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Peeters S, Declerck K, Thomas M, Boudin E, Beckers D, Chivu O, Heinrichs C, Devriendt K, de Zegher F, Van Hul W, Vanden Berghe W, De Schepper J, Rooman R, Mortier G. DNA Methylation Profiling and Genomic Analysis in 20 Children with Short Stature Who Were Born Small for Gestational Age. J Clin Endocrinol Metab 2020; 105:5873625. [PMID: 32685970 DOI: 10.1210/clinem/dgaa465] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/30/2020] [Accepted: 07/15/2020] [Indexed: 12/30/2022]
Abstract
PURPOSE In a significant proportion of children born small for gestational age (SGA) with failure of catch-up growth, the etiology of short stature remains unclear after routine diagnostic workup. We wanted to investigate if extensive analysis of the (epi)genome can unravel the cause of growth failure in a significant portion of these children. PATIENTS AND METHODS Twenty SGA children treated with GH because of short stature were selected from the BELGROW database of the Belgian Society for Pediatric Endocrinology and Diabetology for exome sequencing, single-nucleotide polymorphism (SNP) array and genome-wide methylation analysis to identify the (epi)genetic cause. First-year response to GH was compared with the response of SGA patients in the KIGS database. RESULTS We identified (likely) pathogenic variants in 4 children (from 3 families) using exome sequencing and found pathogenic copy number variants in 2 probands using SNP array. In a child harboring a NSD1-containing microduplication, we identified a DNA methylation signature that is opposite to the genome-wide DNA methylation signature of Sotos syndrome. Moreover, we observed multilocus imprinting disturbances in 2 children in whom no other genomic alteration could be identified. Five of 6 children with a genetic diagnosis had an "above average" response to GH. CONCLUSIONS The study indicates that a more advanced approach with deep genotyping can unravel unexpected (epi)genomic alterations in SGA children with persistent growth failure. Most SGA children with a genetic diagnosis had a good response to GH treatment.
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Affiliation(s)
- Silke Peeters
- Department of Medical Genetics, University of Antwerp and Antwerp University Hospital, Antwerp, Belgium
| | - Ken Declerck
- Laboratory of Protein Chemistry, Proteomics and Epigenetic Signalling (PPES), Department of Biomedical Sciences, University of Antwerp, Antwerp, Belgium
| | - Muriel Thomas
- Belgian Society for Pediatric Endocrinology and Diabetology, Brussels, Belgium
| | - Eveline Boudin
- Department of Medical Genetics, University of Antwerp and Antwerp University Hospital, Antwerp, Belgium
| | - Dominique Beckers
- Unité d'Endocrinologie Pédiatrique, CHU Namur, Université catholique de Louvain, Yvoir, Belgium and Department of Pediatrics, University Hospital Leuven, Leuven, Belgium
| | - Olimpia Chivu
- Department of Pediatrics, Clinique de l'Espérance, Saint-Nicolas, Belgium
| | - Claudine Heinrichs
- Paediatric Endocrinology Unit, Hôpital Universitaire des Enfants Reine Fabiola (HUDERF), Brussels, Belgium
| | - Koenraad Devriendt
- Center for Human Genetics, University of Leuven and the University Hospital Leuven, Leuven, Belgium
| | - Francis de Zegher
- Department of Development & Regeneration, University of Leuven, Leuven, Belgium
| | - Wim Van Hul
- Department of Medical Genetics, University of Antwerp and Antwerp University Hospital, Antwerp, Belgium
| | - Wim Vanden Berghe
- Laboratory of Protein Chemistry, Proteomics and Epigenetic Signalling (PPES), Department of Biomedical Sciences, University of Antwerp, Antwerp, Belgium
| | - Jean De Schepper
- Department of Pediatrics, Vrije Universiteit Brussel, Universitair Ziekenhuis Brussel, Brussels, Belgium and Department of Pediatrics, Universitair Ziekenhuis Gent, Ghent, Belgium
| | | | - Geert Mortier
- Department of Medical Genetics, University of Antwerp and Antwerp University Hospital, Antwerp, Belgium
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Sequence and Evolutionary Features for the Alternatively Spliced Exons of Eukaryotic Genes. Int J Mol Sci 2019; 20:ijms20153834. [PMID: 31390737 PMCID: PMC6695735 DOI: 10.3390/ijms20153834] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2019] [Revised: 07/25/2019] [Accepted: 07/31/2019] [Indexed: 12/22/2022] Open
Abstract
