Animal, Fungi, and Plant Genome Sequences Harbor Different Non-Canonical Splice Sites
Most protein-encoding genes in eukaryotes contain introns, which are interwoven with exons. Introns need to be removed from initial transcripts in order to generate the final messenger RNA (mRNA), which can be translated into an amino acid sequence. Precise excision of introns by the spliceosome req...
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| Format: | Article |
| Language: | English |
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MDPI AG
2020-02-01
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| Series: | Cells |
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| Online Access: | https://www.mdpi.com/2073-4409/9/2/458 |
| _version_ | 1797761822260985856 |
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| author | Katharina Frey Boas Pucker |
| author_facet | Katharina Frey Boas Pucker |
| author_sort | Katharina Frey |
| collection | DOAJ |
| description | Most protein-encoding genes in eukaryotes contain introns, which are interwoven with exons. Introns need to be removed from initial transcripts in order to generate the final messenger RNA (mRNA), which can be translated into an amino acid sequence. Precise excision of introns by the spliceosome requires conserved dinucleotides, which mark the splice sites. However, there are variations of the highly conserved combination of GT at the 5′ end and AG at the 3′ end of an intron in the genome. GC-AG and AT-AC are two major non-canonical splice site combinations, which have been known for years. Recently, various minor non-canonical splice site combinations were detected with numerous dinucleotide permutations. Here, we expand systematic investigations of non-canonical splice site combinations in plants across eukaryotes by analyzing fungal and animal genome sequences. Comparisons of splice site combinations between these three kingdoms revealed several differences, such as an apparently increased CT-AC frequency in fungal genome sequences. Canonical GT-AG splice site combinations in antisense transcripts are a likely explanation for this observation, thus indicating annotation errors. In addition, high numbers of GA-AG splice site combinations were observed in <i>Eurytemora</i> <i>affinis</i> and <i>Oikopleura</i> <i>dioica</i>. A variant in one U1 small nuclear RNA (snRNA) isoform might allow the recognition of GA as a 5′ splice site. In depth investigation of splice site usage based on RNA-Seq read mappings indicates a generally higher flexibility of the 3′ splice site compared to the 5′ splice site across animals, fungi, and plants. |
| first_indexed | 2024-03-12T19:19:34Z |
| format | Article |
| id | doaj.art-1142d3f30ba842c9802f933255261e63 |
| institution | Directory Open Access Journal |
| issn | 2073-4409 |
| language | English |
| last_indexed | 2024-03-12T19:19:34Z |
| publishDate | 2020-02-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Cells |
| spelling | doaj.art-1142d3f30ba842c9802f933255261e632023-08-02T05:16:51ZengMDPI AGCells2073-44092020-02-019245810.3390/cells9020458cells9020458Animal, Fungi, and Plant Genome Sequences Harbor Different Non-Canonical Splice SitesKatharina Frey0Boas Pucker1Genetics and Genomics of Plants, Center for Biotechnology (CeBiTec), Bielefeld University, 33615 Bielefeld, GermanyGenetics and Genomics of Plants, Center for Biotechnology (CeBiTec), Bielefeld University, 33615 Bielefeld, GermanyMost protein-encoding genes in eukaryotes contain introns, which are interwoven with exons. Introns need to be removed from initial transcripts in order to generate the final messenger RNA (mRNA), which can be translated into an amino acid sequence. Precise excision of introns by the spliceosome requires conserved dinucleotides, which mark the splice sites. However, there are variations of the highly conserved combination of GT at the 5′ end and AG at the 3′ end of an intron in the genome. GC-AG and AT-AC are two major non-canonical splice site combinations, which have been known for years. Recently, various minor non-canonical splice site combinations were detected with numerous dinucleotide permutations. Here, we expand systematic investigations of non-canonical splice site combinations in plants across eukaryotes by analyzing fungal and animal genome sequences. Comparisons of splice site combinations between these three kingdoms revealed several differences, such as an apparently increased CT-AC frequency in fungal genome sequences. Canonical GT-AG splice site combinations in antisense transcripts are a likely explanation for this observation, thus indicating annotation errors. In addition, high numbers of GA-AG splice site combinations were observed in <i>Eurytemora</i> <i>affinis</i> and <i>Oikopleura</i> <i>dioica</i>. A variant in one U1 small nuclear RNA (snRNA) isoform might allow the recognition of GA as a 5′ splice site. In depth investigation of splice site usage based on RNA-Seq read mappings indicates a generally higher flexibility of the 3′ splice site compared to the 5′ splice site across animals, fungi, and plants.https://www.mdpi.com/2073-4409/9/2/458splicingspliceosomerna-seqgene structuremrna processingintronssequence conservationsplice site analysis pipeline |
| spellingShingle | Katharina Frey Boas Pucker Animal, Fungi, and Plant Genome Sequences Harbor Different Non-Canonical Splice Sites Cells splicing spliceosome rna-seq gene structure mrna processing introns sequence conservation splice site analysis pipeline |
| title | Animal, Fungi, and Plant Genome Sequences Harbor Different Non-Canonical Splice Sites |
| title_full | Animal, Fungi, and Plant Genome Sequences Harbor Different Non-Canonical Splice Sites |
| title_fullStr | Animal, Fungi, and Plant Genome Sequences Harbor Different Non-Canonical Splice Sites |
| title_full_unstemmed | Animal, Fungi, and Plant Genome Sequences Harbor Different Non-Canonical Splice Sites |
| title_short | Animal, Fungi, and Plant Genome Sequences Harbor Different Non-Canonical Splice Sites |
| title_sort | animal fungi and plant genome sequences harbor different non canonical splice sites |
| topic | splicing spliceosome rna-seq gene structure mrna processing introns sequence conservation splice site analysis pipeline |
| url | https://www.mdpi.com/2073-4409/9/2/458 |
| work_keys_str_mv | AT katharinafrey animalfungiandplantgenomesequencesharbordifferentnoncanonicalsplicesites AT boaspucker animalfungiandplantgenomesequencesharbordifferentnoncanonicalsplicesites |