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Zhao P, Gu L, Gao Y, Pan Z, Liu L, Li X, Zhou H, Yu D, Han X, Qian L, Liu GE, Fang L, Wang Z. Young SINEs in pig genomes impact gene regulation, genetic diversity, and complex traits. Commun Biol 2023; 6:894. [PMID: 37652983 PMCID: PMC10471783 DOI: 10.1038/s42003-023-05234-x] [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: 03/02/2022] [Accepted: 08/09/2023] [Indexed: 09/02/2023] Open
Abstract
Transposable elements (TEs) are a major source of genetic polymorphisms and play a role in chromatin architecture, gene regulatory networks, and genomic evolution. However, their functional role in pigs and contributions to complex traits are largely unknown. We created a catalog of TEs (n = 3,087,929) in pigs and found that young SINEs were predominantly silenced by histone modifications, DNA methylation, and decreased accessibility. However, some transcripts from active young SINEs showed high tissue-specificity, as confirmed by analyzing 3570 RNA-seq samples. We also detected 211,067 dimorphic SINEs in 374 individuals, including 340 population-specific ones associated with local adaptation. Mapping these dimorphic SINEs to genome-wide associations of 97 complex traits in pigs, we found 54 candidate genes (e.g., ANK2 and VRTN) that might be mediated by TEs. Our findings highlight the important roles of young SINEs and provide a supplement for genotype-to-phenotype associations and modern breeding in pigs.
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Affiliation(s)
- Pengju Zhao
- Hainan Institute, Zhejiang University, Yongyou Industry Park, Yazhou Bay Sci-Tech City, Sanya, 572000, China
- College of Animal Sciences, Zhejiang University, Hangzhou, Zhejiang, 310058, China
| | - Lihong Gu
- Institute of Animal Science & Veterinary Medicine, Hainan Academy of Agricultural Sciences, No. 14 Xingdan Road, Haikou, 571100, China
| | - Yahui Gao
- Animal Genomics and Improvement Laboratory, Beltsville Agricultural Research Center, Agricultural Research Service, USDA, Beltsville, MD, 20705, USA
| | - Zhangyuan Pan
- Department of Animal Science, University of California, Davis, CA, 95616, USA
| | - Lei Liu
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518124, China
| | - Xingzheng Li
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518124, China
| | - Huaijun Zhou
- Department of Animal Science, University of California, Davis, CA, 95616, USA
| | - Dongyou Yu
- Hainan Institute, Zhejiang University, Yongyou Industry Park, Yazhou Bay Sci-Tech City, Sanya, 572000, China
- College of Animal Sciences, Zhejiang University, Hangzhou, Zhejiang, 310058, China
| | - Xinyan Han
- Hainan Institute, Zhejiang University, Yongyou Industry Park, Yazhou Bay Sci-Tech City, Sanya, 572000, China
- College of Animal Sciences, Zhejiang University, Hangzhou, Zhejiang, 310058, China
| | - Lichun Qian
- Hainan Institute, Zhejiang University, Yongyou Industry Park, Yazhou Bay Sci-Tech City, Sanya, 572000, China
- College of Animal Sciences, Zhejiang University, Hangzhou, Zhejiang, 310058, China
| | - George E Liu
- Animal Genomics and Improvement Laboratory, Beltsville Agricultural Research Center, Agricultural Research Service, USDA, Beltsville, MD, 20705, USA.
| | - Lingzhao Fang
- Center for Quantitative Genetics and Genomics, Aarhus University, Aarhus, 8000, Denmark.
| | - Zhengguang Wang
- Hainan Institute, Zhejiang University, Yongyou Industry Park, Yazhou Bay Sci-Tech City, Sanya, 572000, China.
- College of Animal Sciences, Zhejiang University, Hangzhou, Zhejiang, 310058, China.
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Stalker L, Backx AG, Tscherner AK, Russell SJ, Foster RA, LaMarre J. cDNA Cloning of Feline PIWIL1 and Evaluation of Expression in the Testis of the Domestic Cat. Int J Mol Sci 2023; 24:ijms24119346. [PMID: 37298298 DOI: 10.3390/ijms24119346] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Revised: 05/12/2023] [Accepted: 05/19/2023] [Indexed: 06/12/2023] Open
Abstract
The PIWI clade of Argonaute proteins is essential for spermatogenesis in all species examined to date. This protein family binds specific classes of small non-coding RNAs known as PIWI-interacting RNAs (piRNAs) which together form piRNA-induced silencing complexes (piRISCs) that are recruited to specific RNA targets through sequence complementarity. These complexes facilitate gene silencing through endonuclease activity and guided recruitment of epigenetic silencing factors. PIWI proteins and piRNAs have been found to play multiple roles in the testis including the maintenance of genomic integrity through transposon silencing and facilitating the turnover of coding RNAs during spermatogenesis. In the present study, we report the first characterization of PIWIL1 in the male domestic cat, a mammalian system predicted to express four PIWI family members. Multiple transcript variants of PIWIL1 were cloned from feline testes cDNA. One isoform shows high homology to PIWIL1 from other mammals, however, the other has characteristics of a "slicer null" isoform, lacking the domain required for endonuclease activity. Expression of PIWIL1 in the male cat appears limited to the testis and correlates with sexual maturity. RNA-immunoprecipitation revealed that feline PIWIL1 binds small RNAs with an average size of 29 nt. Together, these data suggest that the domestic cat has two PIWIL1 isoforms expressed in the mature testis, at least one of which interacts with piRNAs.
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Affiliation(s)
- Leanne Stalker
- Department of Biomedical Sciences, Ontario Veterinary College, University of Guelph, Guelph, ON N1G 2W1, Canada
| | - Alanna G Backx
- Department of Biomedical Sciences, Ontario Veterinary College, University of Guelph, Guelph, ON N1G 2W1, Canada
| | - Allison K Tscherner
- Department of Biomedical Sciences, Ontario Veterinary College, University of Guelph, Guelph, ON N1G 2W1, Canada
| | - Stewart J Russell
- Department of Biomedical Sciences, Ontario Veterinary College, University of Guelph, Guelph, ON N1G 2W1, Canada
| | - Robert A Foster
- Department of Pathobiology, Ontario Veterinary College, University of Guelph, Guelph, ON N1G 2W12, Canada
| | - Jonathan LaMarre
- Department of Biomedical Sciences, Ontario Veterinary College, University of Guelph, Guelph, ON N1G 2W1, Canada
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3
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Nasseri S, Sharifi M, Mehrzad V. Effects of hsa-piR-32877 Suppression with Antisense LNA GapmeRs on the Proliferation and Apoptosis of Human Acute Myeloid Leukemia Cells. INTERNATIONAL JOURNAL OF MOLECULAR AND CELLULAR MEDICINE 2023; 12:18-29. [PMID: 37942262 PMCID: PMC10629728 DOI: 10.22088/ijmcm.bums.12.1.18] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/18/2023] [Revised: 09/15/2023] [Accepted: 09/17/2023] [Indexed: 11/10/2023]
Abstract
Acute myeloid leukemia (AML) is an invasive form of hematologic malignancies which results in the overproduction of myeloid cells in the bone marrow. Aberrant expression of piwi-interacting RNAs (piRNAs) which belong to small non-coding RNAs, play important roles in different cancer cells' progress. hsa- piR- 32877 is up-regulated in AML. Down regulation of hsa-piR-32877 by antisense LNA GapmeRs could be potential for suppression of myeloid cell proliferation and induce myeloid cell apoptosis. We have blocked the expression of hsa-piR-32877 by antisense LNA GapmeRs in human bone marrow blast cells, and the M-07e cell line. Samples were transfected with antisense LNA GapmeRs at 24, 48, and 72 hours. The Quantitative reverse transcriptase polymerase chain reaction (qRT-PCR) was performed to investigate the expression of hsa-piR-32877, CASP3, and CASP9. Both CASP3 and CASP9 play important roles in apoptosis. Cell proliferation was studied via CFSE (carboxyfluorescein diacetate succinimidyl ester) assay. Results showed that hsa-piR-32877 was down-regulated by antisense LNA GapmeRs in the patient and cell line samples. Also, after transfection, cell proliferation and apoptosis decreased and increased, respectively. Our data suggested that hsa-piR-32877 suppression may act as a novel therapeutic method for the inhibition of human leukemic cells proliferation in AML.
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Affiliation(s)
- Sepideh Nasseri
- Department of Genetics and Molecular Biology, School of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran.
| | - Mohammadreza Sharifi
- Department of Genetics and Molecular Biology, School of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran.
| | - Valiollah Mehrzad
- Department of Internal Medicine, Division of Hematology, School of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran.
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4
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Di R, Zhang R, Mwacharo JM, Wang X, He X, Liu Y, Zhang J, Gong Y, Zhang X, Chu M. Characteristics of piRNAs and their comparative profiling in testes of sheep with different fertility. Front Genet 2022; 13:1078049. [PMID: 36568364 PMCID: PMC9768229 DOI: 10.3389/fgene.2022.1078049] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Accepted: 11/23/2022] [Indexed: 12/12/2022] Open
Abstract
As a novel class of small RNAs, piRNAs are highly expressed in the animal gonads and their main known role is to inhibit transposon activity for ensuring the correctness and integrity of genome. In order to explore the characteristics of piRNAs in sheep testis and their possible regulatory roles on male reproduction, deep sequencing technology was used to sequence small RNAs and identify piRNAs in testes of sheep. The length of piRNAs in sheep testes showed a unimodal distribution between 26 and 31 nt, with a peak at 29 nt. These piRNAs exhibited obvious ping-pong signature and strand specificity. In the genome, they were mainly aligned to CDS, intron, repetitive sequence regions and unannotated regions. Furthermore, in transposon analysis, piRNAs were aligned predominantly to LINE, SINE, and LTR types of retrotransposon in sheep testes, and the piRNAs derived from each type showed obvious ping-pong signature. The piRNA clusters identified in sheep testes were mainly distributed on chromosomes 3, 7, 15, 17, 18 and 20. The results combining semen determination with pathway enrichment analysis implied that differentially expressed piRNAs between the testes of rams with different fertility might participate in spermatogenesis by regulating multiple pathways closely related to stabilization of blood-testis barrier and renewal and differentiation of spermatogonial stem cell. Taken together, the study provided new insights into the characteristics, origin and expression patterns of piRNAs in sheep testes tissue, which would help us better understand the role of piRNAs in sheep reproduction.
