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Bakhtiar D, Vondraskova K, Pengelly RJ, Chivers M, Kralovicova J, Vorechovsky I. Exonic splicing code and coordination of divalent metals in proteins. Nucleic Acids Res 2024; 52:1090-1106. [PMID: 38055834 PMCID: PMC10853796 DOI: 10.1093/nar/gkad1161] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2023] [Revised: 11/15/2023] [Accepted: 11/17/2023] [Indexed: 12/08/2023] Open
Abstract
Exonic sequences contain both protein-coding and RNA splicing information but the interplay of the protein and splicing code is complex and poorly understood. Here, we have studied traditional and auxiliary splicing codes of human exons that encode residues coordinating two essential divalent metals at the opposite ends of the Irving-Williams series, a universal order of relative stabilities of metal-organic complexes. We show that exons encoding Zn2+-coordinating amino acids are supported much less by the auxiliary splicing motifs than exons coordinating Ca2+. The handicap of the former is compensated by stronger splice sites and uridine-richer polypyrimidine tracts, except for position -3 relative to 3' splice junctions. However, both Ca2+ and Zn2+ exons exhibit close-to-constitutive splicing in multiple tissues, consistent with their critical importance for metalloprotein function and a relatively small fraction of expendable, alternatively spliced exons. These results indicate that constraints imposed by metal coordination spheres on RNA splicing have been efficiently overcome by the plasticity of exon-intron architecture to ensure adequate metalloprotein expression.
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Affiliation(s)
- Dara Bakhtiar
- University of Southampton, Faculty of Medicine, Southampton SO16 6YD, UK
| | - Katarina Vondraskova
- Slovak Academy of Sciences, Centre of Biosciences, 840 05 Bratislava, Slovak Republic
| | - Reuben J Pengelly
- University of Southampton, Faculty of Medicine, Southampton SO16 6YD, UK
| | - Martin Chivers
- University of Southampton, Faculty of Medicine, Southampton SO16 6YD, UK
| | - Jana Kralovicova
- University of Southampton, Faculty of Medicine, Southampton SO16 6YD, UK
- Slovak Academy of Sciences, Centre of Biosciences, 840 05 Bratislava, Slovak Republic
| | - Igor Vorechovsky
- University of Southampton, Faculty of Medicine, Southampton SO16 6YD, UK
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2
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Beckel MS, Kaufman B, Yanovsky M, Chernomoretz A. Conserved and divergent signals in 5' splice site sequences across fungi, metazoa and plants. PLoS Comput Biol 2023; 19:e1011540. [PMID: 37831726 PMCID: PMC10599564 DOI: 10.1371/journal.pcbi.1011540] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2022] [Revised: 10/25/2023] [Accepted: 09/25/2023] [Indexed: 10/15/2023] Open
Abstract
In eukaryotic organisms the ensemble of 5' splice site sequences reflects the balance between natural nucleotide variability and minimal molecular constraints necessary to ensure splicing fidelity. This compromise shapes the underlying statistical patterns in the composition of donor splice site sequences. The scope of this study was to mine conserved and divergent signals in the composition of 5' splice site sequences. Because 5' donor sequences are a major cue for proper recognition of splice sites, we reasoned that statistical regularities in their composition could reflect the biological functionality and evolutionary history associated with splicing mechanisms. Results: We considered a regularized maximum entropy modeling framework to mine for non-trivial two-site correlations in donor sequence datasets corresponding to 30 different eukaryotes. For each analyzed species, we identified minimal sets of two-site coupling patterns that were able to replicate, at a given regularization level, the observed one-site and two-site frequencies in donor sequences. By performing a systematic and comparative analysis of 5'splice sites we showed that lineage information could be traced from joint di-nucleotide probabilities. We were able to identify characteristic two-site coupling patterns for plants and animals, and propose that they may echo differences in splicing regulation previously reported between these groups.
