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Kozłowska-Masłoń J, Ciomborowska-Basheer J, Kubiak MR, Makałowska I. Evolution of retrocopies in the context of HUSH silencing. Biol Direct 2024; 19:60. [PMID: 39095906 PMCID: PMC11295320 DOI: 10.1186/s13062-024-00507-9] [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: 04/17/2024] [Accepted: 07/29/2024] [Indexed: 08/04/2024] Open
Abstract
Retrotransposition is one of the main factors responsible for gene duplication and thus genome evolution. However, the sequences that undergo this process are not only an excellent source of biological diversity, but in certain cases also pose a threat to the integrity of the DNA. One of the mechanisms that protects against the incorporation of mobile elements is the HUSH complex, which is responsible for silencing long, intronless, transcriptionally active transposed sequences that are rich in adenine on the sense strand. In this study, broad sets of human and porcine retrocopies were analysed with respect to the above factors, taking into account evolution of these molecules. Analysis of expression pattern, genomic structure, transcript length, and nucleotide substitution frequency showed the strong relationship between the expression level and exon length as well as the protective nature of introns. The results of the studies also showed that there is no direct correlation between the expression level and adenine content. However, protein-coding retrocopies, which have a lower adenine content, have a significantly higher expression level than the adenine-rich non-coding but expressed retrocopies. Therefore, although the mechanism of HUSH silencing may be an important part of the regulation of retrocopy expression, it is one component of a more complex molecular network that remains to be elucidated.
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Affiliation(s)
- Joanna Kozłowska-Masłoń
- Institute of Human Biology and Evolution, Faculty of Biology, Adam Mickiewicz University, Uniwersytetu Poznańskiego 6, Poznań, Poland
- Laboratory of Cancer Genetics, Greater Poland Cancer Centre, Garbary 15, Poznań, Poland
| | - Joanna Ciomborowska-Basheer
- Institute of Human Biology and Evolution, Faculty of Biology, Adam Mickiewicz University, Uniwersytetu Poznańskiego 6, Poznań, Poland
- Laboratory of Nature Education and Conservation, Faculty of Biology, Adam Mickiewicz University, Uniwersytetu Poznańskiego 6, Poznań, Poland
| | - Magdalena Regina Kubiak
- Institute of Human Biology and Evolution, Faculty of Biology, Adam Mickiewicz University, Uniwersytetu Poznańskiego 6, Poznań, Poland
| | - Izabela Makałowska
- Institute of Human Biology and Evolution, Faculty of Biology, Adam Mickiewicz University, Uniwersytetu Poznańskiego 6, Poznań, Poland.
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2
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Lughmani H, Patel H, Chakravarti R. Structural Features and Physiological Associations of Human 14-3-3ζ Pseudogenes. Genes (Basel) 2024; 15:399. [PMID: 38674334 PMCID: PMC11049341 DOI: 10.3390/genes15040399] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2024] [Revised: 03/15/2024] [Accepted: 03/19/2024] [Indexed: 04/28/2024] Open
Abstract
There are about 14,000 pseudogenes that are mutated or truncated sequences resembling functional parent genes. About two-thirds of pseudogenes are processed, while others are duplicated. Although initially thought dead, emerging studies indicate they have functional and regulatory roles. We study 14-3-3ζ, an adaptor protein that regulates cytokine signaling and inflammatory diseases, including rheumatoid arthritis, cancer, and neurological disorders. To understand how 14-3-3ζ (gene symbol YWHAZ) performs diverse functions, we examined the human genome and identified nine YWHAZ pseudogenes spread across many chromosomes. Unlike the 32 kb exon-to-exon sequence in YWHAZ, all pseudogenes are much shorter and lack introns. Out of six, four YWHAZ exons are highly conserved, but the untranslated region (UTR) shows significant diversity. The putative amino acid sequence of pseudogenes is 78-97% homologous, resulting in striking structural similarities with the parent protein. The OMIM and Decipher database searches revealed chromosomal loci containing pseudogenes are associated with human diseases that overlap with the parent gene. To the best of our knowledge, this is the first report on pseudogenes of the 14-3-3 family protein and their implications for human health. This bioinformatics-based study introduces a new insight into the complexity of 14-3-3ζ's functions in biology.
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Affiliation(s)
| | | | - Ritu Chakravarti
- Department of Physiology and Pharmacology, The University of Toledo, Toledo, OH 43614, USA; (H.L.); (H.P.)