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Affiliation(s)
- Ran Di
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Ministry of Agriculture and Rural Affairs, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Rensen Zhang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Ministry of Agriculture and Rural Affairs, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China,School of Advanced Agricultural Sciences, Yiyang Vocational & Technical College, Yiyang, China
| | - Joram Mwashigadi Mwacharo
- Small Ruminant Genomics International Center for Agricultural Research in the Dry Areas (ICARDA), Addis Ababa, Ethiopia,Institute of Animal and Veterinary Sciences, SRUC and Center for Tropical Livestock Genetics and Health (CTLGH), Midlothian, United Kingdom
| | - Xiangyu Wang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Ministry of Agriculture and Rural Affairs, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Xiaoyun He
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Ministry of Agriculture and Rural Affairs, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yufang Liu
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Ministry of Agriculture and Rural Affairs, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Jinlong Zhang
- Institute of Animal Husbandry and Veterinary Medicine, Tianjin Academy of Agricultural Sciences, Tianjin, China
| | - Yiming Gong
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Ministry of Agriculture and Rural Affairs, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Xiaosheng Zhang
- Institute of Animal Husbandry and Veterinary Medicine, Tianjin Academy of Agricultural Sciences, Tianjin, China,*Correspondence: Xiaosheng Zhang, ; Mingxing Chu,
| | - Mingxing Chu
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Ministry of Agriculture and Rural Affairs, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China,*Correspondence: Xiaosheng Zhang, ; Mingxing Chu,
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Ma X, Niu X, Huang S, Li S, Ran X, Wang J, Dai X. The piRNAs present in the developing testes of Chinese indigenous Xiang pigs. Theriogenology 2022; 189:92-106. [PMID: 35738035 DOI: 10.1016/j.theriogenology.2022.05.028] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2021] [Revised: 04/21/2022] [Accepted: 05/28/2022] [Indexed: 10/18/2022]
Abstract
The piRNA pathway plays an essential role in defense against transposable elements in the germline tissues of animals and contributes to post-transcriptional regulation of genes. Xiang pigs present an earlier sexual maturation compared with most European pig breeds, but the role that the piRNA pathway plays in the development of Xiang pigs is currently not understood. In this study, we sequenced and analyzed piRNAs expressed in the testes of Xiang pigs at four different ages, and identified endogenous piRNAs which were highly abundant at each time point. The lengths of the identified piRNAs ranged from 24 to 34 nucleotides (nt), with the most abundant length being 29 nt. Additionally, there was a strong bias for uracil at the first position, a slight bias for adenine at position 10 and frequent 5'-10 nt complementary sequences, suggesting that ping-pong-mediated silencing is present in the Xiang pig germline. We observed that the piRNA composition changed from TE-associated piRNAs in two- and three-month-old testes to predominantly gene-derived and intergenic piRNAs in six- and twelve-month-old testes, with a gradual increase in the expression level of piRNAs over the course of testis development. And more than half of piRNA reads mapped to just a few of 473 predicted piRNA clusters. Additionally, we found that several genes were highly enriched by piRNA reads, including CYP19A1, PRMT8, SUZ12, WWOX, SGSM1 and MIF. The functions of these genes are primarily associated with steroidogenesis and histone modification. Changes in piRNA composition and widespread expression patterns during spermatid development indicate that these small ncRNAs may be responsible not only for transposon suppression but also for post-transcriptional regulation of several protein-coding genes essential for normal spermatogenesis.
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Affiliation(s)
- Xinrui Ma
- College of Animal Science/Institute of Agro-Bioengineering/College of Life Science, Key Laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region and Key Laboratory of Animal Genetics, Breeding and Reproduction in the Plateau Mountainous Region (Ministry of Education), Guizhou University, Guiyang, 550025, China.
| | - Xi Niu
- College of Animal Science/Institute of Agro-Bioengineering/College of Life Science, Key Laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region and Key Laboratory of Animal Genetics, Breeding and Reproduction in the Plateau Mountainous Region (Ministry of Education), Guizhou University, Guiyang, 550025, China.
| | - Shihui Huang
- College of Animal Science/Institute of Agro-Bioengineering/College of Life Science, Key Laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region and Key Laboratory of Animal Genetics, Breeding and Reproduction in the Plateau Mountainous Region (Ministry of Education), Guizhou University, Guiyang, 550025, China.
| | - Sheng Li
- College of Animal Science/Institute of Agro-Bioengineering/College of Life Science, Key Laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region and Key Laboratory of Animal Genetics, Breeding and Reproduction in the Plateau Mountainous Region (Ministry of Education), Guizhou University, Guiyang, 550025, China.
| | - Xueqin Ran
- College of Animal Science/Institute of Agro-Bioengineering/College of Life Science, Key Laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region and Key Laboratory of Animal Genetics, Breeding and Reproduction in the Plateau Mountainous Region (Ministry of Education), Guizhou University, Guiyang, 550025, China.
| | - Jiafu Wang
- College of Animal Science/Institute of Agro-Bioengineering/College of Life Science, Key Laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region and Key Laboratory of Animal Genetics, Breeding and Reproduction in the Plateau Mountainous Region (Ministry of Education), Guizhou University, Guiyang, 550025, China.
| | - Xinlan Dai
- College of Animal Science/Institute of Agro-Bioengineering/College of Life Science, Key Laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region and Key Laboratory of Animal Genetics, Breeding and Reproduction in the Plateau Mountainous Region (Ministry of Education), Guizhou University, Guiyang, 550025, China.
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6
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Lima JRS, Azevedo-Pinheiro J, Andrade RB, Khayat AS, de Assumpção PP, Ribeiro-dos-Santos Â, Batista dos Santos SE, Moreira FC. Identification and Characterization of Polymorphisms in piRNA Regions. Curr Issues Mol Biol 2022; 44:942-951. [PMID: 35723347 PMCID: PMC8929088 DOI: 10.3390/cimb44020062] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Revised: 01/06/2022] [Accepted: 01/20/2022] [Indexed: 12/19/2022] Open
Abstract
piRNAs are a class of noncoding RNAs that perform functions in epigenetic regulation and silencing of transposable elements, a mechanism conserved among most mammals. At present, there are more than 30,000 known piRNAs in humans, of which more than 80% are derived from intergenic regions, and approximately 20% are derived from the introns and exons of pre-mRNAs. It was observed that the expression of the piRNA profile is specific in several organs, suggesting that they play functional roles in different tissues. In addition, some studies suggest that changes in regions that encode piRNAs may have an impact on their function. To evaluate the conservation of these regions and explore the existence of a seed region, SNP and INDEL variant rates were investigated in several genomic regions and compared to piRNA region variant rates. Thus, data analysis, data collection, cleaning, treatment, and exploration were implemented using the R programming language with the help of the RStudio platform. We found that piRNA regions are highly conserved after considering INDELs and do not seem to present an identifiable seed region after considering SNPs and INDEL variants. These findings may contribute to future studies attempting to determine how polymorphisms in piRNA regions can impact diseases.
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Affiliation(s)
- José Roberto Sobrinho Lima
- Núcleo de Pesquisas em Oncologia (NPO), Programa de Pós-Graduação em Oncologia e Ciências Médicas, Universidade Federal do Pará, Belém 66073-005, PA, Brazil; (J.R.S.L.); (R.B.A.); (A.S.K.); (P.P.d.A.); (Â.R.-d.-S.); (S.E.B.d.S.)
| | - Jhully Azevedo-Pinheiro
- Laboratório de Genética Humana e Médica (LGHM), Programa de Pós-Graduação em Genética e Biologia Molecular, Universidade Federal do Pará, Belém 66075-110, PA, Brazil;
| | - Roberta Borges Andrade
- Núcleo de Pesquisas em Oncologia (NPO), Programa de Pós-Graduação em Oncologia e Ciências Médicas, Universidade Federal do Pará, Belém 66073-005, PA, Brazil; (J.R.S.L.); (R.B.A.); (A.S.K.); (P.P.d.A.); (Â.R.-d.-S.); (S.E.B.d.S.)
- Laboratório de Genética Humana e Médica (LGHM), Programa de Pós-Graduação em Genética e Biologia Molecular, Universidade Federal do Pará, Belém 66075-110, PA, Brazil;
| | - André Salim Khayat
- Núcleo de Pesquisas em Oncologia (NPO), Programa de Pós-Graduação em Oncologia e Ciências Médicas, Universidade Federal do Pará, Belém 66073-005, PA, Brazil; (J.R.S.L.); (R.B.A.); (A.S.K.); (P.P.d.A.); (Â.R.-d.-S.); (S.E.B.d.S.)
| | - Paulo Pimentel de Assumpção
- Núcleo de Pesquisas em Oncologia (NPO), Programa de Pós-Graduação em Oncologia e Ciências Médicas, Universidade Federal do Pará, Belém 66073-005, PA, Brazil; (J.R.S.L.); (R.B.A.); (A.S.K.); (P.P.d.A.); (Â.R.-d.-S.); (S.E.B.d.S.)
| | - Ândrea Ribeiro-dos-Santos
- Núcleo de Pesquisas em Oncologia (NPO), Programa de Pós-Graduação em Oncologia e Ciências Médicas, Universidade Federal do Pará, Belém 66073-005, PA, Brazil; (J.R.S.L.); (R.B.A.); (A.S.K.); (P.P.d.A.); (Â.R.-d.-S.); (S.E.B.d.S.)
- Laboratório de Genética Humana e Médica (LGHM), Programa de Pós-Graduação em Genética e Biologia Molecular, Universidade Federal do Pará, Belém 66075-110, PA, Brazil;
| | - Sidney Emanuel Batista dos Santos
- Núcleo de Pesquisas em Oncologia (NPO), Programa de Pós-Graduação em Oncologia e Ciências Médicas, Universidade Federal do Pará, Belém 66073-005, PA, Brazil; (J.R.S.L.); (R.B.A.); (A.S.K.); (P.P.d.A.); (Â.R.-d.-S.); (S.E.B.d.S.)
- Laboratório de Genética Humana e Médica (LGHM), Programa de Pós-Graduação em Genética e Biologia Molecular, Universidade Federal do Pará, Belém 66075-110, PA, Brazil;
| | - Fabiano Cordeiro Moreira
- Núcleo de Pesquisas em Oncologia (NPO), Programa de Pós-Graduação em Oncologia e Ciências Médicas, Universidade Federal do Pará, Belém 66073-005, PA, Brazil; (J.R.S.L.); (R.B.A.); (A.S.K.); (P.P.d.A.); (Â.R.-d.-S.); (S.E.B.d.S.)