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Affiliation(s)
- Maximiliano S. Beckel
- Fundación Instituto Leloir, Buenos Aires, Argentina
- Instituto de Investigaciones Bioquímicas de Buenos Aires, Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
| | - Bruno Kaufman
- Fundación Instituto Leloir, Buenos Aires, Argentina
- Instituto de Investigaciones Bioquímicas de Buenos Aires, Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
| | - Marcelo Yanovsky
- Fundación Instituto Leloir, Buenos Aires, Argentina
- Instituto de Investigaciones Bioquímicas de Buenos Aires, Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
| | - Ariel Chernomoretz
- Fundación Instituto Leloir, Buenos Aires, Argentina
- Departamento de Física, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Instituto de Física Interdisciplinaria y Aplicada (INFINA), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
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3
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Fernandez-Castillo E, Barbosa-Santillán LI, Falcon-Morales L, Sánchez-Escobar JJ. Deep Splicer: A CNN Model for Splice Site Prediction in Genetic Sequences. Genes (Basel) 2022; 13:907. [PMID: 35627292 PMCID: PMC9141016 DOI: 10.3390/genes13050907] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Revised: 05/12/2022] [Accepted: 05/13/2022] [Indexed: 02/05/2023] Open
Abstract
Many living organisms have DNA in their cells that is responsible for their biological features. DNA is an organic molecule of two complementary strands of four different nucleotides wound up in a double helix. These nucleotides are adenine (A), thymine (T), guanine (G), and cytosine (C). Genes are DNA sequences containing the information to synthesize proteins. The genes of higher eukaryotic organisms contain coding sequences, known as exons and non-coding sequences, known as introns, which are removed on splice sites after the DNA is transcribed into RNA. Genome annotation is the process of identifying the location of coding regions and determining their function. This process is fundamental for understanding gene structure; however, it is time-consuming and expensive when done by biochemical methods. With technological advances, splice site detection can be done computationally. Although various software tools have been developed to predict splice sites, they need to improve accuracy and reduce false-positive rates. The main goal of this research was to generate Deep Splicer, a deep learning model to identify splice sites in the genomes of humans and other species. This model has good performance metrics and a lower false-positive rate than the currently existing tools. Deep Splicer achieved an accuracy between 93.55% and 99.66% on the genetic sequences of different organisms, while Splice2Deep, another splice site detection tool, had an accuracy between 90.52% and 98.08%. Splice2Deep surpassed Deep Splicer on the accuracy obtained after evaluating C. elegans genomic sequences (97.88% vs. 93.62%) and A. thaliana (95.40% vs. 94.93%); however, Deep Splicer's accuracy was better for H. sapiens (98.94% vs. 97.15%) and D. melanogaster (97.14% vs. 92.30%). The rate of false positives was 0.11% for human genetic sequences and 0.25% for other species' genetic sequences. Another splice prediction tool, Splice Finder, had between 1% and 3% of false positives for human sequences, while other species' sequences had around 4% and 10%.
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Affiliation(s)
- Elisa Fernandez-Castillo
- School of Engineering and Sciences, Monterrey Institute of Technology and Higher Education, Guadalajara 45201, Mexico; (L.I.B.-S.); (L.F.-M.)
| | - Liliana Ibeth Barbosa-Santillán
- School of Engineering and Sciences, Monterrey Institute of Technology and Higher Education, Guadalajara 45201, Mexico; (L.I.B.-S.); (L.F.-M.)
| | - Luis Falcon-Morales
- School of Engineering and Sciences, Monterrey Institute of Technology and Higher Education, Guadalajara 45201, Mexico; (L.I.B.-S.); (L.F.-M.)