Alternative splicing of pre-mRNAs is a crucial mechanism for maintaining protein diversity in eukaryotes without requiring a considerable increase of genes in the number. Due to rapid advances in high-throughput sequencing technologies and computational algorithms, it is anticipated that alternative splicing events will be more intensively studied to address different kinds of biological questions. The occurrences of alternative splicing mean that all exons could be classified to be either constitutively or alternatively spliced depending on whether they are virtually included into all mature mRNAs. From an evolutionary point of view, therefore, the alternatively spliced exons would have been associated with distinctive biological characteristics in comparison with constitutively spliced exons. In this paper, we first outline the representative types of alternative splicing events and exon classification, and then review sequence and evolutionary features for the alternatively spliced exons. The main purpose is to facilitate understanding of the biological implications of alternative splicing in eukaryotes. This knowledge is also helpful to establish computational approaches for predicting the splicing pattern of exons.
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Zou Y, Shao X, Dong D. Inferring the determinants of protein evolutionary rates in mammals. Gene 2016; 584:161-6. [PMID: 26899866 DOI: 10.1016/j.gene.2016.02.021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2015] [Revised: 01/15/2016] [Accepted: 02/15/2016] [Indexed: 11/25/2022]
Abstract
Understanding the determinants of protein evolutionary rates is one of the most fundamental evolutionary questions. Previous studies have revealed that many biological variables are tightly associated with protein evolutionary rates in mammals. However, the dominant role of these biological variables and their combinatorial effects to evolutionary rates of mammalian proteins are still less understood. In this work, we derived a quantitative model to correlate protein evolutionary rates with the levels of these variables. The result showed that only a small number of variables are necessary to accurately predict protein evolutionary rates, among which miRNA regulation plays the most important role. Our result suggested that biological variables are extensively interrelated and suffer from hidden redundancies in determining protein evolutionary rates. Various variables should be considered in a natural ensemble to comprehensively assess the determinants of protein evolutionary rate.
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Affiliation(s)
- Yang Zou
- Laboratory of Molecular Ecology and Evolution, Institute of Estuarine and Coastal Research, East China Normal University, Shanghai 200062, China
| | - Xiaojian Shao
- Department of Human Genetics, McGill University, 740 Dr. Penfield Avenue, H3A 0G1 Montreal, Quebec, Canada
| | - Dong Dong
- Laboratory of Molecular Ecology and Evolution, Institute of Estuarine and Coastal Research, East China Normal University, Shanghai 200062, China.
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Acharya D, Ghosh TC. Global analysis of human duplicated genes reveals the relative importance of whole-genome duplicates originated in the early vertebrate evolution. BMC Genomics 2016; 17:71. [PMID: 26801093 PMCID: PMC4724117 DOI: 10.1186/s12864-016-2392-0] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2015] [Accepted: 01/13/2016] [Indexed: 12/13/2022] Open
Abstract
Background Gene duplication is a genetic mutation that creates functionally redundant gene copies that are initially relieved from selective pressures and may adapt themselves to new functions with time. The levels of gene duplication may vary from small-scale duplication (SSD) to whole genome duplication (WGD). Studies with yeast revealed ample differences between these duplicates: Yeast WGD pairs were functionally more similar, less divergent in subcellular localization and contained a lesser proportion of essential genes. In this study, we explored the differences in evolutionary genomic properties of human SSD and WGD genes, with the identifiable human duplicates coming from the two rounds of whole genome duplication occurred early in vertebrate evolution. Results We observed that these two groups of duplicates were also dissimilar in terms of their evolutionary and genomic properties. But interestingly, this is not like the same observed in yeast. The human WGDs were found to be functionally less similar, diverge more in subcellular level and contain a higher proportion of essential genes than the SSDs, all of which are opposite from yeast. Additionally, we explored that human WGDs were more divergent in their gene expression profile, have higher multifunctionality and are more often associated with disease, and are evolutionarily more conserved than human SSDs. Conclusions Our study suggests that human WGD duplicates are more divergent and entails the adaptation of WGDs to novel and important functions that consequently lead to their evolutionary conservation in the course of evolution. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-2392-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Debarun Acharya
- Bioinformatics Centre, Bose Institute, P 1/12, C.I.T. Scheme VII M, Kolkata, 700054, West Bengal, India
| | - Tapash C Ghosh
- Bioinformatics Centre, Bose Institute, P 1/12, C.I.T. Scheme VII M, Kolkata, 700054, West Bengal, India.