- Correspondence: ; Tel.: +55-091-98107-0858
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Huang S, Yoshitake K, Asakawa S. A Review of Discovery Profiling of PIWI-Interacting RNAs and Their Diverse Functions in Metazoans. Int J Mol Sci 2021; 22:ijms222011166. [PMID: 34681826 PMCID: PMC8538981 DOI: 10.3390/ijms222011166] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Revised: 10/11/2021] [Accepted: 10/14/2021] [Indexed: 12/16/2022] Open
Abstract
PIWI-interacting RNAs (piRNAs) are a class of small non-coding RNAs (sncRNAs) that perform crucial biological functions in metazoans and defend against transposable elements (TEs) in germ lines. Recently, ubiquitously expressed piRNAs were discovered in soma and germ lines using small RNA sequencing (sRNA-seq) in humans and animals, providing new insights into the diverse functions of piRNAs. However, the role of piRNAs has not yet been fully elucidated, and sRNA-seq studies continue to reveal different piRNA activities in the genome. In this review, we summarize a set of simplified processes for piRNA analysis in order to provide a useful guide for researchers to perform piRNA research suitable for their study objectives. These processes can help expand the functional research on piRNAs from previously reported sRNA-seq results in metazoans. Ubiquitously expressed piRNAs have been discovered in the soma and germ lines in Annelida, Cnidaria, Echinodermata, Crustacea, Arthropoda, and Mollusca, but they are limited to germ lines in Chordata. The roles of piRNAs in TE silencing, gene expression regulation, epigenetic regulation, embryonic development, immune response, and associated diseases will continue to be discovered via sRNA-seq.
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Affiliation(s)
- Songqian Huang
- Correspondence: (S.H.); (S.A.); Tel.: +81-3-5841-5296 (S.A.); Fax: +81-3-5841-8166 (S.A.)
| | | | - Shuichi Asakawa
- Correspondence: (S.H.); (S.A.); Tel.: +81-3-5841-5296 (S.A.); Fax: +81-3-5841-8166 (S.A.)
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Rosenkranz D, Zischler H, Gebert D. piRNAclusterDB 2.0: update and expansion of the piRNA cluster database. Nucleic Acids Res 2021; 50:D259-D264. [PMID: 34302483 PMCID: PMC8728273 DOI: 10.1093/nar/gkab622] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2021] [Revised: 06/30/2021] [Accepted: 07/07/2021] [Indexed: 01/14/2023] Open
Abstract
PIWI-interacting RNAs (piRNAs) and their partnering PIWI proteins defend the animal germline against transposable elements and play a crucial role in fertility. Numerous studies in the past have uncovered many additional functions of the piRNA pathway, including gene regulation, anti-viral defense, and somatic transposon repression. Further, comparative analyses across phylogenetic groups showed that the PIWI/piRNA system evolves rapidly and exhibits great evolutionary plasticity. However, the presence of so-called piRNA clusters as the major source of piRNAs is common to nearly all metazoan species. These genomic piRNA-producing loci are highly divergent across taxa and critically influence piRNA populations in different evolutionary lineages. We launched the initial version of the piRNA cluster database to facilitate research on regulation and evolution of piRNA-producing loci across tissues und species. In recent years the amount of small RNA sequencing data that was generated and the abundance of species that were studied has grown rapidly. To keep up with this recent progress, we have released a major update for the piRNA cluster database (https://www.smallrnagroup.uni-mainz.de/piRNAclusterDB), expanding it from 12 to a total of 51 species with hundreds of new datasets, and revised its overall structure to enable easy navigation through this large amount of data.
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Affiliation(s)
- David Rosenkranz
- Institute of Organismic and Molecular Evolution, Anthropology, Johannes Gutenberg University, Mainz 55099, Germany.,Senckenberg Centre for Human Genetics, Facharztzentrum Frankfurt-Nordend gGmbH, Frankfurt am Main 60314, Germany
| | - Hans Zischler
- Institute of Organismic and Molecular Evolution, Anthropology, Johannes Gutenberg University, Mainz 55099, Germany
| | - Daniel Gebert
- Institute of Organismic and Molecular Evolution, Anthropology, Johannes Gutenberg University, Mainz 55099, Germany.,Department of Genetics, University of Cambridge, Downing Street, Cambridge CB2 3EH, UK
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9
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Wang C, Lin H. Roles of piRNAs in transposon and pseudogene regulation of germline mRNAs and lncRNAs. Genome Biol 2021; 22:27. [PMID: 33419460 PMCID: PMC7792047 DOI: 10.1186/s13059-020-02221-x] [Citation(s) in RCA: 48] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2020] [Accepted: 12/07/2020] [Indexed: 12/28/2022] Open
Abstract
PIWI proteins, a subfamily of PAZ/PIWI Domain family RNA-binding proteins, are best known for their function in silencing transposons and germline development by partnering with small noncoding RNAs called PIWI-interacting RNAs (piRNAs). However, recent studies have revealed multifaceted roles of the PIWI-piRNA pathway in regulating the expression of other major classes of RNAs in germ cells. In this review, we summarize how PIWI proteins and piRNAs regulate the expression of many disparate RNAs, describing a highly complex global genomic regulatory relationship at the RNA level through which piRNAs functionally connect all major constituents of the genome in the germline.
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Affiliation(s)
- Chen Wang
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, Shanghai, 201210, China
| | - Haifan Lin
- Yale Stem Cell Center and Department of Cell Biology, Yale University School of Medicine, New Haven, CT, 06519, USA.
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10
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Yu T, Fan K, Özata DM, Zhang G, Fu Y, Theurkauf WE, Zamore PD, Weng Z. Long first exons and epigenetic marks distinguish conserved pachytene piRNA clusters from other mammalian genes. Nat Commun 2021; 12:73. [PMID: 33397987 PMCID: PMC7782496 DOI: 10.1038/s41467-020-20345-3] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2020] [Accepted: 11/17/2020] [Indexed: 02/06/2023] Open
Abstract
In the male germ cells of placental mammals, 26-30-nt-long PIWI-interacting RNAs (piRNAs) emerge when spermatocytes enter the pachytene phase of meiosis. In mice, pachytene piRNAs derive from ~100 discrete autosomal loci that produce canonical RNA polymerase II transcripts. These piRNA clusters bear 5' caps and 3' poly(A) tails, and often contain introns that are removed before nuclear export and processing into piRNAs. What marks pachytene piRNA clusters to produce piRNAs, and what confines their expression to the germline? We report that an unusually long first exon (≥ 10 kb) or a long, unspliced transcript correlates with germline-specific transcription and piRNA production. Our integrative analysis of transcriptome, piRNA, and epigenome datasets across multiple species reveals that a long first exon is an evolutionarily conserved feature of pachytene piRNA clusters. Furthermore, a highly methylated promoter, often containing a low or intermediate level of CG dinucleotides, correlates with germline expression and somatic silencing of pachytene piRNA clusters. Pachytene piRNA precursor transcripts bind THOC1 and THOC2, THO complex subunits known to promote transcriptional elongation and mRNA nuclear export. Together, these features may explain why the major sources of pachytene piRNA clusters specifically generate these unique small RNAs in the male germline of placental mammals.
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Affiliation(s)
- Tianxiong Yu
- Department of Thoracic Surgery, Clinical Translational Research Center, Shanghai Pulmonary Hospital, The School of Life Sciences and Technology, Tongji University, 200092, Shanghai, China
- Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, MA, 01605, USA
| | - Kaili Fan
- Department of Thoracic Surgery, Clinical Translational Research Center, Shanghai Pulmonary Hospital, The School of Life Sciences and Technology, Tongji University, 200092, Shanghai, China
- Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, MA, 01605, USA
| | - Deniz M Özata
- RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, MA, 01605, USA
| | - Gen Zhang
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA, 01605, USA
| | - Yu Fu
- Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, MA, 01605, USA
- Bioinformatics Program, Boston University, 44 Cummington Mall, Boston, MA, 02215, USA
- Oncology Drug Discovery Unit, Takeda Pharmaceuticals, Cambridge, MA, 02139, USA
| | - William E Theurkauf
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA, 01605, USA.
| | - Phillip D Zamore
- RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, MA, 01605, USA.
| | - Zhiping Weng
- Department of Thoracic Surgery, Clinical Translational Research Center, Shanghai Pulmonary Hospital, The School of Life Sciences and Technology, Tongji University, 200092, Shanghai, China.
- Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, MA, 01605, USA.
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11
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Ablondi M, Gòdia M, Rodriguez-Gil JE, Sánchez A, Clop A. Characterisation of sperm piRNAs and their correlation with semen quality traits in swine. Anim Genet 2020; 52:114-120. [PMID: 33226164 DOI: 10.1111/age.13022] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/13/2020] [Indexed: 12/17/2022]
Abstract
Piwi-interacting RNAs (piRNAs) are a class of non-coding RNAs that are essential in the transcriptional silencing of transposable elements and warrant genome stability in the mammalian germline. In this study, we have identified piRNAs in porcine sperm using male germline and zygote datasets from human, mice, cow and pig, and evaluated the relation between their abundances and sperm quality traits. In our analysis, we identified 283 382 piRNAs, 1355 of which correlated with P ≤ 0.01 to at least one semen quality trait. Fifty-seven percent of the correlated piRNAs mapped less than 50 kb apart from any other piRNA in the pig genome. Furthermore, piRNA location was significantly enriched near long interspersed nuclear elements. Moreover, some of the significant piRNAs mapped within or close to genes relevant for fertility or spermatogenesis such as CSNK1G2 and PSMF1.
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Affiliation(s)
- M Ablondi
- Department of Veterinary Science, University of Parma, Parma, 43126, Italy
| | - M Gòdia
- Centre for Research in Agricultural Genomics,, CSIC-IRTA-UAB-UB, Campus UAB, Cerdanyola del Vallès, Catalonia, 08193, Spain
| | - J E Rodriguez-Gil
- Department of Animal Medicine and Surgery, School of Veterinary Sciences, Universitat Autonoma de Barcelona, Cerdanyola del Vallès, Catalonia, 08193, Spain
| | - A Sánchez
- Centre for Research in Agricultural Genomics,, CSIC-IRTA-UAB-UB, Campus UAB, Cerdanyola del Vallès, Catalonia, 08193, Spain.,Departament de Ciència Animal i dels Aliments, School of Veterinary Sciences, Universitat Autonoma de Barcelona, Cerdanyola del Vallès, Catalonia, 08193, Spain
| | - A Clop
- Centre for Research in Agricultural Genomics,, CSIC-IRTA-UAB-UB, Campus UAB, Cerdanyola del Vallès, Catalonia, 08193, Spain.,Consejo Superior de Investigaciones Científicas, Barcelona, Catalonia, 08003, Spain
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12
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Lin Y, Zheng J, Lin D. PIWI-interacting RNAs in human cancer. Semin Cancer Biol 2020; 75:15-28. [PMID: 32877760 DOI: 10.1016/j.semcancer.2020.08.012] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2020] [Revised: 08/16/2020] [Accepted: 08/23/2020] [Indexed: 12/11/2022]
Abstract
P-element-induced wimpy testis (PIWI) interacting RNAs (piRNAs) are a class of small regulatory RNAs mechanistically similar to but much less studied than microRNAs and small interfering RNAs. Today the best understood function of piRNAs is transposon control in animal germ cells, which has earned them the name 'guardians of the germline'. Several molecular/cellular characteristics of piRNAs, including high sequence diversity, lack of secondary structures, and target-oriented generation seem to serve this purpose. Recently, aberrant expressions of piRNAs and PIWI proteins have been implicated in a variety of malignant tumors and associated with cancer hallmarks such as cell proliferation, inhibited apoptosis, invasion, metastasis and increased stemness. Researchers have also demonstrated multiple mechanisms of piRNA-mediated target deregulation associated with cancer initiation, progression or dissemination. We review current research findings on the biogenesis, normal functions and cancer associations of piRNAs, highlighting their potentials as cancer diagnostic/prognostic biomarkers and therapeutic tools. Whenever applicable, we draw connections with other research fields to encourage intercommunity conversations. We also offer recommendations and cautions regarding the general process of cancer-related piRNA studies and the methods/tools used at each step. Finally, we call attention to some issues that, if left unsolved, might impede the future development of this field.