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3
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Batcher K, Varney S, York D, Blacksmith M, Kidd JM, Rebhun R, Dickinson P, Bannasch D. Recent, full-length gene retrocopies are common in canids. Genome Res 2022; 32:1602-1611. [PMID: 35961775 PMCID: PMC9435743 DOI: 10.1101/gr.276828.122] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2022] [Accepted: 07/19/2022] [Indexed: 02/03/2023]
Abstract
Gene retrocopies arise from the reverse transcription and insertion into the genome of processed mRNA transcripts. Although many retrocopies have acquired mutations that render them functionally inactive, most mammals retain active LINE-1 sequences capable of producing new retrocopies. New retrocopies, referred to as retro copy number variants (retroCNVs), may not be identified by standard variant calling techniques in high-throughput sequencing data. Although multiple functional FGF4 retroCNVs have been associated with skeletal dysplasias in dogs, the full landscape of canid retroCNVs has not been characterized. Here, retroCNV discovery was performed on a whole-genome sequencing data set of 293 canids from 76 breeds. We identified retroCNV parent genes via the presence of mRNA-specific 30-mers, and then identified retroCNV insertion sites through discordant read analysis. In total, we resolved insertion sites for 1911 retroCNVs from 1179 parent genes, 1236 of which appeared identical to their parent genes. Dogs had on average 54.1 total retroCNVs and 1.4 private retroCNVs. We found evidence of expression in testes for 12% (14/113) of the retroCNVs identified in six Golden Retrievers, including four chimeric transcripts, and 97 retroCNVs also had significantly elevated F ST across dog breeds, possibly indicating selection. We applied our approach to a subset of human genomes and detected an average of 4.2 retroCNVs per sample, highlighting a 13-fold relative increase of retroCNV frequency in dogs. Particularly in canids, retroCNVs are a largely unexplored source of genetic variation that can contribute to genome plasticity and that should be considered when investigating traits and diseases.
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Affiliation(s)
- Kevin Batcher
- Department of Population Health and Reproduction, University of California, Davis, Davis, California 95616, USA
| | - Scarlett Varney
- Department of Population Health and Reproduction, University of California, Davis, Davis, California 95616, USA
| | - Daniel York
- Department of Surgical and Radiological Sciences, University of California, Davis, Davis, California 95616, USA
| | - Matthew Blacksmith
- Department of Human Genetics, University of Michigan Medical School, Ann Arbor, Michigan 48109, USA
| | - Jeffrey M Kidd
- Department of Human Genetics, University of Michigan Medical School, Ann Arbor, Michigan 48109, USA
- Department of Computational Medicine and Bioinformatics, University of Michigan Medical School, Ann Arbor, Michigan 48109, USA
| | - Robert Rebhun
- Department of Surgical and Radiological Sciences, University of California, Davis, Davis, California 95616, USA
| | - Peter Dickinson
- Department of Surgical and Radiological Sciences, University of California, Davis, Davis, California 95616, USA
| | - Danika Bannasch
- Department of Population Health and Reproduction, University of California, Davis, Davis, California 95616, USA
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4
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Zhang W, Tautz D. Tracing the origin and evolutionary fate of recent gene retrocopies in natural populations of the house mouse. Mol Biol Evol 2021; 39:6481550. [PMID: 34940842 PMCID: PMC8826619 DOI: 10.1093/molbev/msab360] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022] Open
Abstract
Although the contribution of retrogenes to the evolution of genes and genomes has long been recognized, the evolutionary patterns of very recently derived retrocopies that are still polymorphic within natural populations have not been much studied so far. We use here a set of 2,025 such retrocopies in nine house mouse populations from three subspecies (Mus musculus domesticus, M. m. musculus, and M. m. castaneus) to trace their origin and evolutionary fate. We find that ancient house-keeping genes are significantly more likely to generate retrocopies than younger genes and that the propensity to generate a retrocopy depends on its level of expression in the germline. Although most retrocopies are detrimental and quickly purged, we focus here on the subset that appears to be neutral or even adaptive. We show that retrocopies from X-chromosomal parental genes have a higher likelihood to reach elevated frequencies in the populations, confirming the notion of adaptive effects for “out-of-X” retrogenes. Also, retrocopies in intergenic regions are more likely to reach higher population frequencies than those in introns of genes, implying a more detrimental effect when they land within transcribed regions. For a small subset of retrocopies, we find signatures of positive selection, indicating they were involved in a recent adaptation process. We show that the population-specific distribution pattern of retrocopies is phylogenetically informative and can be used to infer population history with a better resolution than with SNP markers.
