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Karimi B, Mokhtari K, Rozbahani H, Peymani M, Nabavi N, Entezari M, Rashidi M, Taheriazam A, Ghaedi K, Hashemi M. Pathological roles of miRNAs and pseudogene-derived lncRNAs in human cancers, and their comparison as prognosis/diagnosis biomarkers. Pathol Res Pract 2024; 253:155014. [PMID: 38128189 DOI: 10.1016/j.prp.2023.155014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/23/2023] [Revised: 12/02/2023] [Accepted: 12/02/2023] [Indexed: 12/23/2023]
Abstract
This review examines and compares the diagnostic and prognostic capabilities of miRNAs and lncRNAs derived from pseudogenes in cancer patients. Additionally, it delves into their roles in cancer pathogenesis. Both miRNAs and pseudogene-derived lncRNAs have undergone thorough investigation as remarkably sensitive and specific cancer biomarkers, offering significant potential for cancer detection and monitoring. . Extensive research is essential to gain a complete understanding of the precise roles these non-coding RNAs play in cancer, allowing the development of novel targeted therapies and biomarkers for improved cancer detection and treatment approaches.
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Affiliation(s)
- Bahareh Karimi
- Department of Cellular and Molecular Biology and Microbiology, Faculty of Biological Science and Technology, University of Isfahan, Isfahan, Iran
| | - Khatere Mokhtari
- Department of Animal Biotechnology, Cell Science Research Center, Royan Institute for Biotechnology, ACECR, Isfahan, Iran
| | - Hossein Rozbahani
- Department of Psychology, North Tehran Branch, Islamic Azad University, Tehran, Iran; Department of Psychology, West Tehran Branch, Islamic Azad University, Tehran, Iran
| | - Maryam Peymani
- Department of Biology, Faculty of Basic Sciences, Shahrekord Branch, Islamic Azad University, Shahrekord, Iran
| | - Noushin Nabavi
- Department of Urologic Sciences and Vancouver Prostate Centre, University of British Columbia, Vancouver, BC V6H3Z6, Canada
| | - Maliheh Entezari
- Farhikhtegan Medical Convergence Sciences Research Center, Farhikhtegan Hospital Tehran Medical Sciences, Islamic Azad University, Tehran, Iran; Department of Genetics, Faculty of Advanced Science and Technology, Tehran Medical Sciences, Islamic Azad University, Tehran, Iran
| | - Mohsen Rashidi
- Department Pharmacology, Faculty of Medicine, Mazandaran University of Medical Sciences, Sari, Iran; The Health of Plant and Livestock Products Research Center, Mazandaran University of Medical Sciences, Sari, Iran.
| | - Afshin Taheriazam
- Department of Genetics, Faculty of Advanced Science and Technology, Tehran Medical Sciences, Islamic Azad University, Tehran, Iran; Department of Orthopedics, Faculty of medicine, Tehran Medical Sciences, Islamic Azad University, Tehran, Iran.
| | - Kamran Ghaedi
- Department of Cell and Molecular Biology and Microbiology, Faculty of Biological Science and Technology, University of Isfahan, Isfahan, Iran.
| | - Mehrdad Hashemi
- Farhikhtegan Medical Convergence Sciences Research Center, Farhikhtegan Hospital Tehran Medical Sciences, Islamic Azad University, Tehran, Iran; Department of Genetics, Faculty of Advanced Science and Technology, Tehran Medical Sciences, Islamic Azad University, Tehran, Iran.
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2
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Yan Y, Tian Y, Wu Z, Zhang K, Yang R. Interchromosomal Colocalization with Parental Genes Is Linked to the Function and Evolution of Mammalian Retrocopies. Mol Biol Evol 2023; 40:msad265. [PMID: 38060983 PMCID: PMC10733166 DOI: 10.1093/molbev/msad265] [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: 07/13/2023] [Revised: 10/25/2023] [Accepted: 11/29/2023] [Indexed: 12/22/2023] Open
Abstract
Retrocopies are gene duplicates arising from reverse transcription of mature mRNA transcripts and their insertion back into the genome. While long being regarded as processed pseudogenes, more and more functional retrocopies have been discovered. How the stripped-down retrocopies recover expression capability and become functional paralogs continually intrigues evolutionary biologists. Here, we investigated the function and evolution of retrocopies in the context of 3D genome organization. By mapping retrocopy-parent pairs onto sequencing-based and imaging-based chromatin contact maps in human and mouse cell lines and onto Hi-C interaction maps in 5 other mammals, we found that retrocopies and their parental genes show a higher-than-expected interchromosomal colocalization frequency. The spatial interactions between retrocopies and parental genes occur frequently at loci in active subcompartments and near nuclear speckles. Accordingly, colocalized retrocopies are more actively transcribed and translated and are more evolutionarily conserved than noncolocalized ones. The active transcription of colocalized retrocopies may result from their permissive epigenetic environment and shared regulatory elements with parental genes. Population genetic analysis of retroposed gene copy number variants in human populations revealed that retrocopy insertions are not entirely random in regard to interchromosomal interactions and that colocalized retroposed gene copy number variants are more likely to reach high frequencies, suggesting that both insertion bias and natural selection contribute to the colocalization of retrocopy-parent pairs. Further dissection implies that reduced selection efficacy, rather than positive selection, contributes to the elevated allele frequency of colocalized retroposed gene copy number variants. Overall, our results hint a role of interchromosomal colocalization in the "resurrection" of initially neutral retrocopies.