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Abstract
The rate and mechanism of protein sequence evolution have been central questions in evolutionary biology since the 1960s. Although the rate of protein sequence evolution depends primarily on the level of functional constraint, exactly what determines functional constraint has remained unclear. The increasing availability of genomic data has enabled much needed empirical examinations on the nature of functional constraint. These studies found that the evolutionary rate of a protein is predominantly influenced by its expression level rather than functional importance. A combination of theoretical and empirical analyses has identified multiple mechanisms behind these observations and demonstrated a prominent role in protein evolution of selection against errors in molecular and cellular processes.
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Affiliation(s)
- Jianzhi Zhang
- Department of Ecology and Evolutionary Biology, University of Michigan, 830 North University Avenue, Ann Arbor, Michigan 48109, USA
| | - Jian-Rong Yang
- Department of Ecology and Evolutionary Biology, University of Michigan, 830 North University Avenue, Ann Arbor, Michigan 48109, USA
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Chuang TJ, Yang MY, Lin CC, Hsieh PH, Hung LY. Comparative genomics of grass EST libraries reveals previously uncharacterized splicing events in crop plants. BMC PLANT BIOLOGY 2015; 15:39. [PMID: 25652661 PMCID: PMC4323234 DOI: 10.1186/s12870-015-0431-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/04/2014] [Accepted: 01/20/2015] [Indexed: 06/04/2023]
Abstract
BACKGROUND Crop plants such as rice, maize and sorghum play economically-important roles as main sources of food, fuel, and animal feed. However, current genome annotations of crop plants still suffer false-positive predictions; a more comprehensive registry of alternative splicing (AS) events is also in demand. Comparative genomics of crop plants is largely unexplored. RESULTS We performed a large-scale comparative analysis (ExonFinder) of the expressed sequence tag (EST) library from nine grass plants against three crop genomes (rice, maize, and sorghum) and identified 2,879 previously-unannotated exons (i.e., novel exons) in the three crops. We validated 81% of the tested exons by RT-PCR-sequencing, supporting the effectiveness of our in silico strategy. Evolutionary analysis reveals that the novel exons, comparing with their flanking annotated ones, are generally under weaker selection pressure at the protein level, but under stronger pressure at the RNA level, suggesting that most of the novel exons also represent novel alternatively spliced variants (ASVs). However, we also observed the consistency of evolutionary rates between certain novel exons and their flanking exons, which provided further evidence of their co-occurrence in the transcripts, suggesting that previously-annotated isoforms might be subject to erroneous predictions. Our validation showed that 54% of the tested genes expressed the newly-identified isoforms that contained the novel exons, rather than the previously-annotated isoforms that excluded them. The consistent results were steadily observed across cultivated (Oryza sativa and O. glaberrima) and wild (O. rufipogon and O. nivara) rice species, asserting the necessity of our curation of the crop genome annotations. Our comparative analyses also inferred the common ancestral transcriptome of grass plants and gain- and loss-of-ASV events. CONCLUSIONS We have reannotated the rice, maize, and sorghum genomes, and showed that evolutionary rates might serve as an indicator for determining whether the identified exons were alternatively spliced. This study not only presents an effective in silico strategy for the improvement of plant annotations, but also provides further insights into the role of AS events in the evolution and domestication of crop plants. ExonFinder and the novel exons/ASVs identified are publicly accessible at http://exonfinder.sourceforge.net/ .
