Comparative Genomics and Evolution of Alternative Splicing: The Pessimists′ Science

Artamonova, Irena I.; Gelfand, Mikhail S.

doi:10.1002/chin.200746273

Cited by 3 publications

(3 citation statements)

References 298 publications

(393 reference statements)

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“…We also find that G4s appear in a subset of species near splice sites ( Fig 6) which suggests that they have emerged as splicing modulators during vertebrate evolution. The presence of additional regulatory mechanisms is in accordance with higher frequencies of alternative splicing events in vertebrates compared to invertebrates (Artamonova & Gelfand 2007). Moreover, G4s display a higher likelihood of DNA mutations (Du et al 2014) and as a result they are likely plastic in nature, enabling rapid splicing changes during evolution and the establishment of new functions through alternative splicing and the generation of isoform diversity.…”

Section: Discussionmentioning

confidence: 73%

Alternative splicing modulation by G-quadruplexes

Soares

Parada

Wong

et al. 2019

Preprint

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Alternative splicing is central to metazoan gene regulation but the regulatory mechanisms involved are only partially understood. Here, we show that G-quadruplex (G4) motifs are enriched ~3-fold both upstream and downstream of splice junctions. Analysis of in vitro G4-seq data corroborates their formation potential. G4s display the highest enrichment at weaker splice sites, which are frequently involved in alternative splicing events. The importance of G4s in RNA as supposed to DNA is emphasized by a higher enrichment for the non-template strand. To explore if G4s are involved in dynamic alternative splicing responses, we analyzed RNA-seq data from mouse and human neuronal cells treated with potassium chloride. We find that G4s are enriched at exons which were skipped following potassium ion treatment. We validate the formation of stable G4s for three candidate splice sites by circular dichroism spectroscopy, UV-melting and fluorescence measurements. Finally, we explore G4 motifs across eleven representative species, and we observe that strong enrichment at splice sites is restricted to mammals and birds.

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Section: Discussionmentioning

confidence: 73%

Alternative splicing modulation by G-quadruplexes

Soares

Parada

Wong

et al. 2019

Preprint

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“…Many studies have been published on the rate of exon insertion and deletion and on the statistics of different types of splicing, but few researchers so far have studied the evolution of transcripts [2]. Harr and Turner showed that most transcripts among Mus subspecies were novel [7].…”

Section: A Backgroundmentioning

confidence: 99%

Inferring Transcript Phylogenies

Christinat

Moret

2011

2011 IEEE International Conference on Bioinformatics and Biomedicine

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Alternative splicing, an unknown mechanism 20 years ago, is now recognized as a major mechanism for proteome and transcriptome diversity, particularly in mammals-some researchers conjecture that up to 90% of human genes are alternatively spliced. Despite much research on exon and intron evolution, little is known about the evolution of transcripts.In this paper, we present a model of transcript evolution and an associated algorithm to reconstruct transcript phylogenies. The evolution of the gene structure-exons and introns-is used as basis for the reconstruction of transcript phylogenies. We apply our model and reconstruction algorithm on two well-studied genes, MAG and PAX6, obtaining results consistent with current knowledge and thereby providing evidence that a phylogenetic analysis of transcripts is feasible and likely to be informative.

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“…Alternative splicing is a well-described biochemical process in which multiple protein isoforms are formed from a single gene, thereby increasing proteomic and functional diversity in eukaryotes (Matlin et al, 2005). Alternative splicing is tightly linked to other processes that lead to the expression of different mRNAs from one gene, such as transcription initiation using alternative promoters and alternative polyadenylation (Artamonova and Gelfand, 2007). In this study, we determined the identities of these two ZEB2 transcripts, analyzed the effects of their protein products on ZEA biosynthesis and identified their protein-interacting partners.…”

Section: Introductionmentioning

confidence: 99%

Autoregulation of ZEB2 expression for zearalenone production in Fusarium graminearum

Park

Son

Min

et al. 2015

Molecular Microbiology

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SummarySeveral Fusarium species produce the polyketide mycotoxin zearalenone (ZEA), a causative agent of hyperestrogenic syndrome in animals that is often found in F. graminearum-infected cereals in temperate regions. The ZEA biosynthetic cluster genes PKS4, PKS13, ZEB1 and ZEB2 encode a reducing polyketide synthase, a non-reducing polyketide synthase, an isoamyl alcohol oxidase and a transcription factor respectively. In this study, the production of two isoforms (ZEB2L and ZEB2S) from the ZEB2 gene in F. graminearum via an alternative promoter was characterized. ZEB2L contains a basic leucine zipper (bZIP) DNA-binding domain at the N-terminus, whereas ZEB2S is an N-terminally truncated form of ZEB2L that lacks the bZIP domain. Interestingly, ZEA triggers the induction of both ZEB2L and ZEB2S transcription. ZEB2L and ZEB2S interact with each other to form a heterodimer that regulates ZEA production by reducing the binding affinity of ZEB2L for the ZEB2L gene promoter. Our study provides insight into the autoregulation of ZEB2 expression by alternative promoter usage and a feedback loop during ZEA production; this regulatory mechanism is similar to that observed in higher eukaryotes.

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Comparative Genomics and Evolution of Alternative Splicing: The Pessimists′ Science

Abstract: ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 200 leading journals. To access a ChemInform Abstract, please click on HTML or PDF.

Cited by 3 publications

References 298 publications

Alternative splicing modulation by G-quadruplexes

Alternative splicing modulation by G-quadruplexes

Inferring Transcript Phylogenies

Autoregulation of ZEB2 expression for zearalenone production in Fusarium graminearum

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