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Affiliation(s)
- Yubin Yan
- College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, China
| | - Yuhan Tian
- College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, China
| | - Zefeng Wu
- College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, China
| | - Kunling Zhang
- College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, China
| | - Ruolin Yang
- College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, China
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3
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Nakamura-García AK, Espinal-Enríquez J. Pseudogenes in Cancer: State of the Art. Cancers (Basel) 2023; 15:4024. [PMID: 37627052 PMCID: PMC10452131 DOI: 10.3390/cancers15164024] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Revised: 07/24/2023] [Accepted: 07/26/2023] [Indexed: 08/27/2023] Open
Abstract
Pseudogenes are duplicates of protein-coding genes that have accumulated multiple detrimental alterations, rendering them unable to produce the protein they encode. Initially disregarded as "junk DNA" due to their perceived lack of functionality, research on their biological roles has been hindered by this assumption. Nevertheless, recent focus has shifted towards these molecules due to their abnormal expression in cancer phenotypes. In this review, our objective is to provide a thorough overview of the current understanding of pseudogene formation, the mechanisms governing their expression, and the roles they may play in promoting tumorigenesis.
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Qian SH, Chen L, Xiong YL, Chen ZX. Evolution and function of developmentally dynamic pseudogenes in mammals. Genome Biol 2022; 23:235. [PMID: 36348461 PMCID: PMC9641868 DOI: 10.1186/s13059-022-02802-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Accepted: 10/23/2022] [Indexed: 11/11/2022] Open
Abstract
BACKGROUND Pseudogenes are excellent markers for genome evolution, which are emerging as crucial regulators of development and disease, especially cancer. However, systematic functional characterization and evolution of pseudogenes remain largely unexplored. RESULTS To systematically characterize pseudogenes, we date the origin of human and mouse pseudogenes across vertebrates and observe a burst of pseudogene gain in these two lineages. Based on a hybrid sequencing dataset combining full-length PacBio sequencing, sample-matched Illumina sequencing, and public time-course transcriptome data, we observe that abundant mammalian pseudogenes could be transcribed, which contribute to the establishment of organ identity. Our analyses reveal that developmentally dynamic pseudogenes are evolutionarily conserved and show an increasing weight during development. Besides, they are involved in complex transcriptional and post-transcriptional modulation, exhibiting the signatures of functional enrichment. Coding potential evaluation suggests that 19% of human pseudogenes could be translated, thus serving as a new way for protein innovation. Moreover, pseudogenes carry disease-associated SNPs and conduce to cancer transcriptome perturbation. CONCLUSIONS Our discovery reveals an unexpectedly high abundance of mammalian pseudogenes that can be transcribed and translated, and these pseudogenes represent a novel regulatory layer. Our study also prioritizes developmentally dynamic pseudogenes with signatures of functional enrichment and provides a hybrid sequencing dataset for further unraveling their biological mechanisms in organ development and carcinogenesis in the future.
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Affiliation(s)
- Sheng Hu Qian
- grid.35155.370000 0004 1790 4137Hubei Hongshan Laboratory, College of Biomedicine and Health, Huazhong Agricultural University, Wuhan, 430070 PR China ,grid.35155.370000 0004 1790 4137Hubei Key Laboratory of Agricultural Bioinformatics, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, 430070 PR China
| | - Lu Chen
- grid.35155.370000 0004 1790 4137Hubei Hongshan Laboratory, College of Biomedicine and Health, Huazhong Agricultural University, Wuhan, 430070 PR China ,grid.35155.370000 0004 1790 4137Hubei Key Laboratory of Agricultural Bioinformatics, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, 430070 PR China
| | - Yu-Li Xiong
- grid.35155.370000 0004 1790 4137Hubei Hongshan Laboratory, College of Biomedicine and Health, Huazhong Agricultural University, Wuhan, 430070 PR China ,grid.35155.370000 0004 1790 4137Hubei Key Laboratory of Agricultural Bioinformatics, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, 430070 PR China
| | - Zhen-Xia Chen
- grid.35155.370000 0004 1790 4137Hubei Hongshan Laboratory, College of Biomedicine and Health, Huazhong Agricultural University, Wuhan, 430070 PR China ,grid.35155.370000 0004 1790 4137Hubei Key Laboratory of Agricultural Bioinformatics, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, 430070 PR China ,grid.35155.370000 0004 1790 4137Interdisciplinary Sciences Institute, Huazhong Agricultural University, Wuhan, 430070 PR China ,grid.35155.370000 0004 1790 4137Shenzhen Institute of Nutrition and Health, Huazhong Agricultural University, Shenzhen, 518124 PR China ,grid.488316.00000 0004 4912 1102Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518124 PR China
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5
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Mascagni F, Usai G, Cavallini A, Porceddu A. Structural characterization and duplication modes of pseudogenes in plants. Sci Rep 2021; 11:5292. [PMID: 33674668 PMCID: PMC7935947 DOI: 10.1038/s41598-021-84778-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2020] [Accepted: 02/19/2021] [Indexed: 11/24/2022] Open