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Affiliation(s)
- Yuan Lin
- Beijing Advanced Innovation Center for Genomics (ICG), Biomedical Pioneering Innovation Center (BIOPIC), Peking University, Beijing, 100871, China.
| | - Jian Zheng
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China and Collaborative Innovation Center for Cancer Medicine, Guangzhou, 510060, China
| | - Dongxin Lin
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China and Collaborative Innovation Center for Cancer Medicine, Guangzhou, 510060, China; Department of Etiology and Carcinogenesis, National Cancer Center/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China
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13
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Jehn J, Treml J, Wulsch S, Ottum B, Erb V, Hewel C, Kooijmans RN, Wester L, Fast I, Rosenkranz D. 5' tRNA halves are highly expressed in the primate hippocampus and might sequence-specifically regulate gene expression. RNA (NEW YORK, N.Y.) 2020; 26:694-707. [PMID: 32144192 PMCID: PMC7266158 DOI: 10.1261/rna.073395.119] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/19/2019] [Accepted: 03/02/2020] [Indexed: 06/10/2023]
Abstract
Fragments of mature tRNAs have long been considered as mere degradation products without physiological function. However, recent reports show that tRNA-derived small RNAs (tsRNAs) play prominent roles in diverse cellular processes across a wide spectrum of species. Contrasting the situation in other small RNA pathways the mechanisms behind these effects appear more diverse, more complex, and are generally less well understood. In addition, surprisingly little is known about the expression profiles of tsRNAs across different tissues and species. Here, we provide an initial overview of tsRNA expression in different species and tissues, revealing very high levels of 5' tRNA halves (5' tRHs) particularly in the primate hippocampus. We further modulated the regulation capacity of selected 5' tRHs in human cells by transfecting synthetic tsRNA mimics ("overexpression") or antisense-RNAs ("inhibition") and identified differentially expressed transcripts based on RNA-seq. We then used a novel k-mer mapping approach to dissect the underlying targeting rules, suggesting that 5' tRHs silence genes in a sequence-specific manner, while the most efficient target sites align to the mid-region of the 5' tRH and are located within the CDS or 3' UTR of the target. This amends previous observations that tsRNAs guide Argonaute proteins to silence their targets via a miRNA-like 5' seed match and suggests a yet unknown mechanism of regulation. Finally, our data suggest that some 5' tRHs that are also able to sequence-specifically stabilize mRNAs as up-regulated mRNAs are also significantly enriched for 5' tRH target sites.
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Affiliation(s)
- Julia Jehn
- Institute of Organismic and Molecular Evolution iOME, Anthropology, Johannes Gutenberg University Mainz, 55099 Mainz, Germany
| | - Jana Treml
- Institute of Organismic and Molecular Evolution iOME, Anthropology, Johannes Gutenberg University Mainz, 55099 Mainz, Germany
| | - Svenja Wulsch
- Institute of Organismic and Molecular Evolution iOME, Anthropology, Johannes Gutenberg University Mainz, 55099 Mainz, Germany
| | - Benjamin Ottum
- Institute of Organismic and Molecular Evolution iOME, Anthropology, Johannes Gutenberg University Mainz, 55099 Mainz, Germany
| | - Verena Erb
- Institute of Organismic and Molecular Evolution iOME, Anthropology, Johannes Gutenberg University Mainz, 55099 Mainz, Germany
| | - Charlotte Hewel
- Institute of Organismic and Molecular Evolution iOME, Anthropology, Johannes Gutenberg University Mainz, 55099 Mainz, Germany
| | - Roxana N Kooijmans
- Primate Brain Bank, Netherlands Institute for Neuroscience, 1105 BA Amsterdam, The Netherlands
| | - Laura Wester
- Institute of Organismic and Molecular Evolution iOME, Anthropology, Johannes Gutenberg University Mainz, 55099 Mainz, Germany
| | - Isabel Fast
- Institute of Organismic and Molecular Evolution iOME, Anthropology, Johannes Gutenberg University Mainz, 55099 Mainz, Germany
| | - David Rosenkranz
- Institute of Organismic and Molecular Evolution iOME, Anthropology, Johannes Gutenberg University Mainz, 55099 Mainz, Germany
- Senckenberg Centre for Human Genetics, 60314 Frankfurt am Main, Germany
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14
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Gebert D, Zischler H, Rosenkranz D. Primate piRNA Cluster Evolution Suggests Limited Relevance of Pseudogenes in piRNA-Mediated Gene Regulation. Genome Biol Evol 2019; 11:1088-1104. [PMID: 30888404 PMCID: PMC6461890 DOI: 10.1093/gbe/evz060] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/16/2019] [Indexed: 12/11/2022] Open
Abstract
PIWI proteins and their guiding Piwi-interacting (pi-) RNAs direct the silencing of target nucleic acids in the animal germline and soma. Although in mammal testes fetal piRNAs are involved in extensive silencing of transposons, pachytene piRNAs have additionally been shown to act in post-transcriptional gene regulation. The bulk of pachytene piRNAs is produced from large genomic loci, named piRNA clusters. Recently, the presence of reversed pseudogenes within piRNA clusters prompted the idea that piRNAs derived from such sequences might direct regulation of their parent genes. Here, we examine primate piRNA clusters and integrated pseudogenes in a comparative approach to gain a deeper understanding about mammalian piRNA cluster evolution and the presumed gene-regulatory role of pseudogene-derived piRNAs. Initially, we provide a broad analysis of the evolutionary relationships of piRNA clusters and their differential activity among six primate species. Subsequently, we show that pseudogenes in reserve orientation relative to piRNA cluster transcription direction generally do not exhibit signs of selection pressure and cause weakly conserved targeting of homologous genes among species, suggesting a lack of functional constraints and thus only a minor significance for gene regulation in most cases. Finally, we report that piRNA-producing loci generally tend to be located in active genomic regions with elevated gene and pseudogene density. Thus, we conclude that the presence of most pseudogenes in piRNA clusters might be regarded as a byproduct of piRNA cluster generation, whereas this does not exclude that some pseudogenes nevertheless play critical roles in individual cases.
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Affiliation(s)
- Daniel Gebert
- Institute of Organismic and Molecular Evolution, Anthropology, Johannes Gutenberg University, Mainz, Germany
| | - Hans Zischler
- Institute of Organismic and Molecular Evolution, Anthropology, Johannes Gutenberg University, Mainz, Germany
| | - David Rosenkranz
- Institute of Organismic and Molecular Evolution, Anthropology, Johannes Gutenberg University, Mainz, Germany
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15
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Spermatozoal mRNAs expression implicated in embryonic development were influenced by dietary folate supplementation of breeder roosters by altering spermatozoal piRNA expression profiles. Theriogenology 2019; 138:102-110. [PMID: 31325740 DOI: 10.1016/j.theriogenology.2019.07.009] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2019] [Revised: 06/20/2019] [Accepted: 07/08/2019] [Indexed: 11/20/2022]
Abstract
Dietary folate intake, together with changes in its metabolism process, have effects on male reproduction, sperm epigenetic patterning and offspring outcome. Previous studies have proven that PIWI-interacting RNAs (piRNAs) play important roles in successful spermatogenesis and regulating genes expression of sperm and offspring embryo. Herein, we fed breeder roosters with five different levels (0, 0.25, 1.25, 2.50, and 5.00 mg/kg) of folate throughout life and found that paternal folate supplementation was beneficial to the growth and organ development of offspring broilers. Further spermatozoal mRNAs sequencing analyses implied that the dietary folate supplementation could regulate the spermatozoal mRNA abundance of genes related to the fetal development. Furthermore, global piRNAs analyses of breeder roosters' sperm revealed that differential concentration of dietary folate supplementation could change piRNAs profiles. Combined mRNAs sequencing and target gene prediction of differentially expressed gene-derived piRNAs, embryonic development and metabolism related pathways and biological processes, which were consisted to the regulatory roles of paternal folate supplementations, were significantly affected by the differentially expressed gene-derived piRNAs based on the GO and KEGG analyses. Overall, our results provided a novel insight into the role of piRNAs in response to folate intake, which will broaden the understanding about the relationship between folate and sperm epigenetic patterning of breeder roosters.
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16
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Identification of piRNAs and piRNA clusters in the testes of the Mongolian horse. Sci Rep 2019; 9:5022. [PMID: 30903011 PMCID: PMC6430771 DOI: 10.1038/s41598-019-41475-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2018] [Accepted: 03/11/2019] [Indexed: 11/10/2022] Open
Abstract
P-element induced wimpy testis-interacting RNAs (piRNAs) are essential for testicular development and spermatogenesis in mammals. Comparative analyses of the molecular mechanisms of spermatogenesis among different organisms are therefore dependent on accurate characterizations of piRNAs. At present, little is known of piRNAs in non-model organisms. Here, we characterize piRNAs in the Mongolian horse, a hardy breed that reproduces under extreme circumstances. A thorough understanding of spermatogenesis and reproduction in this breed may provide insights for the improvement of fecundity and reproductive success in other breeds. We identified 4,936,717 piRNAs and 7,890 piRNA clusters across both testicular developmental stages. Of these, 2,236,377 putative piRNAs were expressed in the mature samples only, and 2,391,271 putative piRNAs were expressed in the immature samples only. Approximately 3,016 piRNA clusters were upregulated in the mature testes as compared to the immature testes, and 4,874 piRNA clusters were downregulated. Functional and pathway analyses indicated that the candidate generating genes of the predicted piRNAs were likely involved in testicular development and spermatogenesis. Our results thus provide information about differential expression patterns in genes associated with testicular development and spermatogenesis in a non-model animal.
