Toward predicting self-splicing and protein-facilitated splicing of group I introns

Vicens, Quentin; Paukstelis, Paul J.; Westhof, Eric; Lambowitz, Alan M.; Cech, Thomas R.

doi:10.1261/rna.1027208

Cited by 49RNA Research and SplicingRNA and protein synthesis mechanismsRNA regulation and disease

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Toward predicting self-splicing and protein-facilitated splicing of group I introns

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Vicens, Quentin, Paukstelis, Paul J., Westhof, Eric, Lambowitz, Alan M., Cech, Thomas R.·2008·RNA

DOI 10.1261/rna.1027208PMC PMC2553746

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Abstract

In the current era of massive discoveries of noncoding RNAs within genomes, being able to infer a function from a nucleotide sequence is of paramount interest. Although studies of individual group I introns have identified self-splicing and nonself-splicing examples, there is no overall understanding of the prevalence of self-splicing or the factors that determine it among the >2300 group I introns sequenced to date. Here, the self-splicing activities of 12 group I introns from various organisms were assayed under six reaction conditions that had been shown previously to promote RNA catalysis for different RNAs. Besides revealing that assessing self-splicing under only one condition can be misleading, this survey emphasizes that in vitro self-splicing efficiency is correlated with the GC content of the intron (>35% GC was generally conductive to self-splicing), and with the ability of the introns to form particular tertiary interactions. Addition of the Neurospora crassa CYT-18 protein activated splicing of two nonself-splicing introns, but inhibited the second step of self-splicing for two others. Together, correlations between sequence, predicted structure and splicing begin to establish rules that should facilitate our ability to predict the self-splicing activity of any group I intron from its sequence.

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Native group I introns have an average intervening region between the 5′ and 3′ splice sites of 300-500 nucleotides.
“Indeed, the intervening region between the 5′ and 3′ splice sites of native group I introns is on average 300–500 nucleotides long22, while the intervening region of the engineered RNA that we constructed was two to four-fold longer.”
From Engineering circular RNA for potent and stable translation in eukaryotic cells (2018) · cites this paper as [22]
The Results section reports that 12 group I introns tested were 183–421 nucleotides long, and Intron selection gives a range of 183–496 nucleotides for introns requested. Neither passage establishes a 300–500-nucleotide average for native group I introns generally. (LLM, conf=0.82)
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Authors: Vicens, Q., Paukstelis, P. J., Westhof, E., Lambowitz, A. M., & Cech, T. R.
Affiliations: Howard Hughes Medical Institute (US)
The University of Texas at Austin (US)
ORCID: Vicens, Quentin
Paukstelis, Paul J.
Lambowitz, Alan M.
Cech, Thomas R.
Venue: RNA
Publisher: Cold Spring Harbor Laboratory
Published: 2008-09-03
Volume: 14
Issue: 10
Pages: 2013-2029
ISSN: 1355-8382 (ISSN-L)
1469-9001
DOI: 10.1261/rna.1027208
PMC: PMC2553746
OpenAlex: W2110018116
Cited by: 49
References: 86
Citations by year: 2026: 2 · 2025: 2 · 2024: 5 · 2023: 3 · 2022: 2 · 2021: 2 · 2018: 5 · 2017: 2 · 2014: 4 · 2013: 4 · 2012: 4
FWCI: 1.92
Type: journal article
Language: en
Open access: bronze
doi.org
Locations: RNA (publishedVersion)
Europe PMC (PubMed Central) (publishedVersion)
PubMed Central (publishedVersion)
PubMed (publishedVersion)
CU Scholar (University of Colorado Boulder) (submittedVersion)
HAL (submittedVersion)
HighWire Press Open Archive (submittedVersion)
Funders: Howard Hughes Medical Institute
National Institutes of Health (GM037951)
National Institute of General Medical Sciences (R37GM037951, R01GM037951, GM037951)
Topics: Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA Research and Splicing
Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA and protein synthesis mechanisms
Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA regulation and disease
Keywords: group I introns, self-splicing, GC content, tertiary interactions, Neurospora crassa, RNA catalysis, sequence-structure-function relationships
MeSH terms: Base Composition, Base Sequence, Catalysis, Introns, Neurospora crassa, Nucleic Acid Conformation, RNA Splicing, RNA, Messenger, Tyrosine-tRNA Ligase, RNA, Catalytic

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Toward predicting self-splicing and protein-facilitated splicing of group I introns

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