Abstract
We identified and characterized the pseudogene complements of five plant species: four dicots (Arabidopsis thaliana, Vitis vinifera, Populus trichocarpa and Phaseolus vulgaris) and one monocot (Oryza sativa). Retroposition was considered of modest importance for pseudogene formation in all investigated species except V. vinifera, which showed an unusually high number of retro-pseudogenes in non coding genic regions. By using a pipeline for the classification of sequence duplicates in plant genomes, we compared the relative importance of whole genome, tandem, proximal, transposed and dispersed duplication modes in the pseudo and functional gene complements. Pseudogenes showed higher tendencies than functional genes to genomic dispersion. Dispersed pseudogenes were prevalently fragmented and showed high sequence divergence at flanking regions. On the contrary, those deriving from whole genome duplication were proportionally less than expected based on observations on functional loci and showed higher levels of flanking sequence conservation than dispersed pseudogenes. Pseudogenes deriving from tandem and proximal duplications were in excess compared to functional loci, probably reflecting the high evolutionary rate associated with these duplication modes in plant genomes. These data are compatible with high rates of sequence turnover at neutral sites and double strand break repairs mediated duplication mechanisms.
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Affiliation(s)
- Flavia Mascagni
- Department of Agricultural, Food, and Environment, University of Pisa, Via del Borghetto 80, 56124, Pisa, Italy
| | - Gabriele Usai
- Department of Agricultural, Food, and Environment, University of Pisa, Via del Borghetto 80, 56124, Pisa, Italy
| | - Andrea Cavallini
- Department of Agricultural, Food, and Environment, University of Pisa, Via del Borghetto 80, 56124, Pisa, Italy
| | - Andrea Porceddu
- Dipartimento di Agraria, Università degli studi di Sassari, Via Enrico de Nicola 1, 07100, Sassari, Italy.
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6
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Feng X, Li H. Higher Rates of Processed Pseudogene Acquisition in Humans and Three Great Apes Revealed by Long-Read Assemblies. Mol Biol Evol 2021; 38:2958-2966. [PMID: 33681998 DOI: 10.1093/molbev/msab062] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
LINE-1-mediated retrotransposition of protein-coding mRNAs is an active process in modern humans for both germline and somatic genomes. Prior works that surveyed human data mostly relied on detecting discordant mappings of paired-end short reads, or exon junctions contained in short reads. Moreover, there have been few genome-wide comparisons between gene retrocopies in great apes and humans. In this study, we introduced a more sensitive and accurate method to identify processed pseudogenes. Our method utilizes long-read assemblies, and more importantly, is able to provide full-length retrocopy sequences as well as flanking regions which are missed by short-read based methods. From 22 human individuals, we pinpointed 40 processed pseudogenes that are not present in the human reference genome GRCh38 and identified 17 pseudogenes that are in GRCh38 but absent from some input individuals. This represents a significantly higher discovery rate than previous reports (39 pseudogenes not in the reference genome out of 939 individuals). We also provided an overview of lineage-specific retrocopies in chimpanzee, gorilla, and orangutan genomes.
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Affiliation(s)
- Xiaowen Feng
- Department of Data Sciences, Dana-Farber Cancer Institute, Boston, MA, USA.,Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - Heng Li
- Department of Data Sciences, Dana-Farber Cancer Institute, Boston, MA, USA.,Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
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7
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Maranda V, Sunstrum FG, Drouin G. Both male and female gamete generating cells produce processed pseudogenes in the human genome. Gene 2018; 684:70-75. [PMID: 30359744 DOI: 10.1016/j.gene.2018.10.061] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2018] [Revised: 09/24/2018] [Accepted: 10/21/2018] [Indexed: 11/25/2022]
Abstract
The human genome contains an unusually large number of processed pseudogenes. The fact that processed pseudogenes are roughly 33% more abundant in our X chromosome than in our autosomes suggests that this overabundance is the result of the fact that human oogenesis is much longer than that of non-mammalian species. Here, we analyze the origins of the processed pseudogenes found on the human Y chromosome to determine whether human spermatogenesis also contribute to this overabundance. Our results show that human processed pseudogenes not only retrotranspose to the Y chromosome, but are also produced by genes on the Y chromosome. Furthermore, the fact that X chromosomes are three times more abundant than Y chromosomes likely explains why the euchromatic density of processed pseudogenes is three times higher in the X chromosome than in the Y chromosome. The large number of processed pseudogenes found in our genome is therefore due to the low substrate specificity of the L1 reverse transcriptase responsible for the reverse transcription of germline mRNA molecules into processed pseudogenes, as well as the life-long production of both male and female gametes.