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17
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Liu Y, Sun Y, Li Y, Bai H, Xu S, Xu H, Ni A, Yang N, Chen J. Identification and differential expression of microRNAs in the testis of chicken with high and low sperm motility. Theriogenology 2018; 122:94-101. [DOI: 10.1016/j.theriogenology.2018.09.010] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2018] [Revised: 09/11/2018] [Accepted: 09/11/2018] [Indexed: 12/19/2022]
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18
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Rojas-Ríos P, Simonelig M. piRNAs and PIWI proteins: regulators of gene expression in development and stem cells. Development 2018; 145:145/17/dev161786. [PMID: 30194260 DOI: 10.1242/dev.161786] [Citation(s) in RCA: 93] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
PIWI proteins and Piwi-interacting RNAs (piRNAs) have established and conserved roles in repressing transposable elements (TEs) in the germline of animals. However, in several biological contexts, a large proportion of piRNAs are not related to TE sequences and, accordingly, functions for piRNAs and PIWI proteins that are independent of TE regulation have been identified. This aspect of piRNA biology is expanding rapidly. Indeed, recent reports have revealed the role of piRNAs in the regulation of endogenous gene expression programs in germ cells, as well as in somatic tissues, challenging dogma in the piRNA field. In this Review, we focus on recent data addressing the biological and developmental functions of piRNAs, highlighting their roles in embryonic patterning, germ cell specification, stem cell biology, neuronal activity and metabolism.
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Affiliation(s)
- Patricia Rojas-Ríos
- mRNA Regulation and Development, IGH, Univ. Montpellier, CNRS, Montpellier 34396, France
| | - Martine Simonelig
- mRNA Regulation and Development, IGH, Univ. Montpellier, CNRS, Montpellier 34396, France
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19
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Jehn J, Gebert D, Pipilescu F, Stern S, Kiefer JST, Hewel C, Rosenkranz D. PIWI genes and piRNAs are ubiquitously expressed in mollusks and show patterns of lineage-specific adaptation. Commun Biol 2018; 1:137. [PMID: 30272016 PMCID: PMC6128900 DOI: 10.1038/s42003-018-0141-4] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2018] [Accepted: 08/17/2018] [Indexed: 12/14/2022] Open
Abstract
PIWI proteins and PIWI-interacting RNAs (piRNAs) suppress transposon activity in animals, thus protecting their genomes from detrimental insertion mutagenesis. Here, we reveal that PIWI genes and piRNAs are ubiquitously expressed in mollusks, similar to the situation in arthropods. We describe lineage-specific adaptations of transposon composition in piRNA clusters in the great pond snail and the pacific oyster, likely reflecting differential transposon activity in gastropods and bivalves. We further show that different piRNA clusters with unique transposon composition are dynamically expressed during oyster development. Finally, bioinformatics analyses suggest that different populations of piRNAs presumably bound to different PIWI paralogs participate in homotypic and heterotypic ping-pong amplification loops in a tissue- and sex-specific manner. Together with recent findings from other animal species, our results support the idea that somatic piRNA expression represents the ancestral state in metazoans.
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Affiliation(s)
- Julia Jehn
- Institute of Organismic and Molecular Evolution, Anthropology, Johannes Gutenberg University Mainz, Anselm-Franz-von-Bentzel-Weg 7, 55099, Mainz, Germany
| | - Daniel Gebert
- Institute of Organismic and Molecular Evolution, Anthropology, Johannes Gutenberg University Mainz, Anselm-Franz-von-Bentzel-Weg 7, 55099, Mainz, Germany
| | - Frank Pipilescu
- Institute of Organismic and Molecular Evolution, Anthropology, Johannes Gutenberg University Mainz, Anselm-Franz-von-Bentzel-Weg 7, 55099, Mainz, Germany
| | - Sarah Stern
- Institute of Organismic and Molecular Evolution, Anthropology, Johannes Gutenberg University Mainz, Anselm-Franz-von-Bentzel-Weg 7, 55099, Mainz, Germany
| | - Julian Simon Thilo Kiefer
- Institute of Organismic and Molecular Evolution, Anthropology, Johannes Gutenberg University Mainz, Anselm-Franz-von-Bentzel-Weg 7, 55099, Mainz, Germany
| | - Charlotte Hewel
- Institute of Organismic and Molecular Evolution, Anthropology, Johannes Gutenberg University Mainz, Anselm-Franz-von-Bentzel-Weg 7, 55099, Mainz, Germany
| | - David Rosenkranz
- Institute of Organismic and Molecular Evolution, Anthropology, Johannes Gutenberg University Mainz, Anselm-Franz-von-Bentzel-Weg 7, 55099, Mainz, Germany.
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20
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Russell SJ, Stalker L, LaMarre J. PIWIs, piRNAs and Retrotransposons: Complex battles during reprogramming in gametes and early embryos. Reprod Domest Anim 2018; 52 Suppl 4:28-38. [PMID: 29052331 DOI: 10.1111/rda.13053] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Gamete and embryo development are indispensable processes for successful reproduction. Cells involved in these processes acquire pluripotency, the ability to differentiate into multiple different cell types, through a series of events known as reprogramming that lead to profound changes in histone and DNA methylation. While essential for pluripotency, this epigenetic remodelling removes constraints that normally limit the expression of genomic sequences known as transposable elements (TEs). Unconstrained TE expression can lead to many deleterious consequences including infertility, so organisms have evolved complex and potent mechanistic arsenals to target and suppress TE expression during reprogramming. This review will focus on the control of transposable elements in gametes and embryos, and one important TE suppressing system known as the PIWI pathway. This broadly conserved, small RNA-targeted silencing mechanism appears critical for fertility in many species and may participate in multiple aspects of gene regulation in reproduction and other contexts.
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Affiliation(s)
- S J Russell
- Department of Biomedical Sciences, University of Guelph, Guelph, ON, Canada
| | - L Stalker
- Department of Biomedical Sciences, University of Guelph, Guelph, ON, Canada
| | - J LaMarre
- Department of Biomedical Sciences, University of Guelph, Guelph, ON, Canada
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21
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Llonga N, Ylla G, Bau J, Belles X, Piulachs MD. Diversity of piRNA expression patterns during the ontogeny of the German cockroach. JOURNAL OF EXPERIMENTAL ZOOLOGY PART B-MOLECULAR AND DEVELOPMENTAL EVOLUTION 2018; 330:288-295. [DOI: 10.1002/jez.b.22815] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/04/2018] [Revised: 05/15/2018] [Accepted: 06/20/2018] [Indexed: 11/08/2022]
Affiliation(s)
- Natalia Llonga
- Institute of Evolutionary Biology; CSIC-Universitat Pompeu Fabra; Barcelona Spain
| | - Guillem Ylla
- Institute of Evolutionary Biology; CSIC-Universitat Pompeu Fabra; Barcelona Spain
- Department of Microbiology and Cell Science; Institute for Food and Agricultural Sciences, Genetics Institute; University of Florida; Gainesville Florida
| | - Josep Bau
- Department of Biosciences; University of Vic - Central University of Catalonia; Vic, Barcelona Spain
| | - Xavier Belles
- Institute of Evolutionary Biology; CSIC-Universitat Pompeu Fabra; Barcelona Spain
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22
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Lecluze E, Jégou B, Rolland AD, Chalmel F. New transcriptomic tools to understand testis development and functions. Mol Cell Endocrinol 2018; 468:47-59. [PMID: 29501799 DOI: 10.1016/j.mce.2018.02.019] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/10/2017] [Revised: 02/26/2018] [Accepted: 02/27/2018] [Indexed: 12/16/2022]
Abstract
The testis plays a central role in the male reproductive system - secreting several hormones including male steroids and producing male gametes. A complex and coordinated molecular program is required for the proper differentiation of testicular cell types and maintenance of their functions in adulthood. The testicular transcriptome displays the highest levels of complexity and specificity across all tissues in a wide range of species. Many studies have used high-throughput sequencing technologies to define the molecular dynamics and regulatory networks in the testis as well as to identify novel genes or gene isoforms expressed in this organ. This review intends to highlight the complementarity of these transcriptomic studies and to show how the use of different sequencing protocols contribute to improve our global understanding of testicular biology.
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Affiliation(s)
- Estelle Lecluze
- Univ Rennes, Inserm, EHESP, Irset (Institut de recherche en santé, Environnement et travail) - UMR_S1085, F-35000 Rennes, France
| | - Bernard Jégou
- Univ Rennes, Inserm, EHESP, Irset (Institut de recherche en santé, Environnement et travail) - UMR_S1085, F-35000 Rennes, France
| | - Antoine D Rolland
- Univ Rennes, Inserm, EHESP, Irset (Institut de recherche en santé, Environnement et travail) - UMR_S1085, F-35000 Rennes, France
| | - Frédéric Chalmel
- Univ Rennes, Inserm, EHESP, Irset (Institut de recherche en santé, Environnement et travail) - UMR_S1085, F-35000 Rennes, France.
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23
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Wu S, Guo J, Zhu L, Yang J, Chen S, Yang X. Identification and characterisation of microRNAs and Piwi-interacting RNAs in cockerels' spermatozoa by Solexa sequencing. Br Poult Sci 2018; 59:371-380. [PMID: 29667432 DOI: 10.1080/00071668.2018.1464123] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
Abstract
1. There has been substantial research focused on the roles of microRNAs (miRNAs) and Piwi-interacting RNAs (piRNAs) derived from mammalian spermatozoa; however, comparatively little is known about the role of spermatozoa-derived miRNAs and piRNAs within breeding cockerels' spermatozoa. 2. A small RNA library of cockerels' spermatozoa was constructed using Illumina high-throughput sequencing technology. Unique sequences with lengths of 18-26 nucleotides were mapped to miRBase 21.0 and unique sequences with lengths of 25-37 nucleotides were mapped to a piRNA database. A total of 1311 miRNAs and 2448 potential piRNAs were identified. Based on stem-loop qRT-PCR, 8 miRNAs were validated. 3. Potential target genes of the abundant miRNAs were predicted, and further Kyoto Encyclopedia of Genes and Genomes database (KEGG) and Gene Ontology (GO) analyses were performed, which revealed that some candidate miRNAs were involved in the spermatogenesis process, spermatozoa epigenetic programming and further embryonic development. 5. GO and KEGG analyses based on mapping genes of expressed piRNAs were performed, which revealed that spermatozoal piRNAs could play important regulatory roles in embryonic development of offspring. 6. The search for endogenous spermatozoa miRNAs and piRNAs will contribute to a preliminary database for functional and molecular mechanistic studies in embryonic development and spermatozoa epigenetic programming.
