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Tajeddin N, Arabfard M, Alizadeh S, Salesi M, Khamse S, Delbari A, Ohadi M. Novel islands of GGC and GCC repeats coincide with human evolution. Gene 2024; 902:148194. [PMID: 38262548 DOI: 10.1016/j.gene.2024.148194] [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: 08/21/2023] [Revised: 10/29/2023] [Accepted: 01/18/2024] [Indexed: 01/25/2024]
Abstract
BACKGROUND Because of high mutation rate, overrepresentation in genic regions, and link with various neurological, neurodegenerative, and movement disorders, GGC and GCC short tandem repeats (STRs) are prone to natural selection. Among a number of lacking data, the 3-repeats of these STRs remain widely unexplored. RESULTS In a genome-wide search in human, here we mapped GGC and GCC STRs of ≥3-repeats, and found novel islands of up to 45 of those STRs, populating spans of 1 to 2 kb of genomic DNA. RGPD4 and NOC4L harbored the densest (GGC)3 (probability 3.09061E-71) and (GCC)3 (probability 1.72376E-61) islands, respectively, and were human-specific. We also found prime instances of directional incremented density of STRs at specific loci in human versus other species, including the FOXK2 and SKI GGC islands. The genes containing those islands significantly diverged in expression in human versus other species, and the proteins encoded by those genes interact closely in a physical interaction network, consequence of which may be human-specific characteristics such as higher order brain functions. CONCLUSION We report novel islands of GGC and GCC STRs of evolutionary relevance to human. The density, and in some instances, periodicity of these islands support them as a novel genomic entity, which need to be further explored in evolutionary, mechanistic, and functional platforms.
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Affiliation(s)
- N Tajeddin
- Iranian Research Center on Aging, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - M Arabfard
- Chemical Injuries Research Center, Systems Biology and Poisonings Institute, Baqiyatallah University of Medical Sciences, Tehran, Iran
| | - S Alizadeh
- Iranian Research Center on Aging, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - M Salesi
- Chemical Injuries Research Center, Systems Biology and Poisonings Institute, Baqiyatallah University of Medical Sciences, Tehran, Iran
| | - S Khamse
- Iranian Research Center on Aging, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - A Delbari
- Iranian Research Center on Aging, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - M Ohadi
- Iranian Research Center on Aging, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran.
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Guitart X, Porubsky D, Yoo D, Dougherty ML, Dishuck PC, Munson KM, Lewis AP, Hoekzema K, Knuth J, Chang S, Pastinen T, Eichler EE. Independent expansion, selection and hypervariability of the TBC1D3 gene family in humans. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.12.584650. [PMID: 38654825 PMCID: PMC11037872 DOI: 10.1101/2024.03.12.584650] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/26/2024]
Abstract
TBC1D3 is a primate-specific gene family that has expanded in the human lineage and has been implicated in neuronal progenitor proliferation and expansion of the frontal cortex. The gene family and its expression have been challenging to investigate because it is embedded in high-identity and highly variable segmental duplications. We sequenced and assembled the gene family using long-read sequencing data from 34 humans and 11 nonhuman primate species. Our analysis shows that this particular gene family has independently duplicated in at least five primate lineages, and the duplicated loci are enriched at sites of large-scale chromosomal rearrangements on chromosome 17. We find that most humans vary along two TBC1D3 clusters where human haplotypes are highly variable in copy number, differing by as many as 20 copies, and structure (structural heterozygosity 90%). We also show evidence of positive selection, as well as a significant change in the predicted human TBC1D3 protein sequence. Lastly, we find that, despite multiple duplications, human TBC1D3 expression is limited to a subset of copies and, most notably, from a single paralog group: TBC1D3-CDKL. These observations may help explain why a gene potentially important in cortical development can be so variable in the human population.
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Affiliation(s)
- Xavi Guitart
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
| | - David Porubsky
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
| | - DongAhn Yoo
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
| | - Max L. Dougherty
- Tisch Cancer Institute, Division of Hematology and Medical Oncology, The Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Philip C. Dishuck
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
| | - Katherine M. Munson
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
| | - Alexandra P. Lewis
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
| | - Kendra Hoekzema
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
| | - Jordan Knuth
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
| | - Stephen Chang
- Department of Biochemistry, Stanford University School of Medicine, Stanford, CA, USA
- Department of Medicine, Division of Cardiovascular Medicine, Stanford University, Stanford, CA, USA
| | - Tomi Pastinen
- Department of Pediatrics, Genomic Medicine Center, Children’s Mercy Kansas City, Kansas City, MO, USA
- Department of Pediatrics, School of Medicine, University of Missouri Kansas City, Kansas City, MO, USA
| | - Evan E. Eichler
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
- Howard Hughes Medical institute, University of Washington, Seattle, WA, USA
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3
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Arabfard M, Tajeddin N, Alizadeh S, Salesi M, Bayat H, Khorram Khorshid HR, Khamse S, Delbari A, Ohadi M. Dyads of GGC and GCC form hotspot colonies that coincide with the evolution of human and other great apes. BMC Genom Data 2024; 25:21. [PMID: 38383300 PMCID: PMC10880355 DOI: 10.1186/s12863-024-01207-z] [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: 07/31/2023] [Accepted: 02/11/2024] [Indexed: 02/23/2024] Open
Abstract
BACKGROUND GGC and GCC short tandem repeats (STRs) are of various evolutionary, biological, and pathological implications. However, the fundamental two-repeats (dyads) of these STRs are widely unexplored. RESULTS On a genome-wide scale, we mapped (GGC)2 and (GCC)2 dyads in human, and found monumental colonies (distance between each dyad < 500 bp) of extraordinary density, and in some instances periodicity. The largest (GCC)2 and (GGC)2 colonies were intergenic, homogeneous, and human-specific, consisting of 219 (GCC)2 on chromosome 2 (probability < 1.545E-219) and 70 (GGC)2 on chromosome 9 (probability = 1.809E-148). We also found that several colonies were shared in other great apes, and directionally increased in density and complexity in human, such as a colony of 99 (GCC)2 on chromosome 20, that specifically expanded in great apes, and reached maximum complexity in human (probability 1.545E-220). Numerous other colonies of evolutionary relevance in human were detected in other largely overlooked regions of the genome, such as chromosome Y and pseudogenes. Several of the genes containing or nearest to those colonies were divergently expressed in human. CONCLUSION In conclusion, (GCC)2 and (GGC)2 form unprecedented genomic colonies that coincide with the evolution of human and other great apes. The extent of the genomic rearrangements leading to those colonies support overlooked recombination hotspots, shared across great apes. The identified colonies deserve to be studied in mechanistic, evolutionary, and functional platforms.
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Affiliation(s)
- M Arabfard
- Chemical Injuries Research Center, Systems Biology and Poisonings Institute, Baqiyatallah University of Medical Sciences, Tehran, Iran
| | - N Tajeddin
- Iranian Research Center on Aging, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
- Department of Biology, Central Tehran Branch, Islamic Azad University, Tehran, Iran
| | - S Alizadeh
- Iranian Research Center on Aging, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - M Salesi
- Chemical Injuries Research Center, Systems Biology and Poisonings Institute, Baqiyatallah University of Medical Sciences, Tehran, Iran
- Research Center for Prevention of Oral and Dental Diseases, Baqiyatallah University of Medical Sciences, Tehran, Iran
| | - H Bayat
- Iranian Research Center on Aging, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - H R Khorram Khorshid
- Personalized Medicine and Genometabolomics Research Center, Hope Generation Foundation, Tehran, Iran
| | - S Khamse
- Iranian Research Center on Aging, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - A Delbari
- Iranian Research Center on Aging, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - M Ohadi
- Iranian Research Center on Aging, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran.
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4
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Zhang R, Quan H, Wang Y, Luo F. Neurogenesis in primates versus rodents and the value of non-human primate models. Natl Sci Rev 2023; 10:nwad248. [PMID: 38025664 PMCID: PMC10659238 DOI: 10.1093/nsr/nwad248] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Revised: 08/21/2023] [Accepted: 09/10/2023] [Indexed: 12/01/2023] Open
Abstract
Neurogenesis, the process of generating neurons from neural stem cells, occurs during both embryonic and adult stages, with each stage possessing distinct characteristics. Dysfunction in either stage can disrupt normal neural development, impair cognitive functions, and lead to various neurological disorders. Recent technological advancements in single-cell multiomics and gene-editing have facilitated investigations into primate neurogenesis. Here, we provide a comprehensive overview of neurogenesis across rodents, non-human primates, and humans, covering embryonic development to adulthood and focusing on the conservation and diversity among species. While non-human primates, especially monkeys, serve as valuable models with closer neural resemblance to humans, we highlight the potential impacts and limitations of non-human primate models on both physiological and pathological neurogenesis research.
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Affiliation(s)
- Runrui Zhang
- State Key Laboratory of Primate Biomedical Research; Institute of Primate Translational Medicine, Kunming University of Science and Technology, Kunming 650500, China
- Yunnan Key Laboratory of Primate Biomedical Research, Kunming 650500, China
| | - Hongxin Quan
- State Key Laboratory of Primate Biomedical Research; Institute of Primate Translational Medicine, Kunming University of Science and Technology, Kunming 650500, China
- Yunnan Key Laboratory of Primate Biomedical Research, Kunming 650500, China
| | - Yinfeng Wang
- State Key Laboratory of Primate Biomedical Research; Institute of Primate Translational Medicine, Kunming University of Science and Technology, Kunming 650500, China
- Yunnan Key Laboratory of Primate Biomedical Research, Kunming 650500, China
| | - Fucheng Luo
- State Key Laboratory of Primate Biomedical Research; Institute of Primate Translational Medicine, Kunming University of Science and Technology, Kunming 650500, China
- Yunnan Key Laboratory of Primate Biomedical Research, Kunming 650500, China
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Wang H, Makowski C, Zhang Y, Qi A, Kaufmann T, Smeland OB, Fiecas M, Yang J, Visscher PM, Chen CH. Chromosomal inversion polymorphisms shape human brain morphology. Cell Rep 2023; 42:112896. [PMID: 37505983 PMCID: PMC10508191 DOI: 10.1016/j.celrep.2023.112896] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Revised: 06/27/2023] [Accepted: 07/13/2023] [Indexed: 07/30/2023] Open
Abstract
The impact of chromosomal inversions on human brain morphology remains underexplored. We studied 35 common inversions classified from genotypes of 33,018 adults with European ancestry. The inversions at 2p22.3, 16p11.2, and 17q21.31 reach genome-wide significance, followed by 8p23.1 and 6p21.33, in their association with cortical and subcortical morphology. The 17q21.31, 8p23.1, and 16p11.2 regions comprise the LRRC37, OR7E, and NPIP duplicated gene families. We find the 17q21.31 MAPT inversion region, known for harboring neurological risk, to be the most salient locus among common variants for shaping and patterning the cortex. Overall, we observe the inverted orientations decreasing brain size, with the exception that the 2p22.3 inversion is associated with increased subcortical volume and the 8p23.1 inversion is associated with increased motor cortex. These significant inversions are in the genomic hotspots of neuropsychiatric loci. Our findings are generalizable to 3,472 children and demonstrate inversions as essential genetic variation to understand human brain phenotypes.
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Affiliation(s)
- Hao Wang
- Center for Multimodal Imaging and Genetics, University of California San Diego, La Jolla, CA 92093, USA
| | - Carolina Makowski
- Center for Multimodal Imaging and Genetics, University of California San Diego, La Jolla, CA 92093, USA
| | - Yanxiao Zhang
- Ludwig Institute for Cancer Research, La Jolla, CA 92093, USA; School of Life Sciences, Westlake University, Hangzhou, Zhejiang 310024, China; Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang 310024, China
| | - Anna Qi
- Center for Multimodal Imaging and Genetics, University of California San Diego, La Jolla, CA 92093, USA
| | - Tobias Kaufmann
- Department of Psychiatry and Psychotherapy, Tübingen Center for Mental Health, University of Tübingen, 72076 Tübingen, Germany; Norwegian Centre for Mental Disorders Research, Oslo University Hospital and University of Oslo, 0450 Oslo, Norway
| | - Olav B Smeland
- Norwegian Centre for Mental Disorders Research, Oslo University Hospital and University of Oslo, 0450 Oslo, Norway
| | - Mark Fiecas
- Division of Biostatistics, University of Minnesota School of Public Health, Minneapolis, MN 55455, USA
| | - Jian Yang
- School of Life Sciences, Westlake University, Hangzhou, Zhejiang 310024, China; Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang 310024, China
| | - Peter M Visscher
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Chi-Hua Chen
- Center for Multimodal Imaging and Genetics, University of California San Diego, La Jolla, CA 92093, USA.