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Jin B, Zhao Y, Dong Y, Liu P, Sun Y, Li X, Zhang X, Chen XG, Gu J. Alternative splicing patterns of doublesex reveal a missing link between Nix and doublesex in the sex determination cascade of Aedes albopictus. INSECT SCIENCE 2021; 28:1601-1620. [PMID: 33179439 DOI: 10.1111/1744-7917.12886] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/08/2020] [Revised: 10/26/2020] [Accepted: 10/28/2020] [Indexed: 05/06/2023]
Abstract
Sexual development in insects is regulated by a complicated hierarchical cascade of sex determination. The primary signals are diverse, whereas the central nexus doublesex (dsx) gene is relatively conserved within the pathway. Aedes (Stegomyia) albopictus is an important vector with an extensive worldwide distribution. We previously reported that Ae. albopictus dsx (Aalbdsx) yields one male- (AalbdsxM ) and three female-specific isoforms (AalbdsxF1-3 ); however, the spatiotemporal expression profiles and mechanisms regulating sex-specific alternative splicing require further investigation. In this study, we demonstrated that the AalbdsxM messenger RNA (mRNA) represents the default pattern when analyzed in human foreskin fibroblasts and HeLa cells. We combined reverse transcription polymerase chain reaction with RNA immunoprecipitation using specific antibodies against tagged Ae. albopictus male-determining factor AalNix and confirmed that AalNix indirectly regulates dsx pre-mRNA and regulates its alternative splicing. During the early embryo stage (0-2 and 4-8 h), maternal dsxF and default splicing dsxM were detected in both sexes; the expression of dsxM then decreased until sufficient AalNix transcripts accumulated in male embryos at 20-24 h. These findings suggest that one or more potential dsx splicing enhancers can shift dsxM to dsxF in both sexes; however, the presence of Nix influences the function of this unknown splicing enhancer and ultimately leads to the formation of dsxM in males. Finally, our results provide important insight into the regulatory mechanism of dsx alternative splicing in the mosquito.
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Affiliation(s)
- Binbin Jin
- Department of Pathogen Biology, Guangdong Provincial Key Laboratory of Tropical Disease Research, School of Public Health, Southern Medical University, Guangzhou, 510515, China
| | - Yijie Zhao
- Department of Pathogen Biology, Guangdong Provincial Key Laboratory of Tropical Disease Research, School of Public Health, Southern Medical University, Guangzhou, 510515, China
| | - Yunqiao Dong
- Reproductive Medical Centre of Guangdong Women and Children Hospital, Guangzhou, 511442, China
| | - Peiwen Liu
- Department of Pathogen Biology, Guangdong Provincial Key Laboratory of Tropical Disease Research, School of Public Health, Southern Medical University, Guangzhou, 510515, China
| | - Yan Sun
- Department of Pathogen Biology, Guangdong Provincial Key Laboratory of Tropical Disease Research, School of Public Health, Southern Medical University, Guangzhou, 510515, China
| | - Xiaocong Li
- Department of Pathogen Biology, Guangdong Provincial Key Laboratory of Tropical Disease Research, School of Public Health, Southern Medical University, Guangzhou, 510515, China
| | - Xin Zhang
- Department of Pathogen Biology, Guangdong Provincial Key Laboratory of Tropical Disease Research, School of Public Health, Southern Medical University, Guangzhou, 510515, China
| | - Xiao-Guang Chen
- Department of Pathogen Biology, Guangdong Provincial Key Laboratory of Tropical Disease Research, School of Public Health, Southern Medical University, Guangzhou, 510515, China
| | - Jinbao Gu
- Department of Pathogen Biology, Guangdong Provincial Key Laboratory of Tropical Disease Research, School of Public Health, Southern Medical University, Guangzhou, 510515, China
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Berkay EG, Elkanova L, Kalaycı T, Uludağ Alkaya D, Altunoğlu U, Cefle K, Mıhçı E, Nur B, Taşdelen E, Bayramoğlu Z, Karaman V, Toksoy G, Güneş N, Öztürk Ş, Palandüz Ş, Kayserili H, Tüysüz B, Uyguner ZO. Skeletal and molecular findings in 51 Cleidocranial dysplasia patients from Turkey. Am J Med Genet A 2021; 185:2488-2495. [PMID: 33987976 DOI: 10.1002/ajmg.a.62261] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2020] [Revised: 04/04/2021] [Accepted: 04/22/2021] [Indexed: 11/07/2022]
Abstract
Loss or decrease of function in runt-related transcription factor 2 encoded by RUNX2 is known to cause a rare autosomal-dominant skeletal disorder, cleidocranial dysplasia (CCD). Clinical spectrum and genetic findings in 51 CCD patients from 30 unrelated families are herein presented. In a majority of the patients, facial abnormalities, such as delayed fontanel closure (89%), parietal and frontal bossing (80%), metopic groove (77%), midface hypoplasia (94%), and abnormal mobility of shoulders (90%), were recorded following clinical examination. In approximately one-half of the subjects, wormian bone (51%), short stature (43%), bell-shaped thorax (42%), wide pubic symphysis (50%), hypoplastic iliac wing (59%), and chef's hat sign (44%) presented in available radiological examinations. Scoliosis was identified in 28% of the patients. Investigation of RUNX2 revealed small sequence alterations in 90% and gross deletions in 10% of the patients; collectively, 23 variants including 11 novel changes (c.29_30insT, c.203delAinsCG, c.423 + 2delT, c.443_454delTACCAGATGGGAinsG, c.505C > T, c.594_595delCTinsG, c.636_637insC, c.685 + 5G > A, c.1088G > T, c.1281delC, Exon 6-9 deletion) presented high allelic heterogeneity. Novel c.29_30insT is unique in affecting the P1-driven long isoform of RUNX2, which is expected to disrupt the N-terminal region of RUNX2; this was shown in two unrelated phenotypically discordant patients. The clinical findings highlighted mild intra-familial genotype-phenotype correlation in our CCD cohort.
