Identification of tumor-associated cassette exons in human cancer through EST-based computational prediction and experimental validation

Valletti, Alessio; Anselmo, Anna; Mangiulli, Marina; Boria, Ilenia; Mignone, Flavio; Merla, Giuseppe; D’Angelo, Vincenzo; Tullo, Apollonia; Sbisà, Elisabetta; D’Erchia, Anna Maria; Pesole, Graziano

doi:10.1186/1476-4598-9-230

Cited by 7 publications

(6 citation statements)

References 45 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Pre-mRNAs of many essential human genes such as glutamate receptor subunits 1–4 (GluR1–4) and voltage-gated sodium channels (SCN genes) undergo mutually exclusive splicing ( 67 , 68 ). MXE clusters often have tissue- and developmental stage-specific expression ( 28 ), and mutations in them have been linked to hereditary diseases ( 69–72 ) and cancer ( 73 , 74 ).…”

Section: Discussionmentioning

confidence: 99%

Multiple competing RNA structures dynamically control alternative splicing in the human ATE1 gene

Kalinina

Skvortsov

Kalmykova

et al. 2020

Nucleic Acids Research

View full text Add to dashboard Cite

The mammalian Ate1 gene encodes an arginyl transferase enzyme with tumor suppressor function that depends on the inclusion of one of the two mutually exclusive exons (MXE), exons 7a and 7b. We report that the molecular mechanism underlying MXE splicing in Ate1 involves five conserved regulatory intronic elements R1–R5, of which R1 and R4 compete for base pairing with R3, while R2 and R5 form an ultra-long-range RNA structure spanning 30 Kb. In minigenes, single and double mutations that disrupt base pairings in R1R3 and R3R4 lead to the loss of MXE splicing, while compensatory triple mutations that restore RNA structure revert splicing to that of the wild type. In the endogenous Ate1 pre-mRNA, blocking the competing base pairings by LNA/DNA mixmers complementary to R3 leads to the loss of MXE splicing, while the disruption of R2R5 interaction changes the ratio of MXE. That is, Ate1 splicing is controlled by two independent, dynamically interacting, and functionally distinct RNA structure modules. Exon 7a becomes more included in response to RNA Pol II slowdown, however it fails to do so when the ultra-long-range R2R5 interaction is disrupted, indicating that exon 7a/7b ratio depends on co-transcriptional RNA folding. In sum, these results demonstrate that splicing is coordinated both in time and in space over very long distances, and that the interaction of these components is mediated by RNA structure.

show abstract

Section: Discussionmentioning

confidence: 99%

Multiple competing RNA structures dynamically control alternative splicing in the human ATE1 gene

Kalinina

Skvortsov

Kalmykova

et al. 2020

Nucleic Acids Research

View full text Add to dashboard Cite

show abstract

“…Pre-mRNAs of many essential human genes such as glutamate receptor subunits 1-4 (GluR1-4) and voltage-gated sodium channels (SCN genes) undergo mutually exclusive splicing (48,49). MXE clusters often have tissue-and developmental stage-specific expression (28), and mutations in them have been linked to hereditary diseases (50)(51)(52)(53) and cancer (54,55).…”

Section: Discussionmentioning

confidence: 99%

Multiple competing RNA structures dynamically control alternative splicing in human ATE1 gene

Kalinina

Skvortsov

Kalmykova

et al. 2020

Preprint

View full text Add to dashboard Cite

The mammalian Ate1 gene encodes an arginyl transferase enzyme, which is essential for embryogenesis, male meiosis, and regulation of the cytoskeleton. Reduced levels of Ate1 are associated with malignant transformations and serve as a prognostic indicator of prostate cancer metastasis. The tumor suppressor function of Ate1 depends on the inclusion of one of the two mutually exclusive exons (MXE), exons 7a and 7b. Here, we report that the molecular mechanism underlying MXE splicing in Ate1 involves five conserved regulatory intronic elements R1-R5, of which R1 and R4 compete for base pairing with R3, while R2 and R5 form an ultra-long-range RNA structure spanning 30 Kb. In minigenes, single and double mutations that disrupt base pairings in R1R3 and R3R4 lead to the loss of MXE splicing, while compensatory triple mutations that restore the RNA structure also revert splicing to that of the wild type. Blocking the competing base pairings by locked nucleic acid (LNA)/DNA mixmers complementary to R3 leads to the loss of MXE splicing, while the disruption of the ultra-longrange R2R5 interaction changes the ratio of mutually exclusive isoforms in the endogenous Ate1 pre-mRNA. The upstream exon 7a becomes more included than the downstream exon 7b in response to RNA Pol II slowdown, however it fails to do so when the ultra-long-range R2R5 interaction is disrupted. In sum, we demonstrated that mutually exclusive splicing in Ate1 is controlled by two independent, dynamically interacting and functionally distinct RNA structure modules. The molecular mechanism proposed here opens new horizons for the development of therapeutic solutions, including antisense correction of splicing.

show abstract

“…Pre-mRNAs of many essential human genes such as glutamate receptor subunits 1-4 (GluR1-4) and voltage-gated sodium channels (SCN genes) undergo mutually exclusive splicing (67,68). MXE clusters often have tissue-and developmental stage-specific expression (28), and mutations in them have been linked to hereditary diseases (69-72) and cancer (73,74).…”

Section: Discussionmentioning

confidence: 99%

Multiple competing RNA structures dynamically control alternative splicing in human ATE1 gene

Pervouchine¹

2020

Preprint

View full text Add to dashboard Cite

The mammalian Ate1 gene encodes an arginyl transferase enzyme with tumor suppressor function that depends on the inclusion of one of the two mutually exclusive exons (MXE), exons 7a and 7b. We report that the molecular mechanism underlying MXE splicing in Ate1 involves five conserved regulatory intronic elements R1-R5, of which R1 and R4 compete for base pairing with R3, while R2 and R5 form an ultra-long-range RNA structure spanning 30 Kb. In minigenes, single and double mutations that disrupt base pairings in R1R3 and R3R4 lead to the loss of MXE splicing, while compensatory triple mutations that restore RNA structure revert splicing to that of the wild type. In the endogenous Ate1 pre-mRNA, blocking the competing base pairings by LNA/DNA mixmers complementary to R3 leads to the loss of MXE splicing, while the disruption of R2R5 interaction changes the ratio of MXE. That is, Ate1 splicing is controlled by two independent, dynamically interacting, and functionally distinct RNA structure modules. Exon 7a becomes more included in response to RNA Pol II slowdown, however it fails to do so when the ultra-long-range R2R5 interaction is disrupted, indicating that exon 7a/7b ratio depends on co-transcriptional RNA folding. In sum, these results demonstrate that splicing is coordinated both in time and in space over very long distances, and that the interaction of these components is mediated by RNA structure.

show abstract

Identification of tumor-associated cassette exons in human cancer through EST-based computational prediction and experimental validation

Cited by 7 publications

References 45 publications

Multiple competing RNA structures dynamically control alternative splicing in the human ATE1 gene

Multiple competing RNA structures dynamically control alternative splicing in the human ATE1 gene

Multiple competing RNA structures dynamically control alternative splicing in human ATE1 gene

Multiple competing RNA structures dynamically control alternative splicing in human ATE1 gene

Contact Info

Product

Resources

About