1
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Crossley ER, Fedorova L, Mulyar O, Freeman R, Khuder S, Fedorov A. Computational identification of ultra-conserved elements in the human genome: a hypothesis on homologous DNA pairing. NAR Genom Bioinform 2024; 6:lqae074. [PMID: 38962254 PMCID: PMC11217675 DOI: 10.1093/nargab/lqae074] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2024] [Revised: 05/29/2024] [Accepted: 06/19/2024] [Indexed: 07/05/2024] Open
Abstract
Thousands of prolonged sequences of human ultra-conserved non-coding elements (UCNEs) share only one common feature: peculiarities in the unique composition of their dinucleotides. Here we investigate whether the numerous weak signals emanating from these dinucleotide arrangements can be used for computational identification of UCNEs within the human genome. For this purpose, we analyzed 4272 UCNE sequences, encompassing 1 393 448 nucleotides, alongside equally sized control samples of randomly selected human genomic sequences. Our research identified nine different features of dinucleotide arrangements that enable differentiation of UCNEs from the rest of the genome. We employed these nine features, implementing three Machine Learning techniques - Support Vector Machine, Random Forest, and Artificial Neural Networks - to classify UCNEs, achieving an accuracy rate of 82-84%, with specific conditions allowing for over 90% accuracy. Notably, the strongest feature for UCNE identification was the frequency ratio between GpC dinucleotides and the sum of GpG and CpC dinucleotides. Additionally, we investigated the entire pool of 31 046 SNPs located within UCNEs for their representation in the ClinVar database, which catalogs human SNPs with known phenotypic effects. The presence of UCNE-associated SNPs in ClinVar aligns with the expectation of a random distribution, emphasizing the enigmatic nature of UCNE phenotypic manifestation.
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Affiliation(s)
- Emily R Crossley
- Program of Bioinformatics and Proteomics/Genomics, University of Toledo, Toledo, OH 43606, USA
| | | | | | | | - Sadik Khuder
- Program of Bioinformatics and Proteomics/Genomics, University of Toledo, Toledo, OH 43606, USA
- Department of Medicine, University of Toledo, Toledo, OH 43606, USA
| | - Alexei Fedorov
- Program of Bioinformatics and Proteomics/Genomics, University of Toledo, Toledo, OH 43606, USA
- CRI Genetics LLC, Santa Monica, CA 90404, USA
- Department of Medicine, University of Toledo, Toledo, OH 43606, USA
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2
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Gibert MK, Sarkar A, Chagari B, Roig-Laboy C, Saha S, Bednarek S, Kefas B, Hanif F, Hudson K, Dube C, Zhang Y, Abounader R. Transcribed Ultraconserved Regions in Cancer. Cells 2022; 11:1684. [PMID: 35626721 PMCID: PMC9139194 DOI: 10.3390/cells11101684] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2022] [Revised: 05/11/2022] [Accepted: 05/17/2022] [Indexed: 11/25/2022] Open
Abstract
Transcribed ultraconserved regions are putative lncRNA molecules that are transcribed from DNA that is 100% conserved in human, mouse, and rat genomes. This is notable, as lncRNAs are typically poorly conserved. TUCRs remain very understudied in many diseases, including cancer. In this review, we summarize the current literature on TUCRs in cancer with respect to expression deregulation, functional roles, mechanisms of action, and clinical perspectives.
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Affiliation(s)
- Myron K. Gibert
- Department of Microbiology, Immunology, and Cancer Biology, School of Medicine, University of Virginia, Charlottesville, VA 22908, USA; (M.K.G.J.); (A.S.); (B.C.); (C.R.-L.); (S.S.); (S.B.); (B.K.); (F.H.); (K.H.); (C.D.); (Y.Z.)
| | - Aditya Sarkar
- Department of Microbiology, Immunology, and Cancer Biology, School of Medicine, University of Virginia, Charlottesville, VA 22908, USA; (M.K.G.J.); (A.S.); (B.C.); (C.R.-L.); (S.S.); (S.B.); (B.K.); (F.H.); (K.H.); (C.D.); (Y.Z.)
| | - Bilhan Chagari
- Department of Microbiology, Immunology, and Cancer Biology, School of Medicine, University of Virginia, Charlottesville, VA 22908, USA; (M.K.G.J.); (A.S.); (B.C.); (C.R.-L.); (S.S.); (S.B.); (B.K.); (F.H.); (K.H.); (C.D.); (Y.Z.)
| | - Christian Roig-Laboy
- Department of Microbiology, Immunology, and Cancer Biology, School of Medicine, University of Virginia, Charlottesville, VA 22908, USA; (M.K.G.J.); (A.S.); (B.C.); (C.R.-L.); (S.S.); (S.B.); (B.K.); (F.H.); (K.H.); (C.D.); (Y.Z.)
| | - Shekhar Saha
- Department of Microbiology, Immunology, and Cancer Biology, School of Medicine, University of Virginia, Charlottesville, VA 22908, USA; (M.K.G.J.); (A.S.); (B.C.); (C.R.-L.); (S.S.); (S.B.); (B.K.); (F.H.); (K.H.); (C.D.); (Y.Z.)
| | - Sylwia Bednarek
- Department of Microbiology, Immunology, and Cancer Biology, School of Medicine, University of Virginia, Charlottesville, VA 22908, USA; (M.K.G.J.); (A.S.); (B.C.); (C.R.-L.); (S.S.); (S.B.); (B.K.); (F.H.); (K.H.); (C.D.); (Y.Z.)
| | - Benjamin Kefas
- Department of Microbiology, Immunology, and Cancer Biology, School of Medicine, University of Virginia, Charlottesville, VA 22908, USA; (M.K.G.J.); (A.S.); (B.C.); (C.R.-L.); (S.S.); (S.B.); (B.K.); (F.H.); (K.H.); (C.D.); (Y.Z.)
| | - Farina Hanif
- Department of Microbiology, Immunology, and Cancer Biology, School of Medicine, University of Virginia, Charlottesville, VA 22908, USA; (M.K.G.J.); (A.S.); (B.C.); (C.R.-L.); (S.S.); (S.B.); (B.K.); (F.H.); (K.H.); (C.D.); (Y.Z.)
