Splicing Enhancers at Intron-Exon Borders Participate in
Acceptor Splice Sites Recognition

J 2020

Splicing Enhancers at Intron-Exon Borders Participate in Acceptor Splice Sites Recognition

KOVÁČOVÁ, Tatiana, Přemysl SOUČEK, Pavla HUJOVÁ, Tomáš FREIBERGER, Lucie GRODECKÁ et. al.

Basic information

Original name

Splicing Enhancers at Intron-Exon Borders Participate in Acceptor Splice Sites Recognition

Authors

KOVÁČOVÁ, Tatiana (703 Slovakia, belonging to the institution), Přemysl SOUČEK (203 Czech Republic, belonging to the institution), Pavla HUJOVÁ (203 Czech Republic, belonging to the institution), Tomáš FREIBERGER (203 Czech Republic, belonging to the institution) and Lucie GRODECKÁ (203 Czech Republic, guarantor)

Edition

International Journal of Molecular Sciences, Basel, Multidisciplinary Digital Publishing Institute, 2020, 1422-0067

Other information

Language

English

Type of outcome

Článek v odborném periodiku

Field of Study

10608 Biochemistry and molecular biology

Country of publisher

Switzerland

Confidentiality degree

není předmětem státního či obchodního tajemství

References:

URL

Impact factor

Impact factor: 5.923

RIV identification code

RIV/00216224:14110/20:00116880

Organization unit

Faculty of Medicine

DOI

http://dx.doi.org/10.3390/ijms21186553

UT WoS

000581229300001

Keywords in English

pre-mRNA splicing; splicing enhancer; U2AF35; acceptor splice site recognition; SRSF1

Abstract

V originále

Acceptor splice site recognition (3 ' splice site: 3 ' ss) is a fundamental step in precursor messenger RNA (pre-mRNA) splicing. Generally, the U2 small nuclear ribonucleoprotein (snRNP) auxiliary factor (U2AF) heterodimer recognizes the 3 ' ss, of which U2AF35 has a dual function: (i) It binds to the intron-exon border of some 3 ' ss and (ii) mediates enhancer-binding splicing activators' interactions with the spliceosome. Alternative mechanisms for 3 ' ss recognition have been suggested, yet they are still not thoroughly understood. Here, we analyzed 3 ' ss recognition where the intron-exon border is bound by a ubiquitous splicing regulator SRSF1. Using the minigene analysis of two model exons and their mutants, BRCA2 exon 12 and VARS2 exon 17, we showed that the exon inclusion correlated much better with the predicted SRSF1 affinity than 3 ' ss quality, which were assessed using the Catalog of Inferred Sequence Binding Preferences of RNA binding proteins (CISBP-RNA) database and maximum entropy algorithm (MaxEnt) predictor and the U2AF35 consensus matrix, respectively. RNA affinity purification proved SRSF1 binding to the model 3 ' ss. On the other hand, knockdown experiments revealed that U2AF35 also plays a role in these exons' inclusion. Most probably, both factors stochastically bind the 3 ' ss, supporting exon recognition, more apparently in VARS2 exon 17. Identifying splicing activators as 3 ' ss recognition factors is crucial for both a basic understanding of splicing regulation and human genetic diagnostics when assessing variants' effects on splicing.

Links

MUNI/A/1099/2019, interní kód MU

Name: Faktory nespecifické imunity u některých imunopatologických stavů (Acronym: nespecif. imunita)

Investor: Masaryk University, Category A

Citovat

KOVÁČOVÁ, Tatiana, Přemysl SOUČEK, Pavla HUJOVÁ, Tomáš FREIBERGER and Lucie GRODECKÁ. Splicing Enhancers at Intron-Exon Borders Participate in Acceptor Splice Sites Recognition. International Journal of Molecular Sciences. Basel: Multidisciplinary Digital Publishing Institute, 2020, vol. 21, No 18, p. 1-18. ISSN 1422-0067. Available from: https://dx.doi.org/10.3390/ijms21186553.

@article{1690936,
   author = {Kováčová, Tatiana and Souček, Přemysl and Hujová, Pavla and Freiberger, Tomáš and Grodecká, Lucie},
   article_location = {Basel},
   article_number = {18},
   doi = {http://dx.doi.org/10.3390/ijms21186553},
   keywords = {pre-mRNA splicing; splicing enhancer; U2AF35; acceptor splice site recognition; SRSF1},
   language = {eng},
   issn = {1422-0067},
   journal = {International Journal of Molecular Sciences},
   title = {Splicing Enhancers at Intron-Exon Borders Participate in Acceptor Splice Sites Recognition},
   url = {https://www.mdpi.com/1422-0067/21/18/6553},
   volume = {21},
   year = {2020}
}

TY  - JOUR
ID  - 1690936
AU  - Kováčová, Tatiana - Souček, Přemysl - Hujová, Pavla - Freiberger, Tomáš - Grodecká, Lucie
PY  - 2020
TI  - Splicing Enhancers at Intron-Exon Borders Participate in Acceptor Splice Sites Recognition
JF  - International Journal of Molecular Sciences
VL  - 21
IS  - 18
SP  - 1-18
EP  - 1-18
PB  - Multidisciplinary Digital Publishing Institute
SN  - 14220067
KW  - pre-mRNA splicing
KW  - splicing enhancer
KW  - U2AF35
KW  - acceptor splice site recognition
KW  - SRSF1
UR  - https://www.mdpi.com/1422-0067/21/18/6553
L2  - https://www.mdpi.com/1422-0067/21/18/6553
N2  - Acceptor splice site recognition (3 ' splice site: 3 ' ss) is a fundamental step in precursor messenger RNA (pre-mRNA) splicing. Generally, the U2 small nuclear ribonucleoprotein (snRNP) auxiliary factor (U2AF) heterodimer recognizes the 3 ' ss, of which U2AF35 has a dual function: (i) It binds to the intron-exon border of some 3 ' ss and (ii) mediates enhancer-binding splicing activators' interactions with the spliceosome. Alternative mechanisms for 3 ' ss recognition have been suggested, yet they are still not thoroughly understood. Here, we analyzed 3 ' ss recognition where the intron-exon border is bound by a ubiquitous splicing regulator SRSF1. Using the minigene analysis of two model exons and their mutants, BRCA2 exon 12 and VARS2 exon 17, we showed that the exon inclusion correlated much better with the predicted SRSF1 affinity than 3 ' ss quality, which were assessed using the Catalog of Inferred Sequence Binding Preferences of RNA binding proteins (CISBP-RNA) database and maximum entropy algorithm (MaxEnt) predictor and the U2AF35 consensus matrix, respectively. RNA affinity purification proved SRSF1 binding to the model 3 ' ss. On the other hand, knockdown experiments revealed that U2AF35 also plays a role in these exons' inclusion. Most probably, both factors stochastically bind the 3 ' ss, supporting exon recognition, more apparently in VARS2 exon 17. Identifying splicing activators as 3 ' ss recognition factors is crucial for both a basic understanding of splicing regulation and human genetic diagnostics when assessing variants' effects on splicing.
ER  -

KOVÁČOVÁ, Tatiana, Přemysl SOUČEK, Pavla HUJOVÁ, Tomáš FREIBERGER and Lucie GRODECKÁ. Splicing Enhancers at Intron-Exon Borders Participate in Acceptor Splice Sites Recognition. \textit{International Journal of Molecular Sciences}. Basel: Multidisciplinary Digital Publishing Institute, 2020, vol.~21, No~18, p.~1-18. ISSN~1422-0067. Available from: https://dx.doi.org/10.3390/ijms21186553.

Detailed Information on Publication Record