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PUF60-activated exons uncover altered 3′ splice-site selection by germline missense mutations in a single RRM

PUF60 is a splicing factor that binds uridine (U)-rich tracts and facilitates association of the U2 small nuclear ribonucleoprotein with primary transcripts. PUF60 deficiency (PD) causes a developmental delay coupled with intellectual disability and spinal, cardiac, ocular and renal defects, but PD...

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Autores principales: Královičová, Jana, Ševčíková, Ivana, Stejskalová, Eva, Obuća, Mina, Hiller, Michael, Staněk, David, Vořechovský, Igor
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Oxford University Press 2018
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6093180/
https://www.ncbi.nlm.nih.gov/pubmed/29788428
http://dx.doi.org/10.1093/nar/gky389
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author Královičová, Jana
Ševčíková, Ivana
Stejskalová, Eva
Obuća, Mina
Hiller, Michael
Staněk, David
Vořechovský, Igor
author_facet Královičová, Jana
Ševčíková, Ivana
Stejskalová, Eva
Obuća, Mina
Hiller, Michael
Staněk, David
Vořechovský, Igor
author_sort Královičová, Jana
collection PubMed
description PUF60 is a splicing factor that binds uridine (U)-rich tracts and facilitates association of the U2 small nuclear ribonucleoprotein with primary transcripts. PUF60 deficiency (PD) causes a developmental delay coupled with intellectual disability and spinal, cardiac, ocular and renal defects, but PD pathogenesis is not understood. Using RNA-Seq, we identify human PUF60-regulated exons and show that PUF60 preferentially acts as their activator. PUF60-activated internal exons are enriched for Us upstream of their 3′ splice sites (3′ss), are preceded by longer AG dinucleotide exclusion zones and more distant branch sites, with a higher probability of unpaired interactions across a typical branch site location as compared to control exons. In contrast, PUF60-repressed exons show U-depletion with lower estimates of RNA single-strandedness. We also describe PUF60-regulated, alternatively spliced isoforms encoding other U-bound splicing factors, including PUF60 partners, suggesting that they are co-regulated in the cell, and identify PUF60-regulated exons derived from transposed elements. PD-associated amino-acid substitutions, even within a single RNA recognition motif (RRM), altered selection of competing 3′ss and branch points of a PUF60-dependent exon and the 3′ss choice was also influenced by alternative splicing of PUF60. Finally, we propose that differential distribution of RNA processing steps detected in cells lacking PUF60 and the PUF60-paralog RBM39 is due to the RBM39 RS domain interactions. Together, these results provide new insights into regulation of exon usage by the 3′ss organization and reveal that germline mutation heterogeneity in RRMs can enhance phenotypic variability at the level of splice-site and branch-site selection.
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spelling pubmed-60931802018-08-22 PUF60-activated exons uncover altered 3′ splice-site selection by germline missense mutations in a single RRM Královičová, Jana Ševčíková, Ivana Stejskalová, Eva Obuća, Mina Hiller, Michael Staněk, David Vořechovský, Igor Nucleic Acids Res Genomics PUF60 is a splicing factor that binds uridine (U)-rich tracts and facilitates association of the U2 small nuclear ribonucleoprotein with primary transcripts. PUF60 deficiency (PD) causes a developmental delay coupled with intellectual disability and spinal, cardiac, ocular and renal defects, but PD pathogenesis is not understood. Using RNA-Seq, we identify human PUF60-regulated exons and show that PUF60 preferentially acts as their activator. PUF60-activated internal exons are enriched for Us upstream of their 3′ splice sites (3′ss), are preceded by longer AG dinucleotide exclusion zones and more distant branch sites, with a higher probability of unpaired interactions across a typical branch site location as compared to control exons. In contrast, PUF60-repressed exons show U-depletion with lower estimates of RNA single-strandedness. We also describe PUF60-regulated, alternatively spliced isoforms encoding other U-bound splicing factors, including PUF60 partners, suggesting that they are co-regulated in the cell, and identify PUF60-regulated exons derived from transposed elements. PD-associated amino-acid substitutions, even within a single RNA recognition motif (RRM), altered selection of competing 3′ss and branch points of a PUF60-dependent exon and the 3′ss choice was also influenced by alternative splicing of PUF60. Finally, we propose that differential distribution of RNA processing steps detected in cells lacking PUF60 and the PUF60-paralog RBM39 is due to the RBM39 RS domain interactions. Together, these results provide new insights into regulation of exon usage by the 3′ss organization and reveal that germline mutation heterogeneity in RRMs can enhance phenotypic variability at the level of splice-site and branch-site selection. Oxford University Press 2018-07-06 2018-05-18 /pmc/articles/PMC6093180/ /pubmed/29788428 http://dx.doi.org/10.1093/nar/gky389 Text en © The Author(s) 2018. Published by Oxford University Press on behalf of Nucleic Acids Research. http://creativecommons.org/licenses/by/4.0/ This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Genomics
Královičová, Jana
Ševčíková, Ivana
Stejskalová, Eva
Obuća, Mina
Hiller, Michael
Staněk, David
Vořechovský, Igor
PUF60-activated exons uncover altered 3′ splice-site selection by germline missense mutations in a single RRM
title PUF60-activated exons uncover altered 3′ splice-site selection by germline missense mutations in a single RRM
title_full PUF60-activated exons uncover altered 3′ splice-site selection by germline missense mutations in a single RRM
title_fullStr PUF60-activated exons uncover altered 3′ splice-site selection by germline missense mutations in a single RRM
title_full_unstemmed PUF60-activated exons uncover altered 3′ splice-site selection by germline missense mutations in a single RRM
title_short PUF60-activated exons uncover altered 3′ splice-site selection by germline missense mutations in a single RRM
title_sort puf60-activated exons uncover altered 3′ splice-site selection by germline missense mutations in a single rrm
topic Genomics
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6093180/
https://www.ncbi.nlm.nih.gov/pubmed/29788428
http://dx.doi.org/10.1093/nar/gky389
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