| | - Kadie Hudson
- Department of Microbiology, Immunology, and Cancer Biology, School of Medicine, University of Virginia, Charlottesville, VA 22908, USA; (M.K.G.J.); (A.S.); (B.C.); (C.R.-L.); (S.S.); (S.B.); (B.K.); (F.H.); (K.H.); (C.D.); (Y.Z.)
| | - Collin Dube
- Department of Microbiology, Immunology, and Cancer Biology, School of Medicine, University of Virginia, Charlottesville, VA 22908, USA; (M.K.G.J.); (A.S.); (B.C.); (C.R.-L.); (S.S.); (S.B.); (B.K.); (F.H.); (K.H.); (C.D.); (Y.Z.)
| | - Ying Zhang
- Department of Microbiology, Immunology, and Cancer Biology, School of Medicine, University of Virginia, Charlottesville, VA 22908, USA; (M.K.G.J.); (A.S.); (B.C.); (C.R.-L.); (S.S.); (S.B.); (B.K.); (F.H.); (K.H.); (C.D.); (Y.Z.)
| | - Roger Abounader
- Department of Microbiology, Immunology, and Cancer Biology, School of Medicine, University of Virginia, Charlottesville, VA 22908, USA; (M.K.G.J.); (A.S.); (B.C.); (C.R.-L.); (S.S.); (S.B.); (B.K.); (F.H.); (K.H.); (C.D.); (Y.Z.)
- Department of Neurology, School of Medicine, University of Virginia, Charlottesville, VA 22908, USA
- NCI Designated Comprehensive Cancer Center, University of Virginia, Charlottesville, VA 22908, USA
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3
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Functional and structural basis of extreme conservation in vertebrate 5' untranslated regions. Nat Genet 2021; 53:729-741. [PMID: 33821006 PMCID: PMC8825242 DOI: 10.1038/s41588-021-00830-1] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2020] [Accepted: 02/26/2021] [Indexed: 01/07/2023]
Abstract
The lack of knowledge about extreme conservation in genomes remains a major gap in our understanding of the evolution of gene regulation. Here, we reveal an unexpected role of extremely conserved 5' untranslated regions (UTRs) in noncanonical translational regulation that is linked to the emergence of essential developmental features in vertebrate species. Endogenous deletion of conserved elements within these 5' UTRs decreased gene expression, and extremely conserved 5' UTRs possess cis-regulatory elements that promote cell-type-specific regulation of translation. We further developed in-cell mutate-and-map (icM2), a new methodology that maps RNA structure inside cells. Using icM2, we determined that an extremely conserved 5' UTR encodes multiple alternative structures and that each single nucleotide within the conserved element maintains the balance of alternative structures important to control the dynamic range of protein expression. These results explain how extreme sequence conservation can lead to RNA-level biological functions encoded in the untranslated regions of vertebrate genomes.
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4
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Woerner AE, Veeramah KR, Watkins JC, Hammer MF. The Role of Phylogenetically Conserved Elements in Shaping Patterns of Human Genomic Diversity. Mol Biol Evol 2020; 35:2284-2295. [PMID: 30113695 DOI: 10.1093/molbev/msy145] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
Evolutionary genetic studies have shown a positive correlation between levels of nucleotide diversity and either rates of recombination or genetic distance to genes. Both positive-directional and purifying selection have been offered as the source of these correlations via genetic hitchhiking and background selection, respectively. Phylogenetically conserved elements (CEs) are short (∼100 bp), widely distributed (comprising ∼5% of genome), sequences that are often found far from genes. While the function of many CEs is unknown, CEs also are associated with reduced diversity at linked sites. Using high coverage (>80×) whole genome data from two human populations, the Yoruba and the CEU, we perform fine scale evaluations of diversity, rates of recombination, and linkage to genes. We find that the local rate of recombination has a stronger effect on levels of diversity than linkage to genes, and that these effects of recombination persist even in regions far from genes. Our whole genome modeling demonstrates that, rather than recombination or GC-biased gene conversion, selection on sites within or linked to CEs better explains the observed genomic diversity patterns. A major implication is that very few sites in the human genome are predicted to be free of the effects of selection. These sites, which we refer to as the human "neutralome," comprise only 1.2% of the autosomes and 5.1% of the X chromosome. Demographic analysis of the neutralome reveals larger population sizes and lower rates of growth for ancestral human populations than inferred by previous analyses.
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Affiliation(s)
- August E Woerner
- ARL Division of Biotechnology, University of Arizona, Tucson, AZ.,Center for Human Identification, University of North Texas Health Science Center, Fort Worth, TX
| | - Krishna R Veeramah
- Department of Ecology and Evolution, Stony Brook University, Stony Brook, NY
| | | | - Michael F Hammer
- ARL Division of Biotechnology, University of Arizona, Tucson, AZ
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5
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Igoshin AV, Gunbin KV, Yudin NS, Voevoda MI. Searching for Signatures of Cold Climate Adaptation in TRPM8 Gene in Populations of East Asian Ancestry. Front Genet 2019; 10:759. [PMID: 31507633 PMCID: PMC6716346 DOI: 10.3389/fgene.2019.00759] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2018] [Accepted: 07/17/2019] [Indexed: 12/14/2022] Open
Abstract
Dispersal of Homo sapiens across the globe during the last 200,000 years was accompanied by adaptation to local climatic conditions, with severe winter temperatures being probably one of the most significant selective forces. The TRPM8 gene codes for a cold-sensing ion channel, and adaptation to low temperatures is the major determinant of its molecular evolution. Here, our aim was to search for signatures of cold climate adaptation in TRPM8 gene using a combined data set of 19 populations of East Asian ancestry from the 1000 Genomes Project and Human Genome Diversity Project. As a result, out of a total of 60 markers under study, none showed significant association with the average winter temperatures at the locations of the studied populations considering the multiple testing thresholds. This might suggest that the principal mode of TRPM8 evolution may be different from widespread models, where adaptive alleles are additive, dominant or recessive, at least in populations with the predominant East Asian component. For example, evolution by means of selectively preferable epistatic interactions among amino acids may have taken place. Despite the lack of strong signals of association, however, a very promising single nucleotide polymorphism (SNP) was found. The SNP rs7577262 is considered the best candidate based on its allelic correlations with winter temperatures, signatures of selective sweep and physiological evidences. The second top SNP, rs17862920, may participate in adaptation as well. Additionally, to assist in interpreting the nominal associations, the other markers reached, we performed SNP prioritization based on functional evidences found in literature and on evolutionary conservativeness.
