1
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Wang J, Shi A, Lyu J. A comprehensive atlas of epigenetic regulators reveals tissue-specific epigenetic regulation patterns. Epigenetics 2023; 18:2139067. [PMID: 36305095 PMCID: PMC9980636 DOI: 10.1080/15592294.2022.2139067] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022] Open
Abstract
Epigenetic machinery contributes to gene regulation in eukaryotic species. However, the machinery including more than 600 epigenetic regulator (ER) genes responsible for reading, writing, and erasing histone modifications and DNA modifications remains largely uncharacterized across species. We compile a comprehensive list of ERs based on an evolutionary analysis across 23 species, which is the most comprehensive ER list in various species until recently. We further perform comparative transcriptomic analyses across different tissues in humans, mice, as well as other amniote species. We observe a consistent tissue-of-origin expression specificity pattern of duplicated ER genes across species and suggest links between expression specificity and ER gene evolution as well as ER function. Additional analyses further suggest that ER duplication can generate tissue-specific ER genes with the same epigenetic substrates, which may be closely related to their regulatory specificity in tissue development. Our work can serve as a foundation to better comprehend the tissue-specific expression patterns of ER genes from an evolutionary perspective and also the functional implications of ERs in tissue-specific epigenetic regulation.
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Affiliation(s)
- Jilu Wang
- Wenzhou Institute, University of Chinese Academy of Sciences, Wenzhou, Zhejiang, People's Republic of China
| | - Aiai Shi
- Wenzhou Institute, University of Chinese Academy of Sciences, Wenzhou, Zhejiang, People's Republic of China
| | - Jie Lyu
- Wenzhou Institute, University of Chinese Academy of Sciences, Wenzhou, Zhejiang, People's Republic of China.,Joint Centre of Translational Medicine, the First Affiliated Hospital of Wenzhou Medical University, Wenzhou, People's Republic of China.,Joint Centre of Translational Medicine, Wenzhou Institute, University of Chinese Academy of Sciences, Wenzhou, Zhejiang, People's Republic of China.,Oujiang Laboratory (Zhejiang Lab for Regenerative Medicine, Vision and Brain Health), Wenzhou, Zhejiang, People's Republic of China
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2
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Vance Z, McLysaght A. Ohnologs and SSD Paralogs Differ in Genomic and Expression Features Related to Dosage Constraints. Genome Biol Evol 2023; 15:evad174. [PMID: 37776514 PMCID: PMC10563793 DOI: 10.1093/gbe/evad174] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Revised: 09/21/2023] [Accepted: 09/26/2023] [Indexed: 10/02/2023] Open
Abstract
Gene duplication is recognized as a critical process in genome evolution; however, many questions about this process remain unanswered. Although gene duplicability has been observed to differ by duplication mechanism and evolutionary rate, there is so far no broad characterization of its determinants. Many features correlate with this difference in duplicability; however, our ability to exploit these observations to advance our understanding of the role of duplication in evolution is hampered by limitations within existing work. In particular, the existence of methodological differences across studies impedes meaningful comparison. Here, we use consistent definitions of duplicability in the human lineage to explore these associations, allow resolution of the impact of confounding factors, and define the overall relevance of individual features. Using a classifier approach and controlling for the confounding effect of duplicate longevity, we find a subset of gene features important in differentiating genes duplicable by small-scale duplication from those duplicable by whole-genome duplication, revealing critical roles for gene dosage and expression costs in duplicability. We further delve into patterns of functional enrichment and find a lack of constraint on duplicate retention in any context for genes duplicable by small-scale duplication.
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Affiliation(s)
- Zoe Vance
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin, Ireland
| | - Aoife McLysaght
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin, Ireland
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3
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Zhu SB, Jiang QH, Chen ZG, Zhou X, Jin YT, Deng Z, Guo FB. Mslar: Microbial synthetic lethal and rescue database. PLoS Comput Biol 2023; 19:e1011218. [PMID: 37289843 DOI: 10.1371/journal.pcbi.1011218] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2022] [Accepted: 05/26/2023] [Indexed: 06/10/2023] Open
Abstract
Synthetic lethality (SL) occurs when mutations in two genes together lead to cell or organism death, while a single mutation in either gene does not have a significant impact. This concept can also be extended to three or more genes for SL. Computational and experimental methods have been developed to predict and verify SL gene pairs, especially for yeast and Escherichia coli. However, there is currently a lack of a specialized platform to collect microbial SL gene pairs. Therefore, we designed a synthetic interaction database for microbial genetics that collects 13,313 SL and 2,994 Synthetic Rescue (SR) gene pairs that are reported in the literature, as well as 86,981 putative SL pairs got through homologous transfer method in 281 bacterial genomes. Our database website provides multiple functions such as search, browse, visualization, and Blast. Based on the SL interaction data in the S. cerevisiae, we review the issue of duplications' essentiality and observed that the duplicated genes and singletons have a similar ratio of being essential when we consider both individual and SL. The Microbial Synthetic Lethal and Rescue Database (Mslar) is expected to be a useful reference resource for researchers interested in the SL and SR genes of microorganisms. Mslar is open freely to everyone and available on the web at http://guolab.whu.edu.cn/Mslar/.
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Affiliation(s)
- Sen-Bin Zhu
- School of Life Science and Technology, Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu, China
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education, and School of Pharmaceutical Sciences, Wuhan University, Wuhan, China
| | - Qian-Hu Jiang
- School of Life Science and Technology, Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu, China
| | - Zhi-Guo Chen
- School of Life Science and Technology, Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu, China
| | - Xiang Zhou
- School of Life Science and Technology, Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu, China
| | - Yan-Ting Jin
- School of Life Science and Technology, Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu, China
| | - Zixin Deng
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education, and School of Pharmaceutical Sciences, Wuhan University, Wuhan, China
| | - Feng-Biao Guo
- Department of Respiratory and Critical Care Medicine, Zhongnan Hospital of Wuhan University, Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education and School of Pharmaceutical Sciences, Wuhan University, Wuhan, China
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4
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Luzuriaga-Neira A, Subramanian K, Alvarez-Ponce D. Functional compensation of mouse duplicates by their paralogs expressed in the same tissues. Genome Biol Evol 2022; 14:evac126. [PMID: 35945673 PMCID: PMC9387915 DOI: 10.1093/gbe/evac126] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Accepted: 07/30/2022] [Indexed: 11/14/2022] Open
Abstract
Analyses in a number of organisms have shown that duplicated genes are less likely to be essential than singletons. This implies that genes can often compensate for the loss of their paralogs. However, it is unclear why the loss of some duplicates can be compensated by their paralogs, whereas the loss of other duplicates cannot. Surprisingly, initial analyses in mice did not detect differences in the essentiality of duplicates and singletons. Only subsequent analyses, using larger gene knockout datasets and controlling for a number of confounding factors, did detect significant differences. Previous studies have not taken into account the tissues in which duplicates are expressed. We hypothesized that in complex organisms, in order for a gene's loss to be compensated by one or more of its paralogs, such paralogs need to be expressed in at least the same set of tissues as the lost gene. To test our hypothesis, we classified mouse duplicates into two categories based on the expression patterns of their paralogs: "compensable duplicates" (those with paralogs expressed in all the tissues in which the gene is expressed) and "non-compensable duplicates" (those whose paralogs are not expressed in all the tissues where the gene is expressed). In agreement with our hypothesis, the essentiality of non-compensable duplicates is similar to that of singletons, whereas compensable duplicates exhibit a substantially lower essentiality. Our results imply that duplicates can often compensate for the loss of their paralogs, but only if they are expressed in the same tissues. Indeed, the compensation ability is more dependent on expression patterns than on protein sequence similarity. The existence of these two kinds of duplicates with different essentialities, which has been overlooked by prior studies, may have hindered the detection of differences between singletons and duplicates.
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5
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Gu X. A Simple Evolutionary Model of Genetic Robustness After Gene Duplication. J Mol Evol 2022; 90:352-361. [PMID: 35913597 DOI: 10.1007/s00239-022-10065-1] [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: 03/01/2022] [Accepted: 06/23/2022] [Indexed: 10/16/2022]
Abstract
When a dispensable gene is duplicated (referred to the ancestral dispensability denoted by O+), genetic buffering and duplicate compensation together maintain the duplicate redundancy, whereas duplicate compensation is the only mechanism when an essential gene is duplicated (referred to the ancestral essentiality denoted by O-). To investigate these evolutionary scenarios of genetic robustness, I formulated a simple mixture model for analyzing duplicate pairs with one of the following states: double dispensable (DD), semi-dispensable (one dispensable one essential, DE), or double essential (EE). This model was applied to the yeast duplicate pairs from a whole-genome duplication (WGD) occurred about 100 million years ago (mya), and the mouse duplicate pairs from a WGD occurred about more than 500 mya. Both case studies revealed that the proportion of essentiality for those duplicates with ancestral essentiality [PE(O-)] was much higher than that for those with ancestral dispensability [PE(O+)]. While it was negligible in the yeast duplicate pairs, PE(O+) (about 20%) was shown statistically significant in the mouse duplicate pairs. These findings, together, support the hypothesis that both sub-functionalization and neo-functionalization may play some roles after gene duplication, though the former may be much faster than the later.
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Affiliation(s)
- Xun Gu
- The Laurence H. Baker Center in Bioinformatics on Biological Statistics, Department of Genetics, Development and Cell Biology, Program of Ecological and Evolutionary Biology, Iowa State University, Ames, IA, 50011, USA.
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6
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Peterson KJ, Beavan A, Chabot PJ, McPeek MA, Pisani D, Fromm B, Simakov O. MicroRNAs as Indicators into the Causes and Consequences of Whole-Genome Duplication Events. Mol Biol Evol 2022; 39:msab344. [PMID: 34865078 PMCID: PMC8789304 DOI: 10.1093/molbev/msab344] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Whole-genome duplications (WGDs) have long been considered the causal mechanism underlying dramatic increases to morphological complexity due to the neo-functionalization of paralogs generated during these events. Nonetheless, an alternative hypothesis suggests that behind the retention of most paralogs is not neo-functionalization, but instead the degree of the inter-connectivity of the intended gene product, as well as the mode of the WGD itself. Here, we explore both the causes and consequences of WGD by examining the distribution, expression, and molecular evolution of microRNAs (miRNAs) in both gnathostome vertebrates as well as chelicerate arthropods. We find that although the number of miRNA paralogs tracks the number of WGDs experienced within the lineage, few of these paralogs experienced changes to the seed sequence, and thus are functionally equivalent relative to their mRNA targets. Nonetheless, in gnathostomes, although the retention of paralogs following the 1R autotetraploidization event is similar across the two subgenomes, the paralogs generated by the gnathostome 2R allotetraploidization event are retained in higher numbers on one subgenome relative to the second, with the miRNAs found on the preferred subgenome showing both higher expression of mature miRNA transcripts and slower molecular evolution of the precursor miRNA sequences. Importantly, WGDs do not result in the creation of miRNA novelty, nor do WGDs correlate to increases in complexity. Instead, it is the number of miRNA seed sequences in the genome itself that not only better correlate to instances in complexification, but also mechanistically explain why complexity increases when new miRNA families are established.