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Affiliation(s)
- Wenyu Zhang
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Biology, August-Thienemann-Str. 2, Plön, D-24306, Germany
| | - Diethard Tautz
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Biology, August-Thienemann-Str. 2, Plön, D-24306, Germany
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5
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Cancer, Retrogenes, and Evolution. Life (Basel) 2021; 11:life11010072. [PMID: 33478113 PMCID: PMC7835786 DOI: 10.3390/life11010072] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2020] [Revised: 01/14/2021] [Accepted: 01/15/2021] [Indexed: 12/18/2022] Open
Abstract
This review summarizes the knowledge about retrogenes in the context of cancer and evolution. The retroposition, in which the processed mRNA from parental genes undergoes reverse transcription and the resulting cDNA is integrated back into the genome, results in additional copies of existing genes. Despite the initial misconception, retroposition-derived copies can become functional, and due to their role in the molecular evolution of genomes, they have been named the “seeds of evolution”. It is convincing that retrogenes, as important elements involved in the evolution of species, also take part in the evolution of neoplastic tumors at the cell and species levels. The occurrence of specific “resistance mechanisms” to neoplastic transformation in some species has been noted. This phenomenon has been related to additional gene copies, including retrogenes. In addition, the role of retrogenes in the evolution of tumors has been described. Retrogene expression correlates with the occurrence of specific cancer subtypes, their stages, and their response to therapy. Phylogenetic insights into retrogenes show that most cancer-related retrocopies arose in the lineage of primates, and the number of identified cancer-related retrogenes demonstrates that these duplicates are quite important players in human carcinogenesis.
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Zeng H, Chen X, Li H, Zhang J, Wei Z, Wang Y. Interpopulation differences of retroduplication variations (RDVs) in rice retrogenes and their phenotypic correlations. Comput Struct Biotechnol J 2021; 19:600-611. [PMID: 33510865 PMCID: PMC7811064 DOI: 10.1016/j.csbj.2020.12.046] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2020] [Revised: 12/29/2020] [Accepted: 12/31/2020] [Indexed: 11/21/2022] Open
Abstract
Retroduplication variation (RDV), a type of retrocopy polymorphism, is considered to have essential biological significance, but its effect on gene function and species phenotype is still poorly understood. To this end, we analyzed the retrocopies and RDVs in 3,010 rice genomes. We calculated the RDV frequencies in the genome of each rice population; detected the mutated, ancestral and expressed retrogenes in rice genomes; and analyzed their RDV influence on rice phenotypic traits. Collectively, 73 RDVs were identified, and 14 RDVs in ancestral retrogenes can significantly affect rice phenotypes. Our research reveals that RDV plays an important role in rice migration, domestication and evolution. We think that RDV is a good molecular breeding marker candidate. To our knowledge, this is the first study on the relationship between retrogene function, expression, RDV and species phenotype.
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Affiliation(s)
- Haiyue Zeng
- State Key Laboratory of Silkworm Genome Biology, Southwest University, Chongqing 400715, China
- Biological Science Research Center, Southwest University, Chongqing 400715, China
- Shennong Class, Southwest University, Chongqing 400715, China
| | - Xingyu Chen
- Shennong Class, Southwest University, Chongqing 400715, China
| | - Hongbo Li
- College of Electronic and Information Engineering, Southwest University, Chongqing 400715
| | - Jun Zhang
- College of Computer & Information Science, Southwest University, Chongqing 400715, China
| | - Zhaoyuan Wei
- State Key Laboratory of Silkworm Genome Biology, Southwest University, Chongqing 400715, China
- Biological Science Research Center, Southwest University, Chongqing 400715, China
| | - Yi Wang
- State Key Laboratory of Silkworm Genome Biology, Southwest University, Chongqing 400715, China
- Biological Science Research Center, Southwest University, Chongqing 400715, China
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Tang W, Mun S, Joshi A, Han K, Liang P. Mobile elements contribute to the uniqueness of human genome with 15,000 human-specific insertions and 14 Mbp sequence increase. DNA Res 2019; 25:521-533. [PMID: 30052927 PMCID: PMC6191304 DOI: 10.1093/dnares/dsy022] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2018] [Accepted: 06/20/2018] [Indexed: 02/02/2023] Open
Abstract
Mobile elements (MEs) collectively contribute to at least 50% of the human genome. Due to their past incremental accumulation and ongoing DNA transposition, MEs serve as a significant source for both inter- and intra-species genetic and phenotypic diversity during primate and human evolution. By making use of the most recent genome sequences for human and many other closely related primates and robust multi-way comparative genomic approach, we identified a total of 14,870 human-specific MEs (HS-MEs) with more than 8,000 being newly identified. Collectively, these HS-MEs contribute to a total of 14.2 Mbp net genome sequence increase. Several new observations were made based on these HS-MEs, including the finding of Y chromosome as a strikingly hot target for HS-MEs and a strong mutual preference for SINE-R/VNTR/Alu (SVAs). Furthermore, ∼8,000 of these HS-MEs were found to locate in the vicinity of ∼4,900 genes, and collectively they contribute to ∼84 kb sequences in the human reference transcriptome in association with over 300 genes, including protein-coding sequences for 40 genes. In conclusion, our results demonstrate that MEs made a significant contribution to the evolution of human genome by participating in gene function in a human-specific fashion.