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Affiliation(s)
- Alexander V. Igoshin
- Sector of the Genetics of Industrial Microorganisms, The Federal Research Center Institute of Cytology and Genetics, The Siberian Branch, The Russian Academy of Sciences, Novosibirsk, Russia
| | - Konstantin V. Gunbin
- Center of Brain Neurobiology and Neurogenetics, The Federal Research Center Institute of Cytology and Genetics, The Siberian Branch, The Russian Academy of Sciences, Novosibirsk, Russia
- V. Zelman Institute for Medicine and Psychology Novosibirsk State University, Novosibirsk, Russia
- Center for Mitochondrial Functional Genomics, Institute of Living Systems, Immanuel Kant Baltic Federal University, Kaliningrad, Russia
| | - Nikolay S. Yudin
- V. Zelman Institute for Medicine and Psychology Novosibirsk State University, Novosibirsk, Russia
- Laboratory of Livestock Molecular Genetics and Breeding, The Federal Research Center Institute of Cytology and Genetics, The Siberian Branch, The Russian Academy of Sciences, Novosibirsk, Russia
| | - Mikhail I. Voevoda
- Laboratory of Human Molecular Genetics, The Federal Research Center Institute of Cytology and Genetics, The Siberian Branch, The Russian Academy of Sciences, Novosibirsk, Russia
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6
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Booker TR, Keightley PD. Understanding the Factors That Shape Patterns of Nucleotide Diversity in the House Mouse Genome. Mol Biol Evol 2019; 35:2971-2988. [PMID: 30295866 PMCID: PMC6278861 DOI: 10.1093/molbev/msy188] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
A major goal of population genetics has been to determine the extent by which selection at linked sites influences patterns of neutral nucleotide diversity in the genome. Multiple lines of evidence suggest that diversity is influenced by both positive and negative selection. For example, in many species there are troughs in diversity surrounding functional genomic elements, consistent with the action of either background selection (BGS) or selective sweeps. In this study, we investigated the causes of the diversity troughs that are observed in the wild house mouse genome. Using the unfolded site frequency spectrum, we estimated the strength and frequencies of deleterious and advantageous mutations occurring in different functional elements in the genome. We then used these estimates to parameterize forward-in-time simulations of chromosomes, using realistic distributions of functional elements and recombination rate variation in order to determine whether selection at linked sites can explain the observed patterns of nucleotide diversity. The simulations suggest that BGS alone cannot explain the dips in diversity around either exons or conserved noncoding elements. A combination of BGS and selective sweeps produces deeper dips in diversity than BGS alone, but the inferred parameters of selection cannot fully explain the patterns observed in the genome. Our results provide evidence of sweeps shaping patterns of nucleotide diversity across the mouse genome and also suggest that infrequent, strongly advantageous mutations play an important role in this. The limitations of using the unfolded site frequency spectrum for inferring the frequency and effects of advantageous mutations are discussed.
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Affiliation(s)
- Tom R Booker
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, United Kingdom.,Department of Forest and Conservation Sciences, University of British Columbia, Vancouver, BC, Canada
| | - Peter D Keightley
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, United Kingdom
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7
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Sharbrough J, Luse M, Boore JL, Logsdon JM, Neiman M. Radical amino acid mutations persist longer in the absence of sex. Evolution 2018. [PMID: 29520921 DOI: 10.1111/evo.13465] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Harmful mutations are ubiquitous and inevitable, and the rate at which these mutations are removed from populations is a critical determinant of evolutionary fate. Closely related sexual and asexual taxa provide a particularly powerful setting to study deleterious mutation elimination because sexual reproduction should facilitate mutational clearance by reducing selective interference between sites and by allowing the production of offspring with different mutational complements than their parents. Here, we compared the rate of removal of conservative (i.e., similar biochemical properties) and radical (i.e., distinct biochemical properties) nonsynonymous mutations from mitochondrial genomes of sexual versus asexual Potamopyrgus antipodarum, a New Zealand freshwater snail characterized by coexisting and ecologically similar sexual and asexual lineages. Our analyses revealed that radical nonsynonymous mutations are cleared at higher rates than conservative changes and that sexual lineages eliminate radical changes more rapidly than asexual counterparts. These results are consistent with reduced efficacy of purifying selection in asexual lineages allowing harmful mutations to remain polymorphic longer than in sexual lineages. Together, these data illuminate some of the population-level processes contributing to mitochondrial mutation accumulation and suggest that mutation accumulation could influence the outcome of competition between sexual and asexual lineages.
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Affiliation(s)
- Joel Sharbrough
- Department of Biology, University of Iowa, Iowa City, Iowa 52242.,Department of Biology, Colorado State University, Fort Collins, Colorado 80523
| | - Meagan Luse
- Department of Biology, University of Iowa, Iowa City, Iowa 52242
| | - Jeffrey L Boore
- Department of Integrative Biology, University of California, Berkeley, Berkeley, California 94720.,Providence St. Joseph Health and Institute for Systems Biology, Seattle, Washington 98109
| | - John M Logsdon
- Department of Biology, University of Iowa, Iowa City, Iowa 52242
| | - Maurine Neiman
- Department of Biology, University of Iowa, Iowa City, Iowa 52242
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8
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Colwell M, Drown M, Showel K, Drown C, Palowski A, Faulk C. Evolutionary conservation of DNA methylation in CpG sites within ultraconserved noncoding elements. Epigenetics 2018; 13:49-60. [PMID: 29372669 PMCID: PMC5836973 DOI: 10.1080/15592294.2017.1411447] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2017] [Revised: 11/14/2017] [Accepted: 11/27/2017] [Indexed: 01/14/2023] Open
Abstract
Ultraconserved noncoding elements (UCNEs) constitute less than 1 Mb of vertebrate genomes and are impervious to accumulating mutations. About 4000 UCNEs exist in vertebrate genomes, each at least 200 nucleotides in length, sharing greater than 95% sequence identity between human and chicken. Despite extreme sequence conservation over 400 million years of vertebrate evolution, we show both ordered interspecies and within-species interindividual variation in DNA methylation in these regions. Here, we surveyed UCNEs with high CpG density in 56 species finding half to be intermediately methylated and the remaining near 0% or 100%. Intermediately methylated UCNEs displayed a greater range of methylation between mouse tissues. In a human population, most UCNEs showed greater variation than the LINE1 transposon, a frequently used epigenetic biomarker. Global methylation was found to be inversely correlated to hydroxymethylation across 60 vertebrates. Within UCNEs, DNA methylation is flexible, conserved between related species, and relaxed from the underlying sequence selection pressure, while remaining heritable through speciation.