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Affiliation(s)
- Vincent Maranda
- Département de biologie et Centre de recherche avancée en génomique environnementale, Université d'Ottawa, Ottawa, Ontario K1N 6N5, Canada
| | - Frédérick G Sunstrum
- Département de biologie et Centre de recherche avancée en génomique environnementale, Université d'Ottawa, Ottawa, Ontario K1N 6N5, Canada
| | - Guy Drouin
- Département de biologie et Centre de recherche avancée en génomique environnementale, Université d'Ottawa, Ottawa, Ontario K1N 6N5, Canada.
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8
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Xiao J, Sekhwal MK, Li P, Ragupathy R, Cloutier S, Wang X, You FM. Pseudogenes and Their Genome-Wide Prediction in Plants. Int J Mol Sci 2016; 17:E1991. [PMID: 27916797 PMCID: PMC5187791 DOI: 10.3390/ijms17121991] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2016] [Revised: 11/20/2016] [Accepted: 11/22/2016] [Indexed: 11/17/2022] Open
Abstract
Pseudogenes are paralogs generated from ancestral functional genes (parents) during genome evolution, which contain critical defects in their sequences, such as lacking a promoter, having a premature stop codon or frameshift mutations. Generally, pseudogenes are functionless, but recent evidence demonstrates that some of them have potential roles in regulation. The majority of pseudogenes are generated from functional progenitor genes either by gene duplication (duplicated pseudogenes) or retro-transposition (processed pseudogenes). Pseudogenes are primarily identified by comparison to their parent genes. Bioinformatics tools for pseudogene prediction have been developed, among which PseudoPipe, PSF and Shiu's pipeline are publicly available. We compared these three tools using the well-annotated Arabidopsis thaliana genome and its known 924 pseudogenes as a test data set. PseudoPipe and Shiu's pipeline identified ~80% of A. thaliana pseudogenes, of which 94% were shared, while PSF failed to generate adequate results. A need for improvement of the bioinformatics tools for pseudogene prediction accuracy in plant genomes was thus identified, with the ultimate goal of improving the quality of genome annotation in plants.
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Affiliation(s)
- Jin Xiao
- Morden Research and Development Centre, Agriculture and Agri-Food Canada, Morden, MB R6M 1Y5, Canada.
- Department of Agronomy, Nanjing Agricultural University, Nanjing 210095, China.
| | - Manoj Kumar Sekhwal
- Morden Research and Development Centre, Agriculture and Agri-Food Canada, Morden, MB R6M 1Y5, Canada.
- Department of Soil Science, University of Saskatchewan, Saskatoon, SK S7N 5A8, Canada.
| | - Pingchuan Li
- Morden Research and Development Centre, Agriculture and Agri-Food Canada, Morden, MB R6M 1Y5, Canada.
| | - Raja Ragupathy
- Department of Plant Science, University of Saskatchewan, Saskatoon, SK S7N 5A2, Canada.
| | - Sylvie Cloutier
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, Ottawa, ON K1A 0C6, Canada.
| | - Xiue Wang
- Department of Agronomy, Nanjing Agricultural University, Nanjing 210095, China.
| | - Frank M You
- Morden Research and Development Centre, Agriculture and Agri-Food Canada, Morden, MB R6M 1Y5, Canada.
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9
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Carelli FN, Hayakawa T, Go Y, Imai H, Warnefors M, Kaessmann H. The life history of retrocopies illuminates the evolution of new mammalian genes. Genome Res 2016; 26:301-14. [PMID: 26728716 PMCID: PMC4772013 DOI: 10.1101/gr.198473.115] [Citation(s) in RCA: 83] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2015] [Accepted: 12/21/2015] [Indexed: 02/03/2023]
Abstract
New genes contribute substantially to adaptive evolutionary innovation, but the functional evolution of new mammalian genes has been little explored at a broad scale. Previous work established mRNA-derived gene duplicates, known as retrocopies, as models for the study of new gene origination. Here we combine mammalian transcriptomic and epigenomic data to unveil the processes underlying the evolution of stripped-down retrocopies into complex new genes. We show that although some robustly expressed retrocopies are transcribed from preexisting promoters, most evolved new promoters from scratch or recruited proto-promoters in their genomic vicinity. In particular, many retrocopy promoters emerged from ancestral enhancers (or bivalent regulatory elements) or are located in CpG islands not associated with other genes. We detected 88–280 selectively preserved retrocopies per mammalian species, illustrating that these mechanisms facilitated the birth of many functional retrogenes during mammalian evolution. The regulatory evolution of originally monoexonic retrocopies was frequently accompanied by exon gain, which facilitated co-option of distant promoters and allowed expression of alternative isoforms. While young retrogenes are often initially expressed in the testis, increased regulatory and structural complexities allowed retrogenes to functionally diversify and evolve somatic organ functions, sometimes as complex as those of their parents. Thus, some retrogenes evolved the capacity to temporarily substitute for their parents during the process of male meiotic X inactivation, while others rendered parental functions superfluous, allowing for parental gene loss. Overall, our reconstruction of the “life history” of mammalian retrogenes highlights retroposition as a general model for understanding new gene birth and functional evolution.