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Affiliation(s)
- Kevin J Peterson
- Department of Biological Sciences, Dartmouth College, Hanover, NH, USA
| | - Alan Beavan
- School of Earth Sciences, University of Bristol, Bristol, United Kingdom
- School of Biological Sciences, University of Bristol, Bristol, United Kingdom
| | - Peter J Chabot
- Department of Biological Sciences, Dartmouth College, Hanover, NH, USA
| | - Mark A McPeek
- Department of Biological Sciences, Dartmouth College, Hanover, NH, USA
| | - Davide Pisani
- School of Earth Sciences, University of Bristol, Bristol, United Kingdom
- School of Biological Sciences, University of Bristol, Bristol, United Kingdom
| | - Bastian Fromm
- Arctic University Museum of Norway, UiT, The Arctic University of Norway, Tromsø, Norway
| | - Oleg Simakov
- Department of Neuroscience and Developmental Biology, University of Vienna, Vienna, Austria
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7
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Vance Z, Niezabitowski L, Hurst LD, McLysaght A. Evidence from Drosophila Supports Higher Duplicability of Faster Evolving Genes. Genome Biol Evol 2022; 14:6501445. [PMID: 35018456 PMCID: PMC8765793 DOI: 10.1093/gbe/evac003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/05/2022] [Indexed: 12/03/2022] Open
Abstract
The faster rate of evolution of duplicated genes relative to singletons has been well documented in multiple lineages. This observation has generally been attributed to a presumed release from constraint following creation of a redundant, duplicate copy. However, it is not obvious that the relationship operates in this direction. An alternative possibility—that the faster rate of evolution predates the duplication event and the observed differences result from a higher propensity to duplicate in fast-evolving genes—has been tested in primates and in insects. However, these studies arrived at different conclusions and clarity is needed on whether these contrasting results relate to differences in methodology or legitimate biological differences between the lineages selected. Here, we test whether duplicable genes are faster evolving independent of duplication in the Drosophila lineage and find that our results support the conclusion that faster evolving genes are more likely to duplicate, in agreement with previous work in primates. Our findings indicate that this characteristic of gene duplication is not restricted to a single lineage and has broad implications for the interpretation of the impact of gene duplication. We identify a subset of “singletons” which defy the general trends and appear to be faster evolving. Further investigation implicates homology detection failure and suggests that these may be duplicable genes with unidentifiable paralogs.
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Affiliation(s)
- Zoe Vance
- Smurfit Institute of Genetics, Trinity College Dublin, Ireland
| | | | - Laurence D Hurst
- Department of Biology and Biochemistry, University of Bath, United Kingdom
| | - Aoife McLysaght
- Smurfit Institute of Genetics, Trinity College Dublin, Ireland
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8
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Ezoe A, Shirai K, Hanada K. Degree of Functional Divergence in Duplicates Is Associated with Distinct Roles in Plant Evolution. Mol Biol Evol 2021; 38:1447-1459. [PMID: 33290522 PMCID: PMC8042753 DOI: 10.1093/molbev/msaa302] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
Gene duplication is a major mechanism to create new genes. After gene duplication, some duplicated genes undergo functionalization, whereas others largely maintain redundant functions. Duplicated genes comprise various degrees of functional diversification in plants. However, the evolutionary fate of high and low diversified duplicates is unclear at genomic scale. To infer high and low diversified duplicates in Arabidopsis thaliana genome, we generated a prediction method for predicting whether a pair of duplicate genes was subjected to high or low diversification based on the phenotypes of knock-out mutants. Among 4,017 pairs of recently duplicated A. thaliana genes, 1,052 and 600 are high and low diversified duplicate pairs, respectively. The predictions were validated based on the phenotypes of generated knock-down transgenic plants. We determined that the high diversified duplicates resulting from tandem duplications tend to have lineage-specific functions, whereas the low diversified duplicates produced by whole-genome duplications are related to essential signaling pathways. To assess the evolutionary impact of high and low diversified duplicates in closely related species, we compared the retention rates and selection pressures on the orthologs of A. thaliana duplicates in two closely related species. Interestingly, high diversified duplicates resulting from tandem duplications tend to be retained in multiple lineages under positive selection. Low diversified duplicates by whole-genome duplications tend to be retained in multiple lineages under purifying selection. Taken together, the functional diversities determined by different duplication mechanisms had distinct effects on plant evolution.
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Affiliation(s)
- Akihiro Ezoe
- Department of Bioscience and Bioinformatics, Kyushu Institute of Technology, Iizuka, Fukuoka, Japan
| | - Kazumasa Shirai
- Department of Bioscience and Bioinformatics, Kyushu Institute of Technology, Iizuka, Fukuoka, Japan
| | - Kousuke Hanada
- Department of Bioscience and Bioinformatics, Kyushu Institute of Technology, Iizuka, Fukuoka, Japan
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9
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Gurumayum S, Jiang P, Hao X, Campos TL, Young ND, Korhonen PK, Gasser RB, Bork P, Zhao XM, He LJ, Chen WH. OGEE v3: Online GEne Essentiality database with increased coverage of organisms and human cell lines. Nucleic Acids Res 2021; 49:D998-D1003. [PMID: 33084874 PMCID: PMC7779042 DOI: 10.1093/nar/gkaa884] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2020] [Revised: 09/24/2020] [Accepted: 09/28/2020] [Indexed: 12/17/2022] Open
Abstract
OGEE is an Online GEne Essentiality database. Gene essentiality is not a static and binary property, rather a context-dependent and evolvable property in all forms of life. In OGEE we collect not only experimentally tested essential and non-essential genes, but also associated gene properties that contributes to gene essentiality. We tagged conditionally essential genes that show variable essentiality statuses across datasets to highlight complex interplays between gene functions and environmental/experimental perturbations. OGEE v3 contains gene essentiality datasets for 91 species; almost doubled from 48 species in previous version. To accommodate recent advances on human cancer essential genes (as known as tumor dependency genes) that could serve as targets for cancer treatment and/or drug development, we expanded the collection of human essential genes from 16 cell lines in previous to 581. These human cancer cell lines were tested with high-throughput experiments such as CRISPR-Cas9 and RNAi; in total, 150 of which were tested by both techniques. We also included factors known to contribute to gene essentiality for these cell lines, such as genomic mutation, methylation and gene expression, along with extensive graphical visualizations for ease of understanding of these factors. OGEE v3 can be accessible freely at https://v3.ogee.info.
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Affiliation(s)
- Sanathoi Gurumayum
- Key Laboratory of Molecular Biophysics of the Ministry of Education, Hubei Key Laboratory of Bioinformatics and Molecular-imaging, Center for Artificial Biology, Department of Bioinformatics and Systems Biology, College of Life Science and Technology, Huazhong University of Science and Technology (HUST), 430074 Wuhan, Hubei, China
| | - Puzi Jiang
- Key Laboratory of Molecular Biophysics of the Ministry of Education, Hubei Key Laboratory of Bioinformatics and Molecular-imaging, Center for Artificial Biology, Department of Bioinformatics and Systems Biology, College of Life Science and Technology, Huazhong University of Science and Technology (HUST), 430074 Wuhan, Hubei, China
| | - Xiaowen Hao
- Key Laboratory of Molecular Biophysics of the Ministry of Education, Hubei Key Laboratory of Bioinformatics and Molecular-imaging, Center for Artificial Biology, Department of Bioinformatics and Systems Biology, College of Life Science and Technology, Huazhong University of Science and Technology (HUST), 430074 Wuhan, Hubei, China
| | - Tulio L Campos
- Department of Veterinary Biosciences, Melbourne Veterinary School, The University of Melbourne, Parkville, Victoria 3010, Australia
- Instituto Aggeu Magalhães, Fundação Oswaldo Cruz (IAM-Fiocruz), Recife, Pernambuco, Brazil
| | - Neil D Young
- Department of Veterinary Biosciences, Melbourne Veterinary School, The University of Melbourne, Parkville, Victoria 3010, Australia
| | - Pasi K Korhonen
- Department of Veterinary Biosciences, Melbourne Veterinary School, The University of Melbourne, Parkville, Victoria 3010, Australia
| | - Robin B Gasser
- Department of Veterinary Biosciences, Melbourne Veterinary School, The University of Melbourne, Parkville, Victoria 3010, Australia
| | - Peer Bork
- European molecular biology laboratory (EMBL), Meyerhof Strasse 1, 69117 Heidelberg, Germany
- Molecular Medicine Partnership Unit, University of Heidelberg and European Molecular Biology Laboratory, 69120 Heidelberg, Germany
- Max-Delbrück-Centre for Molecular Medicine, Robert-Rössle-Straße 10, 13125 Berlin, Germany
- Department of Bioinformatics, Biocenter, University of Würzburg, 97074 Würzburg, Germany
| | - Xing-Ming Zhao
- Institute of Science and Technology for Brain-Inspired Intelligence, Fudan University, 200433 Shanghai, China
- Key Laboratory of Computational Neuroscience and Brain-Inspired Intelligence, Ministry of Education, China
| | - Li-jie He
- Department of Medical Oncology, People's Hospital of Liaoning Province, 110016 Shenyang, China
| | - Wei-Hua Chen
- Key Laboratory of Molecular Biophysics of the Ministry of Education, Hubei Key Laboratory of Bioinformatics and Molecular-imaging, Center for Artificial Biology, Department of Bioinformatics and Systems Biology, College of Life Science and Technology, Huazhong University of Science and Technology (HUST), 430074 Wuhan, Hubei, China
- College of Life Science, Henan Normal University, 453007 Xinxiang, Henan, China
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10
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Conant GC. The lasting after-effects of an ancient polyploidy on the genomes of teleosts. PLoS One 2020; 15:e0231356. [PMID: 32298330 PMCID: PMC7161988 DOI: 10.1371/journal.pone.0231356] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2020] [Accepted: 03/20/2020] [Indexed: 12/20/2022] Open
Abstract
The ancestor of most teleost fishes underwent a whole-genome duplication event three hundred million years ago. Despite its antiquity, the effects of this event are evident both in the structure of teleost genomes and in how the surviving duplicated genes still operate to drive form and function. I inferred a set of shared syntenic regions that survive from the teleost genome duplication (TGD) using eight teleost genomes and the outgroup gar genome (which lacks the TGD). I then phylogenetically modeled the TGD's resolution via shared and independent gene losses and applied a new simulation-based statistical test for the presence of bias toward the preservation of genes from one parental subgenome. On the basis of that test, I argue that the TGD was likely an allopolyploidy. I find that duplicate genes surviving from this duplication in zebrafish are less likely to function in early embryo development than are genes that have returned to single copy at some point in this species' history. The tissues these ohnologs are expressed in, as well as their biological functions, lend support to recent suggestions that the TGD was the source of a morphological innovation in the structure of the teleost retina. Surviving duplicates also appear less likely to be essential than singletons, despite the fact that their single-copy orthologs in mouse are no less essential than other genes.
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Affiliation(s)
- Gavin C. Conant
- Department of Biological Sciences, North Carolina State University, Raleigh, NC, United States of America
- Bioinformatics Research Center, North Carolina State University, Raleigh, NC, United States of America
- Program in Genetics, North Carolina State University, Raleigh, NC, United States of America
- Division of Animal Sciences, University of Missouri, Columbia, MO, United States of America
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11
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Shohat S, Shifman S. Genes essential for embryonic stem cells are associated with neurodevelopmental disorders. Genome Res 2019; 29:1910-1918. [PMID: 31649057 PMCID: PMC6836742 DOI: 10.1101/gr.250019.119] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2019] [Accepted: 10/01/2019] [Indexed: 12/18/2022]
Abstract
Mouse embryonic stem cells (mESCs) are key components in generating mouse models for human diseases and performing basic research on pluripotency, yet the number of genes essential for mESCs is still unknown. We performed a genome-wide screen for essential genes in mESCs and compared it to screens in human cells. We found that essential genes are enriched for basic cellular functions, are highly expressed in mESCs, and tend to lack paralog genes. We discovered that genes that are essential specifically in mESCs play a role in pathways associated with their pluripotent state. We show that 29.5% of human genes intolerant to loss-of-function mutations are essential in mouse or human ESCs, and that the human phenotypes most significantly associated with genes essential for ESCs are neurodevelopmental. Our results provide insights into essential genes in the mouse, the pathways which govern pluripotency, and suggest that many genes associated with neurodevelopmental disorders are essential at very early embryonic stages.
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Affiliation(s)
- Shahar Shohat
- Department of Genetics, The Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem 9190401, Israel
| | - Sagiv Shifman
- Department of Genetics, The Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem 9190401, Israel
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12
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Kabir M, Wenlock S, Doig AJ, Hentges KE. The Essentiality Status of Mouse Duplicate Gene Pairs Correlates with Developmental Co-Expression Patterns. Sci Rep 2019; 9:3224. [PMID: 30824779 PMCID: PMC6397145 DOI: 10.1038/s41598-019-39894-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2018] [Accepted: 01/23/2019] [Indexed: 02/02/2023] Open
Abstract
During the evolution of multicellular eukaryotes, gene duplication occurs frequently to generate new genes and/or functions. A duplicated gene may have a similar function to its ancestral gene. Therefore, it may be expected that duplicated genes are less likely to be critical for the survival of an organism, since there are multiple copies of the gene rendering each individual copy redundant. In this study, we explored the developmental expression patterns of duplicate gene pairs and the relationship between development co-expression and phenotypes resulting from the knockout of duplicate genes in the mouse. We define genes that generate lethal phenotypes in single gene knockout experiments as essential genes. We found that duplicate gene pairs comprised of two essential genes tend to be expressed at different stages of development, compared to duplicate gene pairs with at least one non-essential member, showing that the timing of developmental expression affects the ability of one paralogue to compensate for the loss of the other. Gene essentiality, developmental expression and gene duplication are thus closely linked.