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Affiliation(s)
- Mathia Colwell
- Department of Animal Sciences, University of Minnesota, College of Food, Agricultural, and Natural Resource Sciences, Saint Paul, MN, USA
| | - Melissa Drown
- Department of Animal Sciences, University of Minnesota, College of Food, Agricultural, and Natural Resource Sciences, Saint Paul, MN, USA
| | - Kelly Showel
- Department of Animal Sciences, University of Minnesota, College of Food, Agricultural, and Natural Resource Sciences, Saint Paul, MN, USA
| | - Chelsea Drown
- Department of Animal Sciences, University of Minnesota, College of Food, Agricultural, and Natural Resource Sciences, Saint Paul, MN, USA
| | - Amanda Palowski
- Department of Animal Sciences, University of Minnesota, College of Food, Agricultural, and Natural Resource Sciences, Saint Paul, MN, USA
| | - Christopher Faulk
- Department of Animal Sciences, University of Minnesota, College of Food, Agricultural, and Natural Resource Sciences, Saint Paul, MN, USA
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9
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Booker TR, Ness RW, Keightley PD. The Recombination Landscape in Wild House Mice Inferred Using Population Genomic Data. Genetics 2017; 207:297-309. [PMID: 28751421 PMCID: PMC5586380 DOI: 10.1534/genetics.117.300063] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2017] [Accepted: 07/19/2017] [Indexed: 11/29/2022] Open
Abstract
Characterizing variation in the rate of recombination across the genome is important for understanding several evolutionary processes. Previous analysis of the recombination landscape in laboratory mice has revealed that the different subspecies have different suites of recombination hotspots. It is unknown, however, whether hotspots identified in laboratory strains reflect the hotspot diversity of natural populations or whether broad-scale variation in the rate of recombination is conserved between subspecies. In this study, we constructed fine-scale recombination rate maps for a natural population of the Eastern house mouse, Mus musculus castaneus We performed simulations to assess the accuracy of recombination rate inference in the presence of phase errors, and we used a novel approach to quantify phase error. The spatial distribution of recombination events is strongly positively correlated between our castaneus map, and a map constructed using inbred lines derived predominantly from M. m. domesticus Recombination hotspots in wild castaneus show little overlap, however, with the locations of double-strand breaks in wild-derived house mouse strains. Finally, we also find that genetic diversity in M. m. castaneus is positively correlated with the rate of recombination, consistent with pervasive natural selection operating in the genome. Our study suggests that recombination rate variation is conserved at broad scales between house mouse subspecies, but it is not strongly conserved at fine scales.
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Affiliation(s)
- Tom R Booker
- Institute of Evolutionary Biology, University of Edinburgh, EH9 3FL, United Kingdom
| | - Rob W Ness
- Department of Biology, University of Toronto Mississauga, Ontario, L5L 1C6, Canada
| | - Peter D Keightley
- Institute of Evolutionary Biology, University of Edinburgh, EH9 3FL, United Kingdom
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10
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Harr B, Karakoc E, Neme R, Teschke M, Pfeifle C, Pezer Ž, Babiker H, Linnenbrink M, Montero I, Scavetta R, Abai MR, Molins MP, Schlegel M, Ulrich RG, Altmüller J, Franitza M, Büntge A, Künzel S, Tautz D. Genomic resources for wild populations of the house mouse, Mus musculus and its close relative Mus spretus. Sci Data 2016; 3:160075. [PMID: 27622383 PMCID: PMC5020872 DOI: 10.1038/sdata.2016.75] [Citation(s) in RCA: 87] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2016] [Accepted: 07/29/2016] [Indexed: 12/20/2022] Open
Abstract
Wild populations of the house mouse (Mus musculus) represent the raw genetic material for the classical inbred strains in biomedical research and are a major model system for evolutionary biology. We provide whole genome sequencing data of individuals representing natural populations of M. m. domesticus (24 individuals from 3 populations), M. m. helgolandicus (3 individuals), M. m. musculus (22 individuals from 3 populations) and M. spretus (8 individuals from one population). We use a single pipeline to map and call variants for these individuals and also include 10 additional individuals of M. m. castaneus for which genomic data are publically available. In addition, RNAseq data were obtained from 10 tissues of up to eight adult individuals from each of the three M. m. domesticus populations for which genomic data were collected. Data and analyses are presented via tracks viewable in the UCSC or IGV genome browsers. We also provide information on available outbred stocks and instructions on how to keep them in the laboratory.