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Affiliation(s)
- Francesco Nicola Carelli
- Center for Integrative Genomics, University of Lausanne, 1015 Lausanne, Switzerland; Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
| | - Takashi Hayakawa
- Department of Wildlife Science (Nagoya Railroad Company, Limited), Primate Research Institute, Kyoto University, Inuyama, Aichi 484-8506, Japan; Japan Monkey Center, Inuyama, Aichi 484-0081, Japan
| | - Yasuhiro Go
- Department of Brain Sciences, Center for Novel Science Initiatives, National Institutes of Natural Sciences, Okazaki, Aichi 444-8585, Japan; Department of Developmental Physiology, National Institute for Physiological Sciences, Okazaki, Aichi 444-8585, Japan; Department of Physiological Sciences, School of Life Science, SOKENDAI (The Graduate University for Advanced Studies), Okazaki, Aichi 484-8585, Japan
| | - Hiroo Imai
- Department of Cellular and Molecular Biology, Primate Research Institute, Kyoto University, Inuyama, Aichi 484-8506, Japan
| | - Maria Warnefors
- Center for Integrative Genomics, University of Lausanne, 1015 Lausanne, Switzerland; Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
| | - Henrik Kaessmann
- Center for Integrative Genomics, University of Lausanne, 1015 Lausanne, Switzerland; Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
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10
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Eosinophil-Derived Neurotoxin (EDN/RNase 2) and the Mouse Eosinophil-Associated RNases (mEars): Expanding Roles in Promoting Host Defense. Int J Mol Sci 2015; 16:15442-55. [PMID: 26184157 PMCID: PMC4519907 DOI: 10.3390/ijms160715442] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2015] [Revised: 06/18/2015] [Accepted: 06/30/2015] [Indexed: 12/30/2022] Open
Abstract
The eosinophil-derived neurotoxin (EDN/RNase2) and its divergent orthologs, the mouse eosinophil-associated RNases (mEars), are prominent secretory proteins of eosinophilic leukocytes and are all members of the larger family of RNase A-type ribonucleases. While EDN has broad antiviral activity, targeting RNA viruses via mechanisms that may require enzymatic activity, more recent studies have elucidated how these RNases may generate host defense via roles in promoting leukocyte activation, maturation, and chemotaxis. This review provides an update on recent discoveries, and highlights the versatility of this family in promoting innate immunity.
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11
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Sen K, Ghosh TC. Pseudogenes and their composers: delving in the 'debris' of human genome. Brief Funct Genomics 2013; 12:536-47. [PMID: 23900003 DOI: 10.1093/bfgp/elt026] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
Pseudogenes, the nonfunctional homologs of functional genes and thus exemplified as 'genomic fossils' provide intriguing snapshots of the evolutionary history of human genome. These defunct copies generally arise by retrotransposition or duplication followed by various genetic disablements. In this study, focusing on human pseudogenes and their functional homologues we describe their characteristic features and relevance to protein sequence evolution. We recapitulate that pseudogenes harbor disease-causing degenerative sequence variations in conjunction with the immense disease gene association of their progenitors. Furthermore, we also discuss the issue of functional resurrection and the potentiality observed in some pseudogenes to regulate their functional counterparts.
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Affiliation(s)
- Kamalika Sen
- Bioinformatics Centre, Bose Institute, P 1/12, C.I.T. Scheme VII M, Kolkata 700 054, India. Tel.: +91 33 2355 6626; Fax: +91 33 2355 3886;
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12
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Frequency of intron loss correlates with processed pseudogene abundance: a novel strategy to test the reverse transcriptase model of intron loss. BMC Biol 2013; 11:23. [PMID: 23497167 PMCID: PMC3652778 DOI: 10.1186/1741-7007-11-23] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2013] [Accepted: 03/05/2013] [Indexed: 11/23/2022] Open
Abstract
Background Although intron loss in evolution has been described, the mechanism involved is still unclear. Three models have been proposed, the reverse transcriptase (RT) model, genomic deletion model and double-strand-break repair model. The RT model, also termed mRNA-mediated intron loss, suggests that cDNA molecules reverse transcribed from spliced mRNA recombine with genomic DNA causing intron loss. Many studies have attempted to test this model based on its predictions, such as simultaneous loss of adjacent introns, 3'-side bias of intron loss, and germline expression of intron-lost genes. Evidence either supporting or opposing the model has been reported. The mechanism of intron loss proposed in the RT model shares the process of reverse transcription with the formation of processed pseudogenes. If the RT model is correct, genes that have produced more processed pseudogenes are more likely to undergo intron loss. Results In the present study, we observed that the frequency of intron loss is correlated with processed pseudogene abundance by analyzing a new dataset of intron loss obtained in mice and rats. Furthermore, we found that mRNA molecules of intron-lost genes are mostly translated on free cytoplasmic ribosomes, a feature shared by mRNA molecules of the parental genes of processed pseudogenes and long interspersed elements. This feature is likely convenient for intron-lost gene mRNA molecules to be reverse transcribed. Analyses of adjacent intron loss, 3'-side bias of intron loss, and germline expression of intron-lost genes also support the RT model. Conclusions Compared with previous evidence, the correlation between the abundance of processed pseudogenes and intron loss frequency more directly supports the RT model of intron loss. Exploring such a correlation is a new strategy to test the RT model in organisms with abundant processed pseudogenes.