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Affiliation(s)
- S Wu
- a College of Animal Science and Technology , Northwest A&F University , Yangling , Shaanxi , China
| | - J Guo
- a College of Animal Science and Technology , Northwest A&F University , Yangling , Shaanxi , China
| | - L Zhu
- a College of Animal Science and Technology , Northwest A&F University , Yangling , Shaanxi , China
| | - J Yang
- a College of Animal Science and Technology , Northwest A&F University , Yangling , Shaanxi , China
| | - S Chen
- a College of Animal Science and Technology , Northwest A&F University , Yangling , Shaanxi , China
| | - X Yang
- a College of Animal Science and Technology , Northwest A&F University , Yangling , Shaanxi , China
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Sage AP, Minatel BC, Ng KW, Stewart GL, Dummer TJB, Lam WL, Martinez VD. Oncogenomic disruptions in arsenic-induced carcinogenesis. Oncotarget 2018; 8:25736-25755. [PMID: 28179585 PMCID: PMC5421966 DOI: 10.18632/oncotarget.15106] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2016] [Accepted: 01/24/2017] [Indexed: 12/13/2022] Open
Abstract
Chronic exposure to arsenic affects more than 200 million people worldwide, and has been associated with many adverse health effects, including cancer in several organs. There is accumulating evidence that arsenic biotransformation, a step in the elimination of arsenic from the human body, can induce changes at a genetic and epigenetic level, leading to carcinogenesis. At the genetic level, arsenic interferes with key cellular processes such as DNA damage-repair and chromosomal structure, leading to genomic instability. At the epigenetic level, arsenic places a high demand on the cellular methyl pool, leading to global hypomethylation and hypermethylation of specific gene promoters. These arsenic-associated DNA alterations result in the deregulation of both oncogenic and tumour-suppressive genes. Furthermore, recent reports have implicated aberrant expression of non-coding RNAs and the consequential disruption of signaling pathways in the context of arsenic-induced carcinogenesis. This article provides an overview of the oncogenomic anomalies associated with arsenic exposure and conveys the importance of non-coding RNAs in the arsenic-induced carcinogenic process.
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Affiliation(s)
- Adam P Sage
- Department of Integrative Oncology, British Columbia Cancer Research Centre, Vancouver, British Columbia, Canada
| | - Brenda C Minatel
- Department of Integrative Oncology, British Columbia Cancer Research Centre, Vancouver, British Columbia, Canada
| | - Kevin W Ng
- Department of Integrative Oncology, British Columbia Cancer Research Centre, Vancouver, British Columbia, Canada
| | - Greg L Stewart
- Department of Integrative Oncology, British Columbia Cancer Research Centre, Vancouver, British Columbia, Canada
| | - Trevor J B Dummer
- Centre of Excellence in Cancer Prevention, School of Population and Public Health, University of British Columbia, Vancouver, British Columbia, Canada
| | - Wan L Lam
- Department of Integrative Oncology, British Columbia Cancer Research Centre, Vancouver, British Columbia, Canada
| | - Victor D Martinez
- Department of Integrative Oncology, British Columbia Cancer Research Centre, Vancouver, British Columbia, Canada
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Martinez VD, Firmino NS, Marshall EA, Ng KW, Wadsworth BJ, Anderson C, Lam WL, Bennewith KL. Non-coding RNAs predict recurrence-free survival of patients with hypoxic tumours. Sci Rep 2018; 8:152. [PMID: 29317756 PMCID: PMC5760628 DOI: 10.1038/s41598-017-18462-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2017] [Accepted: 12/12/2017] [Indexed: 12/21/2022] Open
Abstract
Hypoxia promotes tumour aggressiveness and reduces patient survival. A spectrum of poor outcome among patients with hypoxic tumours suggests that additional factors modulate how tumours respond to hypoxia. PIWI-interacting RNAs (piRNAs) are small non-coding RNAs with a pivotal role in genomic stability and epigenetic regulation of gene expression. We reported that cancer type-specific piRNA signatures vary among patients. However, remarkably homogenous piRNA profiles are detected across patients with renal cell carcinoma, a cancer characterized by constitutive upregulation of hypoxia-related signaling induced by common mutation or loss of von Hippel-Lindau factor (VHL). By investigating >3000 piRNA transcriptomes in hypoxic and non-hypoxic tumors from seven organs, we discovered 40 hypoxia-regulated piRNAs and validated this in cells cultured under hypoxia. Moreover, a subset of these hypoxia-regulated piRNAs are regulated by VHL/HIF signaling in vitro. A hypoxia-regulated piRNA-based score (PiSco) was associated with poor RFS for hypoxic tumours, particularly Stage I lung adenocarcinomas, suggesting that hypoxia-regulated piRNA expression can predict tumour recurrence even in early-stage tumours and thus may be of clinical utility.
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Affiliation(s)
- Victor D Martinez
- Department of Integrative Oncology, British Columbia Cancer Agency, Vancouver, B.C, V5Z 1L3, Canada.
| | - Natalie S Firmino
- Department of Integrative Oncology, British Columbia Cancer Agency, Vancouver, B.C, V5Z 1L3, Canada
| | - Erin A Marshall
- Department of Integrative Oncology, British Columbia Cancer Agency, Vancouver, B.C, V5Z 1L3, Canada
| | - Kevin W Ng
- Department of Integrative Oncology, British Columbia Cancer Agency, Vancouver, B.C, V5Z 1L3, Canada
| | - Brennan J Wadsworth
- Department of Integrative Oncology, British Columbia Cancer Agency, Vancouver, B.C, V5Z 1L3, Canada
| | - Christine Anderson
- Department of Integrative Oncology, British Columbia Cancer Agency, Vancouver, B.C, V5Z 1L3, Canada
| | - Wan L Lam
- Department of Integrative Oncology, British Columbia Cancer Agency, Vancouver, B.C, V5Z 1L3, Canada
| | - Kevin L Bennewith
- Department of Integrative Oncology, British Columbia Cancer Agency, Vancouver, B.C, V5Z 1L3, Canada
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26
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Praher D, Zimmermann B, Genikhovich G, Columbus-Shenkar Y, Modepalli V, Aharoni R, Moran Y, Technau U. Characterization of the piRNA pathway during development of the sea anemone Nematostella vectensis. RNA Biol 2017; 14:1727-1741. [PMID: 28783426 PMCID: PMC5731801 DOI: 10.1080/15476286.2017.1349048] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2017] [Revised: 06/22/2017] [Accepted: 06/27/2017] [Indexed: 12/11/2022] Open
Abstract
PIWI-interacting RNAs (piRNAs) and associated proteins comprise a conserved pathway for silencing transposons in metazoan germlines. piRNA pathway components are also expressed in multipotent somatic stem cells in various organisms. piRNA functions have been extensively explored in bilaterian model systems, however, comprehensive studies in non-bilaterian phyla remain limited. Here we investigate the piRNA pathway during the development of Nematostella vectensis, a well-established model system belonging to Cnidaria, the sister group to Bilateria. To date, no population of somatic stem cells has been identified in this organism, despite its long life-span and regenerative capacities that require a constant cell-renewal. We show that Nematostella piRNA pathway components are broadly expressed in early developmental stages, while piRNAs themselves show differential expression, suggesting specific developmental roles of distinct piRNA families. In adults, piRNA associated proteins are enriched in the germline but also expressed in somatic cells, indicating putative stem cell properties. Furthermore, we provide experimental evidence that Nematostella piRNAs cleave transposable elements as well as protein-coding genes. Our results demonstrate that somatic expression of piRNA associated proteins as well as the roles of piRNAs in transposon repression and gene regulation are likely ancestral features that evolved before the split between Cnidaria and Bilateria.
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Affiliation(s)
- Daniela Praher
- Department of Molecular Evolution and Development; Centre of Organismal Systems Biology, Faculty of Life Sciences, University of Vienna; Althanstrasse 14, Wien, Austria
| | - Bob Zimmermann
- Department of Molecular Evolution and Development; Centre of Organismal Systems Biology, Faculty of Life Sciences, University of Vienna; Althanstrasse 14, Wien, Austria
| | - Grigory Genikhovich
- Department of Molecular Evolution and Development; Centre of Organismal Systems Biology, Faculty of Life Sciences, University of Vienna; Althanstrasse 14, Wien, Austria
| | - Yaara Columbus-Shenkar
- Department of Ecology, Evolution and Behavior; Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem; Givat Ram, Jerusalem, Israel
| | - Vengamanaidu Modepalli
- Department of Ecology, Evolution and Behavior; Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem; Givat Ram, Jerusalem, Israel
| | - Reuven Aharoni
- Department of Ecology, Evolution and Behavior; Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem; Givat Ram, Jerusalem, Israel
| | - Yehu Moran
- Department of Ecology, Evolution and Behavior; Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem; Givat Ram, Jerusalem, Israel
| | - Ulrich Technau
- Department of Molecular Evolution and Development; Centre of Organismal Systems Biology, Faculty of Life Sciences, University of Vienna; Althanstrasse 14, Wien, Austria
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Gainetdinov I, Skvortsova Y, Kondratieva S, Funikov S, Azhikina T. Two modes of targeting transposable elements by piRNA pathway in human testis. RNA (NEW YORK, N.Y.) 2017; 23:1614-1625. [PMID: 28842508 PMCID: PMC5648030 DOI: 10.1261/rna.060939.117] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/28/2017] [Accepted: 08/23/2017] [Indexed: 06/07/2023]
Abstract
PIWI proteins and their partner small RNAs, termed piRNAs, are known to control transposable elements (TEs) in the germline. Here, we provide evidence that in humans this control is exerted in two different modes. On the one hand, production of piRNAs specifically targeting evolutionarily youngest TEs (L1HS, L1PA2-L1PA6, LTR12C, SVA) is present both at prenatal and postnatal stages of spermatogenesis and is performed without involvement of piRNA clusters. On the other hand, at postnatal stages, piRNAs deriving from pachytene clusters target "older" TEs and thus complement cluster-independent piRNA production to achieve relevant targeting of virtually all TEs expressed in postnatal testis. We also find that converging transcription of antisense-oriented genes contributes to the origin of genic postnatal prepachytene clusters. Finally, while a fraction of pachytene piRNAs was previously shown to arise from long intergenic noncoding RNAs (lincRNAs, i.e., pachytene piRNA cluster primary transcripts), we ascertain that these are a specific set of lincRNAs that both possess distinguishing epigenetic features and are expressed exclusively in testis.
