J 2019

High-throughput analysis revealed mutations' diverging effects on SMN1 exon 7 splicing

SOUČEK, Přemysl, Kamila RÉBLOVÁ, Michal KRAMÁREK, Lenka RADOVÁ, Tereza GRYMOVÁ et. al.

Basic information

Original name

High-throughput analysis revealed mutations' diverging effects on SMN1 exon 7 splicing

Authors

SOUČEK, Přemysl (203 Czech Republic, belonging to the institution), Kamila RÉBLOVÁ (203 Czech Republic, belonging to the institution), Michal KRAMÁREK (703 Slovakia), Lenka RADOVÁ (203 Czech Republic, belonging to the institution), Tereza GRYMOVÁ (203 Czech Republic), Pavla HUJOVÁ (203 Czech Republic), Tatiana KOVÁČOVÁ (703 Slovakia, belonging to the institution), Matej LEXA (703 Slovakia, belonging to the institution), Lucie GRODECKÁ (203 Czech Republic) and Tomáš FREIBERGER (203 Czech Republic, belonging to the institution)

Edition

RNA BIOLOGY, PHILADELPHIA, TAYLOR & FRANCIS INC, 2019, 1547-6286

Other information

Language

English

Type of outcome

Článek v odborném periodiku

Field of Study

10608 Biochemistry and molecular biology

Country of publisher

United States of America

Confidentiality degree

není předmětem státního či obchodního tajemství

References:

Impact factor

Impact factor: 5.350

RIV identification code

RIV/00216224:14740/19:00107593

Organization unit

Central European Institute of Technology

DOI

UT WoS

000472379600001

Keywords in English

SMN1; cryptic splice sites; U1 snRNA; splicing-affecting mutation; 5 ' ss

Tags

Tags

International impact, Reviewed
Změněno: 15/10/2024 09:10, Ing. Martina Blahová

Abstract

V originále

Splicing-affecting mutations can disrupt gene function by altering the transcript assembly. To ascertain splicing dysregulation principles, we modified a minigene assay for the parallel high-throughput evaluation of different mutations by next-generation sequencing. In our model system, all exonic and six intronic positions of the SMN1 gene's exon 7 were mutated to all possible nucleotide variants, which amounted to 180 unique single-nucleotide mutants and 470 double mutants. The mutations resulted in a wide range of splicing aberrations. Exonic splicing-affecting mutations resulted either in substantial exon skipping, supposedly driven by predicted exonic splicing silencer or cryptic donor splice site (5 ' ss) and de novo 5 ' ss strengthening and use. On the other hand, a single disruption of exonic splicing enhancer was not sufficient to cause major exon skipping, suggesting these elements can be substituted during exon recognition. While disrupting the acceptor splice site led only to exon skipping, some 5 ' ss mutations potentiated the use of three different cryptic 5 ' ss. Generally, single mutations supporting cryptic 5 ' ss use displayed better pre-mRNA/U1 snRNA duplex stability and increased splicing regulatory element strength across the original 5 ' ss. Analyzing double mutants supported the predominating splicing regulatory elements' effect, but U1 snRNA binding could contribute to the global balance of splicing isoforms. Based on these findings, we suggest that creating a new splicing enhancer across the mutated 5 ' ss can be one of the main factors driving cryptic 5 ' ss use.

Links

GA16-11619S, research and development project
Name: Základní vlastnosti DNA mutačních coldspotů/hotspotů v genech asociovaných s dědičnými chorobami
Investor: Czech Science Foundation
MUNI/A/1298/2018, interní kód MU
Name: Vrozené a získané deficience imunitního systému (Acronym: Poruchy imunity)
Investor: Masaryk University, Category A
NV16-34414A, research and development project
Name: Určení genových oblastí náchylných ke vzniku mutací ovlivňujících sestřih mRNA
90091, large research infrastructures
Name: NCMG