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Affiliation(s)
- Bettina Harr
- Max-Planck Institute for Evolutionary Biology, August-Thienemanstrasse 2, 24306 Plön, Germany
| | - Emre Karakoc
- Max-Planck Institute for Evolutionary Biology, August-Thienemanstrasse 2, 24306 Plön, Germany
| | - Rafik Neme
- Max-Planck Institute for Evolutionary Biology, August-Thienemanstrasse 2, 24306 Plön, Germany
| | - Meike Teschke
- Max-Planck Institute for Evolutionary Biology, August-Thienemanstrasse 2, 24306 Plön, Germany
| | - Christine Pfeifle
- Max-Planck Institute for Evolutionary Biology, August-Thienemanstrasse 2, 24306 Plön, Germany
| | - Željka Pezer
- Max-Planck Institute for Evolutionary Biology, August-Thienemanstrasse 2, 24306 Plön, Germany
| | - Hiba Babiker
- Max-Planck Institute for Evolutionary Biology, August-Thienemanstrasse 2, 24306 Plön, Germany
| | - Miriam Linnenbrink
- Max-Planck Institute for Evolutionary Biology, August-Thienemanstrasse 2, 24306 Plön, Germany
| | - Inka Montero
- Max-Planck Institute for Evolutionary Biology, August-Thienemanstrasse 2, 24306 Plön, Germany
| | - Rick Scavetta
- Max-Planck Institute for Evolutionary Biology, August-Thienemanstrasse 2, 24306 Plön, Germany
| | - Mohammad Reza Abai
- Department of Medical Entomology and Vector Control, School of Public Health, Tehran University of Medical Sciences, Tehran 1417613151, Iran
| | - Marta Puente Molins
- Laboratorio de Anatomía Animal, Departamento de Biología Animal, Facultad de Ciencias, Universidad de Vigo, 36200 Vigo, Spain
| | - Mathias Schlegel
- Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Institute for Novel and Emerging Infectious Diseases, Südufer 10, 17493 Greifswald-Insel Riems, Germany
| | - Rainer G Ulrich
- Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Institute for Novel and Emerging Infectious Diseases, Südufer 10, 17493 Greifswald-Insel Riems, Germany
| | - Janine Altmüller
- Cologne Center for Genomics (CCG), University of Cologne, Weyertal 115b, 50931 Cologne, Germany.,Institute of Human Genetics, Universitätsklinik Köln, Kerpener Str. 34, 50931 Köln, Germany
| | - Marek Franitza
- Cologne Center for Genomics (CCG), University of Cologne, Weyertal 115b, 50931 Cologne, Germany.,Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Joseph-Stelzmann-Str. 26, 50931 Cologne, Germany
| | - Anna Büntge
- Max-Planck Institute for Evolutionary Biology, August-Thienemanstrasse 2, 24306 Plön, Germany
| | - Sven Künzel
- Max-Planck Institute for Evolutionary Biology, August-Thienemanstrasse 2, 24306 Plön, Germany
| | - Diethard Tautz
- Max-Planck Institute for Evolutionary Biology, August-Thienemanstrasse 2, 24306 Plön, Germany
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11
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Contrasting Levels of Molecular Evolution on the Mouse X Chromosome. Genetics 2016; 203:1841-57. [PMID: 27317678 DOI: 10.1534/genetics.116.186825] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2016] [Accepted: 06/08/2016] [Indexed: 11/18/2022] Open
Abstract
The mammalian X chromosome has unusual evolutionary dynamics compared to autosomes. Faster-X evolution of spermatogenic protein-coding genes is known to be most pronounced for genes expressed late in spermatogenesis, but it is unclear if these patterns extend to other forms of molecular divergence. We tested for faster-X evolution in mice spanning three different forms of molecular evolution-divergence in protein sequence, gene expression, and DNA methylation-across different developmental stages of spermatogenesis. We used FACS to isolate individual cell populations and then generated cell-specific transcriptome profiles across different stages of spermatogenesis in two subspecies of house mice (Mus musculus), thereby overcoming a fundamental limitation of previous studies on whole tissues. We found faster-X protein evolution at all stages of spermatogenesis and faster-late protein evolution for both X-linked and autosomal genes. In contrast, there was less expression divergence late in spermatogenesis (slower late) on the X chromosome and for autosomal genes expressed primarily in testis (testis-biased). We argue that slower-late expression divergence reflects strong regulatory constraints imposed during this critical stage of sperm development and that these constraints are particularly acute on the tightly regulated sex chromosomes. We also found slower-X DNA methylation divergence based on genome-wide bisulfite sequencing of sperm from two species of mice (M. musculus and M. spretus), although it is unclear whether slower-X DNA methylation reflects development constraints in sperm or other X-linked phenomena. Our study clarifies key differences in patterns of regulatory and protein evolution across spermatogenesis that are likely to have important consequences for mammalian sex chromosome evolution, male fertility, and speciation.
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Seplyarskiy VB, Bazykin GA, Soldatov RA. Polymerase ζ Activity Is Linked to Replication Timing in Humans: Evidence from Mutational Signatures. Mol Biol Evol 2015; 32:3158-72. [PMID: 26376651 DOI: 10.1093/molbev/msv184] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Replication timing is an important determinant of germline mutation patterns, with a higher rate of point mutations in late replicating regions. Mechanisms underlying this association remain elusive. One of the suggested explanations is the activity of error-prone DNA polymerases in late-replicating regions. Polymerase zeta (pol ζ), an essential error-prone polymerase biased toward transversions, also has a tendency to produce dinucleotide mutations (DNMs), complex mutational events that simultaneously affect two adjacent nucleotides. Experimental studies have shown that pol ζ is strongly biased toward GC→AA/TT DNMs. Using primate divergence data, we show that the GC→AA/TT pol ζ mutational signature is the most frequent among DNMs, and its rate exceeds the mean rate of other DNM types by a factor of approximately 10. Unlike the overall rate of DNMs, the pol ζ signature drastically increases with the replication time in the human genome. Finally, the pol ζ signature is enriched in transcribed regions, and there is a strong prevalence of GC→TT over GC→AA DNMs on the nontemplate strand, indicating association with transcription. A recurrently occurring GC→TT DNM in HRAS and SOD1 genes causes the Costello syndrome and amyotrophic lateral sclerosis correspondently; we observe an approximately 1 kb long mutation hotspot enriched by transversions near these DNMs in both cases, suggesting a link between these diseases and pol ζ activity. This study uncovers the genomic preferences of pol ζ, shedding light on a novel cause of mutational heterogeneity along the genome.