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6
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Soto DC, Uribe-Salazar JM, Shew CJ, Sekar A, McGinty S, Dennis MY. Genomic structural variation: A complex but important driver of human evolution. AMERICAN JOURNAL OF BIOLOGICAL ANTHROPOLOGY 2023; 181 Suppl 76:118-144. [PMID: 36794631 PMCID: PMC10329998 DOI: 10.1002/ajpa.24713] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/02/2022] [Revised: 01/21/2023] [Accepted: 02/05/2023] [Indexed: 02/17/2023]
Abstract
Structural variants (SVs)-including duplications, deletions, and inversions of DNA-can have significant genomic and functional impacts but are technically difficult to identify and assay compared with single-nucleotide variants. With the aid of new genomic technologies, it has become clear that SVs account for significant differences across and within species. This phenomenon is particularly well-documented for humans and other primates due to the wealth of sequence data available. In great apes, SVs affect a larger number of nucleotides than single-nucleotide variants, with many identified SVs exhibiting population and species specificity. In this review, we highlight the importance of SVs in human evolution by (1) how they have shaped great ape genomes resulting in sensitized regions associated with traits and diseases, (2) their impact on gene functions and regulation, which subsequently has played a role in natural selection, and (3) the role of gene duplications in human brain evolution. We further discuss how to incorporate SVs in research, including the strengths and limitations of various genomic approaches. Finally, we propose future considerations in integrating existing data and biospecimens with the ever-expanding SV compendium propelled by biotechnology advancements.
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Affiliation(s)
- Daniela C. Soto
- Genome Center, MIND Institute, and Department of Biochemistry & Molecular Medicine, University of California, Davis, CA, USA
- Integrative Genetics and Genomics Graduate Group, University of California, Davis, CA, USA
| | - José M. Uribe-Salazar
- Genome Center, MIND Institute, and Department of Biochemistry & Molecular Medicine, University of California, Davis, CA, USA
- Integrative Genetics and Genomics Graduate Group, University of California, Davis, CA, USA
| | - Colin J. Shew
- Genome Center, MIND Institute, and Department of Biochemistry & Molecular Medicine, University of California, Davis, CA, USA
- Integrative Genetics and Genomics Graduate Group, University of California, Davis, CA, USA
| | - Aarthi Sekar
- Genome Center, MIND Institute, and Department of Biochemistry & Molecular Medicine, University of California, Davis, CA, USA
- Integrative Genetics and Genomics Graduate Group, University of California, Davis, CA, USA
| | - Sean McGinty
- Genome Center, MIND Institute, and Department of Biochemistry & Molecular Medicine, University of California, Davis, CA, USA
- Integrative Genetics and Genomics Graduate Group, University of California, Davis, CA, USA
| | - Megan Y. Dennis
- Genome Center, MIND Institute, and Department of Biochemistry & Molecular Medicine, University of California, Davis, CA, USA
- Integrative Genetics and Genomics Graduate Group, University of California, Davis, CA, USA
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7
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Espinós A, Fernández‐Ortuño E, Negri E, Borrell V. Evolution of genetic mechanisms regulating cortical neurogenesis. Dev Neurobiol 2022; 82:428-453. [PMID: 35670518 PMCID: PMC9543202 DOI: 10.1002/dneu.22891] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2022] [Revised: 04/26/2022] [Accepted: 05/24/2022] [Indexed: 11/20/2022]
Abstract
The size of the cerebral cortex increases dramatically across amniotes, from reptiles to great apes. This is primarily due to different numbers of neurons and glial cells produced during embryonic development. The evolutionary expansion of cortical neurogenesis was linked to changes in neural stem and progenitor cells, which acquired increased capacity of self‐amplification and neuron production. Evolution works via changes in the genome, and recent studies have identified a small number of new genes that emerged in the recent human and primate lineages, promoting cortical progenitor proliferation and increased neurogenesis. However, most of the mammalian genome corresponds to noncoding DNA that contains gene‐regulatory elements, and recent evidence precisely points at changes in expression levels of conserved genes as key in the evolution of cortical neurogenesis. Here, we provide an overview of basic cellular mechanisms involved in cortical neurogenesis across amniotes, and discuss recent progress on genetic mechanisms that may have changed during evolution, including gene expression regulation, leading to the expansion of the cerebral cortex.
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Affiliation(s)
- Alexandre Espinós
- Instituto de Neurociencias CSIC ‐ UMH, 03550 Sant Joan d'Alacant Spain
| | | | - Enrico Negri
- Instituto de Neurociencias CSIC ‐ UMH, 03550 Sant Joan d'Alacant Spain
| | - Víctor Borrell
- Instituto de Neurociencias CSIC ‐ UMH, 03550 Sant Joan d'Alacant Spain
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8
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Damert A. SVA retrotransposons and a low copy repeat in humans and great apes: a mobile connection. Mol Biol Evol 2022; 39:6586216. [PMID: 35574660 PMCID: PMC9132208 DOI: 10.1093/molbev/msac103] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Segmental duplications (SDs) constitute a considerable fraction of primate genomes. They contribute to genetic variation and provide raw material for evolution. Groups of SDs are characterized by the presence of shared core duplicons. One of these core duplicons, low copy repeat (lcr)16a, has been shown to be particularly active in the propagation of interspersed SDs in primates. The underlying mechanisms are, however, only partially understood. Alu short interspersed elements (SINEs) are frequently found at breakpoints and have been implicated in the expansion of SDs. Detailed analysis of lcr16a-containing SDs shows that the hominid-specific SVA (SINE-R-VNTR-Alu) retrotransposon is an integral component of the core duplicon in Asian and African great apes. In orang-utan, it provides breakpoints and contributes to both interchromosomal and intrachromosomal lcr16a mobility by inter-element recombination. Furthermore, the data suggest that in hominines (human, chimpanzee, gorilla) SVA recombination-mediated integration of a circular intermediate is the founding event of a lineage-specific lcr16a expansion. One of the hominine lcr16a copies displays large flanking direct repeats, a structural feature shared by other SDs in the human genome. Taken together, the results obtained extend the range of SVAs’ contribution to genome evolution from RNA-mediated transduction to DNA-based recombination. In addition, they provide further support for a role of circular intermediates in SD mobilization.
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Affiliation(s)
- Annette Damert
- Infection Biology Unit and Primate Genetics Laboratory, German Primate Center, Leibniz Institute for Primate Research, Göttingen, Germany
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9
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Vollger MR, Guitart X, Dishuck PC, Mercuri L, Harvey WT, Gershman A, Diekhans M, Sulovari A, Munson KM, Lewis AP, Hoekzema K, Porubsky D, Li R, Nurk S, Koren S, Miga KH, Phillippy AM, Timp W, Ventura M, Eichler EE. Segmental duplications and their variation in a complete human genome. Science 2022; 376:eabj6965. [PMID: 35357917 PMCID: PMC8979283 DOI: 10.1126/science.abj6965] [Citation(s) in RCA: 104] [Impact Index Per Article: 52.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Despite their importance in disease and evolution, highly identical segmental duplications (SDs) are among the last regions of the human reference genome (GRCh38) to be fully sequenced. Using a complete telomere-to-telomere human genome (T2T-CHM13), we present a comprehensive view of human SD organization. SDs account for nearly one-third of the additional sequence, increasing the genome-wide estimate from 5.4 to 7.0% [218 million base pairs (Mbp)]. An analysis of 268 human genomes shows that 91% of the previously unresolved T2T-CHM13 SD sequence (68.3 Mbp) better represents human copy number variation. Comparing long-read assemblies from human (n = 12) and nonhuman primate (n = 5) genomes, we systematically reconstruct the evolution and structural haplotype diversity of biomedically relevant and duplicated genes. This analysis reveals patterns of structural heterozygosity and evolutionary differences in SD organization between humans and other primates.
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Affiliation(s)
- Mitchell R Vollger
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
| | - Xavi Guitart
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
| | - Philip C Dishuck
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
| | - Ludovica Mercuri
- Department of Biology, University of Bari, Aldo Moro, Bari 70125, Italy
| | - William T Harvey
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
| | - Ariel Gershman
- Department of Molecular Biology and Genetics, Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, USA
| | - Mark Diekhans
- UC Santa Cruz Genomics Institute, University of California Santa Cruz, Santa Cruz, CA, USA
| | - Arvis Sulovari
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
| | - Katherine M Munson
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
| | - Alexandra P Lewis
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
| | - Kendra Hoekzema
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
| | - David Porubsky
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
| | - Ruiyang Li
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
| | - Sergey Nurk
- Genome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Sergey Koren
- Genome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Karen H Miga
- UC Santa Cruz Genomics Institute, University of California Santa Cruz, Santa Cruz, CA, USA
| | - Adam M Phillippy
- Genome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Winston Timp
- Department of Molecular Biology and Genetics, Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, USA
| | - Mario Ventura
- Department of Biology, University of Bari, Aldo Moro, Bari 70125, Italy
| | - Evan E Eichler
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
- Howard Hughes Medical Institute, University of Washington, Seattle, WA, USA
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10
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Abdullaev ET, Umarova IR, Arndt PF. Modelling segmental duplications in the human genome. BMC Genomics 2021; 22:496. [PMID: 34215180 PMCID: PMC8254307 DOI: 10.1186/s12864-021-07789-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2020] [Accepted: 06/10/2021] [Indexed: 11/22/2022] Open
Abstract
Background Segmental duplications (SDs) are long DNA sequences that are repeated in a genome and have high sequence identity. In contrast to repetitive elements they are often unique and only sometimes have multiple copies in a genome. There are several well-studied mechanisms responsible for segmental duplications: non-allelic homologous recombination, non-homologous end joining and replication slippage. Such duplications play an important role in evolution, however, we do not have a full understanding of the dynamic properties of the duplication process. Results We study segmental duplications through a graph representation where nodes represent genomic regions and edges represent duplications between them. The resulting network (the SD network) is quite complex and has distinct features which allow us to make inference on the evolution of segmantal duplications. We come up with the network growth model that explains features of the SD network thus giving us insights on dynamics of segmental duplications in the human genome. Based on our analysis of genomes of other species the network growth model seems to be applicable for multiple mammalian genomes. Conclusions Our analysis suggests that duplication rates of genomic loci grow linearly with the number of copies of a duplicated region. Several scenarios explaining such a preferential duplication rates were suggested. Supplementary Information The online version contains supplementary material available at (10.1186/s12864-021-07789-7).
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Affiliation(s)
- Eldar T Abdullaev
- Department of Computational Molecular Biology, Max Planck Institute for Molecular Genetics, Ihnestraße 63/73, Berlin, 14195, Germany.
| | - Iren R Umarova
- Faculty of Computational Mathematics and Cybernetics, Moscow State University, Leninskiye Gory 1-52, Moscow, 119991, Russia
| | - Peter F Arndt
- Department of Computational Molecular Biology, Max Planck Institute for Molecular Genetics, Ihnestraße 63/73, Berlin, 14195, Germany
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11
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Mosley TJ, Johnston HR, Cutler DJ, Zwick ME, Mulle JG. Sex-specific recombination patterns predict parent of origin for recurrent genomic disorders. BMC Med Genomics 2021; 14:154. [PMID: 34107974 PMCID: PMC8190997 DOI: 10.1186/s12920-021-00999-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2020] [Accepted: 06/02/2021] [Indexed: 11/24/2022] Open
Abstract
BACKGROUND Structural rearrangements of the genome, which generally occur during meiosis and result in large-scale (> 1 kb) copy number variants (CNV; deletions or duplications ≥ 1 kb), underlie genomic disorders. Recurrent pathogenic CNVs harbor similar breakpoints in multiple unrelated individuals and are primarily formed via non-allelic homologous recombination (NAHR). Several pathogenic NAHR-mediated recurrent CNV loci demonstrate biases for parental origin of de novo CNVs. However, the mechanism underlying these biases is not well understood. METHODS We performed a systematic, comprehensive literature search to curate parent of origin data for multiple pathogenic CNV loci. Using a regression framework, we assessed the relationship between parental CNV origin and the male to female recombination rate ratio. RESULTS We demonstrate significant association between sex-specific differences in meiotic recombination and parental origin biases at these loci (p = 1.07 × 10-14). CONCLUSIONS Our results suggest that parental origin of CNVs is largely influenced by sex-specific recombination rates and highlight the need to consider these differences when investigating mechanisms that cause structural variation.