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13
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Casola C, Zekonyte U, Phillips AD, Cooper DN, Hahn MW. Interlocus gene conversion events introduce deleterious mutations into at least 1% of human genes associated with inherited disease. Genome Res 2012; 22:429-35. [PMID: 22090377 PMCID: PMC3290778 DOI: 10.1101/gr.127738.111] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2011] [Accepted: 11/15/2011] [Indexed: 01/06/2023]
Abstract
Establishing the molecular basis of DNA mutations that cause inherited disease is of fundamental importance to understanding the origin, nature, and clinical sequelae of genetic disorders in humans. The majority of disease-associated mutations constitute single-base substitutions and short deletions and/or insertions resulting from DNA replication errors and the repair of damaged bases. However, pathological mutations can also be introduced by nonreciprocal recombination events between paralogous sequences, a phenomenon known as interlocus gene conversion (IGC). IGC events have thus far been linked to pathology in more than 20 human genes. However, the large number of duplicated gene sequences in the human genome implies that many more disease-associated mutations could originate via IGC. Here, we have used a genome-wide computational approach to identify disease-associated mutations derived from IGC events. Our approach revealed hundreds of known pathological mutations that could have been caused by IGC. Further, we identified several dozen high-confidence cases of inherited disease mutations resulting from IGC in ∼1% of all genes analyzed. About half of the donor sequences associated with such mutations are functional paralogous genes, suggesting that epistatic interactions or differential expression patterns will determine the impact upon fitness of specific substitutions between duplicated genes. In addition, we identified thousands of hitherto undescribed and potentially deleterious mutations that could arise via IGC. Our findings reveal the extent of the impact of interlocus gene conversion upon the spectrum of human inherited disease.
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Affiliation(s)
- Claudio Casola
- Department of Biology, Indiana University, Bloomington, Indiana 47405, USA
| | - Ugne Zekonyte
- Department of Biology, Indiana University, Bloomington, Indiana 47405, USA
| | - Andrew D. Phillips
- Institute of Medical Genetics, School of Medicine, Cardiff University, Heath Park, Cardiff CF14 4XN, United Kingdom
| | - David N. Cooper
- Institute of Medical Genetics, School of Medicine, Cardiff University, Heath Park, Cardiff CF14 4XN, United Kingdom
| | - Matthew W. Hahn
- Department of Biology, Indiana University, Bloomington, Indiana 47405, USA
- School of Informatics and Computing, Indiana University, Bloomington, Indiana 47405, USA
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McDonell L, Drouin G. The abundance of processed pseudogenes derived from glycolytic genes is correlated with their expression level. Genome 2012; 55:147-51. [PMID: 22309162 DOI: 10.1139/g2012-002] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The abundance of processed pseudogenes in different vertebrate species is known to be proportional to the length of their oogenesis. However, this hypothesis cannot explain why, in a given species, certain genes produce more processed pseudogenes than others. In particular, one would expect that all genes of the glycolytic pathway would generate roughly the same number of processed pseudogenes. However, some glycolitic genes generate more processed pseudogenes than others. Here, we show that there is a positive correlation between the abundance of processed pseudogene generated from glycolytic genes and their level of expression. The variation in expression level of different glycolytic genes likely reflects the fact that some of them, such a GAPDH, have functions other than those they play in glycolysis. Furthermore, the age distribution of GAPDH-processed pseudogenes corresponds to the age distribution of LINE1 elements, which are the source of the reverse transcriptase that generates processed pseudogenes. These results support the hypothesis that gene expression levels affect the level of processed pseudogene production.