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Affiliation(s)
| | - Min-Yu Yang
- Genomics Research Center, Academia Sinica, Taipei, 11529, Taiwan.
| | - Chuang-Chieh Lin
- Genomics Research Center, Academia Sinica, Taipei, 11529, Taiwan.
| | - Ping-Hung Hsieh
- Genomics Research Center, Academia Sinica, Taipei, 11529, Taiwan.
| | - Li-Yuan Hung
- Genomics Research Center, Academia Sinica, Taipei, 11529, Taiwan.
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Lin PS, Chen FC, Kuo SF, Kung YH. Assessing the relationship of evolutionary rates and functional variables by mixture estimating equations. Stat Probab Lett 2014. [DOI: 10.1016/j.spl.2014.07.031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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Chen FC, Chuang TJ, Lin HY, Hsu MK. The evolution of the coding exome of the Arabidopsis species--the influences of DNA methylation, relative exon position, and exon length. BMC Evol Biol 2014; 14:145. [PMID: 24965500 PMCID: PMC4079183 DOI: 10.1186/1471-2148-14-145] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2014] [Accepted: 06/19/2014] [Indexed: 11/10/2022] Open
Abstract
Background The evolution of the coding exome is a major driving force of functional divergence both between species and between protein isoforms. Exons at different positions in the transcript or in different transcript isoforms may (1) mutate at different rates due to variations in DNA methylation level; and (2) serve distinct biological roles, and thus be differentially targeted by natural selection. Furthermore, intrinsic exonic features, such as exon length, may also affect the evolution of individual exons. Importantly, the evolutionary effects of these intrinsic/extrinsic features may differ significantly between animals and plants. Such inter-lineage differences, however, have not been systematically examined. Results Here we examine how DNA methylation at CpG dinucleotides (CpG methylation), in the context of intrinsic exonic features (exon length and relative exon position in the transcript), influences the evolution of coding exons of Arabidopsis thaliana. We observed fairly different evolutionary patterns in A. thaliana as compared with those reported for animals. Firstly, the mutagenic effect of CpG methylation is the strongest for internal exons and the weakest for first exons despite the stringent selective constraints on the former group. Secondly, the mutagenic effect of CpG methylation increases significantly with length in first exons but not in the other two exon groups. Thirdly, CpG methylation level is correlated with evolutionary rates (dS, dN, and the dN/dS ratio) with markedly different patterns among the three exon groups. The correlations are generally positive, negative, and mixed for first, last, and internal exons, respectively. Fourthly, exon length is a CpG methylation-independent indicator of evolutionary rates, particularly for dN and the dN/dS ratio in last and internal exons. Finally, the evolutionary patterns of coding exons with regard to CpG methylation differ significantly between Arabidopsis species and mammals. Conclusions Our results suggest that intrinsic features, including relative exonic position in the transcript and exon length, play an important role in the evolution of A. thaliana coding exons. Furthermore, CpG methylation is correlated with exonic evolutionary rates differentially between A. thaliana and animals, and may have served different biological roles in the two lineages.
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Affiliation(s)
- Feng-Chi Chen
- Institute of Population Health Sciences, National Health Research Institutes, Miaoli County, Taiwan.