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Affiliation(s)
- Mitra Kabir
- Division of Evolution and Genomic Sciences, Faculty of Biology, Medicine and Health, Manchester Academic Health Science Centre, University of Manchester, Oxford Road, Manchester, M13 9PT, UK
| | - Stephanie Wenlock
- Division of Evolution and Genomic Sciences, Faculty of Biology, Medicine and Health, Manchester Academic Health Science Centre, University of Manchester, Oxford Road, Manchester, M13 9PT, UK
- Department of Pathology, Cambridge Genomic Services, University of Cambridge, Cambridge, CB2 1QP, UK
| | - Andrew J Doig
- Manchester Institute of Biotechnology and School of Biological Sciences, Faculty of Biology, Medicine and Health, Manchester Academic Health Science Centre, University of Manchester, 131 Princess Street, Manchester, M1 7DN, UK
| | - Kathryn E Hentges
- Division of Evolution and Genomic Sciences, Faculty of Biology, Medicine and Health, Manchester Academic Health Science Centre, University of Manchester, Oxford Road, Manchester, M13 9PT, UK.
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13
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Sacerdot C, Louis A, Bon C, Berthelot C, Roest Crollius H. Chromosome evolution at the origin of the ancestral vertebrate genome. Genome Biol 2018; 19:166. [PMID: 30333059 PMCID: PMC6193309 DOI: 10.1186/s13059-018-1559-1] [Citation(s) in RCA: 110] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2018] [Accepted: 10/04/2018] [Indexed: 11/30/2022] Open
Abstract
BACKGROUND It has been proposed that more than 450 million years ago, two successive whole genome duplications took place in a marine chordate lineage before leading to the common ancestor of vertebrates. A precise reconstruction of these founding events would provide a framework to better understand the impact of these early whole genome duplications on extant vertebrates. RESULTS We reconstruct the evolution of chromosomes at the beginning of vertebrate evolution. We first compare 61 extant animal genomes to reconstruct the highly contiguous order of genes in a 326-million-year-old ancestral Amniota genome. In this genome, we establish a well-supported list of duplicated genes originating from the two whole genome duplications to identify tetrads of duplicated chromosomes. From this, we reconstruct a chronology in which a pre-vertebrate genome composed of 17 chromosomes duplicated to 34 chromosomes and was subject to seven chromosome fusions before duplicating again into 54 chromosomes. After the separation of the lineage of Gnathostomata (jawed vertebrates) from Cyclostomata (extant jawless fish), four more fusions took place to form the ancestral Euteleostomi (bony vertebrates) genome of 50 chromosomes. CONCLUSIONS These results firmly establish the occurrence of two whole genome duplications in the lineage that precedes the ancestor of vertebrates, resolving in particular the ambiguity raised by the analysis of the lamprey genome. This work provides a foundation for studying the evolution of vertebrate chromosomes from the standpoint of a common ancestor and particularly the pattern of duplicate gene retention and loss that resulted in the gene composition of extant vertebrate genomes.
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Affiliation(s)
- Christine Sacerdot
- Institut de Biologie de l'Ecole Normale Supérieure (IBENS), Ecole Normale Supérieure, CNRS, INSERM, PSL Research University, 75005, Paris, France
| | - Alexandra Louis
- Institut de Biologie de l'Ecole Normale Supérieure (IBENS), Ecole Normale Supérieure, CNRS, INSERM, PSL Research University, 75005, Paris, France
| | - Céline Bon
- Institut de Biologie de l'Ecole Normale Supérieure (IBENS), Ecole Normale Supérieure, CNRS, INSERM, PSL Research University, 75005, Paris, France
- Present Address: Laboratoire Éco-Anthropologie et Ethnobiologie, UMR 7206 CNRS - Muséum National d'Histoire Naturelle, Université Paris Diderot, Sorbonne Paris Cité, F-75016, Paris, France
| | | | - Hugues Roest Crollius
- Institut de Biologie de l'Ecole Normale Supérieure (IBENS), Ecole Normale Supérieure, CNRS, INSERM, PSL Research University, 75005, Paris, France.
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14
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Roux J, Liu J, Robinson-Rechavi M. Selective Constraints on Coding Sequences of Nervous System Genes Are a Major Determinant of Duplicate Gene Retention in Vertebrates. Mol Biol Evol 2018; 34:2773-2791. [PMID: 28981708 PMCID: PMC5850798 DOI: 10.1093/molbev/msx199] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
The evolutionary history of vertebrates is marked by three ancient whole-genome duplications: two successive rounds in the ancestor of vertebrates, and a third one specific to teleost fishes. Biased loss of most duplicates enriched the genome for specific genes, such as slow evolving genes, but this selective retention process is not well understood. To understand what drives the long-term preservation of duplicate genes, we characterized duplicated genes in terms of their expression patterns. We used a new method of expression enrichment analysis, TopAnat, applied to in situ hybridization data from thousands of genes from zebrafish and mouse. We showed that the presence of expression in the nervous system is a good predictor of a higher rate of retention of duplicate genes after whole-genome duplication. Further analyses suggest that purifying selection against the toxic effects of misfolded or misinteracting proteins, which is particularly strong in nonrenewing neural tissues, likely constrains the evolution of coding sequences of nervous system genes, leading indirectly to the preservation of duplicate genes after whole-genome duplication. Whole-genome duplications thus greatly contributed to the expansion of the toolkit of genes available for the evolution of profound novelties of the nervous system at the base of the vertebrate radiation.
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Affiliation(s)
- Julien Roux
- Département d'Ecologie et d'Evolution, Université de Lausanne, Lausanne, Switzerland.,Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Jialin Liu
- Département d'Ecologie et d'Evolution, Université de Lausanne, Lausanne, Switzerland.,Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Marc Robinson-Rechavi
- Département d'Ecologie et d'Evolution, Université de Lausanne, Lausanne, Switzerland.,Swiss Institute of Bioinformatics, Lausanne, Switzerland
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15
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Rodrigo G, Fares MA. Intrinsic adaptive value and early fate of gene duplication revealed by a bottom-up approach. eLife 2018; 7:29739. [PMID: 29303479 PMCID: PMC5771667 DOI: 10.7554/elife.29739] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2017] [Accepted: 01/04/2018] [Indexed: 02/06/2023] Open
Abstract
The population genetic mechanisms governing the preservation of gene duplicates, especially in the critical very initial phase, have remained largely unknown. Here, we demonstrate that gene duplication confers per se a weak selective advantage in scenarios of fitness trade-offs. Through a precise quantitative description of a model system, we show that a second gene copy serves to reduce gene expression inaccuracies derived from pervasive molecular noise and suboptimal gene regulation. We then reveal that such an accuracy in the phenotype yields a selective advantage in the order of 0.1% on average, which would allow the positive selection of gene duplication in populations with moderate/large sizes. This advantage is greater at higher noise levels and intermediate concentrations of the environmental molecule, when fitness trade-offs become more evident. Moreover, we discuss how the genome rearrangement rates greatly condition the eventual fixation of duplicates. Overall, our theoretical results highlight an original adaptive value for cells carrying new-born duplicates, broadly analyze the selective conditions that determine their early fates in different organisms, and reconcile population genetics with evolution by gene duplication.
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Affiliation(s)
- Guillermo Rodrigo
- Instituto de Biología Molecular y Celular de Plantas, CSIC - UPV, Valencia, Spain.,Instituto de Biología Integrativa y de Sistemas, CSIC - UV, Paterna, Spain
| | - Mario A Fares
- Instituto de Biología Molecular y Celular de Plantas, CSIC - UPV, Valencia, Spain.,Instituto de Biología Integrativa y de Sistemas, CSIC - UV, Paterna, Spain.,Trinity College Dublin, University of Dublin, Dublin, Ireland
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16
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Sekine M, Makino T. Inference of Causative Genes for Alzheimer's Disease Due to Dosage Imbalance. Mol Biol Evol 2017; 34:2396-2407. [PMID: 28666362 DOI: 10.1093/molbev/msx183] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Copy number variations (CNVs) have recently drawn attention as an important genetic factor for diseases, especially common neuropsychiatric disorders including Alzheimer's disease (AD). Because most of the pathogenic CNV regions overlap with multiple genes, it has been challenging to identify the true disease-causing genes amongst them. Notably, a recent study reported that CNV regions containing ohnologs, which are dosage-sensitive genes, are likely to be deleterious. Utilizing the unique feature of ohnologs could be useful for identifying causative genes with pathogenic CNVs, however its effectiveness is still unclear. Although it has been reported that AD is strongly affected by CNVs, most of AD-causing genes with pathogenic CNVs have not been identified yet. Here, we show that dosage-sensitive ohnologs within CNV regions reported in patients with AD are related to the nervous system and are highly expressed in the brain, similar to other known susceptible genes for AD. We found that CNV regions in patients with AD contained dosage-sensitive genes, which are ohnologs not overlapping with control CNV regions, frequently. Furthermore, these dosage-sensitive genes in pathogenic CNV regions had a strong enrichment in the nervous system for mouse knockout phenotype and high expression in the brain similar to the known susceptible genes for AD. Our results demonstrated that selecting dosage-sensitive ohnologs out of multiple genes with pathogenic CNVs is effective in identifying the causative genes for AD. This methodology can be applied to other diseases caused by dosage imbalance and might help to establish the medical diagnosis by analysis of CNVs.
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Affiliation(s)
- Mizuka Sekine
- Department of Biology, Faculty of Science, Tohoku University, Sendai, Japan
| | - Takashi Makino
- Department of Ecology and Evolutionary Biology, Graduate School of Life Sciences, Tohoku University, Sendai, Japan
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17
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Abstract
For a subset of genes in our genome a change in gene dosage, by duplication or deletion, causes a phenotypic effect. These dosage-sensitive genes may confer an advantage upon copy number change, but more typically they are associated with disease, including heart disease, cancers and neuropsychiatric disorders. This gene copy number sensitivity creates characteristic evolutionary constraints that can serve as a diagnostic to identify dosage-sensitive genes. Though the link between copy number change and disease is well-established, the mechanism of pathogenicity is usually opaque. We propose that gene expression level may provide a common basis for the pathogenic effects of many copy number variants.
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Affiliation(s)
- Alan M Rice
- Smurfit Institute of Genetics, Trinity College Dublin, University of Dublin, Dublin 2, Ireland
| | - Aoife McLysaght
- Smurfit Institute of Genetics, Trinity College Dublin, University of Dublin, Dublin 2, Ireland.