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Affiliation(s)
- Wanxiangfu Tang
- Department of Biological Sciences, Brock University, St. Catharines, ON, Canada
| | - Seyoung Mun
- Department of Nanobiomedical Science & BK21 PLUS NBM Global Research, Center for Regenerative Medicine, Dankook University, Cheonan, Republic of Korea
| | - Aditya Joshi
- Department of Biological Sciences, Brock University, St. Catharines, ON, Canada
| | - Kyudong Han
- Department of Nanobiomedical Science & BK21 PLUS NBM Global Research, Center for Regenerative Medicine, Dankook University, Cheonan, Republic of Korea
| | - Ping Liang
- Department of Biological Sciences, Brock University, St. Catharines, ON, Canada
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8
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Rosikiewicz W, Kabza M, Kosinski JG, Ciomborowska-Basheer J, Kubiak MR, Makalowska I. RetrogeneDB-a database of plant and animal retrocopies. DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION 2018; 2017:3964680. [PMID: 29220443 PMCID: PMC5509963 DOI: 10.1093/database/bax038] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/20/2017] [Accepted: 04/14/2017] [Indexed: 01/08/2023]
Abstract
For a long time, retrocopies were considered ‘junk DNA’, but numerous studies have shown that retrocopies may gain functionality and become so-called retrogenes. Retrogenes may code fully functional proteins that coexist with parental gene products or may even replace them. Retrocopies may also function as regulatory RNAs and, for example, become a source of small interfering RNAs, act as trans natural antisense transcripts or as alternative targets for miRNAs. Numerous researchers have emphasized that retrogenes play a crucial role in various organisms’ developmental stages and diseases. Despite the ever-growing evidence of the importance of retrocopies, resources dedicated to retroposition are very limited. Here, we report an update of the RetrogeneDB, which, to the best of our knowledge, is the largest database dedicated to retrocopies. It provides annotations of 86 458 retrocopies in 62 animal and 37 plant species. The database contains information about the retrocopies’ localization, open reading frame conservation, expression, RNA Polymerase II activity and the alternative transcription start site studies. Orthologous relationships between retrogenes were also determined, which made retrocopy conservation studies much more valuable. Additionally, based on the RNA-Seq data from the Geuvadis project, the expression levels of retrocopies were estimated in a total of 50 individuals from 5 human populations. The information is now presented in a new, more user-friendly web interface, with easy access to the source data, which may be used for the downstream analysis. RetrogeneDB is freely available at http://yeti.amu.edu.pl/retrogenedb. Database URL:http://yeti.amu.edu.pl/retrogenedb Secondary database URL:http://rhesus.amu.edu.pl/retrogenedb
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Affiliation(s)
- Wojciech Rosikiewicz
- Department of Integrative Genomics, Institute of Anthropology, Faculty of Biology, Adam Mickiewicz University in Poznan, Umultowska 89, 61-614, Poznan, Poland
| | - Michal Kabza
- Department of Integrative Genomics, Institute of Anthropology, Faculty of Biology, Adam Mickiewicz University in Poznan, Umultowska 89, 61-614, Poznan, Poland
| | - Jan G Kosinski
- Department of Integrative Genomics, Institute of Anthropology, Faculty of Biology, Adam Mickiewicz University in Poznan, Umultowska 89, 61-614, Poznan, Poland
| | - Joanna Ciomborowska-Basheer
- Department of Integrative Genomics, Institute of Anthropology, Faculty of Biology, Adam Mickiewicz University in Poznan, Umultowska 89, 61-614, Poznan, Poland
| | - Magdalena R Kubiak
- Department of Integrative Genomics, Institute of Anthropology, Faculty of Biology, Adam Mickiewicz University in Poznan, Umultowska 89, 61-614, Poznan, Poland
| | - Izabela Makalowska
- Department of Integrative Genomics, Institute of Anthropology, Faculty of Biology, Adam Mickiewicz University in Poznan, Umultowska 89, 61-614, Poznan, Poland