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Affiliation(s)
- Ezgi Gizem Berkay
- Department of Medical Genetics, Istanbul Medical Faculty, Istanbul University, Istanbul, Turkey
| | - Leyla Elkanova
- Department of Pediatric Genetics, Istanbul University-Cerrahpasa, Cerrahpasa Medical School, Istanbul, Turkey
| | - Tuğba Kalaycı
- Division of Medical Genetics, Department of Internal Medicine, Istanbul Medical Faculty, Istanbul University, Istanbul, Turkey
| | - Dilek Uludağ Alkaya
- Department of Pediatric Genetics, Istanbul University-Cerrahpasa, Cerrahpasa Medical School, Istanbul, Turkey
| | - Umut Altunoğlu
- Department of Medical Genetics, Istanbul Medical Faculty, Istanbul University, Istanbul, Turkey.,Medical Genetics Department, Koç University School of Medicine (KUSoM), Istanbul, Turkey
| | - Kıvanç Cefle
- Division of Medical Genetics, Department of Internal Medicine, Istanbul Medical Faculty, Istanbul University, Istanbul, Turkey
| | - Ercan Mıhçı
- Division of Medical Genetics, Department of Pediatrics, Akdeniz University Medical School, Antalya, Turkey
| | - Banu Nur
- Division of Medical Genetics, Department of Pediatrics, Akdeniz University Medical School, Antalya, Turkey
| | - Elifcan Taşdelen
- Department of Medical Genetics, School of Medicine, Ankara University, Ankara, Turkey
| | - Zuhal Bayramoğlu
- Department of Radiology, Istanbul Medical Faculty, Istanbul University, Istanbul, Turkey
| | - Volkan Karaman
- Department of Medical Genetics, Istanbul Medical Faculty, Istanbul University, Istanbul, Turkey
| | - Güven Toksoy
- Department of Medical Genetics, Istanbul Medical Faculty, Istanbul University, Istanbul, Turkey
| | - Nilay Güneş
- Department of Pediatric Genetics, Istanbul University-Cerrahpasa, Cerrahpasa Medical School, Istanbul, Turkey
| | - Şükrü Öztürk
- Division of Medical Genetics, Department of Internal Medicine, Istanbul Medical Faculty, Istanbul University, Istanbul, Turkey
| | - Şükrü Palandüz
- Division of Medical Genetics, Department of Internal Medicine, Istanbul Medical Faculty, Istanbul University, Istanbul, Turkey
| | - Hülya Kayserili
- Department of Medical Genetics, Istanbul Medical Faculty, Istanbul University, Istanbul, Turkey.,Medical Genetics Department, Koç University School of Medicine (KUSoM), Istanbul, Turkey
| | - Beyhan Tüysüz
- Department of Pediatric Genetics, Istanbul University-Cerrahpasa, Cerrahpasa Medical School, Istanbul, Turkey
| | - Zehra Oya Uyguner
- Department of Medical Genetics, Istanbul Medical Faculty, Istanbul University, Istanbul, Turkey
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An extended catalogue of tandem alternative splice sites in human tissue transcriptomes. PLoS Comput Biol 2021; 17:e1008329. [PMID: 33826604 PMCID: PMC8055015 DOI: 10.1371/journal.pcbi.1008329] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2020] [Revised: 04/19/2021] [Accepted: 03/22/2021] [Indexed: 12/18/2022] Open
Abstract
Tandem alternative splice sites (TASS) is a special class of alternative splicing events that are characterized by a close tandem arrangement of splice sites. Most TASS lack functional characterization and are believed to arise from splicing noise. Based on the RNA-seq data from the Genotype Tissue Expression project, we present an extended catalogue of TASS in healthy human tissues and analyze their tissue-specific expression. The expression of TASS is usually dominated by one major splice site (maSS), while the expression of minor splice sites (miSS) is at least an order of magnitude lower. Among 46k miSS with sufficient read support, 9k (20%) are significantly expressed above the expected noise