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18
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Power provides protection: Genetic robustness in yeast depends on the capacity to generate energy. PLoS Genet 2017; 13:e1006768. [PMID: 28493864 PMCID: PMC5444853 DOI: 10.1371/journal.pgen.1006768] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2017] [Revised: 05/25/2017] [Accepted: 04/19/2017] [Indexed: 11/19/2022] Open
Abstract
The functional basis of genetic robustness, the ability of organisms to suppress the effects of mutations, remains incompletely understood. We exposed a set of 15 strains of Saccharomyces cerevisiae form diverse environments to increasing doses of the chemical mutagen EMS. The number of the resulting random mutations was similar for all tested strains. However, there were differences in immediate mortality after the mutagenic treatment and in defective growth of survivors. An analysis of gene expression revealed that immediate mortality was lowest in strains with lowest expression of transmembrane proteins, which are rich in thiol groups and thus vulnerable to EMS. A signal of genuine genetic robustness was detected for the other trait, the ability to grow well despite bearing non-lethal mutations. Increased tolerance of such mutations correlated with high expression of genes responsible for the oxidative energy metabolism, suggesting that the negative effect of mutations can be buffered if enough energy is available. We confirmed this finding in three additional tests of the ability to grow on (i) fermentable or non-fermentable sources of carbon, (ii) under chemical inhibition of the electron transport chain and (iii) during overexpression of its key component, cytochrome c. Our results add the capacity to generate energy as a general mechanism of genetic robustness. The ability to suppress phenotypic effects of mutations is termed genetic robustness. Its functional basis and evolutionary origin remain insufficiently understood despite decades of research. In fact, it is still largely untested whether genetic robustness is a trait of substantial, within-species variation. We used a model organism, Saccharomyces cerevisiae, to study both phenotypic signs and functional underpinnings of genetic robustness. We introduced random mutations into a set of well-characterized yeast strain. There was considerable variation in the growth rate among clones recovered after mutagenesis, which is an indication of genetic robustness. Using available data on gene expression for our strains, we found that genetic robustness was strongest among strains with enhanced expression of genes related to the energy metabolism. We reasoned that, regardless of the specific mutations, the capacity to generate metabolic energy may be a general underlying mechanism for buffering the effects of random mutations across the genome. We confirmed this hypothesis in further experiments in which we showed that genetic robustness decreases when the energy metabolism is compromised and increases when it is boosted.
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19
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Chen WH, Lu G, Chen X, Zhao XM, Bork P. OGEE v2: an update of the online gene essentiality database with special focus on differentially essential genes in human cancer cell lines. Nucleic Acids Res 2017; 45:D940-D944. [PMID: 27799467 PMCID: PMC5210522 DOI: 10.1093/nar/gkw1013] [Citation(s) in RCA: 98] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2016] [Revised: 10/14/2016] [Accepted: 10/18/2016] [Indexed: 01/14/2023] Open
Abstract
OGEE is an Online GEne Essentiality database. To enhance our understanding of the essentiality of genes, in OGEE we collected experimentally tested essential and non-essential genes, as well as associated gene properties known to contribute to gene essentiality. We focus on large-scale experiments, and complement our data with text-mining results. We organized tested genes into data sets according to their sources, and tagged those with variable essentiality statuses across data sets as conditionally essential genes, intending to highlight the complex interplay between gene functions and environments/experimental perturbations. Developments since the last public release include increased numbers of species and gene essentiality data sets, inclusion of non-coding essential sequences and genes with intermediate essentiality statuses. In addition, we included 16 essentiality data sets from cancer cell lines, corresponding to 9 human cancers; with OGEE, users can easily explore the shared and differentially essential genes within and between cancer types. These genes, especially those derived from cell lines that are similar to tumor samples, could reveal the oncogenic drivers, paralogous gene expression pattern and chromosomal structure of the corresponding cancer types, and can be further screened to identify targets for cancer therapy and/or new drug development. OGEE is freely available at http://ogee.medgenius.info.
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Affiliation(s)
- Wei-Hua Chen
- Key Laboratory of Molecular Biophysics of the Ministry of Education, Hubei Key Laboratory of Bioinformatics and Molecular-imaging, Department of Bioinformatics and Systems Biology, College of Life Science and Technology, Huazhong University of Science and Technology (HUST), 430074 Wuhan, Hubei, China
| | - Guanting Lu
- Department of Blood Transfusion, Tangdu Hospital, the Fourth Military Medical University, No 1, Xinsi Road, Chanba District, 710000 Xi'an, China
| | - Xiao Chen
- Department of Computer Science and Technology, Tongji University, Shanghai 201804, China
| | - Xing-Ming Zhao
- Department of Computer Science and Technology, Tongji University, Shanghai 201804, China
| | - Peer Bork
- European molecular biology laboratory (EMBL), Meyerhofstrasse 1, 69117 Heidelberg, Germany
- Molecular Medicine Partnership Unit, University of Heidelberg and European Molecular Biology Laboratory, 69120 Heidelberg, Germany
- Max-Delbrück-Centre for Molecular Medicine, Robert-Rössle-Straße 10, 13125 Berlin, Germany
- Department of Bioinformatics, Biocenter, University of Würzburg, 97074 Würzburg, Germany
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20
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Pires JC, Conant GC. Robust Yet Fragile: Expression Noise, Protein Misfolding, and Gene Dosage in the Evolution of Genomes. Annu Rev Genet 2016; 50:113-131. [PMID: 27617972 DOI: 10.1146/annurev-genet-120215-035400] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The complex manner in which organisms respond to changes in their gene dosage has long fascinated geneticists. Oddly, although the existence of dominance implies that dosage reductions often have mild phenotypes, extra copies of whole chromosomes (aneuploidy) are generally strongly deleterious. Even more paradoxically, an extra copy of the genome is better tolerated than is aneuploidy. We review the resolution of this paradox, highlighting the roles of biochemistry, protein aggregation, and disruption of cellular microstructure in that explanation. Returning to life's curious combination of robustness and sensitivity to dosage changes, we argue that understanding how biological robustness evolved makes these observations less inexplicable. We propose that noise in gene expression and evolutionary strategies for its suppression play a role in generating dosage phenotypes. Finally, we outline an unappreciated mechanism for the preservation of duplicate genes, namely preservation to limit expression noise, arguing that it is particularly relevant in polyploid organisms.
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Affiliation(s)
- J Chris Pires
- Division of Biological Sciences.,Informatics Institute, and
| | - Gavin C Conant
- Informatics Institute, and.,Division of Animal Sciences, University of Missouri, Columbia, Missouri, 65211-5300;
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21
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Yoshida K, Makino T, Kitano J. Accumulation of Deleterious Mutations on the Neo-Y Chromosome of Japan Sea Stickleback (Gasterosteus nipponicus). J Hered 2016; 108:63-68. [DOI: 10.1093/jhered/esw054] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2016] [Accepted: 08/22/2016] [Indexed: 12/22/2022] Open
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22
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Lan X, Pritchard JK. Coregulation of tandem duplicate genes slows evolution of subfunctionalization in mammals. Science 2016; 352:1009-13. [PMID: 27199432 DOI: 10.1126/science.aad8411] [Citation(s) in RCA: 120] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2015] [Accepted: 04/02/2016] [Indexed: 12/14/2022]
Abstract
Gene duplication is a fundamental process in genome evolution. However, most young duplicates are degraded by loss-of-function mutations, and the factors that allow some duplicate pairs to survive long-term remain controversial. One class of models to explain duplicate retention invokes sub- or neofunctionalization, whereas others focus on sharing of gene dosage. RNA-sequencing data from 46 human and 26 mouse tissues indicate that subfunctionalization of expression evolves slowly and is rare among duplicates that arose within the placental mammals, possibly because tandem duplicates are coregulated by shared genomic elements. Instead, consistent with the dosage-sharing hypothesis, most young duplicates are down-regulated to match expression levels of single-copy genes. Thus, dosage sharing of expression allows for the initial survival of mammalian duplicates, followed by slower functional adaptation enabling long-term preservation.
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Affiliation(s)
- Xun Lan
- Department of Genetics, Stanford University, Stanford, CA, USA. Howard Hughes Medical Institute, Stanford University, Stanford, CA, USA.
| | - Jonathan K Pritchard
- Department of Genetics, Stanford University, Stanford, CA, USA. Department of Biology, Stanford University, Stanford, CA, USA. Howard Hughes Medical Institute, Stanford University, Stanford, CA, USA.
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23
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Xie T, Yang QY, Wang XT, McLysaght A, Zhang HY. Spatial Colocalization of Human Ohnolog Pairs Acts to Maintain Dosage-Balance. Mol Biol Evol 2016; 33:2368-75. [PMID: 27297469 PMCID: PMC4989111 DOI: 10.1093/molbev/msw108] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Ohnologs -paralogous gene pairs generated by whole genome duplication- are enriched for dosage sensitive genes, that is, genes that have a phenotype due to copy number changes. Dosage sensitive genes frequently occur in the same metabolic pathway and in physically interacting proteins. Accumulating evidence reveals that functionally related genes tend to co-localize in the three-dimensional (3D) arrangement of chromosomes. We query whether the spatial distribution of ohnologs has implications for their dosage balance. We analyzed the colocalization frequency of ohnologs based on chromatin interaction datasets of seven human cell lines and found that ohnolog pairs exhibit higher spatial proximity in 3D nuclear organization than other paralog pairs and than randomly chosen ohnologs in the genome. We also found that colocalized ohnologs are more resistant to copy number variations and more likely to be disease-associated genes, which indicates a stronger dosage balance in ohnologs with high spatial proximity. This phenomenon is further supported by the stronger similarity of gene co-expression and of gene ontology terms of colocalized ohnologs. In addition, for a large fraction of ohnologs, the spatial colocalization is conserved in mouse cells, suggestive of functional constraint on their 3D positioning in the nucleus.
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Affiliation(s)
- Ting Xie
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan P. R. China
| | - Qing-Yong Yang
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan P. R. China
| | - Xiao-Tao Wang
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan P. R. China
| | - Aoife McLysaght
- Smurfit Institute of Genetics, Trinity College Dublin, University of Dublin, Dublin, Ireland
| | - Hong-Yu Zhang
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan P. R. China
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24
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Zimmer F, Harrison PW, Dessimoz C, Mank JE. Compensation of Dosage-Sensitive Genes on the Chicken Z Chromosome. Genome Biol Evol 2016; 8:1233-42. [PMID: 27044516 PMCID: PMC4860703 DOI: 10.1093/gbe/evw075] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/26/2016] [Indexed: 12/15/2022] Open
Abstract
In many diploid species, sex determination is linked to a pair of sex chromosomes that evolved from a pair of autosomes. In these organisms, the degeneration of the sex-limited Y or W chromosome causes a reduction in gene dose in the heterogametic sex for X- or Z-linked genes. Variations in gene dose are detrimental for large chromosomal regions when they span dosage-sensitive genes, and many organisms were thought to evolve complete mechanisms of dosage compensation to mitigate this. However, the recent realization that a wide variety of organisms lack complete mechanisms of sex chromosome dosage compensation has presented a perplexing question: How do organisms with incomplete dosage compensation avoid deleterious effects of gene dose differences between the sexes? Here we use expression data from the chicken (Gallus gallus) to show that ohnologs, duplicated genes known to be dosage-sensitive, are preferentially dosage-compensated on the chicken Z chromosome. Our results indicate that even in the absence of a complete and chromosome wide dosage compensation mechanism, dosage-sensitive genes are effectively dosage compensated on the Z chromosome.
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Affiliation(s)
- Fabian Zimmer
- Department of Genetics Evolution and Environment, University College London, London, United Kingdom
| | - Peter W Harrison
- Department of Genetics Evolution and Environment, University College London, London, United Kingdom
| | - Christophe Dessimoz
- Department of Genetics Evolution and Environment, University College London, London, United Kingdom Department of Ecology and Evolution & Center for Integrative Genomics, University of Lausanne, Biophore 1015, Lausanne, Switzerland Swiss Institute of Bioinformatics, Biophore, 1015 Lausanne, Switzerland
| | - Judith E Mank
- Department of Genetics Evolution and Environment, University College London, London, United Kingdom
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25
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Abstract
The recent increase in genomic data is revealing an unexpected perspective of gene loss as a pervasive source of genetic variation that can cause adaptive phenotypic diversity. This novel perspective of gene loss is raising new fundamental questions. How relevant has gene loss been in the divergence of phyla? How do genes change from being essential to dispensable and finally to being lost? Is gene loss mostly neutral, or can it be an effective way of adaptation? These questions are addressed, and insights are discussed from genomic studies of gene loss in populations and their relevance in evolutionary biology and biomedicine.