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Tian L, Khan A, Ning Z, Yuan K, Zhang C, Lou H, Yuan Y, Xu S. Genome-wide comparison of allele-specific gene expression between African and European populations. Hum Mol Genet 2018; 27:1067-1077. [DOI: 10.1093/hmg/ddy027] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2017] [Accepted: 01/05/2018] [Indexed: 11/12/2022] Open
Affiliation(s)
- Lei Tian
- Chinese Academy of Sciences Key Laboratory of Computational Biology, Max Planck Independent Research Group on Population Genomics, CAS-MPG Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, CAS, Shanghai 200031, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Asifullah Khan
- Chinese Academy of Sciences Key Laboratory of Computational Biology, Max Planck Independent Research Group on Population Genomics, CAS-MPG Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, CAS, Shanghai 200031, China
- Department of Biochemistry, Abdul Wali Khan University Mardan, Mardan-23200 KP, Pakistan
| | - Zhilin Ning
- Chinese Academy of Sciences Key Laboratory of Computational Biology, Max Planck Independent Research Group on Population Genomics, CAS-MPG Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, CAS, Shanghai 200031, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Kai Yuan
- Chinese Academy of Sciences Key Laboratory of Computational Biology, Max Planck Independent Research Group on Population Genomics, CAS-MPG Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, CAS, Shanghai 200031, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Chao Zhang
- Chinese Academy of Sciences Key Laboratory of Computational Biology, Max Planck Independent Research Group on Population Genomics, CAS-MPG Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, CAS, Shanghai 200031, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Haiyi Lou
- Chinese Academy of Sciences Key Laboratory of Computational Biology, Max Planck Independent Research Group on Population Genomics, CAS-MPG Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, CAS, Shanghai 200031, China
| | - Yuan Yuan
- Chinese Academy of Sciences Key Laboratory of Computational Biology, Max Planck Independent Research Group on Population Genomics, CAS-MPG Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, CAS, Shanghai 200031, China
| | - Shuhua Xu
- Chinese Academy of Sciences Key Laboratory of Computational Biology, Max Planck Independent Research Group on Population Genomics, CAS-MPG Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, CAS, Shanghai 200031, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- School of Life Science and Technology, Shanghai Tech University, Shanghai 201210, China
- Collaborative Innovation Center of Genetics and Development, Shanghai 200438, China
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Protein-Coding Genes' Retrocopies and Their Functions. Viruses 2017; 9:v9040080. [PMID: 28406439 PMCID: PMC5408686 DOI: 10.3390/v9040080] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2017] [Revised: 04/07/2017] [Accepted: 04/11/2017] [Indexed: 12/11/2022] Open
Abstract
Transposable elements, often considered to be not important for survival, significantly contribute to the evolution of transcriptomes, promoters, and proteomes. Reverse transcriptase, encoded by some transposable elements, can be used in trans to produce a DNA copy of any RNA molecule in the cell. The retrotransposition of protein-coding genes requires the presence of reverse transcriptase, which could be delivered by either non-long terminal repeat (non-LTR) or LTR transposons. The majority of these copies are in a state of “relaxed” selection and remain “dormant” because they are lacking regulatory regions; however, many become functional. In the course of evolution, they may undergo subfunctionalization, neofunctionalization, or replace their progenitors. Functional retrocopies (retrogenes) can encode proteins, novel or similar to those encoded by their progenitors, can be used as alternative exons or create chimeric transcripts, and can also be involved in transcriptional interference and participate in the epigenetic regulation of parental gene expression. They can also act in trans as natural antisense transcripts, microRNA (miRNA) sponges, or a source of various small RNAs. Moreover, many retrocopies of protein-coding genes are linked to human diseases, especially various types of cancer.