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Affiliation(s)
- Trenell J Mosley
- Graduate Program in Genetics and Molecular Biology, Laney Graduate School, Emory University, 201 Dowman Drive, Atlanta, GA, 30322, USA
- Department of Human Genetics, Emory University School of Medicine, 615 Michael Street, Whitehead Building Suite 300, Atlanta, GA, 30322, USA
| | - H Richard Johnston
- Department of Human Genetics, Emory University School of Medicine, 615 Michael Street, Whitehead Building Suite 300, Atlanta, GA, 30322, USA
- Emory Integrated Computational Core, Emory University, 101 Woodruff Circle, Atlanta, GA, 30322, USA
| | - David J Cutler
- Department of Human Genetics, Emory University School of Medicine, 615 Michael Street, Whitehead Building Suite 300, Atlanta, GA, 30322, USA
| | - Michael E Zwick
- Department of Human Genetics, Emory University School of Medicine, 615 Michael Street, Whitehead Building Suite 300, Atlanta, GA, 30322, USA
- Department of Pediatrics, Emory University School of Medicine, 2015 Uppergate Drive, Atlanta, GA, 30322, USA
| | - Jennifer G Mulle
- Department of Human Genetics, Emory University School of Medicine, 615 Michael Street, Whitehead Building Suite 300, Atlanta, GA, 30322, USA.
- Department of Epidemiology, Rollins School of Public Health, Emory University, 1518 Clifton Road NE, Atlanta, GA, 30322, USA.
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12
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Gualtieri CT. Genomic Variation, Evolvability, and the Paradox of Mental Illness. Front Psychiatry 2021; 11:593233. [PMID: 33551865 PMCID: PMC7859268 DOI: 10.3389/fpsyt.2020.593233] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/10/2020] [Accepted: 11/27/2020] [Indexed: 12/30/2022] Open
Abstract
Twentieth-century genetics was hard put to explain the irregular behavior of neuropsychiatric disorders. Autism and schizophrenia defy a principle of natural selection; they are highly heritable but associated with low reproductive success. Nevertheless, they persist. The genetic origins of such conditions are confounded by the problem of variable expression, that is, when a given genetic aberration can lead to any one of several distinct disorders. Also, autism and schizophrenia occur on a spectrum of severity, from mild and subclinical cases to the overt and disabling. Such irregularities reflect the problem of missing heritability; although hundreds of genes may be associated with autism or schizophrenia, together they account for only a small proportion of cases. Techniques for higher resolution, genomewide analysis have begun to illuminate the irregular and unpredictable behavior of the human genome. Thus, the origins of neuropsychiatric disorders in particular and complex disease in general have been illuminated. The human genome is characterized by a high degree of structural and behavioral variability: DNA content variation, epistasis, stochasticity in gene expression, and epigenetic changes. These elements have grown more complex as evolution scaled the phylogenetic tree. They are especially pertinent to brain development and function. Genomic variability is a window on the origins of complex disease, neuropsychiatric disorders, and neurodevelopmental disorders in particular. Genomic variability, as it happens, is also the fuel of evolvability. The genomic events that presided over the evolution of the primate and hominid lineages are over-represented in patients with autism and schizophrenia, as well as intellectual disability and epilepsy. That the special qualities of the human genome that drove evolution might, in some way, contribute to neuropsychiatric disorders is a matter of no little interest.
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13
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Benton ML, Abraham A, LaBella AL, Abbot P, Rokas A, Capra JA. The influence of evolutionary history on human health and disease. Nat Rev Genet 2021; 22:269-283. [PMID: 33408383 PMCID: PMC7787134 DOI: 10.1038/s41576-020-00305-9] [Citation(s) in RCA: 97] [Impact Index Per Article: 32.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/26/2020] [Indexed: 01/29/2023]
Abstract
Nearly all genetic variants that influence disease risk have human-specific origins; however, the systems they influence have ancient roots that often trace back to evolutionary events long before the origin of humans. Here, we review how advances in our understanding of the genetic architectures of diseases, recent human evolution and deep evolutionary history can help explain how and why humans in modern environments become ill. Human populations exhibit differences in the prevalence of many common and rare genetic diseases. These differences are largely the result of the diverse environmental, cultural, demographic and genetic histories of modern human populations. Synthesizing our growing knowledge of evolutionary history with genetic medicine, while accounting for environmental and social factors, will help to achieve the promise of personalized genomics and realize the potential hidden in an individual's DNA sequence to guide clinical decisions. In short, precision medicine is fundamentally evolutionary medicine, and integration of evolutionary perspectives into the clinic will support the realization of its full potential.
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Affiliation(s)
- Mary Lauren Benton
- grid.152326.10000 0001 2264 7217Department of Biomedical Informatics, Vanderbilt University School of Medicine, Nashville, TN USA ,grid.252890.40000 0001 2111 2894Department of Computer Science, Baylor University, Waco, TX USA
| | - Abin Abraham
- grid.152326.10000 0001 2264 7217Vanderbilt Genetics Institute, Vanderbilt University, Nashville, TN USA ,grid.152326.10000 0001 2264 7217Vanderbilt University Medical Center, Vanderbilt University, Nashville, TN USA
| | - Abigail L. LaBella
- grid.152326.10000 0001 2264 7217Department of Biological Sciences, Vanderbilt University, Nashville, TN USA
| | - Patrick Abbot
- grid.152326.10000 0001 2264 7217Department of Biological Sciences, Vanderbilt University, Nashville, TN USA
| | - Antonis Rokas
- grid.152326.10000 0001 2264 7217Department of Biomedical Informatics, Vanderbilt University School of Medicine, Nashville, TN USA ,grid.152326.10000 0001 2264 7217Vanderbilt Genetics Institute, Vanderbilt University, Nashville, TN USA ,grid.152326.10000 0001 2264 7217Department of Biological Sciences, Vanderbilt University, Nashville, TN USA
| | - John A. Capra
- grid.152326.10000 0001 2264 7217Department of Biomedical Informatics, Vanderbilt University School of Medicine, Nashville, TN USA ,grid.152326.10000 0001 2264 7217Department of Biological Sciences, Vanderbilt University, Nashville, TN USA ,grid.266102.10000 0001 2297 6811Bakar Computational Health Sciences Institute and Department of Epidemiology and Biostatistics, University of California, San Francisco, CA USA
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14
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Abstract
The mammalian cerebral cortex is the pinnacle of brain evolution, reaching its maximum complexity in terms of neuron number, diversity and functional circuitry. The emergence of this outstanding complexity begins during embryonic development, when a limited number of neural stem and progenitor cells manage to generate myriads of neurons in the appropriate numbers, types and proportions, in a process called neurogenesis. Here we review the current knowledge on the regulation of cortical neurogenesis, beginning with a description of the types of progenitor cells and their lineage relationships. This is followed by a review of the determinants of neuron fate, the molecular and genetic regulatory mechanisms, and considerations on the evolution of cortical neurogenesis in vertebrates leading to humans. We finish with an overview on how dysregulation of neurogenesis is a leading cause of human brain malformations and functional disabilities.
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Affiliation(s)
- Ana Villalba
- Instituto de Neurociencias, Consejo Superior de Investigaciones Científicas & Universidad Miguel Hernández, Sant Joan d'Alacant, Spain
| | - Magdalena Götz
- Institute for Stem Cell Research, Helmholtz Zentrum München & Biomedical Center, Ludwig-Maximilians Universitaet, Planegg-Martinsried, Germany
| | - Víctor Borrell
- Instituto de Neurociencias, Consejo Superior de Investigaciones Científicas & Universidad Miguel Hernández, Sant Joan d'Alacant, Spain.
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15
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Single-cell strand sequencing of a macaque genome reveals multiple nested inversions and breakpoint reuse during primate evolution. Genome Res 2020; 30:1680-1693. [PMID: 33093070 PMCID: PMC7605249 DOI: 10.1101/gr.265322.120] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Accepted: 09/02/2020] [Indexed: 12/14/2022]
Abstract
Rhesus macaque is an Old World monkey that shared a common ancestor with human ∼25 Myr ago and is an important animal model for human disease studies. A deep understanding of its genetics is therefore required for both biomedical and evolutionary studies. Among structural variants, inversions represent a driving force in speciation and play an important role in disease predisposition. Here we generated a genome-wide map of inversions between human and macaque, combining single-cell strand sequencing with cytogenetics. We identified 375 total inversions between 859 bp and 92 Mbp, increasing by eightfold the number of previously reported inversions. Among these, 19 inversions flanked by segmental duplications overlap with recurrent copy number variants associated with neurocognitive disorders. Evolutionary analyses show that in 17 out of 19 cases, the Hominidae orientation of these disease-associated regions is always derived. This suggests that duplicated sequences likely played a fundamental role in generating inversions in humans and great apes, creating architectures that nowadays predispose these regions to disease-associated genetic instability. Finally, we identified 861 genes mapping at 156 inversions breakpoints, with some showing evidence of differential expression in human and macaque cell lines, thus highlighting candidates that might have contributed to the evolution of species-specific features. This study depicts the most accurate fine-scale map of inversions between human and macaque using a two-pronged integrative approach, such as single-cell strand sequencing and cytogenetics, and represents a valuable resource toward understanding of the biology and evolution of primate species.
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16
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Van Bibber NW, Haerle C, Khalife R, Dayhoff GW, Uversky VN. Intrinsic Disorder in Human Proteins Encoded by Core Duplicon Gene Families. J Phys Chem B 2020; 124:8050-8070. [PMID: 32880174 DOI: 10.1021/acs.jpcb.0c07676] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Segmental duplications (i.e., highly homologous DNA fragments greater than 1 kb in length that are present within a genome at more than one site) are typically found in genome regions that are prone to rearrangements. A noticeable fraction of the human genome (∼5%) includes segmental duplications (or duplicons) that are assumed to play a number of vital roles in human evolution, human-specific adaptation, and genomic instability. Despite their importance for crucial events such as synaptogenesis, neuronal migration, and neocortical expansion, these segmental duplications continue to be rather poorly characterized. Of particular interest are the core duplicon gene (CDG) families, which are replicates sharing common "core" DNA among the randomly attached pieces and which expand along single chromosomes and might harbor newly acquired protein domains. Another important feature of proteins encoded by CDG families is their multifunctionality. Although it seems that these proteins might possess many characteristic features of intrinsically disordered proteins, to the best of our knowledge, a systematic investigation of the intrinsic disorder predisposition of the proteins encoded by core duplicon gene families has not been conducted yet. To fill this gap and to determine the degree to which these proteins might be affected by intrinsic disorder, we analyzed a set of human proteins encoded by the members of 10 core duplicon gene families, such as NBPF, RGPD, GUSBP, PMS2P, SPATA31, TRIM51, GOLGA8, NPIP, TBC1D3, and LRRC37. Our analysis revealed that the vast majority of these proteins are highly disordered, with their disordered regions often being utilized as means for the protein-protein interactions and/or targeted for numerous posttranslational modifications of different nature.
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Affiliation(s)
- Nathan W Van Bibber
- Department of Molecular Medicine Morsani College of Medicine, University of South Florida, 12901 Bruce B. Downs Boulevard, Tampa, Florida 33612, United States
| | - Cornelia Haerle
- Department of Molecular Medicine Morsani College of Medicine, University of South Florida, 12901 Bruce B. Downs Boulevard, Tampa, Florida 33612, United States
| | - Roy Khalife
- Department of Molecular Medicine Morsani College of Medicine, University of South Florida, 12901 Bruce B. Downs Boulevard, Tampa, Florida 33612, United States
| | - Guy W Dayhoff
- Department of Chemistry, College of Art and Sciences, University of South Florida, Tampa, Florida 33620, United States
| | - Vladimir N Uversky
- Department of Molecular Medicine Morsani College of Medicine, University of South Florida, 12901 Bruce B. Downs Boulevard, Tampa, Florida 33612, United States.,USF Health Byrd Alzheimer's Research Institute, Morsani College of Medicine, University of South Florida, 12901 Bruce B. Downs Boulevard, Tampa, Florida 33612, United States.,Institute for Biological Instrumentation, Russian Academy of Sciences, Federal Research Center "Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences", 4 Institutskaya St., Pushchino, 142290, Moscow Region, Russia
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17
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Chicote JU, López-Sánchez M, Marquès-Bonet T, Callizo J, Pérez-Jurado LA, García-España A. Circular DNA intermediates in the generation of large human segmental duplications. BMC Genomics 2020; 21:593. [PMID: 32847497 PMCID: PMC7450558 DOI: 10.1186/s12864-020-06998-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2020] [Accepted: 08/17/2020] [Indexed: 11/28/2022] Open
Abstract
Background Duplications of large genomic segments provide genetic diversity in genome evolution. Despite their importance, how these duplications are generated remains uncertain, particularly for distant duplicated genomic segments. Results Here we provide evidence of the participation of circular DNA intermediates in the single generation of some large human segmental duplications. A specific reversion of sequence order from A-B/C-D to B-A/D-C between duplicated segments and the presence of only microhomologies and short indels at the evolutionary breakpoints suggest a circularization of the donor ancestral locus and an accidental replicative interaction with the acceptor locus. Conclusions This novel mechanism of random genomic mutation could explain several distant genomic duplications including some of the ones that took place during recent human evolution.
