Nucleotides in both donor and acceptor splice sites are
responsible for choice in NAGNAG tandem splice sites

J 2021

Nucleotides in both donor and acceptor splice sites are responsible for choice in NAGNAG tandem splice sites

HUJOVÁ, Pavla; Přemysl SOUČEK; Lenka RADOVÁ; Michal KRAMAREK; Tatiana KOVÁČOVÁ et al.

Basic information

Original name

Nucleotides in both donor and acceptor splice sites are responsible for choice in NAGNAG tandem splice sites

Authors

HUJOVÁ, Pavla; Přemysl SOUČEK; Lenka RADOVÁ; Michal KRAMAREK; Tatiana KOVÁČOVÁ and Tomáš FREIBERGER

Edition

Cellular and molecular life sciences, BASEL, SPRINGER BASEL AG, 2021, 1420-682X

Other information

Language

English

Type of outcome

Article in a journal

Field of Study

10608 Biochemistry and molecular biology

Country of publisher

Switzerland

Confidentiality degree

is not subject to a state or trade secret

References:

URL

Impact factor

Impact factor: 9.234

Marked to be transferred to RIV

Yes

RIV identification code

RIV/00216224:14110/21:00123981

Organization unit

Faculty of Medicine

Keywords in English

RNA splicing; Alternative splicing; Splicing isoform; NAG choice

Abstract

In the original language

Among alternative splicing events in the human transcriptome, tandem NAGNAG acceptor splice sites represent an appreciable proportion. Both proximal and distal NAG can be used to produce two splicing isoforms differing by three nucleotides. In some cases, the upstream exon can be alternatively spliced as well, which further increases the number of possible transcripts. In this study, we showed that NAG choice in tandem splice site depends considerably not only on the concerned acceptor, but also on the upstream donor splice site sequence. Using an extensive set of experiments with systematically modified two-exonic minigene systems of AFAP1L2 or CSTD gene, we recognized the third and fifth intronic upstream donor splice site position and the tandem acceptor splice site region spanning from -10 to +2, including NAGNAG itself, as the main drivers. In addition, competition between different branch points and their composition were also shown to play a significant role in NAG choice. All these nucleotide effects appeared almost additive, which explained the high variability in proximal versus distal NAG usage.

Links

MUNI/A/1099/2019, interní kód MU

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

Investor: Masaryk University, Category A

MUNI/A/1412/2020, interní kód MU

Name: Patogenetický význam nespecifické imunity u některých poruch imunitního systému (Acronym: Nespecifická imunita)

Investor: Masaryk University

Cite

HUJOVÁ, Pavla; Přemysl SOUČEK; Lenka RADOVÁ; Michal KRAMAREK; Tatiana KOVÁČOVÁ and Tomáš FREIBERGER. Nucleotides in both donor and acceptor splice sites are responsible for choice in NAGNAG tandem splice sites. Cellular and molecular life sciences. BASEL: SPRINGER BASEL AG, 2021, vol. 78, 21-22, p. 6979-6993. ISSN 1420-682X. Available from: https://doi.org/10.1007/s00018-021-03943-2.

@article{1828124,
   author = {Hujová, Pavla and Souček, Přemysl and Radová, Lenka and Kramarek, Michal and Kováčová, Tatiana and Freiberger, Tomáš},
   article_location = {BASEL},
   article_number = {21-22},
   doi = {https://doi.org/10.1007/s00018-021-03943-2},
   keywords = {RNA splicing; Alternative splicing; Splicing isoform; NAG choice},
   language = {eng},
   issn = {1420-682X},
   journal = {Cellular and molecular life sciences},
   title = {Nucleotides in both donor and acceptor splice sites are responsible for choice in NAGNAG tandem splice sites},
   url = {https://link.springer.com/article/10.1007%2Fs00018-021-03943-2},
   volume = {78},
   year = {2021}
}

TY  - JOUR
ID  - 1828124
AU  - Hujová, Pavla - Souček, Přemysl - Radová, Lenka - Kramarek, Michal - Kováčová, Tatiana - Freiberger, Tomáš
PY  - 2021
TI  - Nucleotides in both donor and acceptor splice sites are responsible for choice in NAGNAG tandem splice sites
JF  - Cellular and molecular life sciences
VL  - 78
IS  - 21-22
SP  - 6979-6993
EP  - 6979-6993
PB  - SPRINGER BASEL AG
SN  - 1420682X
KW  - RNA splicing
KW  - Alternative splicing
KW  - Splicing isoform
KW  - NAG choice
UR  - https://link.springer.com/article/10.1007%2Fs00018-021-03943-2
N2  - Among alternative splicing events in the human transcriptome, tandem NAGNAG acceptor splice sites represent an appreciable proportion. Both proximal and distal NAG can be used to produce two splicing isoforms differing by three nucleotides. In some cases, the upstream exon can be alternatively spliced as well, which further increases the number of possible transcripts. In this study, we showed that NAG choice in tandem splice site depends considerably not only on the concerned acceptor, but also on the upstream donor splice site sequence. Using an extensive set of experiments with systematically modified two-exonic minigene systems of AFAP1L2 or CSTD gene, we recognized the third and fifth intronic upstream donor splice site position and the tandem acceptor splice site region spanning from -10 to +2, including NAGNAG itself, as the main drivers. In addition, competition between different branch points and their composition were also shown to play a significant role in NAG choice. All these nucleotide effects appeared almost additive, which explained the high variability in proximal versus distal NAG usage.
ER  -

HUJOVÁ, Pavla; Přemysl SOUČEK; Lenka RADOVÁ; Michal KRAMAREK; Tatiana KOVÁČOVÁ and Tomáš FREIBERGER. Nucleotides in both donor and acceptor splice sites are responsible for choice in NAGNAG tandem splice sites. \textit{Cellular and molecular life sciences}. BASEL: SPRINGER BASEL AG, 2021, vol.~78, 21-22, p.~6979-6993. ISSN~1420-682X. Available from: https://doi.org/10.1007/s00018-021-03943-2.

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