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11
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Emergence and evolution of inter-specific segregating retrocopies in cynomolgus monkey (Macaca fascicularis) and rhesus macaque (Macaca mulatta). Sci Rep 2016; 6:32598. [PMID: 27600022 PMCID: PMC5013489 DOI: 10.1038/srep32598] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2016] [Accepted: 08/10/2016] [Indexed: 11/13/2022] Open
Abstract
Retroposition is an RNA-mediated mechanism to generate gene duplication, and is believed to play an important role in genome evolution and phenotypic adaptation in various species including primates. Previous studies suggested an elevated rate of recent retroposition in the rhesus macaque genome. To better understand the impact of retroposition on macaque species which have undergone an adaptive radiation approximately 3–6 million years ago, we developed a bioinformatics pipeline to identify recently derived retrocopies in cynomolgus monkeys. As a result, we identified seven experimentally validated young retrocopies, all of which are polymorphic in cynomolgus monkeys. Unexpectedly, five of them are also present in rhesus monkeys and are still segregating. Molecular evolutionary analysis indicates that the observed inter-specific polymorphism is attribute to ancestral polymorphism. Further population genetics analysis provided strong evidence of balancing selection on at least one case (Crab-eating monkey retrocopy 6, or CER6) in both species. CER6 is in adjacent with an immunoglobulin related gene and may be involved in host-pathogen interaction, a well-known target of balancing selection. Altogether, our data support that retroposition is an important force to shape genome evolution and species adaptation.
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Mori S, Hayashi M, Inagaki S, Oshima T, Tateishi K, Fujii H, Suzuki S. Identification of Multiple Forms of RNA Transcripts Associated with Human-Specific Retrotransposed Gene Copies. Genome Biol Evol 2016; 8:2288-96. [PMID: 27389689 PMCID: PMC5010893 DOI: 10.1093/gbe/evw156] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
The human genome contains thousands of retrocopies, mostly as processed pseudogenes, which were recently shown to be prevalently transcribed. In particular, those specifically acquired in the human lineage are able to modulate gene expression in a manner that contributed to the evolution of human-specific traits. Therefore, knowledge of the human-specific retrocopies that are transcribed or their full-length transcript structure contributes to better understand human genome evolution. In this study, we identified 16 human-specific retrocopies that harbor 5' CpG islands by in silico analysis and showed that 12 were transcribed in normal tissues and cancer cell lines with a variety of expression patterns, including cancer-specific expression. Determination of the structure of the transcripts associated with the retrocopies revealed that none were transcribed from their 5' CpG islands, but rather, from inside the 3' UTR and the nearby 5' flanking region of the retrocopies as well as the promoter of neighboring genes. The multiple forms of the transcripts, such as chimeric and individual transcripts in both the sense and antisense orientation, might have introduced novel post-transcriptional regulation into the genome during human evolution. These results shed light on the potential role of human-specific retrocopies in the evolution of gene regulation and genomic disorders.
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Affiliation(s)
- Saori Mori
- Epigenomics Division, Frontier Agriscience and Technology Center, Faculty of Agriculture, Shinshu University, Kami-Ina, Nagano, Japan
| | - Masaaki Hayashi
- Epigenomics Division, Frontier Agriscience and Technology Center, Faculty of Agriculture, Shinshu University, Kami-Ina, Nagano, Japan
| | - Shun Inagaki
- Epigenomics Division, Frontier Agriscience and Technology Center, Faculty of Agriculture, Shinshu University, Kami-Ina, Nagano, Japan
| | - Takuji Oshima
- Epigenomics Division, Frontier Agriscience and Technology Center, Faculty of Agriculture, Shinshu University, Kami-Ina, Nagano, Japan
| | - Ken Tateishi
- Epigenomics Division, Frontier Agriscience and Technology Center, Faculty of Agriculture, Shinshu University, Kami-Ina, Nagano, Japan
| | - Hiroshi Fujii
- Department of Interdisciplinary Genome Sciences and Cell Metabolism, Institute for Biomedical Sciences, Interdisciplinary Cluster for Cutting Edge Research, Shinshu University, Kami-Ina, Nagano, Japan
| | - Shunsuke Suzuki
- Epigenomics Division, Frontier Agriscience and Technology Center, Faculty of Agriculture, Shinshu University, Kami-Ina, Nagano, Japan Department of Interdisciplinary Genome Sciences and Cell Metabolism, Institute for Biomedical Sciences, Interdisciplinary Cluster for Cutting Edge Research, Shinshu University, Kami-Ina, Nagano, Japan
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