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Affiliation(s)
- Javier U Chicote
- Research Unit, Hospital Universitari de Tarragona Joan XXIII, Institut d'Investigació Sanitària Pere Virgili, Universitat Rovira i Virgili, 43005, Tarragona, Spain
| | - Marcos López-Sánchez
- Genetics Unit, Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra, 08003, Barcelona, Spain.,Hospital del Mar Research Institute (IMIM) and Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), 08003, Barcelona, Spain
| | - Tomàs Marquès-Bonet
- Institut de Biologia Evolutiva (CSIC-UPF), Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra, 08003, Barcelona, Spain.,Catalan Institution of Research and Advanced Studies (ICREA), 08010, Barcelona, Spain.,CNAG-CRG, Centre for Genomic Regulation, Barcelona Institute of Science and Technology (BIST), 08028, Barcelona, Spain
| | - José Callizo
- Department of Ophthalmology, Hospital Universitari de Tarragona Joan XXIII, Institut d'Investigació Sanitària Pere Virgili, Universitat Rovira i Virgili, 43005, Tarragona, Spain
| | - Luis A Pérez-Jurado
- Genetics Unit, Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra, 08003, Barcelona, Spain. .,Hospital del Mar Research Institute (IMIM) and Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), 08003, Barcelona, Spain. .,SA Clinical Genetics, Women's and Children's Hospital, South Australian Health and Medical Research Institute (SAHMRI) & University of Adelaide, Adelaide, SA, 5000, Australia.
| | - Antonio García-España
- Research Unit, Hospital Universitari de Tarragona Joan XXIII, Institut d'Investigació Sanitària Pere Virgili, Universitat Rovira i Virgili, 43005, Tarragona, Spain.
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18
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Lengyel A, Pinti É, Pikó H, Jávorszky E, David D, Tihanyi M, Gönczi É, Kiss E, Tóth Z, Tory K, Fekete G, Haltrich I. Clinical and genetic findings in Hungarian pediatric patients carrying chromosome 16p copy number variants and a review of the literature. Eur J Med Genet 2020; 63:104027. [PMID: 32758661 DOI: 10.1016/j.ejmg.2020.104027] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2020] [Revised: 07/10/2020] [Accepted: 07/25/2020] [Indexed: 11/27/2022]
Abstract
The short arm of chromosome 16 (16p) is enriched for segmental duplications, making it susceptible to recurrent, reciprocal rearrangements implicated in the etiology of several phenotypes, including intellectual disability, speech disorders, developmental coordination disorder, autism spectrum disorders, attention deficit hyperactivity disorders, obesity and congenital skeletal disorders. In our clinical study 73 patients were analyzed by chromosomal microarray, and results were confirmed by fluorescence in situ hybridization or polymerase chain reaction. All patients underwent detailed clinical evaluation, with special emphasis on behavioral symptoms. 16p rearrangements were identified in 10 individuals. We found six pathogenic deletions and duplications of the recurrent regions within 16p11.2: one patient had a deletion of the distal 16p11.2 region associated with obesity, while four individuals had duplications, and one patient a deletion of the proximal 16p11.2 region. The other four patients carried 16p variations as second-site genomic alterations, acting as possible modifying genetic factors. We present the phenotypic and genotypic results of our patients and discuss our findings in relation to the available literature.
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Affiliation(s)
- Anna Lengyel
- II Department of Pediatrics, Semmelweis University, Budapest, Hungary.
| | - Éva Pinti
- II Department of Pediatrics, Semmelweis University, Budapest, Hungary
| | - Henriett Pikó
- I Department of Internal Medicine, Semmelweis University, Budapest, Hungary
| | - Eszter Jávorszky
- I Department of Pediatrics, Semmelweis University, Budapest, Hungary
| | - Dezső David
- Department of Human Genetics, National Health Institute Dr. Ricardo Jorge, Lisbon, Portugal
| | - Mariann Tihanyi
- Department of Genetics, Zala County Hospital, Zalaegerszeg, Hungary
| | - Éva Gönczi
- II Department of Pediatrics, Semmelweis University, Budapest, Hungary
| | - Eszter Kiss
- II Department of Pediatrics, Semmelweis University, Budapest, Hungary
| | - Zsuzsa Tóth
- II Department of Pediatrics, Semmelweis University, Budapest, Hungary
| | - Kálmán Tory
- I Department of Pediatrics, Semmelweis University, Budapest, Hungary
| | - György Fekete
- II Department of Pediatrics, Semmelweis University, Budapest, Hungary
| | - Irén Haltrich
- II Department of Pediatrics, Semmelweis University, Budapest, Hungary
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19
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Bekpen C, Tautz D. Human core duplicon gene families: game changers or game players? Brief Funct Genomics 2020; 18:402-411. [PMID: 31529038 PMCID: PMC6920530 DOI: 10.1093/bfgp/elz016] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2019] [Revised: 05/01/2019] [Accepted: 06/24/2019] [Indexed: 01/09/2023] Open
Abstract
Illuminating the role of specific gene duplications within the human lineage can provide insights into human-specific adaptations. The so-called human core duplicon gene families have received particular attention in this respect, due to special features, such as expansion along single chromosomes, newly acquired protein domains and signatures of positive selection. Here, we summarize the data available for 10 such families and include some new analyses. A picture emerges that suggests broad functions for these protein families, possibly through modification of core cellular pathways. Still, more dedicated studies are required to elucidate the function of core-duplicons gene families and how they have shaped adaptations and evolution of humans.
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Affiliation(s)
| | - Diethard Tautz
- Max-Planck Institute for Evolutionary Biology, 24306 Plön, Germany
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20
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Brasó-Vives M, Povolotskaya IS, Hartasánchez DA, Farré X, Fernandez-Callejo M, Raveendran M, Harris RA, Rosene DL, Lorente-Galdos B, Navarro A, Marques-Bonet T, Rogers J, Juan D. Copy number variants and fixed duplications among 198 rhesus macaques (Macaca mulatta). PLoS Genet 2020; 16:e1008742. [PMID: 32392208 PMCID: PMC7241854 DOI: 10.1371/journal.pgen.1008742] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2019] [Revised: 05/21/2020] [Accepted: 03/27/2020] [Indexed: 01/01/2023] Open
Abstract
The rhesus macaque is an abundant species of Old World monkeys and a valuable model organism for biomedical research due to its close phylogenetic relationship to humans. Copy number variation is one of the main sources of genomic diversity within and between species and a widely recognized cause of inter-individual differences in disease risk. However, copy number differences among rhesus macaques and between the human and macaque genomes, as well as the relevance of this diversity to research involving this nonhuman primate, remain understudied. Here we present a high-resolution map of sequence copy number for the rhesus macaque genome constructed from a dataset of 198 individuals. Our results show that about one-eighth of the rhesus macaque reference genome is composed of recently duplicated regions, either copy number variable regions or fixed duplications. Comparison with human genomic copy number maps based on previously published data shows that, despite overall similarities in the genome-wide distribution of these regions, there are specific differences at the chromosome level. Some of these create differences in the copy number profile between human disease genes and their rhesus macaque orthologs. Our results highlight the importance of addressing the number of copies of target genes in the design of experiments and cautions against human-centered assumptions in research conducted with model organisms. Overall, we present a genome-wide copy number map from a large sample of rhesus macaque individuals representing an important novel contribution concerning the evolution of copy number in primate genomes.
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Affiliation(s)
- Marina Brasó-Vives
- Institut de Biologia Evolutiva (CSIC-Universitat Pompeu Fabra), Parc de Recerca Biomèdica de Barcelona, Barcelona, Catalonia, Spain
- Laboratoire de Biométrie et Biologie Évolutive UMR 5558, Université de Lyon, Université Lyon 1, CNRS, Villeurbanne, France
| | - Inna S. Povolotskaya
- Veltischev Research and Clinical Institute for Pediatrics of the Pirogov Russian National Research Medical University, Moscow, Russia
| | - Diego A. Hartasánchez
- Institut de Biologia Evolutiva (CSIC-Universitat Pompeu Fabra), Parc de Recerca Biomèdica de Barcelona, Barcelona, Catalonia, Spain
| | - Xavier Farré
- Institut de Biologia Evolutiva (CSIC-Universitat Pompeu Fabra), Parc de Recerca Biomèdica de Barcelona, Barcelona, Catalonia, Spain
| | - Marcos Fernandez-Callejo
- National Centre for Genomic Analysis-Centre for Genomic Regulation, Barcelona Institute of Science and Technology, Barcelona, Catalonia, Spain
| | - Muthuswamy Raveendran
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, United States of America
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America
| | - R. Alan Harris
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, United States of America
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America
| | - Douglas L. Rosene
- Department of Anatomy and Neurobiology, Boston University School of Medicine, Boston, Massachusetts, United States of America
| | - Belen Lorente-Galdos
- Department of Neuroscience, Yale School of Medicine, New Haven, Connecticut, United States of America
| | - Arcadi Navarro
- Institut de Biologia Evolutiva (CSIC-Universitat Pompeu Fabra), Parc de Recerca Biomèdica de Barcelona, Barcelona, Catalonia, Spain
- National Institute for Bioinformatics (INB), Barcelona, Catalonia, Spain
- Institució Catalana de Recerca i Estudis Avançats, Barcelona, Catalonia, Spain
| | - Tomas Marques-Bonet
- Institut de Biologia Evolutiva (CSIC-Universitat Pompeu Fabra), Parc de Recerca Biomèdica de Barcelona, Barcelona, Catalonia, Spain
- National Centre for Genomic Analysis-Centre for Genomic Regulation, Barcelona Institute of Science and Technology, Barcelona, Catalonia, Spain
- Institució Catalana de Recerca i Estudis Avançats, Barcelona, Catalonia, Spain
- Institut Català de Paleontologia Miquel Crusafont, Universitat Autònoma de Barcelona, Cerdanyola del Vallès, Catalonia, Spain
| | - Jeffrey Rogers
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, United States of America
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America
| | - David Juan
- Institut de Biologia Evolutiva (CSIC-Universitat Pompeu Fabra), Parc de Recerca Biomèdica de Barcelona, Barcelona, Catalonia, Spain
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21
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Maggiolini FAM, Cantsilieris S, D’Addabbo P, Manganelli M, Coe BP, Dumont BL, Sanders AD, Pang AWC, Vollger MR, Palumbo O, Palumbo P, Accadia M, Carella M, Eichler EE, Antonacci F. Genomic inversions and GOLGA core duplicons underlie disease instability at the 15q25 locus. PLoS Genet 2019; 15:e1008075. [PMID: 30917130 PMCID: PMC6436712 DOI: 10.1371/journal.pgen.1008075] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2018] [Accepted: 03/07/2019] [Indexed: 11/19/2022] Open
Abstract
Human chromosome 15q25 is involved in several disease-associated structural rearrangements, including microdeletions and chromosomal markers with inverted duplications. Using comparative fluorescence in situ hybridization, strand-sequencing, single-molecule, real-time sequencing and Bionano optical mapping analyses, we investigated the organization of the 15q25 region in human and nonhuman primates. We found that two independent inversions occurred in this region after the fission event that gave rise to phylogenetic chromosomes XIV and XV in humans and great apes. One of these inversions is still polymorphic in the human population today and may confer differential susceptibility to 15q25 microdeletions and inverted duplications. The inversion breakpoints map within segmental duplications containing core duplicons of the GOLGA gene family and correspond to the site of an ancestral centromere, which became inactivated about 25 million years ago. The inactivation of this centromere likely released segmental duplications from recombination repression typical of centromeric regions. We hypothesize that this increased the frequency of ectopic recombination creating a hotspot of hominid inversions where dispersed GOLGA core elements now predispose this region to recurrent genomic rearrangements associated with disease.
