crosstissue variation of isoform ratio at §17.0%. Finally, a study that used deep RNA-seq data to analyze NAGNAG isoforms genome-wide, came to the conclusion that 73% of human and 28% mouse NAGNAGs are significantly tissue-specific.…”

“…6,16,30,[34][35][36] However, what also seems important for the potential relevance of changes in TASS splicing is the dynamic range imposed by regulation, in comparison to other AS classes. Early case reports of human genes with TASS showed almost constant isoform ratios, for example in NR3C1, ATN1, IGF1R, SCN5A, ING4, whereas some showed differential isoform ratios, for example in EDA and CACNA1A (reviewed in ref 17).…”

Merging Absolute and Relative Quantitative PCR Data to Quantify STAT3 Splice Variant Transcripts

“…STAT3 auto-regulates its own expression 37 , and the protocol described above may help to elucidate whether ratios of STAT3 splice variants contribute to regulating this positive feedback loop. The protocol could be used to study shifts in splice variant ratios as observed in cells at differing densities 38 or over the course of development: it is known that the STAT3 α/β ratio changes at the protein level during hematopoiesis 16 . Sundin et al found that an intronic single nucleotide polymorphism biased splicing of exon 12 in STAT3 of a patient with Job's syndrome 39 .…”