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Affiliation(s)
- Vladimir B Seplyarskiy
- Institute of Information Transmission Problems (Kharkevich Institute) of the Russian Academy of Sciences, Moscow, Russia Department of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow, Russia Pirogov Russian National Research Medical University, Moscow, Russia
| | - Georgii A Bazykin
- Institute of Information Transmission Problems (Kharkevich Institute) of the Russian Academy of Sciences, Moscow, Russia Department of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow, Russia Pirogov Russian National Research Medical University, Moscow, Russia
| | - Ruslan A Soldatov
- Institute of Information Transmission Problems (Kharkevich Institute) of the Russian Academy of Sciences, Moscow, Russia Department of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow, Russia
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McCole RB, Fonseka CY, Koren A, Wu CT. Abnormal dosage of ultraconserved elements is highly disfavored in healthy cells but not cancer cells. PLoS Genet 2014; 10:e1004646. [PMID: 25340765 PMCID: PMC4207606 DOI: 10.1371/journal.pgen.1004646] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2014] [Accepted: 08/04/2014] [Indexed: 12/17/2022] Open
Abstract
Ultraconserved elements (UCEs) are strongly depleted from segmental duplications and copy number variations (CNVs) in the human genome, suggesting that deletion or duplication of a UCE can be deleterious to the mammalian cell. Here we address the process by which CNVs become depleted of UCEs. We begin by showing that depletion for UCEs characterizes the most recent large-scale human CNV datasets and then find that even newly formed de novo CNVs, which have passed through meiosis at most once, are significantly depleted for UCEs. In striking contrast, CNVs arising specifically in cancer cells are, as a rule, not depleted for UCEs and can even become significantly enriched. This observation raises the possibility that CNVs that arise somatically and are relatively newly formed are less likely to have established a CNV profile that is depleted for UCEs. Alternatively, lack of depletion for UCEs from cancer CNVs may reflect the diseased state. In support of this latter explanation, somatic CNVs that are not associated with disease are depleted for UCEs. Finally, we show that it is possible to observe the CNVs of induced pluripotent stem (iPS) cells become depleted of UCEs over time, suggesting that depletion may be established through selection against UCE-disrupting CNVs without the requirement for meiotic divisions.
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Affiliation(s)
- Ruth B. McCole
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Chamith Y. Fonseka
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, United States of America
- Biological and Biomedical Sciences PhD program, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Amnon Koren
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, United States of America
- Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, Massachusetts, United States of America
| | - C.-ting Wu
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, United States of America
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De Silva DR, Nichols R, Elgar G. Purifying selection in deeply conserved human enhancers is more consistent than in coding sequences. PLoS One 2014; 9:e103357. [PMID: 25062004 PMCID: PMC4111549 DOI: 10.1371/journal.pone.0103357] [Citation(s) in RCA: 8] [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: 08/01/2013] [Accepted: 07/01/2014] [Indexed: 12/30/2022] Open
Abstract
Comparison of polymorphism at synonymous and non-synonymous sites in protein-coding DNA can provide evidence for selective constraint. Non-coding DNA that forms part of the regulatory landscape presents more of a challenge since there is not such a clear-cut distinction between sites under stronger and weaker selective constraint. Here, we consider putative regulatory elements termed Conserved Non-coding Elements (CNEs) defined by their high level of sequence identity across all vertebrates. Some mutations in these regions have been implicated in developmental disorders; we analyse CNE polymorphism data to investigate whether such deleterious effects are widespread in humans. Single nucleotide variants from the HapMap and 1000 Genomes Projects were mapped across nearly 2000 CNEs. In the 1000 Genomes data we find a significant excess of rare derived alleles in CNEs relative to coding sequences; this pattern is absent in HapMap data, apparently obscured by ascertainment bias. The distribution of polymorphism within CNEs is not uniform; we could identify two categories of sites by exploiting deep vertebrate alignments: stretches that are non-variant, and those that have at least one substitution. The conserved category has fewer polymorphic sites and a greater excess of rare derived alleles, which can be explained by a large proportion of sites under strong purifying selection within humans--higher than that for non-synonymous sites in most protein coding regions, and comparable to that at the strongly conserved trans-dev genes. Conversely, the more evolutionarily labile CNE sites have an allele frequency distribution not significantly different from non-synonymous sites. Future studies should exploit genome-wide re-sequencing to obtain better coverage in selected non-coding regions, given the likelihood that mutations in evolutionarily conserved enhancer sequences are deleterious. Discovery pipelines should validate non-coding variants to aid in identifying causal and risk-enhancing variants in complex disorders, in contrast to the current focus on exome sequencing.
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Affiliation(s)
- Dilrini R. De Silva
- Systems Biology, MRC National Institute for Medical Research, Mill Hill, London, United Kingdom
- School of Biological and Chemical Sciences, Queen Mary University of London, London, United Kingdom
| | - Richard Nichols
- School of Biological and Chemical Sciences, Queen Mary University of London, London, United Kingdom
| | - Greg Elgar
- Systems Biology, MRC National Institute for Medical Research, Mill Hill, London, United Kingdom
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Abstract
Evolutionary conservation has been an accurate predictor of functional elements across the first decade of metazoan genomics. More recently, there has been a move to define functional elements instead from biochemical annotations. Evolutionary methods are, however, more comprehensive than biochemical approaches can be and can assess quantitatively, especially for subtle effects, how biologically important--how injurious after mutation--different types of elements are. Evolutionary methods are thus critical for understanding the large fraction (up to 10%) of the human genome that does not encode proteins and yet might convey function. These methods can also capture the ephemeral nature of much noncoding functional sequence, with large numbers of functional elements having been gained and lost rapidly along each mammalian lineage. Here, we review how different strengths of purifying selection have impacted on protein-coding and non-protein-coding loci and on transcription factor binding sites in mammalian and fruit fly genomes.