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Affiliation(s)
| | - Stuart Cantsilieris
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, United States of America
| | - Pietro D’Addabbo
- Dipartimento di Biologia, Università degli Studi di Bari “Aldo Moro”, Bari, Italy
| | - Michele Manganelli
- Dipartimento di Biologia, Università degli Studi di Bari “Aldo Moro”, Bari, Italy
| | - Bradley P. Coe
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, United States of America
| | - Beth L. Dumont
- The Jackson Laboratory, Bar Harbor, ME, United States of America
| | - Ashley D. Sanders
- European Molecular Biology Laboratory (EMBL), Genome Biology Unit, Meyerhofstraße 1, Heidelberg, Germany
| | | | - Mitchell R. Vollger
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, United States of America
| | - Orazio Palumbo
- Medical Genetics Unit, IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotondo (FG), Italy
| | - Pietro Palumbo
- Medical Genetics Unit, IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotondo (FG), Italy
| | - Maria Accadia
- Medical Genetics Service, Hospital “Cardinale G. Panico”, Via San Pio X n°4, Tricase, LE, Italy
| | - Massimo Carella
- Medical Genetics Unit, IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotondo (FG), Italy
| | - Evan E. Eichler
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, United States of America
- Howard Hughes Medical Institute, University of Washington, Seattle, WA, United States of America
| | - Francesca Antonacci
- Dipartimento di Biologia, Università degli Studi di Bari “Aldo Moro”, Bari, Italy
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22
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Abstract
What made us human? Gene expression changes clearly played a significant part in human evolution, but pinpointing the causal regulatory mutations is hard. Comparative genomics enabled the identification of human accelerated regions (HARs) and other human-specific genome sequences. The major challenge in the past decade has been to link diverged sequences to uniquely human biology. This review discusses approaches to this problem, progress made at the molecular level, and prospects for moving towards genetic causes for uniquely human biology.
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Affiliation(s)
- Lucía F Franchini
- Instituto de Investigaciones en Ingeniería Genética y Biología Molecular (INGEBI), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
| | - Katherine S Pollard
- Gladstone Institutes, San Francisco, CA, 94158, USA. .,Department of Epidemiology & Biostatistics, Institute for Human Genetics, Institute for Computational Health Sciences, University of California, San Francisco, CA, 94158, USA.
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Chujo T, Yamazaki T, Kawaguchi T, Kurosaka S, Takumi T, Nakagawa S, Hirose T. Unusual semi-extractability as a hallmark of nuclear body-associated architectural noncoding RNAs. EMBO J 2017; 36:1447-1462. [PMID: 28404604 PMCID: PMC5430218 DOI: 10.15252/embj.201695848] [Citation(s) in RCA: 83] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2016] [Revised: 02/02/2017] [Accepted: 03/09/2017] [Indexed: 12/21/2022] Open
Abstract
NEAT1_2 long noncoding RNA (lncRNA) is the molecular scaffold of paraspeckle nuclear bodies. Here, we report an improved RNA extraction method: extensive needle shearing or heating of cell lysate in RNA extraction reagent improved NEAT1_2 extraction by 20-fold (a property we term "semi-extractability"), whereas using a conventional method NEAT1_2 was trapped in the protein phase. The improved extraction method enabled us to estimate that approximately 50 NEAT1_2 molecules are present in a single paraspeckle. Another architectural lncRNA, IGS16, also exhibited similar semi-extractability. A comparison of RNA-seq data from needle-sheared and control samples revealed the existence of multiple semi-extractable RNAs, many of which were localized in subnuclear granule-like structures. The semi-extractability of NEAT1_2 correlated with its association with paraspeckle proteins and required the prion-like domain of the RNA-binding protein FUS This observation suggests that tenacious RNA-protein and protein-protein interactions, which drive nuclear body formation, are responsible for semi-extractability. Our findings provide a foundation for the discovery of the architectural RNAs that constitute nuclear bodies.
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Affiliation(s)
- Takeshi Chujo
- Institute for Genetic Medicine, Hokkaido University, Sapporo Hokkaido, Japan
| | - Tomohiro Yamazaki
- Institute for Genetic Medicine, Hokkaido University, Sapporo Hokkaido, Japan
| | - Tetsuya Kawaguchi
- Institute for Genetic Medicine, Hokkaido University, Sapporo Hokkaido, Japan
| | | | - Toru Takumi
- Brain Science Institute, RIKEN, Wako Saitama, Japan
| | - Shinichi Nakagawa
- Faculty of Pharmaceutical Sciences, Hokkaido University, Sapporo Hokkaido, Japan
| | - Tetsuro Hirose
- Institute for Genetic Medicine, Hokkaido University, Sapporo Hokkaido, Japan
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Bekpen C, Künzel S, Xie C, Eaaswarkhanth M, Lin YL, Gokcumen O, Akdis CA, Tautz D. Segmental duplications and evolutionary acquisition of UV damage response in the SPATA31 gene family of primates and humans. BMC Genomics 2017; 18:222. [PMID: 28264649 PMCID: PMC5338094 DOI: 10.1186/s12864-017-3595-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2016] [Accepted: 02/20/2017] [Indexed: 12/11/2022] Open
Abstract
Background Segmental duplications are an abundant source for novel gene functions and evolutionary adaptations. This mechanism of generating novelty was very active during the evolution of primates particularly in the human lineage. Here, we characterize the evolution and function of the SPATA31 gene family (former designation FAM75A), which was previously shown to be among the gene families with the strongest signal of positive selection in hominoids. The mouse homologue for this gene family is a single copy gene expressed during spermatogenesis. Results We show that in primates, the SPATA31 gene duplicated into SPATA31A and SPATA31C types and broadened the expression into many tissues. Each type became further segmentally duplicated in the line towards humans with the largest number of full-length copies found for SPATA31A in humans. Copy number estimates of SPATA31A based on digital PCR show an average of 7.5 with a range of 5–11 copies per diploid genome among human individuals. The primate SPATA31 genes also acquired new protein domains that suggest an involvement in UV response and DNA repair. We generated antibodies and show that the protein is re-localized from the nucleolus to the whole nucleus upon UV-irradiation suggesting a UV damage response. We used CRISPR/Cas mediated mutagenesis to knockout copies of the gene in human primary fibroblast cells. We find that cell lines with reduced functional copies as well as naturally occurring low copy number HFF cells show enhanced sensitivity towards UV-irradiation. Conclusion The acquisition of new SPATA31 protein functions and its broadening of expression may be related to the evolution of the diurnal life style in primates that required a higher UV tolerance. The increased segmental duplications in hominoids as well as its fast evolution suggest the acquisition of further specific functions particularly in humans. Electronic supplementary material The online version of this article (doi:10.1186/s12864-017-3595-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Cemalettin Bekpen
- Max-Planck Institute for Evolutionary Biology, August-Thienemann Strasse 2, 24306, Plön, Germany.
| | - Sven Künzel
- Max-Planck Institute for Evolutionary Biology, August-Thienemann Strasse 2, 24306, Plön, Germany
| | - Chen Xie
- Max-Planck Institute for Evolutionary Biology, August-Thienemann Strasse 2, 24306, Plön, Germany
| | - Muthukrishnan Eaaswarkhanth
- Department of Biological Sciences, State University of New York at Buffalo, Buffalo, 14260-1300, NY, USA.,Present address: Population Genomics and Genetic Epidemiology Unit, Dasman Diabetes Institute, P.O.Box 1180, Dasman, 15462, Kuwait
| | - Yen-Lung Lin
- Department of Biological Sciences, State University of New York at Buffalo, Buffalo, 14260-1300, NY, USA
| | - Omer Gokcumen
- Department of Biological Sciences, State University of New York at Buffalo, Buffalo, 14260-1300, NY, USA
| | - Cezmi A Akdis
- Swiss Institute of Allergy and Asthma Research (SIAF), Davos, CH-7270, Switzerland
| | - Diethard Tautz
- Max-Planck Institute for Evolutionary Biology, August-Thienemann Strasse 2, 24306, Plön, Germany.
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Kim YJ, Ahn K, Gim JA, Oh MH, Han K, Kim HS. Gene structure variation in segmental duplication block C of human chromosome 7q 11.23 during primate evolution. Gene 2015. [PMID: 26196062 DOI: 10.1016/j.gene.2015.07.060] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
Segmental duplication, or low-copy repeat (LCR) event, occurs during primate evolution and is an important source of genomic diversity, including gain or loss of gene function. The human chromosome 7q 11.23 is related to the William-Beuren syndrome and contains large region-specific LCRs composed of blocks A, B, and C that have different copy numbers in humans and different primates. We analyzed the structure of POM121, NSUN5, FKBP6, and TRIM50 genes in the LCRs of block C. Based on computational analysis, POM121B created by a segmental duplication acquired a new exonic region, whereas NSUN5B (NSUN5C) showed structural variation by integration of HERV-K LTR after duplication from the original NSUN5 gene. The TRIM50 gene originally consists of seven exons, whereas the duplicated TRIM73 and TRIM74 genes present five exons because of homologous recombination-mediated deletion. In addition, independent duplication events of the FKBP6 gene generated two pseudogenes at different genomic locations. In summary, these clustered genes are created by segmental duplication, indicating that they show dynamic evolutionary events, leading to structure variation in the primate genome.
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Affiliation(s)
- Yun-Ji Kim
- Department of Nanobiomedical Science & BK21 PLUS NBM Global Research Center for Regenerative Medicine, Dankook University, Cheonan 330-714, Republic of Korea; DKU-Theragen Institute for NGS Analysis (DTiNa), Cheonan 330-714, Republic of Korea
| | - Kung Ahn
- TBI, Theragen BiO Institute, TheragenEtex, Suwon 443-270, Republic of Korea
| | - Jeong-An Gim
- Department of Biological Sciences, College of Natural Sciences, Pusan National University, Busan 609-735, Republic of Korea
| | - Man Hwan Oh
- Department of Nanobiomedical Science & BK21 PLUS NBM Global Research Center for Regenerative Medicine, Dankook University, Cheonan 330-714, Republic of Korea
| | - Kyudong Han
- Department of Nanobiomedical Science & BK21 PLUS NBM Global Research Center for Regenerative Medicine, Dankook University, Cheonan 330-714, Republic of Korea; DKU-Theragen Institute for NGS Analysis (DTiNa), Cheonan 330-714, Republic of Korea
| | - Heui-Soo Kim
- Department of Biological Sciences, College of Natural Sciences, Pusan National University, Busan 609-735, Republic of Korea.
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Skinner BM, Sargent CA, Churcher C, Hunt T, Herrero J, Loveland JE, Dunn M, Louzada S, Fu B, Chow W, Gilbert J, Austin-Guest S, Beal K, Carvalho-Silva D, Cheng W, Gordon D, Grafham D, Hardy M, Harley J, Hauser H, Howden P, Howe K, Lachani K, Ellis PJI, Kelly D, Kerry G, Kerwin J, Ng BL, Threadgold G, Wileman T, Wood JMD, Yang F, Harrow J, Affara NA, Tyler-Smith C. The pig X and Y Chromosomes: structure, sequence, and evolution. Genome Res 2015; 26:130-9. [PMID: 26560630 PMCID: PMC4691746 DOI: 10.1101/gr.188839.114] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2014] [Accepted: 11/09/2015] [Indexed: 12/19/2022]
Abstract
We have generated an improved assembly and gene annotation of the pig X Chromosome, and a first draft assembly of the pig Y Chromosome, by sequencing BAC and fosmid clones from Duroc animals and incorporating information from optical mapping and fiber-FISH. The X Chromosome carries 1033 annotated genes, 690 of which are protein coding. Gene order closely matches that found in primates (including humans) and carnivores (including cats and dogs), which is inferred to be ancestral. Nevertheless, several protein-coding genes present on the human X Chromosome were absent from the pig, and 38 pig-specific X-chromosomal genes were annotated, 22 of which were olfactory receptors. The pig Y-specific Chromosome sequence generated here comprises 30 megabases (Mb). A 15-Mb subset of this sequence was assembled, revealing two clusters of male-specific low copy number genes, separated by an ampliconic region including the HSFY gene family, which together make up most of the short arm. Both clusters contain palindromes with high sequence identity, presumably maintained by gene conversion. Many of the ancestral X-related genes previously reported in at least one mammalian Y Chromosome are represented either as active genes or partial sequences. This sequencing project has allowed us to identify genes--both single copy and amplified--on the pig Y Chromosome, to compare the pig X and Y Chromosomes for homologous sequences, and thereby to reveal mechanisms underlying pig X and Y Chromosome evolution.