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Affiliation(s)
- Laura McDonell
- Département de biologie et Centre de recherche avancée en génomique environnementale, Université d'Ottawa, Ottawa, ON, Canada
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15
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Sen K, Podder S, Ghosh TC. On the quest for selective constraints shaping the expressivity of the genes casting retropseudogenes in human. BMC Genomics 2011; 12:401. [PMID: 21824418 PMCID: PMC3162935 DOI: 10.1186/1471-2164-12-401] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2010] [Accepted: 08/08/2011] [Indexed: 02/04/2023] Open
Abstract
Background Pseudogenes, the nonfunctional homologues of functional genes are now coming to light as important resources regarding the study of human protein evolution. Processed pseudogenes arising by reverse transcription and reinsertion can provide molecular record on the dynamics and evolution of genomes. Researches on the progenitors of human processed pseudogenes delved out their highly expressed and evolutionarily conserved characters. They are reported to be short and GC-poor indicating their high efficiency for retrotransposition. In this article we focused on their high expressivity and explored the factors contributing for that and their relevance in the milieu of protein sequence evolution. Results We here, analyzed the high expressivity of these genes configuring processed or retropseudogenes by their immense connectivity in protein-protein interaction network, an inclination towards alternative splicing mechanism, a lower rate of mRNA disintegration and a slower evolutionary rate. While the unusual trend of the upraised disorder in contrast with the high expressivity of the proteins encoded by processed pseudogene ancestors is accredited by a predominance of hub-protein encoding genes, a high propensity of repeat sequence containing genes, elevated protein stability and the functional constraint to perform the transcription regulatory jobs. Linear regression analysis demonstrates mRNA decay rate and protein intrinsic disorder as the influential factors controlling the expressivity of these retropseudogene ancestors while the latter one is found to have the most significant regulatory power. Conclusions Our findings imply that, the affluence of disordered regions elevating the network attachment to be involved in important cellular assignments and the stability in transcriptional level are acting as the prevailing forces behind the high expressivity of the human genes configuring processed pseudogenes.
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Affiliation(s)
- Kamalika Sen
- Bioinformatics Centre, Bose Institute, P 1/12, C,I,T, Scheme VII M, Kolkata- 700 054, India
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16
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Abstract
The human septins are part of a gene family, that is a group of genes with similar sequences and usually but not invariably share similar functions that are descended from a common ancestor. Here we review our current knowledge of the human septin gene family and highlight areas of uncertainty. Currently 13 human septin genes are known (SEPT1 to SEPT12 and SEPT14). What was known as SEPT13 is now defined as one of many SEPT7 related pseudogenes. The family is characterized by complex genomics and extensive (but not universal) splicing, giving rise to a plethora of septin isoforms. For only a few members of the family do we have a comprehensive insight into these transcripts and isoforms. Given the formation of countless septin homotypic and heterotypic interactions our understanding of the biology and pathobiology of the septin family will require a detailed understanding of the genomics, transcriptomics and regulation of all members of this diverse and complex family.
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Affiliation(s)
- S E Hilary Russell
- Centre for Cancer Research and Cell Biology, Queens University Belfast, Belfast, Northern Ireland, UK.
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17
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Atianand MK, Fuchs T, Harton JA. Recent evolution of the NF-κB and inflammasome regulating protein POP2 in primates. BMC Evol Biol 2011; 11:56. [PMID: 21362197 PMCID: PMC3056782 DOI: 10.1186/1471-2148-11-56] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2010] [Accepted: 03/01/2011] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Pyrin-only protein 2 (POP2) is a small human protein comprised solely of a pyrin domain that inhibits NF-κB p65/RelA and blocks the formation of functional IL-1β processing inflammasomes. Pyrin proteins are abundant in mammals and several, like POP2, have been linked to activation or regulation of inflammatory processes. Because POP2 knockout mice would help probe the biological role of inflammatory regulation, we thus considered whether POP2 is common in the mammalian lineage. RESULTS BLAST searches revealed that POP2 is absent from the available genomes of not only mice and rats, but those of other domestic mammals and New World monkeys as well. POP2 is however present in the genome of the primate species most closely related to humans including Pan troglodytes (chimpanzees), Macaca mulatta (rhesus macaques) and others. Interestingly, chimpanzee POP2 is identical to human POP2 (huPOP2) at both the DNA and protein level. Macaque POP2 (mqPOP2), although highly conserved is not identical to the human sequence; however, both functions of the human protein are retained. Further, POP2 appears to have arisen in the mammalian genome relatively recently (~25 mya) and likely derived from retrogene insertion of NLRP2. CONCLUSION Our findings support the hypothesis that the NLR loci of mammals, encoding proteins involved in innate and adaptive immunity as well as mammalian development, have been subject to recent and strong selective pressures. Since POP2 is capable of regulating signaling events and processes linked to innate immunity and inflammation, its presence in the genomes of hominids and Old World primates further suggests that additional regulation of these signals is important in these species.