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Choi SS, Hannenhalli S. Three independent determinants of protein evolutionary rate. J Mol Evol 2013; 76:98-111. [PMID: 23400388 DOI: 10.1007/s00239-013-9543-6] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2012] [Accepted: 01/16/2013] [Indexed: 12/15/2022]
Abstract
One of the most widely accepted ideas related to the evolutionary rates of proteins is that functionally important residues or regions evolve slower than other regions, a reasonable outcome of which should be a slower evolutionary rate of the proteins with a higher density of functionally important sites. Oddly, the role of functional importance, mainly measured by essentiality, in determining evolutionary rate has been challenged in recent studies. Several variables other than protein essentiality, such as expression level, gene compactness, protein-protein interactions, etc., have been suggested to affect protein evolutionary rate. In the present review, we try to refine the concept of functional importance of a gene, and consider three factors-functional importance, expression level, and gene compactness, as independent determinants of evolutionary rate of a protein, based not only on their known correlation with evolutionary rate but also on a reasonable mechanistic model. We suggest a framework based on these mechanistic models to correctly interpret the correlations between evolutionary rates and the various variables as well as the interrelationships among the variables.
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Affiliation(s)
- Sun Shim Choi
- Department of Medical Biotechnology, College of Biomedical Science, and Institute of Bioscience & Biotechnology, Kangwon National University, Chuncheon, South Korea.
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Gelly JC, Lin HY, de Brevern AG, Chuang TJ, Chen FC. Selective constraint on human pre-mRNA splicing by protein structural properties. Genome Biol Evol 2012; 4:966-75. [PMID: 22936073 PMCID: PMC3468958 DOI: 10.1093/gbe/evs071] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Alternative splicing (AS) is a major mechanism of increasing proteome diversity in complex organisms. Different AS transcript isoforms may be translated into peptide sequences of significantly different lengths and amino acid compositions. One important question, then, is how AS is constrained by protein structural requirements while peptide sequences may be significantly changed in AS events. Here, we address this issue by examining whether the intactness of three-dimensional protein structural units (compact units in protein structures, namely protein units [PUs]) tends to be preserved in AS events in human. We show that PUs tend to occur in constitutively spliced exons and to overlap constitutive exon boundaries. Furthermore, when PUs are located at the boundaries between two alternatively spliced exons (ASEs), these neighboring ASEs tend to co-occur in different transcript isoforms. In addition, such PU-spanned ASE pairs tend to have a higher frequency of being included in transcript isoforms. ASE regions that overlap with PUs also have lower nonsynonymous-to-synonymous substitution rate ratios than those that do not overlap with PUs, indicating stronger negative selection pressure in PU-overlapped ASE regions. Of note, we show that PUs have protein domain- and structural orderness-independent effects on messenger RNA (mRNA) splicing. Overall, our results suggest that fine-scale protein structural requirements have significant influences on the splicing patterns of human mRNAs.
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Affiliation(s)
- Jean-Christophe Gelly
- INSERM, UMR-S 665, Dynamique des Structures et Interactions des Macromolécules Biologiques, Paris, France
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Wu GCT, Chen FC. Determinants of exon-level evolutionary rates in Arabidopsis species. Evol Bioinform Online 2012; 8:389-415. [PMID: 22844194 PMCID: PMC3399485 DOI: 10.4137/ebo.s9743] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022] Open
Abstract
What causes the variations in evolutionary rates is fundamental to molecular evolution. However, in plants, the causes of within-gene evolutionary rate variations remain underexplored. Here we use the principal component regression to examine the contributions of eleven exon features to the within-gene variations in nonsynonymous substitution rate (d(N)), synonymous substitution rate (d(S)), and the d(N)/d(S) ratio in Arabidopsis species. We demonstrate that exon features related to protein structural-functional constraints and mRNA splicing account for the largest proportions of within-gene variations in d(N)/d(S) and d(N). Meanwhile, for d(S), a combination of expression level, exon length, and structural-functional features explains the largest proportion of within-gene variances. Our results suggest that the determinants of within-gene variations differ from those of between-gene variations in evolutionary rates. Furthermore, the relative importance of different exon features also differs between plants and animals. Our study thus may shed a new light on the evolution of plant genes.
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Affiliation(s)
- Gideon C-T Wu
- Graduate Institute of Life Sciences, National Defense Medical Center, 114 Taiwan
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