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Affiliation(s)
- Ildar Gainetdinov
- Department of Genomics and Postgenomic Technologies, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, 117997, Russia
| | - Yulia Skvortsova
- Department of Genomics and Postgenomic Technologies, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, 117997, Russia
| | - Sofia Kondratieva
- Department of Genomics and Postgenomic Technologies, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, 117997, Russia
| | - Sergey Funikov
- Department of Structural, Functional and Evolutionary Genomics, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, 119991, Russia
| | - Tatyana Azhikina
- Department of Genomics and Postgenomic Technologies, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, 117997, Russia
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Wu S, Li Y, Chen S, Liang S, Ren X, Guo W, Sun Q, Yang X. Effect of dietary Astragalus Polysaccharide supplements on testicular piRNA expression profiles of breeding cocks. Int J Biol Macromol 2017; 103:957-964. [DOI: 10.1016/j.ijbiomac.2017.05.122] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2017] [Revised: 05/08/2017] [Accepted: 05/19/2017] [Indexed: 01/04/2023]
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Cui L, Fang L, Shi B, Qiu S, Ye Y. Spermatozoa Expression of piR-31704, piR-39888, and piR-40349 and Their Correlation to Sperm Concentration and Fertilization Rate After ICSI. Reprod Sci 2017; 25:733-739. [DOI: 10.1177/1933719117725822] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Long Cui
- Department of Reproductive Endocrinology, Women’s Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Li Fang
- Department of Reproductive Endocrinology, Women’s Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Biwei Shi
- Department of Reproductive Endocrinology, Women’s Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Sunquan Qiu
- Department of Reproductive Endocrinology, Women’s Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Yinghui Ye
- Department of Reproductive Endocrinology, Women’s Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
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30
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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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31
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Chen C, Wu H, Shen D, Wang S, Zhang L, Wang X, Gao B, Wu T, Li B, Li K, Song C. Comparative profiling of small RNAs of pig seminal plasma and ejaculated and epididymal sperm. Reproduction 2017; 153:785-796. [PMID: 28314792 DOI: 10.1530/rep-17-0014] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2017] [Revised: 03/16/2017] [Accepted: 03/17/2017] [Indexed: 12/19/2022]
Abstract
The similarities and differences of small RNAs in seminal plasma, epididymal sperm and ejaculated sperm remain largely undefined. We conducted a systematic comparative analysis of small RNA profiles in pig ejaculated sperm, epididymal sperm and seminal plasma and found that the diversity distribution of small RNA species was generally similar, whereas the abundance of small RNAs is dramatically different across the three libraries; miRNAs and small RNAs derived from rRNA, tRNA, small nuclear RNA, 7SK RNA, NRON RNA and cis-regulatory RNA were enriched in the three libraries, but piRNA was absent. A large population of small RNAs from ejaculated sperm are ejaculated sperm specific, and only 8-30% of small RNAs overlapped with those of epididymal sperm or seminal plasma and a small proportion (5-18%) of small RNAs were shared in the three libraries, suggesting that, in addition to the testes, sperm RNAs may also originate from seminal plasma, epididymis as well as other resources. Most miRNAs were co-distributed but differentially expressed across the three libraries, with epididymal sperm exhibiting the highest abundance, followed by ejaculated sperm and seminal plasma. The prediction of target genes of the top 10 highly expressed miRNAs across the three libraries revealed that these miRNAs may be involved in spermatogenesis, zygote development and the interaction between the environment and animals. Our study provides the first description of the similarities and differences of small RNA profiles in ejaculated sperm, epididymal sperm and seminal plasma and indicates that sperm RNA may have origins other than the testes.
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Affiliation(s)
- Cai Chen
- The Key Laboratory for Domestic Animal Genetic Resources and Breeding of the Ministry of Agriculture of ChinaInstitute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China.,Joint International Research Laboratory of Agriculture and Agri-Product SafetyCollege of Animal Science & Technology, Yangzhou University, Yangzhou, Jiangsu, China
| | - Han Wu
- Joint International Research Laboratory of Agriculture and Agri-Product SafetyCollege of Animal Science & Technology, Yangzhou University, Yangzhou, Jiangsu, China
| | - Dan Shen
- Joint International Research Laboratory of Agriculture and Agri-Product SafetyCollege of Animal Science & Technology, Yangzhou University, Yangzhou, Jiangsu, China
| | - Saisai Wang
- Joint International Research Laboratory of Agriculture and Agri-Product SafetyCollege of Animal Science & Technology, Yangzhou University, Yangzhou, Jiangsu, China
| | - Li Zhang
- Joint International Research Laboratory of Agriculture and Agri-Product SafetyCollege of Animal Science & Technology, Yangzhou University, Yangzhou, Jiangsu, China
| | - Xiaoyan Wang
- Joint International Research Laboratory of Agriculture and Agri-Product SafetyCollege of Animal Science & Technology, Yangzhou University, Yangzhou, Jiangsu, China
| | - Bo Gao
- Joint International Research Laboratory of Agriculture and Agri-Product SafetyCollege of Animal Science & Technology, Yangzhou University, Yangzhou, Jiangsu, China
| | - Tianwen Wu
- The Key Laboratory for Domestic Animal Genetic Resources and Breeding of the Ministry of Agriculture of ChinaInstitute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Bichun Li
- Joint International Research Laboratory of Agriculture and Agri-Product SafetyCollege of Animal Science & Technology, Yangzhou University, Yangzhou, Jiangsu, China
| | - Kui Li
- The Key Laboratory for Domestic Animal Genetic Resources and Breeding of the Ministry of Agriculture of ChinaInstitute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Chengyi Song
- The Key Laboratory for Domestic Animal Genetic Resources and Breeding of the Ministry of Agriculture of ChinaInstitute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China .,Joint International Research Laboratory of Agriculture and Agri-Product SafetyCollege of Animal Science & Technology, Yangzhou University, Yangzhou, Jiangsu, China
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Russell S, Patel M, Gilchrist G, Stalker L, Gillis D, Rosenkranz D, LaMarre J. Bovine piRNA-like RNAs are associated with both transposable elements and mRNAs. Reproduction 2017; 153:305-318. [DOI: 10.1530/rep-16-0620] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2016] [Revised: 11/20/2016] [Accepted: 12/13/2016] [Indexed: 01/01/2023]
Abstract
PIWI proteins and their associated piRNAs have been the focus of intensive research in the past decade; therefore, their participation in the maintenance of genomic integrity during spermatogenesis has been well established. Recent studies have suggested important roles for the PIWI/piRNA system outside of gametogenesis, based on the presence of piRNAs and PIWI proteins in several somatic tissues, cancers, and the early embryo. Here, we investigated the small RNA complement present in bovine gonads, gametes, and embryos through next-generation sequencing. A distinct piRNA population was present in the testis as expected. However, we also found a large population of slightly shorter, 24–27 nt piRNA-like RNA (pilRNAs) in pools of oocytes and zygotes. These oocyte and embryo pilRNAs exhibited many of the canonical characteristics of piRNAs including a 1U bias, the presence of a ‘ping-pong’ signature, genomic clustering, and transposable element targeting. Some of the major transposons targeted by oocyte and zygote pilRNA were from the LINE RTE and ERV1 classes. We also identified pools of pilRNA potentially derived from, or targeted at, specific mRNA sequences. We compared the frequency of these gene-associated pilRNAs to the fold change in the expression of respective mRNAs from two previously reported transcriptome datasets. We observed significant negative correlations between the number of pilRNAs targeting mRNAs, and their fold change in expression between the 4–8 cell and 8–16 cell stages. Together, these results represent one of the first characterizations of the PIWI/piRNA pathway in the translational bovine model, and in the novel context of embryogenesis.
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Small RNA Sequencing in Cells and Exosomes Identifies eQTLs and 14q32 as a Region of Active Export. G3-GENES GENOMES GENETICS 2017; 7:31-39. [PMID: 27799337 PMCID: PMC5217120 DOI: 10.1534/g3.116.036137] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Exosomes are small extracellular vesicles that carry heterogeneous cargo, including RNA, between cells. Increasing evidence suggests that exosomes are important mediators of intercellular communication and biomarkers of disease. Despite this, the variability of exosomal RNA between individuals has not been well quantified. To assess this variability, we sequenced the small RNA of cells and exosomes from a 17-member family. Across individuals, we show that selective export of miRNAs occurs not only at the level of specific transcripts, but that a cluster of 74 mature miRNAs on chromosome 14q32 is massively exported in exosomes while mostly absent from cells. We also observe more interindividual variability between exosomal samples than between cellular ones and identify four miRNA expression quantitative trait loci shared between cells and exosomes. Our findings indicate that genomically colocated miRNAs can be exported together and highlight the variability in exosomal miRNA levels between individuals as relevant for exosome use as diagnostics.
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Sivagurunathan S, Palanisamy K, Arunachalam JP, Chidambaram S. Possible role of HIWI2 in modulating tight junction proteins in retinal pigment epithelial cells through Akt signaling pathway. Mol Cell Biochem 2016; 427:145-156. [DOI: 10.1007/s11010-016-2906-8] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2016] [Accepted: 12/03/2016] [Indexed: 12/22/2022]
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Sarkar A, Volff JN, Vaury C. piRNAs and their diverse roles: a transposable element-driven tactic for gene regulation? FASEB J 2016; 31:436-446. [PMID: 27799346 DOI: 10.1096/fj.201600637rr] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2016] [Accepted: 10/14/2016] [Indexed: 01/12/2023]
Abstract
P-element-induced wimpy testis (PIWI)-interacting RNAs (piRNAs) are small, noncoding RNAs known for silencing transposable elements (TEs) in the germline of animals. Most genomes host TEs, which are notorious for mobilizing themselves and endangering survival of the host if not controlled. By silencing TEs in the germline, piRNAs prevent harmful mutations from being passed on to the next generation. How piRNAs are generated and how they silence TEs were the focus of researchers ever since their discovery. Now a spate of recent papers are beginning to tell us that piRNAs can play roles beyond TE silencing and are involved in diverse cellular processes from mRNA regulation to development or genome rearrangement. In this review, we discuss some of these recently reported roles. Data on these new roles are often rudimentary, and the involvement of piRNAs in these processes is yet to be definitely established. What is interesting is that the reports are on animals widely separated on the phylogenetic tree of life and that piRNAs were also found outside the gonadal tissues. Some of these piRNAs map to TE sequences, prompting us to hypothesize that genomes may have co-opted the TE-derived piRNA system for their own regulation.-Sarkar, A., Volff, J.-N., Vaury, C. piRNAs and their diverse roles: a transposable element-driven tactic for gene regulation?