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Affiliation(s)
- Maninjay K Atianand
- Center for Immunology and Microbial Disease, Albany Medical College, Albany, New York 12208, USA
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18
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McNulty SN, Foster JM, Mitreva M, Dunning Hotopp JC, Martin J, Fischer K, Wu B, Davis PJ, Kumar S, Brattig NW, Slatko BE, Weil GJ, Fischer PU. Endosymbiont DNA in endobacteria-free filarial nematodes indicates ancient horizontal genetic transfer. PLoS One 2010; 5:e11029. [PMID: 20543958 PMCID: PMC2882956 DOI: 10.1371/journal.pone.0011029] [Citation(s) in RCA: 98] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2010] [Accepted: 05/19/2010] [Indexed: 11/24/2022] Open
Abstract
BACKGROUND Wolbachia are among the most abundant symbiotic microbes on earth; they are present in about 66% of all insect species, some spiders, mites and crustaceans, and most filarial nematode species. Infected filarial nematodes, including many pathogens of medical and veterinary importance, depend on Wolbachia for proper development and survival. The mechanisms behind this interdependence are not understood. Interestingly, a minority of filarial species examined to date are naturally Wolbachia-free. METHODOLOGY/PRINCIPAL FINDINGS We used 454 pyrosequencing to survey the genomes of two distantly related Wolbachia-free filarial species, Acanthocheilonema viteae and Onchocerca flexuosa. This screen identified 49 Wolbachia-like DNA sequences in A. viteae and 114 in O. flexuosa. qRT-PCR reactions detected expression of 30 Wolbachia-like sequences in A. viteae and 56 in O. flexuosa. Approximately half of these appear to be transcribed from pseudogenes. In situ hybridization showed that two of these pseudogene transcripts were specifically expressed in developing embryos and testes of both species. CONCLUSIONS/SIGNIFICANCE These results strongly suggest that the last common ancestor of extant filarial nematodes was infected with Wolbachia and that this former endosymbiont contributed to their genome evolution. Horizontally transferred Wolbachia DNA may explain the ability of some filarial species to live and reproduce without the endosymbiont while other species cannot.
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Affiliation(s)
- Samantha N. McNulty
- Infectious Diseases Division, Department of Internal Medicine, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Jeremy M. Foster
- New England Biolabs, Ipswich, Massachusetts, United States of America
| | - Makedonka Mitreva
- The Genome Center, Department of Genetics, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Julie C. Dunning Hotopp
- Institute for Genome Sciences, Department of Microbiology and Immunology, University of Maryland Baltimore, Baltimore, Maryland, United States of America
| | - John Martin
- The Genome Center, Department of Genetics, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Kerstin Fischer
- Infectious Diseases Division, Department of Internal Medicine, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Bo Wu
- New England Biolabs, Ipswich, Massachusetts, United States of America
| | - Paul J. Davis
- New England Biolabs, Ipswich, Massachusetts, United States of America
| | - Sanjay Kumar
- New England Biolabs, Ipswich, Massachusetts, United States of America
| | | | - Barton E. Slatko
- New England Biolabs, Ipswich, Massachusetts, United States of America
| | - Gary J. Weil
- Infectious Diseases Division, Department of Internal Medicine, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Peter U. Fischer
- Infectious Diseases Division, Department of Internal Medicine, Washington University School of Medicine, St. Louis, Missouri, United States of America
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Slatko BE, Taylor MJ, Foster JM. The Wolbachia endosymbiont as an anti-filarial nematode target. Symbiosis 2010; 51:55-65. [PMID: 20730111 PMCID: PMC2918796 DOI: 10.1007/s13199-010-0067-1] [Citation(s) in RCA: 111] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2009] [Accepted: 05/13/2010] [Indexed: 01/05/2023]
Abstract
Human disease caused by parasitic filarial nematodes is a major cause of global morbidity. The parasites are transmitted by arthropod intermediate hosts and are responsible for lymphatic filariasis (elephantiasis) or onchocerciasis (river blindness). Within these filarial parasites are intracellular alpha-proteobacteria, Wolbachia, that were first observed almost 30 years ago. The obligate endosymbiont has been recognized as a target for anti-filarial nematode chemotherapy as evidenced by the loss of worm fertility and viability upon antibiotic treatment in an extensive series of human trials. While current treatments with doxycycline and rifampicin are not practical for widespread use due to the length of required treatments and contraindications, anti-Wolbachia targeting nevertheless appears a promising alternative for filariasis control in situations where current programmatic strategies fail or are unable to be delivered and it provides a superior efficacy for individual therapy. The mechanisms that underlie the symbiotic relationship between Wolbachia and its nematode hosts remain elusive. Comparative genomics, bioinfomatic and experimental analyses have identified a number of potential interactions, which may be drug targets. One candidate is de novo heme biosynthesis, due to its absence in the genome sequence of the host nematode, Brugia malayi, but presence in Wolbachia and its potential roles in worm biology. We describe this and several additional candidate targets, as well as our approaches for understanding the nature of the host-symbiont relationship.
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Affiliation(s)
- Barton E. Slatko
- Molecular Parasitology Division, New England Biolabs, 240 County Road, Ipswich, MA 01938 USA
| | - Mark J. Taylor
- Filariasis Research Laboratory, Molecular and Biochemical Parasitology, Liverpool School of Tropical Medicine, Pembroke Place, Liverpool, L3 5QA UK
| | - Jeremy M. Foster
- Molecular Parasitology Division, New England Biolabs, 240 County Road, Ipswich, MA 01938 USA
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