level, and among them 2.5k are expressed tissue-specifically. We found significant correlations between tissue-specific expression of RNA-binding proteins (RBP), tissue-specific expression of miSS, and miSS response to RBP inactivation by shRNA. In combination with RBP profiling by eCLIP, this allowed prediction of novel cases of tissue-specific splicing regulation including a miSS in QKI mRNA that is likely regulated by PTBP1. The analysis of human primary cell transcriptomes suggested that both tissue-specific and cell-type-specific factors contribute to the regulation of miSS expression. More than 20% of tissue-specific miSS affect structured protein regions and may adjust protein-protein interactions or modify the stability of the protein core. The significantly expressed miSS evolve under the same selection pressure as maSS, while other miSS lack signatures of evolutionary selection and conservation. Using mixture models, we estimated that not more than 15% of maSS and not more than 54% of tissue-specific miSS are noisy, while the proportion of noisy splice sites among non-significantly expressed miSS is above 63%. Pre-mRNA splicing is an important step in the processing of the genomic information during gene expression. During splicing, introns are excised from a gene transcript, and the remaining exons are ligated. Our work concerns one its particular subtype, which involves the so-called tandem alternative splice sites, a group of closely located exon borders that are used alternatively. We analyzed RNA-seq measurements of gene expression provided by the Genotype-Tissue Expression (GTEx) project, the largest to-date collection of such measurements in healthy human tissues, and constructed a detailed catalogue of tandem alternative splice sites. Within this catalogue, we characterized patterns of tissue-specific expression, regulation, impact on protein structure, and evolutionary selection acting on tandem alternative splice sites. In a number of genes, we predicted regulatory mechanisms that could be responsible for choosing one of many tandem alternative splice sites. The results of this study provide an invaluable resource for molecular biologists studying alternative splicing.
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Górski AZ, Piwowar M. Nucleotide spacing distribution analysis for human genome. Mamm Genome 2021; 32:123-128. [PMID: 33723659 PMCID: PMC8012312 DOI: 10.1007/s00335-021-09865-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Accepted: 03/02/2021] [Indexed: 11/30/2022]
Abstract
The distribution of nucleotides spacing in human genome was investigated. An analysis of the frequency of occurrence in the human genome of different sequence lengths flanked by one type of nucleotide was carried out showing that the distribution has no self-similar (fractal) structure. The results nevertheless revealed several characteristic features: (i) the distribution for short-range spacing is quite similar to the purely stochastic sequences; (ii) the distribution for long-range spacing essentially deviates from the random sequence distribution, showing strong long-range correlations; (iii) the differences between (A, T) and (C, G) nucleotides are quite significant; (iv) the spacing distribution displays tiny oscillations.
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Affiliation(s)
- Andrzej Z Górski
- Polish Academy of Sciences, Institute of Nuclear Physics, Radzikowskiego 152 st, 31-342, Kraków, Poland
| | - Monika Piwowar
- Jagiellonian University, Collegium Medicum, Kopernika 7E st, 31-034, Kraków, Poland.
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