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Affiliation(s)
- Benjamin M Skinner
- Department of Pathology, University of Cambridge, Cambridge CB2 1QP, United Kingdom
| | - Carole A Sargent
- Department of Pathology, University of Cambridge, Cambridge CB2 1QP, United Kingdom
| | - Carol Churcher
- Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, United Kingdom
| | - Toby Hunt
- Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, United Kingdom
| | - Javier Herrero
- European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, Cambridge CB10 1SD, United Kingdom; Bill Lyons Informatics Centre, UCL Cancer Institute, University College London, London WC1E 6BT, United Kingdom
| | - Jane E Loveland
- Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, United Kingdom
| | - Matt Dunn
- Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, United Kingdom
| | - Sandra Louzada
- Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, United Kingdom
| | - Beiyuan Fu
- Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, United Kingdom
| | - William Chow
- Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, United Kingdom
| | - James Gilbert
- Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, United Kingdom
| | | | - Kathryn Beal
- European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, Cambridge CB10 1SD, United Kingdom
| | - Denise Carvalho-Silva
- European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, Cambridge CB10 1SD, United Kingdom
| | - William Cheng
- Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, United Kingdom
| | - Daria Gordon
- Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, United Kingdom
| | - Darren Grafham
- Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, United Kingdom
| | - Matt Hardy
- Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, United Kingdom
| | - Jo Harley
- Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, United Kingdom
| | - Heidi Hauser
- Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, United Kingdom
| | - Philip Howden
- Department of Pathology, University of Cambridge, Cambridge CB2 1QP, United Kingdom; Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, United Kingdom
| | - Kerstin Howe
- Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, United Kingdom
| | - Kim Lachani
- Department of Pathology, University of Cambridge, Cambridge CB2 1QP, United Kingdom
| | - Peter J I Ellis
- Department of Pathology, University of Cambridge, Cambridge CB2 1QP, United Kingdom
| | - Daniel Kelly
- Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, United Kingdom
| | - Giselle Kerry
- Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, United Kingdom
| | - James Kerwin
- Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, United Kingdom
| | - Bee Ling Ng
- Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, United Kingdom
| | - Glen Threadgold
- Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, United Kingdom
| | - Thomas Wileman
- Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, United Kingdom
| | - Jonathan M D Wood
- Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, United Kingdom
| | - Fengtang Yang
- Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, United Kingdom
| | - Jen Harrow
- Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, United Kingdom
| | - Nabeel A Affara
- Department of Pathology, University of Cambridge, Cambridge CB2 1QP, United Kingdom
| | - Chris Tyler-Smith
- Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, United Kingdom
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Ottolini B, Hornsby MJ, Abujaber R, MacArthur JAL, Badge RM, Schwarzacher T, Albertson DG, Bevins CL, Solnick JV, Hollox EJ. Evidence of convergent evolution in humans and macaques supports an adaptive role for copy number variation of the β-defensin-2 gene. Genome Biol Evol 2014; 6:3025-38. [PMID: 25349268 PMCID: PMC4255768 DOI: 10.1093/gbe/evu236] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
β-defensins are a family of important peptides of innate immunity, involved in host defense, immunomodulation, reproduction, and pigmentation. Genes encoding β-defensins show evidence of birth-and-death evolution, adaptation by amino acid sequence changes, and extensive copy number variation (CNV) within humans and other species. The role of CNV in the adaptation of β-defensins to new functions remains unclear, as does the adaptive role of CNV in general. Here, we fine-map CNV of a cluster of β-defensins in humans and rhesus macaques. Remarkably, we found that the structure of the CNV is different between primates, with distinct mutational origins and CNV boundaries defined by retroviral long terminal repeat elements. Although the human β-defensin CNV region is 322 kb and encompasses several genes, including β-defensins, a long noncoding RNA gene, and testes-specific zinc-finger transcription factors, the orthologous region in the rhesus macaque shows CNV of a 20-kb region, containing only a single gene, the ortholog of the human β-defensin-2 gene. Despite its independent origins, the range of gene copy numbers in the rhesus macaque is similar to humans. In addition, the rhesus macaque gene has been subject to divergent positive selection at the amino acid level following its initial duplication event between 3 and 9.5 Ma, suggesting adaptation of this gene as the macaque successfully colonized novel environments outside Africa. Therefore, the molecular phenotype of β-defensin-2 CNV has undergone convergent evolution, and this gene shows evidence of adaptation at the amino acid level in rhesus macaques.
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Affiliation(s)
| | - Michael J Hornsby
- Department of Microbiology and Immunology, University of California Davis School of Medicine
| | - Razan Abujaber
- Department of Genetics, University of Leicester, United Kingdom
| | - Jacqueline A L MacArthur
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco Present address: European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Richard M Badge
- Department of Genetics, University of Leicester, United Kingdom
| | | | - Donna G Albertson
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco Present address: Bluestone Center for Clinical Research, New York University College of Dentistry, New York, New York
| | - Charles L Bevins
- Department of Microbiology and Immunology, University of California Davis School of Medicine
| | - Jay V Solnick
- Department of Microbiology and Immunology, University of California Davis School of Medicine Department of Medicine, Center for Comparative Medicine, and the California National Primate Research Center, University of California
| | - Edward J Hollox
- Department of Genetics, University of Leicester, United Kingdom
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Keeney JG, Dumas L, Sikela JM. The case for DUF1220 domain dosage as a primary contributor to anthropoid brain expansion. Front Hum Neurosci 2014; 8:427. [PMID: 25009482 PMCID: PMC4067907 DOI: 10.3389/fnhum.2014.00427] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2013] [Accepted: 05/28/2014] [Indexed: 12/14/2022] Open
Abstract
Here we present the hypothesis that increasing copy number (dosage) of sequences encoding DUF1220 protein domains is a major contributor to the evolutionary increase in brain size, neuron number, and cognitive capacity that is associated with the primate order. We further propose that this relationship is restricted to the anthropoid sub-order of primates, with DUF1220 copy number markedly increasing in monkeys, further in apes, and most extremely in humans where the greatest number of copies (~272 haploid copies) is found. We show that this increase closely parallels the increase in brain size and neuron number that has occurred among anthropoid primate species. We also provide evidence linking DUF1220 copy number to brain size within the human species, both in normal populations and in individuals associated with brain size pathologies (1q21-associated microcephaly and macrocephaly). While we believe these and other findings presented here strongly suggest increase in DUF1220 copy number is a key contributor to anthropoid brain expansion, the data currently available rely largely on correlative measures that, though considerable, do not yet provide direct evidence for a causal connection. Nevertheless, we believe the evidence presented is sufficient to provide the basis for a testable model which proposes that DUF1220 protein domain dosage increase is a main contributor to the increase in brain size and neuron number found among the anthropoid primate species and that is at its most extreme in human.
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Affiliation(s)
- Jonathon G Keeney
- Department of Biochemistry and Molecular Genetics and Human Medical Genetics and Neuroscience Programs, University of Colorado School of Medicine, Anschutz Medical Campus Aurora, CO, USA
| | - Laura Dumas
- Department of Biochemistry and Molecular Genetics and Human Medical Genetics and Neuroscience Programs, University of Colorado School of Medicine, Anschutz Medical Campus Aurora, CO, USA
| | - James M Sikela
- Department of Biochemistry and Molecular Genetics and Human Medical Genetics and Neuroscience Programs, University of Colorado School of Medicine, Anschutz Medical Campus Aurora, CO, USA
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30
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Zhang C, Wang J, Marowsky NC, Long M, Wing RA, Fan C. High occurrence of functional new chimeric genes in survey of rice chromosome 3 short arm genome sequences. Genome Biol Evol 2013; 5:1038-48. [PMID: 23651622 PMCID: PMC3673630 DOI: 10.1093/gbe/evt071] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
In an effort to identify newly evolved genes in rice, we searched the genomes of Asian-cultivated rice Oryza sativa ssp. japonica and its wild progenitors, looking for lineage-specific genes. Using genome pairwise comparison of approximately 20-Mb DNA sequences from the chromosome 3 short arm (Chr3s) in six rice species, O. sativa, O. nivara, O. rufipogon, O. glaberrima, O. barthii, and O. punctata, combined with synonymous substitution rate tests and other evidence, we were able to identify potential recently duplicated genes, which evolved within the last 1 Myr. We identified 28 functional O. sativa genes, which likely originated after O. sativa diverged from O. glaberrima. These genes account for around 1% (28/3,176) of all annotated genes on O. sativa's Chr3s. Among the 28 new genes, two recently duplicated segments contained eight genes. Fourteen of the 28 new genes consist of chimeric gene structure derived from one or multiple parental genes and flanking targeting sequences. Although the majority of these 28 new genes were formed by single or segmental DNA-based gene duplication and recombination, we found two genes that were likely originated partially through exon shuffling. Sequence divergence tests between new genes and their putative progenitors indicated that new genes were most likely evolving under natural selection. We showed all 28 new genes appeared to be functional, as suggested by Ka/Ks analysis and the presence of RNA-seq, cDNA, expressed sequence tag, massively parallel signature sequencing, and/or small RNA data. The high rate of new gene origination and of chimeric gene formation in rice may demonstrate rice's broad diversification, domestication, its environmental adaptation, and the role of new genes in rice speciation.
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Affiliation(s)
- Chengjun Zhang
- Department of Ecology and Evolution, University of Chicago, USA
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Currall BB, Chiang C, Talkowski ME, Morton CC. Mechanisms for Structural Variation in the Human Genome. CURRENT GENETIC MEDICINE REPORTS 2013; 1:81-90. [PMID: 23730541 DOI: 10.1007/s40142-013-0012-8] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
It has been known for several decades that genetic variation involving changes to chromosomal structure (i.e., structural variants) can contribute to disease; however this relationship has been brought into acute focus in recent years largely based on innovative new genomics approaches and technology. Structural variants (SVs) arise from improperly repaired DNA double-strand breaks (DSB). DSBs are a frequent occurrence in all cells and two major pathways are involved in their repair: homologous recombination and non-homologous end joining. Errors during these repair mechanisms can result in SVs that involve losses, gains and rearrangements ranging from a few nucleotides to entire chromosomal arms. Factors such as rearrangements, hotspots and induced DSBs are implicated in the formation of SVs. While de novo SVs are often associated with disease, some SVs are conserved within human subpopulations and may have had a meaningful influence on primate evolution. As the ability to sequence the whole human genome rapidly evolves, the diversity of SVs is illuminated, including very complex rearrangements involving multiple DSBs in a process recently designated as "chromothripsis". Elucidating mechanisms involved in the etiology of SVs informs disease pathogenesis as well as the dynamic function associated with the biology and evolution of human genomes.
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Affiliation(s)
- Benjamin B Currall
- Departments of Obstetrics, Gynecology and Reproductive Biology, Brigham and Women's Hospital and Harvard Medical School, New Research Building, Room 160D, 77 Avenue Louis Pasteur, Boston, MA 02115, USA. Harvard Medical School, Boston, MA, USA
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Lorente-Galdos B, Bleyhl J, Santpere G, Vives L, Ramírez O, Hernandez J, Anglada R, Cooper GM, Navarro A, Eichler EE, Marques-Bonet T. Accelerated exon evolution within primate segmental duplications. Genome Biol 2013; 14:R9. [PMID: 23360670 PMCID: PMC3906575 DOI: 10.1186/gb-2013-14-1-r9] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2012] [Revised: 12/20/2012] [Accepted: 01/29/2013] [Indexed: 01/27/2023] Open
Abstract
BACKGROUND The identification of signatures of natural selection has long been used as an approach to understanding the unique features of any given species. Genes within segmental duplications are overlooked in most studies of selection due to the limitations of draft nonhuman genome assemblies and to the methodological reliance on accurate gene trees, which are difficult to obtain for duplicated genes. RESULTS In this work, we detected exons with an accumulation of high-quality nucleotide differences between the human assembly and shotgun sequencing reads from single human and macaque individuals. Comparing the observed rates of nucleotide differences between coding exons and their flanking intronic sequences with a likelihood-ratio test, we identified 74 exons with evidence for rapid coding sequence evolution during the evolution of humans and Old World monkeys. Fifty-five percent of rapidly evolving exons were either partially or totally duplicated, which is a significant enrichment of the 6% rate observed across all human coding exons. CONCLUSIONS Our results provide a more comprehensive view of the action of selection upon segmental duplications, which are the most complex regions of our genomes. In light of these findings, we suggest that segmental duplications could be subjected to rapid evolution more frequently than previously thought.