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26
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Zielezinski A, Karlowski WM. Early origin and adaptive evolution of the GW182 protein family, the key component of RNA silencing in animals. RNA Biol 2016; 12:761-70. [PMID: 26106978 PMCID: PMC4615383 DOI: 10.1080/15476286.2015.1051302] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The GW182 proteins are a key component of the miRNA-dependent post-transcriptional silencing pathway in animals. They function as scaffold proteins to mediate the interaction of Argonaute (AGO)-containing complexes with cytoplasmic poly(A)-binding proteins (PABP) and PAN2-PAN3 and CCR4-NOT deadenylases. The AGO-GW182 complexes mediate silencing of the target mRNA through induction of translational repression and/or mRNA degradation. Although the GW182 proteins are a subject of extensive experimental research in the recent years, very little is known about their origin and evolution. Here, based on complex functional annotation and phylogenetic analyses, we reveal 448 members of the GW182 protein family from the earliest animals to humans. Our results indicate that a single-copy GW182/TNRC6C progenitor gene arose with the emergence of multicellularity and it multiplied in the last common ancestor of vertebrates in 2 rounds of whole genome duplication (WGD) resulting in 3 genes. Before the divergence of vertebrates, both the AGO- and CCR4-NOT-binding regions of GW182s showed significant acceleration in the accumulation of amino acid changes, suggesting functional adaptation toward higher specificity to the molecules of the silencing complex. We conclude that the silencing ability of the GW182 proteins improves with higher position in the taxonomic classification and increasing complexity of the organism. The first reconstruction of the molecular journey of GW182 proteins from the ancestral metazoan protein to the current mammalian configuration provides new insight into development of the miRNA-dependent post-transcriptional silencing pathway in animals.
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Affiliation(s)
- Andrzej Zielezinski
- a Department of Computational Biology; Institute of Molecular Biology and Biotechnology; Adam Mickiewicz University ; Poznan , Poland
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27
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Wang T, Birsoy K, Hughes NW, Krupczak KM, Post Y, Wei JJ, Lander ES, Sabatini DM. Identification and characterization of essential genes in the human genome. Science 2015; 350:1096-101. [PMID: 26472758 PMCID: PMC4662922 DOI: 10.1126/science.aac7041] [Citation(s) in RCA: 1104] [Impact Index Per Article: 122.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2014] [Accepted: 10/01/2015] [Indexed: 12/13/2022]
Abstract
Large-scale genetic analysis of lethal phenotypes has elucidated the molecular underpinnings of many biological processes. Using the bacterial clustered regularly interspaced short palindromic repeats (CRISPR) system, we constructed a genome-wide single-guide RNA library to screen for genes required for proliferation and survival in a human cancer cell line. Our screen revealed the set of cell-essential genes, which was validated with an orthogonal gene-trap-based screen and comparison with yeast gene knockouts. This set is enriched for genes that encode components of fundamental pathways, are expressed at high levels, and contain few inactivating polymorphisms in the human population. We also uncovered a large group of uncharacterized genes involved in RNA processing, a number of whose products localize to the nucleolus. Last, screens in additional cell lines showed a high degree of overlap in gene essentiality but also revealed differences specific to each cell line and cancer type that reflect the developmental origin, oncogenic drivers, paralogous gene expression pattern, and chromosomal structure of each line. These results demonstrate the power of CRISPR-based screens and suggest a general strategy for identifying liabilities in cancer cells.
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Affiliation(s)
- Tim Wang
- Department of Biology, Massachusetts Institute of Technology, Cambridge MA 02139, USA. Whitehead Institute for Biomedical Research, 9 Cambridge Center, Cambridge, MA 02142, USA. Broad Institute of MIT and Harvard, 7 Cambridge Center, Cambridge, MA 02142, USA. David H. Koch Institute for Integrative Cancer Research at MIT, Cambridge, MA 02139, USA
| | - Kıvanç Birsoy
- Department of Biology, Massachusetts Institute of Technology, Cambridge MA 02139, USA. Whitehead Institute for Biomedical Research, 9 Cambridge Center, Cambridge, MA 02142, USA. Broad Institute of MIT and Harvard, 7 Cambridge Center, Cambridge, MA 02142, USA. David H. Koch Institute for Integrative Cancer Research at MIT, Cambridge, MA 02139, USA
| | - Nicholas W Hughes
- Broad Institute of MIT and Harvard, 7 Cambridge Center, Cambridge, MA 02142, USA
| | - Kevin M Krupczak
- Whitehead Institute for Biomedical Research, 9 Cambridge Center, Cambridge, MA 02142, USA. Broad Institute of MIT and Harvard, 7 Cambridge Center, Cambridge, MA 02142, USA. David H. Koch Institute for Integrative Cancer Research at MIT, Cambridge, MA 02139, USA
| | - Yorick Post
- Whitehead Institute for Biomedical Research, 9 Cambridge Center, Cambridge, MA 02142, USA. Broad Institute of MIT and Harvard, 7 Cambridge Center, Cambridge, MA 02142, USA. David H. Koch Institute for Integrative Cancer Research at MIT, Cambridge, MA 02139, USA
| | - Jenny J Wei
- Department of Biology, Massachusetts Institute of Technology, Cambridge MA 02139, USA. Whitehead Institute for Biomedical Research, 9 Cambridge Center, Cambridge, MA 02142, USA
| | - Eric S Lander
- Department of Biology, Massachusetts Institute of Technology, Cambridge MA 02139, USA. Broad Institute of MIT and Harvard, 7 Cambridge Center, Cambridge, MA 02142, USA. Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA.
| | - David M Sabatini
- Department of Biology, Massachusetts Institute of Technology, Cambridge MA 02139, USA. Whitehead Institute for Biomedical Research, 9 Cambridge Center, Cambridge, MA 02142, USA. Broad Institute of MIT and Harvard, 7 Cambridge Center, Cambridge, MA 02142, USA. David H. Koch Institute for Integrative Cancer Research at MIT, Cambridge, MA 02139, USA. Howard Hughes Medical Institute, Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
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Miura S, Tate S, Kumar S. Using Disease-Associated Coding Sequence Variation to Investigate Functional Compensation by Human Paralogous Proteins. Evol Bioinform Online 2015; 11:245-51. [PMID: 26604664 PMCID: PMC4631161 DOI: 10.4137/ebo.s30594] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2015] [Revised: 09/14/2015] [Accepted: 09/18/2015] [Indexed: 11/09/2022] Open
Abstract
Gene duplication enables the functional diversification in species. It is thought that duplicated genes may be able to compensate if the function of one of the gene copies is disrupted. This possibility is extensively debated with some studies reporting proteome-wide compensation, whereas others suggest functional compensation among only recent gene duplicates or no compensation at all. We report results from a systematic molecular evolutionary analysis to test the predictions of the functional compensation hypothesis. We contrasted the density of Mendelian disease-associated single nucleotide variants (dSNVs) in proteins with no discernable paralogs (singletons) with the dSNV density in proteins found in multigene families. Under the functional compensation hypothesis, we expected to find greater numbers of dSNVs in singletons due to the lack of any compensating partners. Our analyses produced an opposite pattern; paralogs have over 35% higher dSNV density than singletons. We found that these patterns are concordant with similar differences in the rates of amino acid evolution (ie, functional constraints), as the proteins with paralogs have evolved 33% slower than singletons. Our evolutionary constraint explanation is robust to differences in family sizes, ages (young vs. old duplicates), and degrees of amino acid sequence similarities among paralogs. Therefore, disease-associated human variation does not exhibit significant signals of functional compensation among paralogous proteins, but rather an evolutionary constraint hypothesis provides a better explanation for the observed patterns of disease-associated and neutral polymorphisms in the human genome.
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Affiliation(s)
- Sayaka Miura
- Institute for Genomics and Evolutionary Medicine, Temple University, Philadelphia, PA, USA
| | - Stephanie Tate
- School of Life Sciences, Arizona State University, Tempe, AZ, USA
| | - Sudhir Kumar
- Institute for Genomics and Evolutionary Medicine, Temple University, Philadelphia, PA, USA. ; Department of Biology, Temple University, Philadelphia, PA, USA. ; Center for Excellence in Genome Medicine and Research, King Abdulaziz University, Jeddah, Saudi Arabia
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29
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Kryuchkova-Mostacci N, Robinson-Rechavi M. Tissue-Specific Evolution of Protein Coding Genes in Human and Mouse. PLoS One 2015; 10:e0131673. [PMID: 26121354 PMCID: PMC4488272 DOI: 10.1371/journal.pone.0131673] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2015] [Accepted: 06/04/2015] [Indexed: 12/23/2022] Open
Abstract
Protein-coding genes evolve at different rates, and the influence of different parameters, from gene size to expression level, has been extensively studied. While in yeast gene expression level is the major causal factor of gene evolutionary rate, the situation is more complex in animals. Here we investigate these relations further, especially taking in account gene expression in different organs as well as indirect correlations between parameters. We used RNA-seq data from two large datasets, covering 22 mouse tissues and 27 human tissues. Over all tissues, evolutionary rate only correlates weakly with levels and breadth of expression. The strongest explanatory factors of purifying selection are GC content, expression in many developmental stages, and expression in brain tissues. While the main component of evolutionary rate is purifying selection, we also find tissue-specific patterns for sites under neutral evolution and for positive selection. We observe fast evolution of genes expressed in testis, but also in other tissues, notably liver, which are explained by weak purifying selection rather than by positive selection.
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Affiliation(s)
- Nadezda Kryuchkova-Mostacci
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Marc Robinson-Rechavi
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
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30
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Fares MA. The origins of mutational robustness. Trends Genet 2015; 31:373-81. [PMID: 26013677 DOI: 10.1016/j.tig.2015.04.008] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2015] [Revised: 04/27/2015] [Accepted: 04/28/2015] [Indexed: 11/17/2022]
Abstract
Biological systems are resistant to genetic changes; a property known as mutational robustness, the origin of which remains an open question. In recent years, researchers have explored emergent properties of biological systems and mechanisms of genetic redundancy to reveal how mutational robustness emerges and persists. Several mechanisms have been proposed to explain the origin of mutational robustness, including molecular chaperones and gene duplication. The latter has received much attention, but its role in robustness remains controversial. Here, I examine recent findings linking genetic redundancy through gene duplication and mutational robustness. Experimental evolution and genome resequencing have made it possible to test the role of gene duplication in tolerating mutations at both the coding and regulatory levels. This evidence as well as previous findings on regulatory reprogramming of duplicates support the role of gene duplication in the origin of robustness.
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Affiliation(s)
- Mario A Fares
- Instituto de Biología Molecular y Celular de Plantas (CSIC-UPV), Valencia, Spain; Department of Genetics, Smurfit Institute of Genetics, University of Dublin, Trinity College Dublin, Dublin, Ireland.
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Acharya D, Mukherjee D, Podder S, Ghosh TC. Investigating different duplication pattern of essential genes in mouse and human. PLoS One 2015; 10:e0120784. [PMID: 25751152 PMCID: PMC4353620 DOI: 10.1371/journal.pone.0120784] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2014] [Accepted: 01/27/2015] [Indexed: 11/18/2022] Open
Abstract
Gene duplication is one of the major driving forces shaping genome and organism evolution and thought to be itself regulated by some intrinsic properties of the gene. Comparing the essential genes among mouse and human, we observed that the essential genes avoid duplication in mouse while prefer to remain duplicated in humans. In this study, we wanted to explore the reasons behind such differences in gene essentiality by cross-species comparison of human and mouse. Moreover, we examined essential genes that are duplicated in humans are functionally more redundant than that in mouse. The proportion of paralog pseudogenization of essential genes is higher in mouse than that of humans. These duplicates of essential genes are under stringent dosage regulation in human than in mouse. We also observed slower evolutionary rate in the paralogs of human essential genes than the mouse counterpart. Together, these results clearly indicate that human essential genes are retained as duplicates to serve as backed up copies that may shield themselves from harmful mutations.