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Affiliation(s)
- Wilfried Haerty
- MRC Functional Genomics Unit, Department of Physiology, Anatomy, and Genetics, University of Oxford, Oxford OX1 3PT, United Kingdom; ,
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Halligan DL, Kousathanas A, Ness RW, Harr B, Eöry L, Keane TM, Adams DJ, Keightley PD. Contributions of protein-coding and regulatory change to adaptive molecular evolution in murid rodents. PLoS Genet 2013; 9:e1003995. [PMID: 24339797 PMCID: PMC3854965 DOI: 10.1371/journal.pgen.1003995] [Citation(s) in RCA: 89] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2013] [Accepted: 10/16/2013] [Indexed: 12/22/2022] Open
Abstract
The contribution of regulatory versus protein change to adaptive evolution has long been controversial. In principle, the rate and strength of adaptation within functional genetic elements can be quantified on the basis of an excess of nucleotide substitutions between species compared to the neutral expectation or from effects of recent substitutions on nucleotide diversity at linked sites. Here, we infer the nature of selective forces acting in proteins, their UTRs and conserved noncoding elements (CNEs) using genome-wide patterns of diversity in wild house mice and divergence to related species. By applying an extension of the McDonald-Kreitman test, we infer that adaptive substitutions are widespread in protein-coding genes, UTRs and CNEs, and we estimate that there are at least four times as many adaptive substitutions in CNEs and UTRs as in proteins. We observe pronounced reductions in mean diversity around nonsynonymous sites (whether or not they have experienced a recent substitution). This can be explained by selection on multiple, linked CNEs and exons. We also observe substantial dips in mean diversity (after controlling for divergence) around protein-coding exons and CNEs, which can also be explained by the combined effects of many linked exons and CNEs. A model of background selection (BGS) can adequately explain the reduction in mean diversity observed around CNEs. However, BGS fails to explain the wide reductions in mean diversity surrounding exons (encompassing ∼100 Kb, on average), implying that there is a substantial role for adaptation within exons or closely linked sites. The wide dips in diversity around exons, which are hard to explain by BGS, suggest that the fitness effects of adaptive amino acid substitutions could be substantially larger than substitutions in CNEs. We conclude that although there appear to be many more adaptive noncoding changes, substitutions in proteins may dominate phenotypic evolution. We present an analysis of the genome sequences of multiple wild house mice. Wild house mice are about ten times more genetically diverse than humans, reflecting the large effective population size of the species. This manifests itself as more effective natural selection acting against deleterious mutations and favouring advantageous mutations in mice than in humans. We show that there are strong signals of adaptive evolution at many sites in the genome. We estimate that 80% of adaptive changes in the genome are in gene regulatory elements and only 20% are in protein-coding genes. We find that nucleotide diversity is markedly reduced close to gene regulatory elements and protein-coding gene sequences. The reductions around regulatory elements can be explained by selection purging deleterious mutations that occur in the elements themselves, but this process only partially explains the diversity reductions around protein-coding genes. Recurrent adaptive evolution, which can also cause local reductions in diversity via selective sweeps, may be necessary to fully explain the patterns in diversity that we observe surrounding genes. Although most adaptive molecular evolution appears to be regulatory, adaptive phenotypic change may principally be driven by structural change in proteins.
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Affiliation(s)
- Daniel L. Halligan
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, United Kingdom
| | | | - Rob W. Ness
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, United Kingdom
| | - Bettina Harr
- Max-Planck Institute for Evolutionary Biology, Plön, Germany
| | - Lél Eöry
- The Roslin Institute and R(D)SVS, University of Edinburgh, Midlothian, United Kingdom
| | - Thomas M. Keane
- The Wellcome Trust Sanger Institute, Hinxton, Cambridge, United Kingdom
| | - David J. Adams
- The Wellcome Trust Sanger Institute, Hinxton, Cambridge, United Kingdom
| | - Peter D. Keightley
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, United Kingdom
- * E-mail:
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Terekhanova NV, Bazykin GA, Neverov A, Kondrashov AS, Seplyarskiy VB. Prevalence of multinucleotide replacements in evolution of primates and Drosophila. Mol Biol Evol 2013; 30:1315-25. [PMID: 23447710 PMCID: PMC3649671 DOI: 10.1093/molbev/mst036] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Evolution of sequences mostly involves independent changes at different sites. However, substitutions at neighboring sites may co-occur as multinucleotide replacement events (MNRs). Here, we compare noncoding sequences of several species of primates, and of three species of Drosophila fruit flies, in a phylogenetic analysis of the replacements that occurred between species at nearby nucleotide sites. Both in primates and in Drosophila, the frequency of single-nucleotide replacements is substantially elevated within 10 nucleotides from other replacements that occurred on the same lineage but not on another lineage. The data imply that dinucleotide replacements (DNRs) affecting sites at distances of up to 10 nucleotides from each other are responsible for 2.3% of single-nucleotide replacements in primate genomes and for 5.6% in Drosophila genomes. Among these DNRs, 26% and 69%, respectively, are in fact parts of replacements of three or more trinucleotide replacements (TNRs). The plurality of MNRs affect nearby nucleotides, so that at least six times as many DNRs affect two adjacent nucleotide sites than sites 10 nucleotides apart. Still, approximately 60% of DNRs, and approximately 90% of TNRs, span distances more than two (or three) nucleotides. MNRs make a major contribution to the observed clustering of substitutions: In the human–chimpanzee comparison, DNRs are responsible for 50% of cases when two nearby replacements are observed on the human lineage, and TNRs are responsible for 83% of cases when three replacements at three immediately adjacent sites are observed on the human lineage. The prevalence of MNRs matches that is observed in data on de novo mutations and is also observed in the regions with the lowest sequence conservation, suggesting that MNRs mainly have mutational origin; however, epistatic selection and/or gene conversion may also play a role.
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Affiliation(s)
- Nadezhda V Terekhanova
- Department of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow, Russia
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Ryu T, Seridi L, Ravasi T. The evolution of ultraconserved elements with different phylogenetic origins. BMC Evol Biol 2012; 12:236. [PMID: 23217155 PMCID: PMC3556307 DOI: 10.1186/1471-2148-12-236] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2012] [Accepted: 11/09/2012] [Indexed: 11/10/2022] Open
Abstract
Background Ultraconserved elements of DNA have been identified in vertebrate and invertebrate genomes. These elements have been found to have diverse functions, including enhancer activities in developmental processes. The evolutionary origins and functional roles of these elements in cellular systems, however, have not yet been determined. Results Here, we identified a wide range of ultraconserved elements common to distant species, from primitive aquatic organisms to terrestrial species with complicated body systems, including some novel elements conserved in fruit fly and human. In addition to a well-known association with developmental genes, these DNA elements have a strong association with genes implicated in essential cell functions, such as epigenetic regulation, apoptosis, detoxification, innate immunity, and sensory reception. Interestingly, we observed that ultraconserved elements clustered by sequence similarity. Furthermore, species composition and flanking genes of clusters showed lineage-specific patterns. Ultraconserved elements are highly enriched with binding sites to developmental transcription factors regardless of how they cluster. Conclusion We identified large numbers of ultraconserved elements across distant species. Specific classes of these conserved elements seem to have been generated before the divergence of taxa and fixed during the process of evolution. Our findings indicate that these ultraconserved elements are not the exclusive property of higher modern eukaryotes, but rather transmitted from their metazoan ancestors.
