Genome-wide analyses supported by RNA-Seq reveal non-canonical splice sites in plant genomes
Pucker B, Brockington SF (2018)
BMC Genomics 19(1): 980.
Zeitschriftenaufsatz
| Veröffentlicht | Englisch
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Autor*in
Pucker, BoasUniBi
;
Brockington, Samuel F.
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Einrichtung
Abstract / Bemerkung
Background:
Most eukaryotic genes comprise exons and introns thus requiring the precise removal of introns from pre-mRNAs to enable protein biosynthesis. U2 and U12 spliceosomes catalyze this step by recognizing motifs on the transcript in order to remove the introns. A process which is dependent on precise definition of exon-intron borders by splice sites, which are consequently highly conserved across species. Only very few combinations of terminal dinucleotides are frequently observed at intron ends, dominated by the canonical GT-AG splice sites on the DNA level.
Results:
Here we investigate the occurrence of diverse combinations of dinucleotides at predicted splice sites. Analyzing 121 plant genome sequences based on their an notation revealed strong splice site conservation across species, annotation errors, and true biological divergence from canonical splice sites. The frequency of non-canonical splice sites clearly correlates with their divergence from canonical ones indicating either an accumulation of probably neutral mutations, or evolution towards canonical splice sites. Strong conservation across multiple species and non-random accumulation of substitutions in splice sites indicate a functional relevance of non-canonical splice sites. The average composition of splice sites across all investigated species is 98.7% for GT-AG, 1.2% for GC-AG, 0.06% for AT-AC, and 0.09% for minor non-canonical splice sites. RNA-Seq data sets of 35 species were incorporated to validate non-canonical splice site predictions through gaps in sequencing reads alignments and to demonstrate the expression of affected genes.
Conclusion:
We conclude that bona fide non-canonical splice sites are present and appear to be functionally relevantinmostplantgenomes, although at low abundance.
Erscheinungsjahr
2018
Zeitschriftentitel
BMC Genomics
Band
19
Ausgabe
1
Art.-Nr.
980
Urheberrecht / Lizenzen
ISSN
1471-2164
eISSN
1471-2164
Finanzierungs-Informationen
Open-Access-Publikationskosten wurden durch die Deutsche Forschungsgemeinschaft und die Universität Bielefeld gefördert.
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https://pub.uni-bielefeld.de/record/2932870
Zitieren
Pucker B, Brockington SF. Genome-wide analyses supported by RNA-Seq reveal non-canonical splice sites in plant genomes. BMC Genomics. 2018;19(1): 980.
Pucker, B., & Brockington, S. F. (2018). Genome-wide analyses supported by RNA-Seq reveal non-canonical splice sites in plant genomes. BMC Genomics, 19(1), 980. doi:10.1186/s12864-018-5360-z
Pucker, Boas, and Brockington, Samuel F. 2018. “Genome-wide analyses supported by RNA-Seq reveal non-canonical splice sites in plant genomes”. BMC Genomics 19 (1): 980.
Pucker, B., and Brockington, S. F. (2018). Genome-wide analyses supported by RNA-Seq reveal non-canonical splice sites in plant genomes. BMC Genomics 19:980.
Pucker, B., & Brockington, S.F., 2018. Genome-wide analyses supported by RNA-Seq reveal non-canonical splice sites in plant genomes. BMC Genomics, 19(1): 980.
B. Pucker and S.F. Brockington, “Genome-wide analyses supported by RNA-Seq reveal non-canonical splice sites in plant genomes”, BMC Genomics, vol. 19, 2018, : 980.
Pucker, B., Brockington, S.F.: Genome-wide analyses supported by RNA-Seq reveal non-canonical splice sites in plant genomes. BMC Genomics. 19, : 980 (2018).
Pucker, Boas, and Brockington, Samuel F. “Genome-wide analyses supported by RNA-Seq reveal non-canonical splice sites in plant genomes”. BMC Genomics 19.1 (2018): 980.
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1001 Genomes Consortium. Electronic address: magnus.nordborg@gmi.oeaw.ac.at; 1001 Genomes Consortium, Alonso-Blanco C, Andrade J, Becker C, Bemm F, Bergelson J, Borgwardt KM, Cao J, Chae E, Dezwaan TM, Ding W, Ecker JR, Exposito-Alonso M, Farlow A, Fitz J, Gan X, Grimm DG, Hancock AM, Henz SR, Holm S, Horton M, Jarsulic M, Kerstetter RA, Korte A, Korte P, Lanz C, Lee CR, Meng D, Michael TP, Mott R, Muliyati NW, Nagele T, Nagler M, Nizhynska V, Nordborg M, Novikova PY, Pico FX, Platzer A, Rabanal FA, Rodriguez A, Rowan BA, Salome PA, Schmid KJ, Schmitz RJ, Seren U, Sperone FG, Sudkamp M, Svardal H, Tanzer MM, Todd D, Volchenboum SL, Wang C, Wang G, Wang X, Weckwerth W, Weigel D, Zhou X., Cell 166(2), 2016
PMID: 27293186
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Muir P, Li S, Lou S, Wang D, Spakowicz DJ, Salichos L, Zhang J, Weinstock GM, Isaacs F, Rozowsky J, Gerstein M., Genome Biol. 17(), 2016
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Muir P, Li S, Lou S, Wang D, Spakowicz DJ, Salichos L, Zhang J, Weinstock GM, Isaacs F, Rozowsky J, Gerstein M., Genome Biol. 17(), 2016
PMID: 27009100
AUTHOR UNKNOWN, 0
AUTHOR UNKNOWN, 0
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Goodall GJ, Filipowicz W., EMBO J. 10(9), 1991
PMID: 1868837
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De novo Nd-1 genome assembly reveals genomic diversity of Arabidopsis thaliana and facilitates genome-wide non-canonical splice site analysis across plant species
Pucker B (2019)
Bielefeld: Universität Bielefeld.
Pucker B (2019)
Bielefeld: Universität Bielefeld.
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PMID: 30594132
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Preprint: 10.1101/428318
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