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Affiliation(s)
- Debarun Acharya
- Bioinformatics Centre, Bose Institute, Kolkata, West Bengal, India
| | - Dola Mukherjee
- Bioinformatics Centre, Bose Institute, Kolkata, West Bengal, India
| | - Soumita Podder
- Bioinformatics Centre, Bose Institute, Kolkata, West Bengal, India
| | - Tapash C. Ghosh
- Bioinformatics Centre, Bose Institute, Kolkata, West Bengal, India
- * E-mail:
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32
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Diversification of the light-harvesting complex gene family via intra- and intergenic duplications in the coral symbiotic alga Symbiodinium. PLoS One 2015; 10:e0119406. [PMID: 25741697 PMCID: PMC4351107 DOI: 10.1371/journal.pone.0119406] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2014] [Accepted: 01/12/2015] [Indexed: 12/22/2022] Open
Abstract
The light-harvesting complex (LHC) is an essential component in light energy capture and transduction to facilitate downstream photosynthetic reactions in plant and algal chloroplasts. The unicellular dinoflagellate alga Symbiodinium is an endosymbiont of cnidarian animals, including corals and sea anemones, and provides carbohydrates generated through photosynthesis to host animals. Although Symbiodinium possesses a unique LHC gene family, called chlorophyll a-chlorophyll c2-peridinin protein complex (acpPC), its genome-level diversity and evolutionary trajectories have not been investigated. Here, we describe a phylogenetic analysis revealing that many of the LHCs are encoded by highly duplicated genes with multi-subunit polyprotein structures in the nuclear genome of Symbiodinium minutum. This analysis provides an extended list of the LHC gene family in a single organism, including 80 loci encoding polyproteins composed of 145 LHC subunits recovered in the phylogenetic tree. In S. minutum, 5 phylogenetic groups of the Lhcf-type gene family, which is exclusively conserved in algae harboring secondary plastids of red algal origin, were identified. Moreover, 5 groups of the Lhcr-type gene family, of which members are known to be associated with PSI in red algal plastids and secondary plastids of red algal origin, were identified. Notably, members classified within a phylogenetic group of the Lhcf-type (group F1) are highly duplicated, which may explain the presence of an unusually large number of LHC genes in this species. Some gene units were homologous to other units within single loci of the polyprotein genes, whereas intergenic homologies between separate loci were conspicuous in other cases, implying that gene unit ‘shuffling’ by gene conversion and/or genome rearrangement might have been a driving force for diversification. These results suggest that vigorous intra- and intergenic gene duplication events have resulted in the genomic framework of photosynthesis in coral symbiont dinoflagellate algae.
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Tanaka K, Diekmann Y, Hazbun A, Hijazi A, Vreede B, Roch F, Sucena É. Multispecies Analysis of Expression Pattern Diversification in the Recently Expanded Insect Ly6 Gene Family. Mol Biol Evol 2015; 32:1730-47. [PMID: 25743545 PMCID: PMC4476152 DOI: 10.1093/molbev/msv052] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Gene families often consist of members with diverse expression domains reflecting their functions in a wide variety of tissues. However, how the expression of individual members, and thus their tissue-specific functions, diversified during the course of gene family expansion is not well understood. In this study, we approached this question through the analysis of the duplication history and transcriptional evolution of a rapidly expanding subfamily of insect Ly6 genes. We analyzed different insect genomes and identified seven Ly6 genes that have originated from a single ancestor through sequential duplication within the higher Diptera. We then determined how the original embryonic expression pattern of the founding gene diversified by characterizing its tissue-specific expression in the beetle Tribolium castaneum, the butterfly Bicyclus anynana, and the mosquito Anopheles stephensi and those of its duplicates in three higher dipteran species, representing various stages of the duplication history (Megaselia abdita, Ceratitis capitata, and Drosophila melanogaster). Our results revealed that frequent neofunctionalization episodes contributed to the increased expression breadth of this subfamily and that these events occurred after duplication and speciation events at comparable frequencies. In addition, at each duplication node, we consistently found asymmetric expression divergence. One paralog inherited most of the tissue-specificities of the founder gene, whereas the other paralog evolved drastically reduced expression domains. Our approach attests to the power of combining a well-established duplication history with a comprehensive coverage of representative species in acquiring unequivocal information about the dynamics of gene expression evolution in gene families.
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Affiliation(s)
| | | | | | - Assia Hijazi
- Centre de Biologie du Développement, CNRS UMR 5547, Université de Toulouse UPS, Toulouse, France
| | | | - Fernando Roch
- Centre de Biologie du Développement, CNRS UMR 5547, Université de Toulouse UPS, Toulouse, France
| | - Élio Sucena
- Instituto Gulbenkian de Ciência, Oeiras, Portugal Departamento de Biologia Animal, Faculdade de Ciências, Edifício C2, Universidade de Lisboa, Lisboa, Portugal
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34
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Singh PP, Affeldt S, Malaguti G, Isambert H. Human dominant disease genes are enriched in paralogs originating from whole genome duplication. PLoS Comput Biol 2014; 10:e1003754. [PMID: 25080083 PMCID: PMC4117431 DOI: 10.1371/journal.pcbi.1003754] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Affiliation(s)
| | - Séverine Affeldt
- CNRS-UMR168, UPMC, Institut Curie, Research Center, Paris, France
| | - Giulia Malaguti
- CNRS-UMR168, UPMC, Institut Curie, Research Center, Paris, France
| | - Hervé Isambert
- CNRS-UMR168, UPMC, Institut Curie, Research Center, Paris, France
- * E-mail:
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35
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Effect of duplicate genes on mouse genetic robustness: an update. BIOMED RESEARCH INTERNATIONAL 2014; 2014:758672. [PMID: 25110693 PMCID: PMC4119742 DOI: 10.1155/2014/758672] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/15/2014] [Revised: 06/15/2014] [Accepted: 06/16/2014] [Indexed: 12/28/2022]
Abstract
In contrast to S. cerevisiae and C. elegans, analyses based on the current knockout (KO) mouse phenotypes led to the conclusion that duplicate genes had almost no role in mouse genetic robustness. It has been suggested that the bias of mouse KO database toward ancient duplicates may possibly cause this knockout duplicate puzzle, that is, a very similar proportion of essential genes (PE) between duplicate genes and singletons. In this paper, we conducted an extensive and careful analysis for the mouse KO phenotype data and corroborated a strong effect of duplicate genes on mouse genetics robustness. Moreover, the effect of duplicate genes on mouse genetic robustness is duplication-age dependent, which holds after ruling out the potential confounding effect from coding-sequence conservation, protein-protein connectivity, functional bias, or the bias of duplicates generated by whole genome duplication (WGD). Our findings suggest that two factors, the sampling bias toward ancient duplicates and very ancient duplicates with a proportion of essential genes higher than that of singletons, have caused the mouse knockout duplicate puzzle; meanwhile, the effect of genetic buffering may be correlated with sequence conservation as well as protein-protein interactivity.
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36
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Chen WH, Zhao XM, van Noort V, Bork P. Comments on "Human dominant disease genes are enriched in paralogs originating from whole genome duplication". PLoS Comput Biol 2014; 10:e1003758. [PMID: 25077479 PMCID: PMC4117415 DOI: 10.1371/journal.pcbi.1003758] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Affiliation(s)
- Wei-Hua Chen
- European Molecular Biology Laboratory (EMBL) Heidelberg, Heidelberg, Germany
| | - Xing-Ming Zhao
- Department of Computer Science, School of Electronics and Information Engineering, Tongji University, Shanghai, China
| | - Vera van Noort
- European Molecular Biology Laboratory (EMBL) Heidelberg, Heidelberg, Germany
| | - Peer Bork
- European Molecular Biology Laboratory (EMBL) Heidelberg, Heidelberg, Germany
- Max-Delbrück-Centrum für Molekulare Medizin (MDC), Berlin, Germany
- * E-mail:
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37
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Hart T, Brown KR, Sircoulomb F, Rottapel R, Moffat J. Measuring error rates in genomic perturbation screens: gold standards for human functional genomics. Mol Syst Biol 2014; 10:733. [PMID: 24987113 PMCID: PMC4299491 DOI: 10.15252/msb.20145216] [Citation(s) in RCA: 218] [Impact Index Per Article: 21.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Technological advancement has opened the door to systematic genetics in mammalian cells.
Genome-scale loss-of-function screens can assay fitness defects induced by partial gene knockdown,
using RNA interference, or complete gene knockout, using new CRISPR techniques. These screens can
reveal the basic blueprint required for cellular proliferation. Moreover, comparing healthy to
cancerous tissue can uncover genes that are essential only in the tumor; these genes are targets for
the development of specific anticancer therapies. Unfortunately, progress in this field has been
hampered by off-target effects of perturbation reagents and poorly quantified error rates in
large-scale screens. To improve the quality of information derived from these screens, and to
provide a framework for understanding the capabilities and limitations of CRISPR technology, we
derive gold-standard reference sets of essential and nonessential genes, and provide a Bayesian
classifier of gene essentiality that outperforms current methods on both RNAi and CRISPR screens.
Our results indicate that CRISPR technology is more sensitive than RNAi and that both techniques
have nontrivial false discovery rates that can be mitigated by rigorous analytical methods.
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Affiliation(s)
- Traver Hart
- Donnelly Centre and Banting and Best Department of Medical Research, University of Toronto, Toronto, ON, Canada
| | - Kevin R Brown
- Donnelly Centre and Banting and Best Department of Medical Research, University of Toronto, Toronto, ON, Canada
| | - Fabrice Sircoulomb
- Campbell Family Cancer Research Institute, Ontario Cancer Institute, Princess Margaret Hospital University Health Network, Toronto, ON, Canada
| | - Robert Rottapel
- Campbell Family Cancer Research Institute, Ontario Cancer Institute, Princess Margaret Hospital University Health Network, Toronto, ON, Canada Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada Division of Rheumatology, Department of Medicine, St. Michael's Hospital, Toronto, ON, Canada
| | - Jason Moffat
- Donnelly Centre and Banting and Best Department of Medical Research, University of Toronto, Toronto, ON, Canada Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
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38
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Tinti M, Dissanayake K, Synowsky S, Albergante L, MacKintosh C. Identification of 2R-ohnologue gene families displaying the same mutation-load skew in multiple cancers. Open Biol 2014; 4:140029. [PMID: 24806839 PMCID: PMC4042849 DOI: 10.1098/rsob.140029] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2014] [Accepted: 04/09/2014] [Indexed: 12/12/2022] Open
Abstract
The complexity of signalling pathways was boosted at the origin of the vertebrates, when two rounds of whole genome duplication (2R-WGD) occurred. Those genes and proteins that have survived from the 2R-WGD-termed 2R-ohnologues-belong to families of two to four members, and are enriched in signalling components relevant to cancer. Here, we find that while only approximately 30% of human transcript-coding genes are 2R-ohnologues, they carry 42-60% of the gene mutations in 30 different cancer types. Across a subset of cancer datasets, including melanoma, breast, lung adenocarcinoma, liver and medulloblastoma, we identified 673 2R-ohnologue families in which one gene carries mutations at multiple positions, while sister genes in the same family are relatively mutation free. Strikingly, in 315 of the 322 2R-ohnologue families displaying such a skew in multiple cancers, the same gene carries the heaviest mutation load in each cancer, and usually the second-ranked gene is also the same in each cancer. Our findings inspire the hypothesis that in certain cancers, heterogeneous combinations of genetic changes impair parts of the 2R-WGD signalling networks and force information flow through a limited set of oncogenic pathways in which specific non-mutated 2R-ohnologues serve as effectors. The non-mutated 2R-ohnologues are therefore potential therapeutic targets. These include proteins linked to growth factor signalling, neurotransmission and ion channels.
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Affiliation(s)
- Michele Tinti
- Division of Cell and Developmental Biology, College of Life Sciences, University of Dundee, Dundee DD1 5EH, UK
| | - Kumara Dissanayake
- Division of Cell and Developmental Biology, College of Life Sciences, University of Dundee, Dundee DD1 5EH, UK
| | - Silvia Synowsky
- MRC Protein Phosphorylation and Ubiquitylation Unit, University of Dundee, Dundee DD1 5EH, UK
| | - Luca Albergante
- Division of Cell and Developmental Biology, College of Life Sciences, University of Dundee, Dundee DD1 5EH, UK
- Division of Computational Biology, College of Life Sciences, University of Dundee, Dundee DD1 5EH, UK
| | - Carol MacKintosh
- Division of Cell and Developmental Biology, College of Life Sciences, University of Dundee, Dundee DD1 5EH, UK
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Tamate SC, Kawata M, Makino T. Contribution of nonohnologous duplicated genes to high habitat variability in mammals. Mol Biol Evol 2014; 31:1779-86. [PMID: 24714078 DOI: 10.1093/molbev/msu128] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The mechanism by which genetic systems affect environmental adaptation is a focus of considerable attention in the fields of ecology, evolution, and conservation. However, the genomic characteristics that constrain adaptive evolution have remained unknown. A recent study showed that the proportion of duplicated genes in whole Drosophila genomes correlated with environmental variability within habitat, but it remains unclear whether the correlation is observed even in vertebrates whose genomes including a large number of duplicated genes generated by whole-genome duplication (WGD). Here, we focus on fully sequenced mammalian genomes that experienced WGD in early vertebrate lineages and show that the proportion of small-scale duplication (SSD) genes in the genome, but not that of WGD genes, is significantly correlated with habitat variability. Moreover, species with low habitat variability have a higher proportion of lost duplicated genes, particularly SSD genes, than those with high habitat variability. These results indicate that species that inhabit variable environments may maintain more SSD genes in their genomes and suggest that SSD genes are important for adapting to novel environments and surviving environmental changes. These insights may be applied to predicting invasive and endangered species.