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Affiliation(s)
- Belen Lorente-Galdos
- IBE, Institute of Evolutionary Biology (Universitat Pompeu Fabra-CSIC), PRBB, Doctor Aiguader, 88, 08003, Barcelona, Catalonia, Spain
- National Institute for Bioinformatics (INB), PRBB, Doctor Aiguader, 88, 08003, Barcelona, Catalonia, Spain
| | - Jonathan Bleyhl
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, Washington 98195, USA
| | - Gabriel Santpere
- IBE, Institute of Evolutionary Biology (Universitat Pompeu Fabra-CSIC), PRBB, Doctor Aiguader, 88, 08003, Barcelona, Catalonia, Spain
| | - Laura Vives
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, Washington 98195, USA
| | - Oscar Ramírez
- IBE, Institute of Evolutionary Biology (Universitat Pompeu Fabra-CSIC), PRBB, Doctor Aiguader, 88, 08003, Barcelona, Catalonia, Spain
| | - Jessica Hernandez
- IBE, Institute of Evolutionary Biology (Universitat Pompeu Fabra-CSIC), PRBB, Doctor Aiguader, 88, 08003, Barcelona, Catalonia, Spain
| | - Roger Anglada
- IBE, Institute of Evolutionary Biology (Universitat Pompeu Fabra-CSIC), PRBB, Doctor Aiguader, 88, 08003, Barcelona, Catalonia, Spain
| | - Gregory M Cooper
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, Washington 98195, USA
| | - Arcadi Navarro
- IBE, Institute of Evolutionary Biology (Universitat Pompeu Fabra-CSIC), PRBB, Doctor Aiguader, 88, 08003, Barcelona, Catalonia, Spain
- National Institute for Bioinformatics (INB), PRBB, Doctor Aiguader, 88, 08003, Barcelona, Catalonia, Spain
- Institucio Catalana de Recerca i Estudis Avançats (ICREA), PRBB, Doctor Aiguader, 88, 08003, Barcelona, Catalonia, Spain
| | - Evan E Eichler
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, Washington 98195, USA
- Howard Hughes Medical Institute, Seattle, Washington 98195, USA
| | - Tomas Marques-Bonet
- IBE, Institute of Evolutionary Biology (Universitat Pompeu Fabra-CSIC), PRBB, Doctor Aiguader, 88, 08003, Barcelona, Catalonia, Spain
- Institucio Catalana de Recerca i Estudis Avançats (ICREA), PRBB, Doctor Aiguader, 88, 08003, Barcelona, Catalonia, Spain
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Zhang Y, Haraksingh R, Grubert F, Abyzov A, Gerstein M, Weissman S, Urban AE. Child development and structural variation in the human genome. Child Dev 2013; 84:34-48. [PMID: 23311762 DOI: 10.1111/cdev.12051] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Structural variation of the human genome sequence is the insertion, deletion, or rearrangement of stretches of DNA sequence sized from around 1,000 to millions of base pairs. Over the past few years, structural variation has been shown to be far more common in human genomes than previously thought. Very little is currently known about the effects of structural variation on normal child development, but such effects could be of considerable significance. This review provides an overview of the phenomenon of structural variation in the human genome sequence, describing the novel genomics technologies that are revolutionizing the way structural variation is studied and giving examples of genomic structural variations that affect child development.
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Robinson CM, Singh G, Lee JY, Dehghan S, Rajaiya J, Liu EB, Yousuf MA, Betensky RA, Jones MS, Dyer DW, Seto D, Chodosh J. Molecular evolution of human adenoviruses. Sci Rep 2013; 3:1812. [PMID: 23657240 PMCID: PMC3648800 DOI: 10.1038/srep01812] [Citation(s) in RCA: 176] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2013] [Accepted: 04/22/2013] [Indexed: 11/15/2022] Open
Abstract
The recent emergence of highly virulent human adenoviruses (HAdVs) with new tissue tropisms underscores the need to determine their ontogeny. Here we report complete high quality genome sequences and analyses for all the previously unsequenced HAdV serotypes (n = 20) within HAdV species D. Analysis of nucleotide sequence variability for these in conjunction with another 40 HAdV prototypes, comprising all seven HAdV species, confirmed the uniquely hypervariable regions within species. The mutation rate among HAdV-Ds was low when compared to other HAdV species. Homologous recombination was identified in at least two of five examined hypervariable regions for every virus, suggesting the evolution of HAdV-Ds has been highly dependent on homologous recombination. Patterns of alternating GC and AT rich motifs correlated well with hypervariable region recombination sites across the HAdV-D genomes, suggesting foci of DNA instability lead to formulaic patterns of homologous recombination and confer agility to adenovirus evolution.
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Affiliation(s)
- Christopher M. Robinson
- Department of Ophthalmology, Howe Laboratory, Massachusetts Eye and Ear Infirmary, Harvard Medical School, Boston, MA, 02114, USA
| | - Gurdeep Singh
- Department of Ophthalmology, Howe Laboratory, Massachusetts Eye and Ear Infirmary, Harvard Medical School, Boston, MA, 02114, USA
| | - Jeong Yoon Lee
- Department of Ophthalmology, Howe Laboratory, Massachusetts Eye and Ear Infirmary, Harvard Medical School, Boston, MA, 02114, USA
| | - Shoaleh Dehghan
- Bioinformatics and Computational Biology Program, School of Systems Biology, George Mason University, Manassas, VA, 20110, USA
- Chemistry Department, American University, Washington, DC 20016 USA
| | - Jaya Rajaiya
- Department of Ophthalmology, Howe Laboratory, Massachusetts Eye and Ear Infirmary, Harvard Medical School, Boston, MA, 02114, USA
| | - Elizabeth B. Liu
- Bioinformatics and Computational Biology Program, School of Systems Biology, George Mason University, Manassas, VA, 20110, USA
| | - Mohammad A. Yousuf
- Department of Ophthalmology, Howe Laboratory, Massachusetts Eye and Ear Infirmary, Harvard Medical School, Boston, MA, 02114, USA
| | - Rebecca A. Betensky
- Department of Biostatistics, Harvard School of Public Health, Boston, MA 02115 USA
| | - Morris S. Jones
- Division of Infectious Diseases, Naval Medical Center San Diego, San Diego, CA, 92136, USA
| | - David W. Dyer
- Department of Microbiology and Immunology, University of Oklahoma Health Sciences Center, Oklahoma City, OK, 73104, USA
| | - Donald Seto
- Bioinformatics and Computational Biology Program, School of Systems Biology, George Mason University, Manassas, VA, 20110, USA
| | - James Chodosh
- Department of Ophthalmology, Howe Laboratory, Massachusetts Eye and Ear Infirmary, Harvard Medical School, Boston, MA, 02114, USA
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Giannuzzi G, Siswara P, Malig M, Marques-Bonet T, Mullikin JC, Ventura M, Eichler EE. Evolutionary dynamism of the primate LRRC37 gene family. Genome Res 2012; 23:46-59. [PMID: 23064749 PMCID: PMC3530683 DOI: 10.1101/gr.138842.112] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Core duplicons in the human genome represent ancestral duplication modules shared by the majority of intrachromosomal duplication blocks within a given chromosome. These cores are associated with the emergence of novel gene families in the hominoid lineage, but their genomic organization and gene characterization among other primates are largely unknown. Here, we investigate the genomic organization and expression of the core duplicon on chromosome 17 that led to the expansion of LRRC37 during primate evolution. A comparison of the LRRC37 gene family organization in human, orangutan, macaque, marmoset, and lemur genomes shows the presence of both orthologous and species-specific gene copies in all primate lineages. Expression profiling in mouse, macaque, and human tissues reveals that the ancestral expression of LRRC37 was restricted to the testis. In the hominid lineage, the pattern of LRRC37 became increasingly ubiquitous, with significantly higher levels of expression in the cerebellum and thymus, and showed a remarkable diversity of alternative splice forms. Transfection studies in HeLa cells indicate that the human FLAG-tagged recombinant LRRC37 protein is secreted after cleavage of a transmembrane precursor and its overexpression can induce filipodia formation.
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Affiliation(s)
- Giuliana Giannuzzi
- Dipartimento di Biologia, Università degli Studi di Bari Aldo Moro, Bari 70126, Italy
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Li Y, Xiao J, Wu J, Duan J, Liu Y, Ye X, Zhang X, Guo X, Gu Y, Zhang L, Jia J, Kong X. A tandem segmental duplication (TSD) in green revolution gene Rht-D1b region underlies plant height variation. THE NEW PHYTOLOGIST 2012; 196:282-291. [PMID: 22849513 DOI: 10.1111/j.1469-8137.2012.04243.x] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
• Rht-D1c (Rht10) carried by Chinese wheat (Triticum aestivum) line Aibian 1 is an allele at the Rht-D1 locus. Among the Rht-1 alleles, little is known about Rht-D1c although it determines an extreme dwarf phenotype in wheat. • Here, we cloned and functionally characterized Rht-D1c using a combination of Southern blotting, target region sequencing, gene expression analysis and transgenic experiments. • We found that the Rht-D1c allele was generated through a tandem segmental duplication (TSD) of a > 1 Mb region, resulting in two copies of the Rht-D1b. Two copies of Rht-D1b in the TSD were three-fold more effective in reducing plant height than a single copy, and transformation with a segment containing the tandemly duplicated copy of Rht-D1b resulted in the same level of reduction of plant height as the original copy in Aibian 1. • Our results suggest that changes in gene copy number are one of the important sources of genetic diversity and some of these changes could be directly associated with important traits in crops.
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Affiliation(s)
- Yiyuan Li
- College of Biology Sciences, China Agricultural University, No. 2 Yuanmingyuan West Road, Haidian District, Beijing 100094, China
- Key Laboratory of Crop Gene Resources and Germplasm Enhancement, Ministry of Agriculture, National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Jianhui Xiao
- Key Laboratory of Crop Gene Resources and Germplasm Enhancement, Ministry of Agriculture, National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Jiajie Wu
- Key Laboratory of Crop Gene Resources and Germplasm Enhancement, Ministry of Agriculture, National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Jialei Duan
- College of Biology Sciences, China Agricultural University, No. 2 Yuanmingyuan West Road, Haidian District, Beijing 100094, China
- Key Laboratory of Crop Gene Resources and Germplasm Enhancement, Ministry of Agriculture, National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Yue Liu
- Key Laboratory of Crop Gene Resources and Germplasm Enhancement, Ministry of Agriculture, National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Xingguo Ye
- Key Laboratory of Crop Gene Resources and Germplasm Enhancement, Ministry of Agriculture, National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Xin Zhang
- Key Laboratory of Crop Gene Resources and Germplasm Enhancement, Ministry of Agriculture, National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Xiuping Guo
- Key Laboratory of Crop Gene Resources and Germplasm Enhancement, Ministry of Agriculture, National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Yongqiang Gu
- United States Department of Agriculture, Agricultural Research Service, Western Regional Research Center, 800 Buchanan Street, Albany, CA 94710, USA
| | - Lichao Zhang
- Key Laboratory of Crop Gene Resources and Germplasm Enhancement, Ministry of Agriculture, National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Jizeng Jia
- Key Laboratory of Crop Gene Resources and Germplasm Enhancement, Ministry of Agriculture, National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Xiuying Kong
- Key Laboratory of Crop Gene Resources and Germplasm Enhancement, Ministry of Agriculture, National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China
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O’Bleness MS, Dickens CM, Dumas LJ, Kehrer-Sawatzki H, Wyckoff GJ, Sikela JM. Evolutionary history and genome organization of DUF1220 protein domains. G3 (BETHESDA, MD.) 2012; 2:977-86. [PMID: 22973535 PMCID: PMC3429928 DOI: 10.1534/g3.112.003061] [Citation(s) in RCA: 60] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/09/2012] [Accepted: 06/05/2012] [Indexed: 12/04/2022]
Abstract
DUF1220 protein domains exhibit the most extreme human lineage-specific (HLS) copy number increase of any protein coding region in the human genome and have recently been linked to evolutionary and pathological changes in brain size (e.g., 1q21-associated microcephaly). These findings lend support to the view that DUF1220 domain dosage is a key factor in the determination of primate (and human) brain size. Here we analyze 41 animal genomes and present the most complete account to date of the evolutionary history and genome organization of DUF1220 domains and the gene family that encodes them (NBPF). Included among the novel features identified by this analysis is a DUF1220 domain precursor in nonmammalian vertebrates, a unique predicted promoter common to all mammalian NBPF genes, six distinct clades into which DUF1220 sequences can be subdivided, and a previously unknown member of the NBPF gene family (NBPF25). Most importantly, we show that the exceptional HLS increase in DUF1220 copy number (from 102 in our last common ancestor with chimp to 272 in human; an average HLS increase of ~28 copies every million years since the Homo/Pan split) was driven by intragenic domain hyperamplification. This increase primarily involved a 4.7 kb, tandemly repeated three DUF1220 domain unit we have named the HLS DUF1220 triplet, a motif that is a likely candidate to underlie key properties unique to the Homo sapiens brain. Interestingly, all copies of the HLS DUF1220 triplet lie within a human-specific pericentric inversion that also includes the 1q12 C-band, a polymorphic heterochromatin expansion that is unique to the human genome. Both cytogenetic features likely played key roles in the rapid HLS DUF1220 triplet hyperamplification, which is among the most striking genomic changes specific to the human lineage.