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Affiliation(s)
- Taewoo Ryu
- Integrative Systems Biology Lab, Division of Biological and Environmental Sciences & Engineering, King Abdullah University of Science and Technology, Thuwal, 23955-6900, Kingdom of Saudi Arabia.
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Genin A, Desir J, Lambert N, Biervliet M, Van Der Aa N, Pierquin G, Killian A, Tosi M, Urbina M, Lefort A, Libert F, Pirson I, Abramowicz M. Kinetochore KMN network gene CASC5 mutated in primary microcephaly. Hum Mol Genet 2012; 21:5306-17. [PMID: 22983954 DOI: 10.1093/hmg/dds386] [Citation(s) in RCA: 85] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
Several genes expressed at the centrosome or spindle pole have been reported to underlie autosomal recessive primary microcephaly (MCPH), a neurodevelopmental disorder consisting of an important brain size reduction present since birth, associated with mild-to-moderate mental handicap and no other neurological feature nor associated malformation. Here, we report a mutation of CASC5 (aka Blinkin, or KNL1, or hSPC105) in MCPH patients from three consanguineous families, in one of which we initially reported the MCPH4 locus. The combined logarithm of odds score of the three families was >6. All patients shared a very rare homozygous mutation of CASC5. The mutation induced skipping of exon 18 with subsequent frameshift and truncation of the predicted protein. CASC5 is part of the KMN network of the kinetochore and is required for proper microtubule attachment to the chromosome centromere and for spindle-assembly checkpoint (SAC) activation during mitosis. Like MCPH gene ASPM, CASC5 is upregulated in the ventricular zone (VZ) of the human fetal brain. CASC5 binds BUB1, BUBR1, ZWINT-1 and interestingly it binds to MIS12 through a protein domain which is truncated by the mutation. CASC5 localized at the equatorial plate like ZWINT-1 and BUBR1, while ASPM, CEP152 and PCTN localized at the spindle poles in our patients and in controls. Comparison of primate and rodent lineages indicates accelerated evolution of CASC5 in the human lineage. Our data provide strong evidence for CASC5 as a novel MCPH gene, and underscore the role of kinetochore integrity in proper volumetric development of the human brain.
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Affiliation(s)
- Anne Genin
- Institute of Interdisciplinary Research IRIBHM , Université Libre de Bruxelles, Anderlecht, Belgium
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Bazykin GA, Kondrashov AS. Major role of positive selection in the evolution of conservative segments of Drosophila proteins. Proc Biol Sci 2012; 279:3409-17. [PMID: 22673359 PMCID: PMC3396909 DOI: 10.1098/rspb.2012.0776] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
Slow evolution of conservative segments of coding and non-coding DNA is caused by the action of negative selection, which removes new mutations. However, the mode of selection that affects the few substitutions that do occur within such segments remains unclear. Here, we show that the fraction of allele replacements that were driven by positive selection, and the strength of this selection, is the highest within the conservative segments of Drosophila protein-coding genes. The McDonald–Kreitman test, applied to the data on variation in Drosophila melanogaster and in Drosophila simulans, indicates that within the most conservative protein segments, approximately 72 per cent (approx. 80%) of allele replacements were driven by positive selection, as opposed to only approximately 44 per cent (approx. 53%) at rapidly evolving segments. Data on multiple non-synonymous substitutions at a codon lead to the same conclusion and additionally indicate that positive selection driving allele replacements at conservative sites is the strongest, as it accelerates evolution by a factor of approximately 40, as opposed to a factor of approximately 5 at rapidly evolving sites. Thus, random drift plays only a minor role in the evolution of conservative DNA segments, and those relatively rare allele replacements that occur within such segments are mostly driven by substantial positive selection.
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Affiliation(s)
- Georgii A Bazykin
- Department of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Vorbyevy Gory 1-73, Moscow 119992, Russia
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Harrison RJ. Understanding genetic variation and function- the applications of next generation sequencing. Semin Cell Dev Biol 2012; 23:230-6. [DOI: 10.1016/j.semcdb.2012.01.006] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2011] [Revised: 01/10/2012] [Accepted: 01/12/2012] [Indexed: 12/31/2022]
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Denver DR, Wilhelm LJ, Howe DK, Gafner K, Dolan PC, Baer CF. Variation in base-substitution mutation in experimental and natural lineages of Caenorhabditis nematodes. Genome Biol Evol 2012; 4:513-22. [PMID: 22436997 PMCID: PMC3342874 DOI: 10.1093/gbe/evs028] [Citation(s) in RCA: 91] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Variation among lineages in the mutation process has the potential to impact diverse biological processes ranging from susceptibilities to genetic disease to the mode and tempo of molecular evolution. The combination of high-throughput DNA sequencing (HTS) with mutation-accumulation (MA) experiments has provided a powerful approach to genome-wide mutation analysis, though insights into mutational variation have been limited by the vast evolutionary distances among the few species analyzed. We performed a HTS analysis of MA lines derived from four Caenorhabditis nematode natural genotypes: C. elegans N2 and PB306 and C. briggsae HK104 and PB800. Total mutation rates did not differ among the four sets of MA lines. A mutational bias toward G:C→A:T transitions and G:C→T:A transversions was observed in all four sets of MA lines. Chromosome-specific rates were mostly stable, though there was some evidence for a slightly elevated X chromosome mutation rate in PB306. Rates were homogeneous among functional coding sequence types and across autosomal cores, arms, and tips. Mutation spectra were similar among the four MA line sets but differed significantly when compared with patterns of natural base-substitution polymorphism for 13/14 comparisons performed. Our findings show that base-substitution mutation processes in these closely related animal lineages are mostly stable but differ from natural polymorphism patterns in these two species.
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Affiliation(s)
- Dee R Denver
- Department of Zoology and Center for Genome Research and Biocomputing, Oregon State University, OR, USA.
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