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Affiliation(s)
- Satoshi C Tamate
- Department of Ecology and Evolutionary Biology, Graduate School of Life Sciences, Tohoku University, Aoba-ku, Sendai, Japan
| | - Masakado Kawata
- Department of Ecology and Evolutionary Biology, Graduate School of Life Sciences, Tohoku University, Aoba-ku, Sendai, Japan
| | - Takashi Makino
- Department of Ecology and Evolutionary Biology, Graduate School of Life Sciences, Tohoku University, Aoba-ku, Sendai, JapanDepartment of Ecology and Evolutionary Biology, Graduate School of Life Sciences, Tohoku University, Aoba-ku, Sendai, Japan
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Abstract
A number of rare copy number variants (CNVs), including both deletions and duplications, have been associated with developmental disorders, including schizophrenia, autism, intellectual disability, and epilepsy. Pathogenicity may derive from dosage sensitivity of one or more genes contained within the CNV locus. To understand pathophysiology, the specific disease-causing gene(s) within each CNV need to be identified. In the present study, we test the hypothesis that ohnologs (genes retained after ancestral whole-genome duplication events, which are frequently dosage sensitive) are overrepresented in pathogenic CNVs. We selected three sets of genes implicated in copy number pathogenicity: (i) genes mapping within rare disease-associated CNVs, (ii) genes within de novo CNVs under negative genetic selection, and (iii) genes identified by clinical array comparative genome hybridization studies as potentially pathogenic. We compared the proportion of ohnologs between these gene sets and control genes, mapping to CNVs not known to be disease associated. We found that ohnologs are significantly overrepresented in genes mapping to pathogenic CNVs, irrespective of how CNVs were identified, with over 90% containing an ohnolog, compared with control CNVs >100 kb, where only about 30% contained an ohnolog. In some CNVs, such as del15p11.2 (CYFIP1) and dup/del16p13.11 (NDE1), the most plausible prior candidate gene was also an ohnolog, as were the genes VIPR2 and NRXN1, each found in short CNVs containing no other genes. Our results support the hypothesis that ohnologs represent critical dosage-sensitive elements of the genome, possibly responsible for some of the deleterious phenotypes observed for pathogenic CNVs and as such are readily identifiable candidate genes for further study.
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41
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Cheng J, Wu W, Zhang Y, Li X, Jiang X, Wei G, Tao S. A new computational strategy for predicting essential genes. BMC Genomics 2013; 14:910. [PMID: 24359534 PMCID: PMC3880044 DOI: 10.1186/1471-2164-14-910] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2013] [Accepted: 11/29/2013] [Indexed: 12/17/2022] Open
Abstract
Background Determination of the minimum gene set for cellular life is one of the central goals in biology. Genome-wide essential gene identification has progressed rapidly in certain bacterial species; however, it remains difficult to achieve in most eukaryotic species. Several computational models have recently been developed to integrate gene features and used as alternatives to transfer gene essentiality annotations between organisms. Results We first collected features that were widely used by previous predictive models and assessed the relationships between gene features and gene essentiality using a stepwise regression model. We found two issues that could significantly reduce model accuracy: (i) the effect of multicollinearity among gene features and (ii) the diverse and even contrasting correlations between gene features and gene essentiality existing within and among different species. To address these issues, we developed a novel model called feature-based weighted Naïve Bayes model (FWM), which is based on Naïve Bayes classifiers, logistic regression, and genetic algorithm. The proposed model assesses features and filters out the effects of multicollinearity and diversity. The performance of FWM was compared with other popular models, such as support vector machine, Naïve Bayes model, and logistic regression model, by applying FWM to reciprocally predict essential genes among and within 21 species. Our results showed that FWM significantly improves the accuracy and robustness of essential gene prediction. Conclusions FWM can remarkably improve the accuracy of essential gene prediction and may be used as an alternative method for other classification work. This method can contribute substantially to the knowledge of the minimum gene sets required for living organisms and the discovery of new drug targets.
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Affiliation(s)
| | | | | | | | | | - Gehong Wei
- College of Life Science, State Key Laboratory of Crop Stress Biology for Arid Areas, Northwest A&F University, Yangling, Shaanxi, China.
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42
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Abstract
During the course of evolution, genomes acquire novel genetic elements as sources of functional and phenotypic diversity, including new genes that originated in recent evolution. In the past few years, substantial progress has been made in understanding the evolution and phenotypic effects of new genes. In particular, an emerging picture is that new genes, despite being present in the genomes of only a subset of species, can rapidly evolve indispensable roles in fundamental biological processes, including development, reproduction, brain function and behaviour. The molecular underpinnings of how new genes can develop these roles are starting to be characterized. These recent discoveries yield fresh insights into our broad understanding of biological diversity at refined resolution.
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43
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White JK, Gerdin AK, Karp NA, Ryder E, Buljan M, Bussell JN, Salisbury J, Clare S, Ingham NJ, Podrini C, Houghton R, Estabel J, Bottomley JR, Melvin DG, Sunter D, Adams NC, Tannahill D, Logan DW, Macarthur DG, Flint J, Mahajan VB, Tsang SH, Smyth I, Watt FM, Skarnes WC, Dougan G, Adams DJ, Ramirez-Solis R, Bradley A, Steel KP. Genome-wide generation and systematic phenotyping of knockout mice reveals new roles for many genes. Cell 2013; 154:452-64. [PMID: 23870131 PMCID: PMC3717207 DOI: 10.1016/j.cell.2013.06.022] [Citation(s) in RCA: 378] [Impact Index Per Article: 34.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2013] [Revised: 05/10/2013] [Accepted: 06/17/2013] [Indexed: 02/06/2023]
Abstract
Mutations in whole organisms are powerful ways of interrogating gene function in a realistic context. We describe a program, the Sanger Institute Mouse Genetics Project, that provides a step toward the aim of knocking out all genes and screening each line for a broad range of traits. We found that hitherto unpublished genes were as likely to reveal phenotypes as known genes, suggesting that novel genes represent a rich resource for investigating the molecular basis of disease. We found many unexpected phenotypes detected only because we screened for them, emphasizing the value of screening all mutants for a wide range of traits. Haploinsufficiency and pleiotropy were both surprisingly common. Forty-two percent of genes were essential for viability, and these were less likely to have a paralog and more likely to contribute to a protein complex than other genes. Phenotypic data and more than 900 mutants are openly available for further analysis. PaperClip
Large openly available resource of targeted mouse mutants and phenotypic data Screen for broad range of disease features and traits Many novel phenotypes suggest functions for both studied and unstudied genes Haploinsufficiency and pleiotropy are common
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44
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Bush SJ, Castillo-Morales A, Tovar-Corona JM, Chen L, Kover PX, Urrutia AO. Presence-absence variation in A. thaliana is primarily associated with genomic signatures consistent with relaxed selective constraints. Mol Biol Evol 2013; 31:59-69. [PMID: 24072814 PMCID: PMC3879440 DOI: 10.1093/molbev/mst166] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
The sequencing of multiple genomes of the same plant species has revealed polymorphic gene and exon loss. Genes associated with disease resistance are overrepresented among those showing structural variations, suggesting an adaptive role for gene and exon presence–absence variation (PAV). To shed light on the possible functional relevance of polymorphic coding region loss and the mechanisms driving this process, we characterized genes that have lost entire exons or their whole coding regions in 17 fully sequenced Arabidopsis thaliana accessions. We found that although a significant enrichment in genes associated with certain functional categories is observed, PAV events are largely restricted to genes with signatures of reduced essentiality: PAV genes tend to be newer additions to the genome, tissue specific, and lowly expressed. In addition, PAV genes are located in regions of lower gene density and higher transposable element density. Partial coding region PAV events were associated with only a marginal reduction in gene expression level in the affected accession and occurred in genes with higher levels of alternative splicing in the Col-0 accession. Together, these results suggest that although adaptive scenarios cannot be ruled out, PAV events can be explained without invoking them.
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Affiliation(s)
- Stephen J Bush
- Department of Biology and Biochemistry, University of Bath, Bath, United Kingdom
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45
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Capra JA, Stolzer M, Durand D, Pollard KS. How old is my gene? Trends Genet 2013; 29:659-68. [PMID: 23915718 DOI: 10.1016/j.tig.2013.07.001] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2013] [Revised: 06/13/2013] [Accepted: 07/03/2013] [Indexed: 11/26/2022]
Abstract
Gene functions, interactions, disease associations, and ecological distributions are all correlated with gene age. However, it is challenging to estimate the intricate series of evolutionary events leading to a modern-day gene and then to reduce this history to a single age estimate. Focusing on eukaryotic gene families, we introduce a framework that can be used to compare current strategies for quantifying gene age, discuss key differences between these methods, and highlight several common problems. We argue that genes with complex evolutionary histories do not have a single well-defined age. As a result, care must be taken to articulate the goals and assumptions of any analysis that uses gene age estimates. Recent algorithmic advances offer the promise of gene age estimates that are fast, accurate, and consistent across gene families. This will enable a shift to integrated genome-wide analyses of all events in gene evolutionary histories in the near future.
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Affiliation(s)
- John A Capra
- Center for Human Genetics Research and Department of Biomedical Informatics, Vanderbilt University, Nashville, TN 37232, USA
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Alvarez-Ponce D, Fares MA. Evolutionary rate and duplicability in the Arabidopsis thaliana protein-protein interaction network. Genome Biol Evol 2013; 4:1263-74. [PMID: 23160177 PMCID: PMC3542556 DOI: 10.1093/gbe/evs101] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Genes show a bewildering variation in their patterns of molecular evolution, as a result of the action of different levels and types of selective forces. The factors underlying this variation are, however, still poorly understood. In the last decade, the position of proteins in the protein-protein interaction network has been put forward as a determinant factor of the evolutionary rate and duplicability of their encoding genes. This conclusion, however, has been based on the analysis of the limited number of microbes and animals for which interactome-level data are available (essentially, Escherichia coli, yeast, worm, fly, and humans). Here, we study, for the first time, the relationship between the position of proteins in the high-density interactome of a plant (Arabidopsis thaliana) and the patterns of molecular evolution of their encoding genes. We found that genes whose encoded products act at the center of the network are more evolutionarily constrained than those acting at the network periphery. This trend remains significant when potential confounding factors (gene expression level and breadth, duplicability, function, and length of the encoded products) are controlled for. Even though the correlation between centrality measures and rates of evolution is generally weak, for some functional categories, it is comparable in strength to (or even stronger than) the correlation between evolutionary rates and expression levels or breadths. In addition, genes encoding interacting proteins in the network evolve at relatively similar rates. Finally, Arabidopsis proteins encoded by duplicated genes are more highly connected than those encoded by singleton genes. This observation is in agreement with the patterns observed in humans, but in contrast with those observed in E. coli, yeast, worm, and fly (whose duplicated genes tend to act at the periphery of the network), implying that the relationship between duplicability and centrality inverted at least twice during eukaryote evolution. Taken together, these results indicate that the structure of the A. thaliana network constrains the evolution of its components at multiple levels.