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Affiliation(s)
- Majesta S. O’Bleness
- Department of Biochemistry and Molecular Genetics, Human Medical Genetics and Neuroscience Programs, University of Colorado School of Medicine, Aurora, Colorado 80045
| | - C. Michael Dickens
- Department of Biochemistry and Molecular Genetics, Human Medical Genetics and Neuroscience Programs, University of Colorado School of Medicine, Aurora, Colorado 80045
| | - Laura J. Dumas
- Department of Biochemistry and Molecular Genetics, Human Medical Genetics and Neuroscience Programs, University of Colorado School of Medicine, Aurora, Colorado 80045
| | | | - Gerald J. Wyckoff
- Division of Molecular Biology and Biochemistry, School of Biological Sciences, University of Missouri, Kansas City, Missouri 64110
| | - James M. Sikela
- Department of Biochemistry and Molecular Genetics, Human Medical Genetics and Neuroscience Programs, University of Colorado School of Medicine, Aurora, Colorado 80045
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George CM, Alani E. Multiple cellular mechanisms prevent chromosomal rearrangements involving repetitive DNA. Crit Rev Biochem Mol Biol 2012; 47:297-313. [PMID: 22494239 PMCID: PMC3337352 DOI: 10.3109/10409238.2012.675644] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Repetitive DNA is present in the eukaryotic genome in the form of segmental duplications, tandem and interspersed repeats, and satellites. Repetitive sequences can be beneficial by serving specific cellular functions (e.g. centromeric and telomeric DNA) and by providing a rapid means for adaptive evolution. However, such elements are also substrates for deleterious chromosomal rearrangements that affect fitness and promote human disease. Recent studies analyzing the role of nuclear organization in DNA repair and factors that suppress non-allelic homologous recombination (NAHR) have provided insights into how genome stability is maintained in eukaryotes. In this review, we outline the types of repetitive sequences seen in eukaryotic genomes and how recombination mechanisms are regulated at the DNA sequence, cell organization, chromatin structure, and cell cycle control levels to prevent chromosomal rearrangements involving these sequences.
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Affiliation(s)
- Carolyn M George
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853-2703, USA
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Bekpen C, Tastekin I, Siswara P, Akdis CA, Eichler EE. Primate segmental duplication creates novel promoters for the LRRC37 gene family within the 17q21.31 inversion polymorphism region. Genome Res 2012; 22:1050-8. [PMID: 22419166 PMCID: PMC3371713 DOI: 10.1101/gr.134098.111] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
The LRRC37 gene family maps to a complex region of the human genome and has been subjected to multiple rounds of segmental duplication. We investigate the expression and regulation of this gene family in multiple tissues and organisms and show a testis-specific expression of this gene family in mouse but a more ubiquitous pattern of expression among primates. Evolutionary and phylogenetic analyses support a model in which new alternative promoters have been acquired during primate evolution. We identify two promoters, Cl8 and particularly Cl3, both of which are highly active in the cerebellum and fetal brain in human and have been duplicated from a promoter region of two unrelated genes, BPTF and DND1, respectively. Two of these more broadly expressed gene family members, LRRC37A1 and A4, define the boundary of a common human inversion polymorphism mapping to chromosome 17q21.31 (the MAPT locus)—a region associated with risk for frontal temporal dementia, Parkinsonism, and intellectual disability. We propose that the regulation of the LRRC37 family occurred in a stepwise manner, acquiring foreign promoters from BPTF and DND1 via segmental duplication. This unusual evolutionary trajectory altered the regulation of the LRRC37 family, leading to increased expression in the fetal brain and cerebellum.
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40
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Weise A, Mrasek K, Klein E, Mulatinho M, Llerena JC, Hardekopf D, Pekova S, Bhatt S, Kosyakova N, Liehr T. Microdeletion and microduplication syndromes. J Histochem Cytochem 2012; 60:346-58. [PMID: 22396478 DOI: 10.1369/0022155412440001] [Citation(s) in RCA: 94] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
The widespread use of whole genome analysis based on array comparative genomic hybridization in diagnostics and research has led to a continuously growing number of microdeletion and microduplication syndromes (MMSs) connected to certain phenotypes. These MMSs also include increasing instances in which the critical region can be reciprocally deleted or duplicated. This review catalogues the currently known MMSs and the corresponding critical regions including phenotypic consequences. Besides the pathogenic pathways leading to such rearrangements, the different detection methods and their limitations are discussed. Finally, the databases available for distinguishing between reported benign or pathogenic copy number alterations are highlighted. Overall, a review of MMSs that previously were also denoted "genomic disorders" or "contiguous gene syndromes" is given.
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Affiliation(s)
- Anja Weise
- Jena University Hospital, Friedrich Schiller University, Institute of Human Genetics, Jena, Germany.
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41
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Antic D, Impera L, Fekete MD, Djordjevic V, Storlazzi CT, Elezovic I. Novel chromosomal translocation (17;22)(q12;q12) in a case of myelodisplastic syndrome characterized with signs of hemolytic anemia at presentation. Gene 2012; 493:161-4. [PMID: 22138479 DOI: 10.1016/j.gene.2011.11.002] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2011] [Accepted: 11/01/2011] [Indexed: 11/15/2022]
Abstract
Myelodysplastic syndromes (MDS) are clonal stem cell diseases that can result in cytopenias, dysplasia in one or more cell lineages, infective hematopoiesis, and increase the risk of progression to acute myeloid leukemia (AML). MDSs are characterized by several recurrent cytogenetic defects, which can affect diagnosis, prognosis, and treatment. Some of that chromosomal alterations are associated with very poor prognosis. Conventional cytogenetics cannot accurately define the rearranged karyotype. Instead, molecular cytogenetics analyses can provide important diagnostic and prognostic information for patients affected by MDS, allowing the characterization of the whole mutational spectrum and, mainly, novel chromosomal lesions. In this paper, we report a MDS case with a novel chromosomal translocation [t(17;22)(q12;q22)], described for the first time here. Following Giemsa-banding karyotyping, fluorescent in situ hybridization analyses, by using chromosome-specific probes, displayed the breakpoint regions at chromosomes 17 and 22, within which intra and inter-chromosomal segmental duplications (SD) are present. Because of the occurrence of SDs in breakpoint region, it was not possible to finely define the genomic regions where breaks fell. Further investigations could be required to better understand the molecular basis of the novel translocation t(17;22)(q12;q12) acting in MDS context and to explain if SDs could contribute to the pathogenesis of MDS.
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Affiliation(s)
- Darko Antic
- Clinic for hematology, Clinical Center Serbia, Koste Todorovica 2, 11 000 Belgrade, Serbia.
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42
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Quinlan AR, Hall IM. Characterizing complex structural variation in germline and somatic genomes. Trends Genet 2011; 28:43-53. [PMID: 22094265 DOI: 10.1016/j.tig.2011.10.002] [Citation(s) in RCA: 71] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2011] [Revised: 10/02/2011] [Accepted: 10/03/2011] [Indexed: 10/15/2022]
Abstract
Genome structural variation (SV) is a major source of genetic diversity in mammals and a hallmark of cancer. Although SV is typically defined by its canonical forms (duplication, deletion, insertion, inversion and translocation), recent breakpoint mapping studies have revealed a surprising number of 'complex' variants that evade simple classification. Complex SVs are defined by clustered breakpoints that arose through a single mutation but cannot be explained by one simple end-joining or recombination event. Some complex variants exhibit profoundly complicated rearrangements between distinct loci from multiple chromosomes, whereas others involve more subtle alterations at a single locus. These diverse and unpredictable features present a challenge for SV mapping experiments. Here, we review current knowledge of complex SV in mammals, and outline techniques for identifying and characterizing complex variants using next-generation DNA sequencing.
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Affiliation(s)
- Aaron R Quinlan
- Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, Charlottesville, VA 22908, USA
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43
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Cooper DN, Bacolla A, Férec C, Vasquez KM, Kehrer-Sawatzki H, Chen JM. On the sequence-directed nature of human gene mutation: the role of genomic architecture and the local DNA sequence environment in mediating gene mutations underlying human inherited disease. Hum Mutat 2011; 32:1075-99. [PMID: 21853507 PMCID: PMC3177966 DOI: 10.1002/humu.21557] [Citation(s) in RCA: 94] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2011] [Accepted: 06/17/2011] [Indexed: 12/21/2022]
Abstract
Different types of human gene mutation may vary in size, from structural variants (SVs) to single base-pair substitutions, but what they all have in common is that their nature, size and location are often determined either by specific characteristics of the local DNA sequence environment or by higher order features of the genomic architecture. The human genome is now recognized to contain "pervasive architectural flaws" in that certain DNA sequences are inherently mutation prone by virtue of their base composition, sequence repetitivity and/or epigenetic modification. Here, we explore how the nature, location and frequency of different types of mutation causing inherited disease are shaped in large part, and often in remarkably predictable ways, by the local DNA sequence environment. The mutability of a given gene or genomic region may also be influenced indirectly by a variety of noncanonical (non-B) secondary structures whose formation is facilitated by the underlying DNA sequence. Since these non-B DNA structures can interfere with subsequent DNA replication and repair and may serve to increase mutation frequencies in generalized fashion (i.e., both in the context of subtle mutations and SVs), they have the potential to serve as a unifying concept in studies of mutational mechanisms underlying human inherited disease.
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Affiliation(s)
- David N Cooper
- Institute of Medical Genetics, School of Medicine, Cardiff University, Cardiff, United Kingdom.
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Bengesser K, Cooper DN, Steinmann K, Kluwe L, Chuzhanova NA, Wimmer K, Tatagiba M, Tinschert S, Mautner VF, Kehrer-Sawatzki H. A novel third type of recurrent NF1 microdeletion mediated by nonallelic homologous recombination between LRRC37B-containing low-copy repeats in 17q11.2. Hum Mutat 2010; 31:742-51. [PMID: 20506354 DOI: 10.1002/humu.21254] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
Large microdeletions encompassing the neurofibromatosis type-1 (NF1) gene and its flanking regions at 17q11.2 belong to the group of genomic disorders caused by aberrant recombination between segmental duplications. The most common NF1 microdeletions (type-1) span 1.4-Mb and have breakpoints located within NF1-REPs A and C, low-copy repeats (LCRs) containing LRRC37-core duplicons. We have identified a novel type of recurrent NF1 deletion mediated by nonallelic homologous recombination (NAHR) between the highly homologous NF1-REPs B and C. The breakpoints of these approximately 1.0-Mb ("type-3") NF1 deletions were characterized at the DNA sequence level in three unrelated patients. Recombination regions, spanning 275, 180, and 109-bp, respectively, were identified within the LRRC37B-P paralogues of NF1-REPs B and C, and were found to contain sequences capable of non-B DNA formation. Both LCRs contain LRRC37-core duplicons, abundant and highly dynamic sequences in the human genome. NAHR between LRRC37-containing LCRs at 17q21.31 is known to have mediated the 970-kb polymorphic inversions of the MAPT-locus that occurred independently in different primate species, but also underlies the syndromes associated with recurrent 17q21.31 microdeletions and reciprocal microduplications. The novel NF1 microdeletions reported here provide further evidence for the unusually high recombinogenic potential of LRRC37-containing LCRs in the human genome.
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45
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Abstract
Ever since the pre-molecular era, the birth of new genes with novel functions has been considered to be a major contributor to adaptive evolutionary innovation. Here, I review the origin and evolution of new genes and their functions in eukaryotes, an area of research that has made rapid progress in the past decade thanks to the genomics revolution. Indeed, recent work has provided initial whole-genome views of the different types of new genes for a large number of different organisms. The array of mechanisms underlying the origin of new genes is compelling, extending way beyond the traditionally well-studied source of gene duplication. Thus, it was shown that novel genes also regularly arose from messenger RNAs of ancestral genes, protein-coding genes metamorphosed into new RNA genes, genomic parasites were co-opted as new genes, and that both protein and RNA genes were composed from scratch (i.e., from previously nonfunctional sequences). These mechanisms then also contributed to the formation of numerous novel chimeric gene structures. Detailed functional investigations uncovered different evolutionary pathways that led to the emergence of novel functions from these newly minted sequences and, with respect to animals, attributed a potentially important role to one specific tissue--the testis--in the process of gene birth. Remarkably, these studies also demonstrated that novel genes of the various types significantly impacted the evolution of cellular, physiological, morphological, behavioral, and reproductive phenotypic traits. Consequently, it is now firmly established that new genes have indeed been major contributors to the origin of adaptive evolutionary novelties.
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Affiliation(s)
- Henrik Kaessmann
- Center for Integrative Genomics, University of Lausanne, CH-1015 Lausanne, Switzerland.
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