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Affiliation(s)
- David Alvarez-Ponce
- Department of Abiotic Stress, Integrative and Systems Biology Laboratory, Instituto de Biología Molecular y Celular de Plantas, Consejo Superior de Investigaciones Científicias (CSIC-UPV), Valencia, Spain.
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Woods S, Coghlan A, Rivers D, Warnecke T, Jeffries SJ, Kwon T, Rogers A, Hurst LD, Ahringer J. Duplication and retention biases of essential and non-essential genes revealed by systematic knockdown analyses. PLoS Genet 2013; 9:e1003330. [PMID: 23675306 PMCID: PMC3649981 DOI: 10.1371/journal.pgen.1003330] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2012] [Accepted: 01/04/2013] [Indexed: 11/19/2022] Open
Abstract
When a duplicate gene has no apparent loss-of-function phenotype, it is commonly considered that the phenotype has been masked as a result of functional redundancy with the remaining paralog. This is supported by indirect evidence showing that multi-copy genes show loss-of-function phenotypes less often than single-copy genes and by direct tests of phenotype masking using select gene sets. Here we take a systematic genome-wide RNA interference approach to assess phenotype masking in paralog pairs in the Caenorhabditis elegans genome. Remarkably, in contrast to expectations, we find that phenotype masking makes only a minor contribution to the low knockdown phenotype rate for duplicate genes. Instead, we find that non-essential genes are highly over-represented among duplicates, leading to a low observed loss-of-function phenotype rate. We further find that duplicate pairs derived from essential and non-essential genes have contrasting evolutionary dynamics: whereas non-essential genes are both more often successfully duplicated (fixed) and lost, essential genes are less often duplicated but upon successful duplication are maintained over longer periods. We expect the fundamental evolutionary duplication dynamics presented here to be broadly applicable. Duplicate genes occur in all organisms. It has been found that mutations in duplicate genes cause defects much less often than when single copy genes are mutated. It is widely believed that this is due to functional redundancy—that is, the two genes can carry out similar functions so that the non-mutated duplicate gene can cover for or “mask” the phenotype of the mutation in the first duplicate. To determine whether this hypothesis is true, it is necessary to test systematically whether defects indeed occur in the organism when both duplicate genes are inhibited. We have for the first time carried out such an analysis in a multicellular organism, the nematode Caenorhabditis elegans. In contrast to expectations, we observed that when both copies of duplicate genes are inhibited deleterious effects are very rare. We show that this is because duplicate genes are much more often non-essential compared to genes where there is only a single copy. Non-essential genes are also lost from the genome much more often than essential genes. However, when essential genes are duplicated, they remain present in the genome over longer periods. Our results give a framework to explain the evolutionary dynamics of duplications in the genome.
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Affiliation(s)
- Shane Woods
- The Gurdon Institute and Department of Genetics, University of Cambridge, Cambridge, United Kingdom
| | - Avril Coghlan
- Department of Microbiology, University College Cork, Cork, Ireland
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom
| | - David Rivers
- The Gurdon Institute and Department of Genetics, University of Cambridge, Cambridge, United Kingdom
| | - Tobias Warnecke
- Department of Biology and Biochemistry, University of Bath, Bath, Somerset, United Kingdom
| | - Sean J. Jeffries
- The Gurdon Institute and Department of Genetics, University of Cambridge, Cambridge, United Kingdom
| | - Taejoon Kwon
- The Gurdon Institute and Department of Genetics, University of Cambridge, Cambridge, United Kingdom
| | - Anthony Rogers
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Laurence D. Hurst
- Department of Biology and Biochemistry, University of Bath, Bath, Somerset, United Kingdom
- * E-mail: (LDH); (JA)
| | - Julie Ahringer
- The Gurdon Institute and Department of Genetics, University of Cambridge, Cambridge, United Kingdom
- * E-mail: (LDH); (JA)
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Talavera D, Robertson DL, Lovell SC. The role of protein interactions in mediating essentiality and synthetic lethality. PLoS One 2013; 8:e62866. [PMID: 23638160 PMCID: PMC3639263 DOI: 10.1371/journal.pone.0062866] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2012] [Accepted: 03/27/2013] [Indexed: 11/18/2022] Open
Abstract
Genes are characterized as essential if their knockout is associated with a lethal phenotype, and these "essential genes" play a central role in biological function. In addition, some genes are only essential when deleted in pairs, a phenomenon known as synthetic lethality. Here we consider genes displaying synthetic lethality as "essential pairs" of genes, and analyze the properties of yeast essential genes and synthetic lethal pairs together. As gene duplication initially produces an identical pair or sets of genes, it is often invoked as an explanation for synthetic lethality. However, we find that duplication explains only a minority of cases of synthetic lethality. Similarly, disruption of metabolic pathways leads to relatively few examples of synthetic lethality. By contrast, the vast majority of synthetic lethal gene pairs code for proteins with related functions that share interaction partners. We also find that essential genes and synthetic lethal pairs cluster in the protein-protein interaction network. These results suggest that synthetic lethality is strongly dependent on the formation of protein-protein interactions. Compensation by duplicates does not usually occur mainly because the genes involved are recent duplicates, but is more commonly due to functional similarity that permits preservation of essential protein complexes. This unified view, combining genes that are individually essential with those that form essential pairs, suggests that essentiality is a feature of physical interactions between proteins protein-protein interactions, rather than being inherent in gene and protein products themselves.
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Affiliation(s)
- David Talavera
- Faculty of Life Sciences, University of Manchester, Manchester, United Kingdom
| | - David L. Robertson
- Faculty of Life Sciences, University of Manchester, Manchester, United Kingdom
| | - Simon C. Lovell
- Faculty of Life Sciences, University of Manchester, Manchester, United Kingdom
- * E-mail:
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Tropeano M, Ahn JW, Dobson RJB, Breen G, Rucker J, Dixit A, Pal DK, McGuffin P, Farmer A, White PS, Andrieux J, Vassos E, Ogilvie CM, Curran S, Collier DA. Male-biased autosomal effect of 16p13.11 copy number variation in neurodevelopmental disorders. PLoS One 2013; 8:e61365. [PMID: 23637818 PMCID: PMC3630198 DOI: 10.1371/journal.pone.0061365] [Citation(s) in RCA: 95] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2012] [Accepted: 03/08/2013] [Indexed: 01/26/2023] Open
Abstract
Copy number variants (CNVs) at chromosome 16p13.11 have been associated with a range of neurodevelopmental disorders including autism, ADHD, intellectual disability and schizophrenia. Significant sex differences in prevalence, course and severity have been described for a number of these conditions but the biological and environmental factors underlying such sex-specific features remain unclear. We tested the burden and the possible sex-biased effect of CNVs at 16p13.11 in a sample of 10,397 individuals with a range of neurodevelopmental conditions, clinically referred for array comparative genomic hybridisation (aCGH); cases were compared with 11,277 controls. In order to identify candidate phenotype-associated genes, we performed an interval-based analysis and investigated the presence of ohnologs at 16p13.11; finally, we searched the DECIPHER database for previously identified 16p13.11 copy number variants. In the clinical referral series, we identified 46 cases with CNVs of variable size at 16p13.11, including 28 duplications and 18 deletions. Patients were referred for various phenotypes, including developmental delay, autism, speech delay, learning difficulties, behavioural problems, epilepsy, microcephaly and physical dysmorphisms. CNVs at 16p13.11 were also present in 17 controls. Association analysis revealed an excess of CNVs in cases compared with controls (OR = 2.59; p = 0.0005), and a sex-biased effect, with a significant enrichment of CNVs only in the male subgroup of cases (OR = 5.62; p = 0.0002), but not in females (OR = 1.19, p = 0.673). The same pattern of results was also observed in the DECIPHER sample. Interval-based analysis showed a significant enrichment of case CNVs containing interval II (OR = 2.59; p = 0.0005), located in the 0.83 Mb genomic region between 15.49-16.32 Mb, and encompassing the four ohnologs NDE1, MYH11, ABCC1 and ABCC6. Our data confirm that duplications and deletions at 16p13.11 represent incompletely penetrant pathogenic mutations that predispose to a range of neurodevelopmental disorders, and suggest a sex-limited effect on the penetrance of the pathological phenotypes at the 16p13.11 locus.
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Affiliation(s)
- Maria Tropeano
- MRC Social, Genetic and Developmental Psychiatry Centre, Institute of Psychiatry, King’s College London, London, United Kingdom
| | - Joo Wook Ahn
- Department of Cytogenetics, Guy's and St Thomas’ NHS Foundation Trust, London, United Kingdom
| | - Richard J. B. Dobson
- MRC Social, Genetic and Developmental Psychiatry Centre, Institute of Psychiatry, King’s College London, London, United Kingdom
| | - Gerome Breen
- MRC Social, Genetic and Developmental Psychiatry Centre, Institute of Psychiatry, King’s College London, London, United Kingdom
| | - James Rucker
- MRC Social, Genetic and Developmental Psychiatry Centre, Institute of Psychiatry, King’s College London, London, United Kingdom
| | - Abhishek Dixit
- MRC Social, Genetic and Developmental Psychiatry Centre, Institute of Psychiatry, King’s College London, London, United Kingdom
| | - Deb K. Pal
- Department of Clinical Neuroscience, Institute of Psychiatry, King’s College London, London, United Kingdom
| | - Peter McGuffin
- MRC Social, Genetic and Developmental Psychiatry Centre, Institute of Psychiatry, King’s College London, London, United Kingdom
| | - Anne Farmer
- MRC Social, Genetic and Developmental Psychiatry Centre, Institute of Psychiatry, King’s College London, London, United Kingdom
| | - Peter S. White
- Center for Biomedical Informatics, The Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, United States of America
- Division of Oncology, The Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, United States of America
| | - Joris Andrieux
- Institut de Génétique Médicale, CHRU de Lille, Lille, France
| | - Evangelos Vassos
- MRC Social, Genetic and Developmental Psychiatry Centre, Institute of Psychiatry, King’s College London, London, United Kingdom
| | - Caroline Mackie Ogilvie
- Department of Cytogenetics, Guy's and St Thomas’ NHS Foundation Trust, London, United Kingdom
| | - Sarah Curran
- MRC Social, Genetic and Developmental Psychiatry Centre, Institute of Psychiatry, King’s College London, London, United Kingdom
| | - David A Collier
- MRC Social, Genetic and Developmental Psychiatry Centre, Institute of Psychiatry, King’s College London, London, United Kingdom
- Discovery Neuroscience Research, Eli Lilly and Company Ltd, Lilly Research Laboratories, Erl Wood Manor, Windlesham, Surrey, United Kingdom
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50
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Doherty A, Alvarez-Ponce D, McInerney JO. Increased genome sampling reveals a dynamic relationship between gene duplicability and the structure of the primate protein-protein interaction network. Mol Biol Evol 2012; 29:3563-73. [PMID: 22723304 DOI: 10.1093/molbev/mss165] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
Although gene duplications occur at a higher rate, only a small fraction of these are retained. The position of a gene's encoded product in the protein-protein interaction network has recently emerged as a determining factor of gene duplicability. However, the direction of the relationship between network centrality and duplicability is not universal: In Escherichia coli, yeast, fly, and worm, duplicated genes more often act at the periphery of the network, whereas in humans, such genes tend to occupy the most central positions. Herein, we have inferred duplication events that took place in the different branches of the primate phylogeny. In agreement with previous observations, we found that duplications generally affected the most central network genes, which is presumably the process that has most influenced the trend in humans. However, the opposite trend--that is, duplication being more common in genes whose encoded products are peripheral in the network--is observed for three recent branches, including, quite counterintuitively, the external branch leading to humans. This indicates a shift in the relationship between centrality and duplicability during primate evolution. Furthermore, we found that genes encoding interacting proteins exhibit phylogenetic tree topologies that are more similar than expected for random pairs and that genes duplicated in a given branch of the phylogeny tend to interact with those that duplicated in the same lineage. These results indicate that duplication of a gene increases the likelihood of duplication of its interacting partners. Our observations indicate that the structure of the primate protein-protein interaction network affects gene duplicability in previously unrecognized ways.
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Affiliation(s)
- Aoife Doherty
- Department of Biology, National University of Ireland Maynooth, Maynooth, County Kildare, Ireland
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