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Affiliation(s)
- Arpita Sarkar
- Laboratoire de Génétique, Reproduction et Développement (GReD), Centre National de la Recherche Scientifique, INSERM, Université Clermont Auvergne, Clermont-Ferrand,France; and
| | - Jean-Nicolas Volff
- Institut de Génomique Fonctionnelle de Lyon, Ecole Normale Supérieure de Lyon, Lyon, France
| | - Chantal Vaury
- Laboratoire de Génétique, Reproduction et Développement (GReD), Centre National de la Recherche Scientifique, INSERM, Université Clermont Auvergne, Clermont-Ferrand,France; and
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36
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Abstract
Understanding the molecular mechanisms behind the capacity of cancer cells to adapt to the tumor microenvironment and to anticancer therapies is a major challenge. In this context, cancer is believed to be an evolutionary process where random mutations and the selection process shape the mutational pattern and phenotype of cancer cells. This article challenges the notion of randomness of some cancer-associated mutations by describing molecular mechanisms involving stress-mediated biogenesis of mRNA-derived small RNAs able to target and increase the local mutation rate of the genomic loci they originate from. It is proposed that the probability of some mutations at specific loci could be increased in a stress-specific and RNA-depending manner. This would increase the probability of generating mutations that could alleviate stress situations, such as those triggered by anticancer drugs. Such a mechanism is made possible because tumor- and anticancer drug-associated stress situations trigger both cellular reprogramming and inflammation, which leads cancer cells to express molecular tools allowing them to “attack” and mutate their own genome in an RNA-directed manner.
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Affiliation(s)
- Didier Auboeuf
- Univ Lyon, ENS de Lyon, Univ Claude Bernard, CNRS UMR 5239, INSERM U1210, Laboratory of Biology and Modelling of the Cell, Lyon, France
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37
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Xu L, Qiu L, Chang G, Guo Q, Liu X, Bi Y, Zhang Y, Wang H, Li Z, Guo X, Wan F, Zhang Y, Xu Q, Chen G. Discovery of piRNAs Pathway Associated with Early-Stage Spermatogenesis in Chicken. PLoS One 2016; 11:e0151780. [PMID: 27045806 PMCID: PMC4821617 DOI: 10.1371/journal.pone.0151780] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2016] [Accepted: 03/03/2016] [Indexed: 01/10/2023] Open
Abstract
Piwi-interacting RNAs (piRNAs) play a key role in spermatogenesis. Here, we describe the piRNAs profiling of primordial germ cells (PGCs), spermatogonial stem cells (SSCs), and the spermatogonium (Sp) during early-stage spermatogenesis in chicken. We obtained 31,361,989 reads from PGCs, 31,757,666 reads from SSCs, and 46,448,327 reads from Sp cells. The length distribution of piRNAs in the three samples showed peaks at 33 nt. The resulting genes were subsequently annotated against the Gene Ontology (GO) database. Five genes (RPL7A, HSPA8, Pum1, CPXM2, and PRKCA) were found to be involved in cellular processes. Interactive pathway analysis (IPA) further revealed three important pathways in early-stage spermatogenesis including the FGF, Wnt, and EGF receptor signaling pathways. The gene Pum1 was found to promote germline stem cell proliferation, but it also plays a role in spermatogenesis. In conclusion, we revealed characteristics of piRNAs during early spermatogonial development in chicken and provided the basis for future research.
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Affiliation(s)
- Lu Xu
- College of Animal Science & Technology, Yangzhou University, Yangzhou, Jiangsu, 225009, China
| | - Lingling Qiu
- College of Animal Science & Technology, Yangzhou University, Yangzhou, Jiangsu, 225009, China
| | - Guobin Chang
- College of Animal Science & Technology, Yangzhou University, Yangzhou, Jiangsu, 225009, China
- * E-mail: (GBC); (GHC)
| | - Qixin Guo
- College of Animal Science & Technology, Yangzhou University, Yangzhou, Jiangsu, 225009, China
| | - Xiangping Liu
- Poultry Institute, Chinese Academy of Agricultural Sciences, Yangzhou, Jiangsu, 225003, China
| | - Yulin Bi
- College of Animal Science & Technology, Yangzhou University, Yangzhou, Jiangsu, 225009, China
| | - Yu Zhang
- College of Animal Science & Technology, Yangzhou University, Yangzhou, Jiangsu, 225009, China
| | - Hongzhi Wang
- Poultry Institute, Chinese Academy of Agricultural Sciences, Yangzhou, Jiangsu, 225003, China
| | - Zhiteng Li
- College of Animal Science & Technology, Yangzhou University, Yangzhou, Jiangsu, 225009, China
| | - Xiaoming Guo
- College of Animal Science & Technology, Yangzhou University, Yangzhou, Jiangsu, 225009, China
| | - Fang Wan
- College of Animal Science & Technology, Yangzhou University, Yangzhou, Jiangsu, 225009, China
| | - Yang Zhang
- College of Animal Science & Technology, Yangzhou University, Yangzhou, Jiangsu, 225009, China
| | - Qi Xu
- College of Animal Science & Technology, Yangzhou University, Yangzhou, Jiangsu, 225009, China
| | - Guohong Chen
- College of Animal Science & Technology, Yangzhou University, Yangzhou, Jiangsu, 225009, China
- * E-mail: (GBC); (GHC)
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38
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Ng KW, Anderson C, Marshall EA, Minatel BC, Enfield KSS, Saprunoff HL, Lam WL, Martinez VD. Piwi-interacting RNAs in cancer: emerging functions and clinical utility. Mol Cancer 2016; 15:5. [PMID: 26768585 PMCID: PMC4714483 DOI: 10.1186/s12943-016-0491-9] [Citation(s) in RCA: 140] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2015] [Accepted: 01/05/2016] [Indexed: 12/29/2022] Open
Abstract
PIWI-interacting RNAs (piRNAs) are emerging players in cancer genomics. Originally described in the germline, there are over 20,000 piRNA genes in the human genome. In contrast to microRNAs, piRNAs interact with PIWI proteins, another member of the Argonaute family, and function primarily in the nucleus. There, they are involved in the epigenetic silencing of transposable elements in addition to the transcriptional regulation of genes. It has recently been demonstrated that piRNAs are also expressed across a variety of human somatic tissue types in a tissue-specific manner. An increasing number of studies have shown that aberrant piRNA expression is a signature feature across multiple tumour types; however, their specific tumorigenic functions remain unclear. In this article, we discuss the emerging functional roles of piRNAs in a variety of cancers, and highlight their potential clinical utilities.
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Affiliation(s)
- Kevin W Ng
- Department of Integrative Oncology, BC Cancer Agency, Vancouver, Canada.
| | - Christine Anderson
- Department of Integrative Oncology, BC Cancer Agency, Vancouver, Canada.
| | - Erin A Marshall
- Department of Integrative Oncology, BC Cancer Agency, Vancouver, Canada.
| | - Brenda C Minatel
- Department of Integrative Oncology, BC Cancer Agency, Vancouver, Canada.
| | - Katey S S Enfield
- Department of Integrative Oncology, BC Cancer Agency, Vancouver, Canada.
| | | | - Wan L Lam
- Department of Integrative Oncology, BC Cancer Agency, Vancouver, Canada.
| | - Victor D Martinez
- Department of Integrative Oncology, BC Cancer Agency, Vancouver, Canada.
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Chirn GW, Rahman R, Sytnikova YA, Matts JA, Zeng M, Gerlach D, Yu M, Berger B, Naramura M, Kile BT, Lau NC. Conserved piRNA Expression from a Distinct Set of piRNA Cluster Loci in Eutherian Mammals. PLoS Genet 2015; 11:e1005652. [PMID: 26588211 PMCID: PMC4654475 DOI: 10.1371/journal.pgen.1005652] [Citation(s) in RCA: 56] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2015] [Accepted: 10/15/2015] [Indexed: 12/18/2022] Open
Abstract
The Piwi pathway is deeply conserved amongst animals because one of its essential functions is to repress transposons. However, many Piwi-interacting RNAs (piRNAs) do not base-pair to transposons and remain mysterious in their targeting function. The sheer number of piRNA cluster (piC) loci in animal genomes and infrequent piRNA sequence conservation also present challenges in determining which piC loci are most important for development. To address this question, we determined the piRNA expression patterns of piC loci across a wide phylogenetic spectrum of animals, and reveal that most genic and intergenic piC loci evolve rapidly in their capacity to generate piRNAs, regardless of known transposon silencing function. Surprisingly, we also uncovered a distinct set of piC loci with piRNA expression conserved deeply in Eutherian mammals. We name these loci Eutherian-Conserved piRNA cluster (ECpiC) loci. Supporting the hypothesis that conservation of piRNA expression across ~100 million years of Eutherian evolution implies function, we determined that one ECpiC locus generates abundant piRNAs antisense to the STOX1 transcript, a gene clinically associated with preeclampsia. Furthermore, we confirmed reduced piRNAs in existing mouse mutations at ECpiC-Asb1 and -Cbl, which also display spermatogenic defects. The Asb1 mutant testes with strongly reduced Asb1 piRNAs also exhibit up-regulated gene expression profiles. These data indicate ECpiC loci may be specially adapted to support Eutherian reproduction. Animal genomes from flies to humans contain many hundreds of non-coding elements called Piwi-interacting RNAs (piRNAs) cluster loci (piC loci). Some of these elements generate piRNAs that direct the silencing of transposable elements, which are pervasive genetic parasites. However, we lack an understanding of the targeting function for the remaining bulk of piRNAs because their loci are not complementarity to transposable elements. In addition, the field does not know if all piC loci are quickly evolving, or if some piC loci might be deeply conserved in piRNA expression, an indication of its potentially functional importance. Our study confirms the highly rapid evolution in piRNA expression capacity for the majority of piC loci in flies and mammals, with many clade- and species-specific piC loci expression patterns. In spite of this, we also discover a cohort of piC loci that are deeply conserved in piRNA expression from the human to the dog, a significantly broad phylogenetic spectrum of eutherian mammals. However, this conservation in piRNA expression ends at non-eutherian mammals like marsupials and monotremes. Existing mutations in two of these Eutherian-Conserved piC (ECpiC) loci impair mouse reproduction and abrogate piRNA production. Therefore, we suggest these ECpiC loci are conserved for piRNA expression due to their important function in eutherian reproduction and stand out as prime candidates for future genetic studies.
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Affiliation(s)
- Gung-wei Chirn
- Department of Biology and Rosenstiel Basic Medical Science Research Center, Brandeis University, Waltham, Massachusetts, United States of America
| | - Reazur Rahman
- Department of Biology and Rosenstiel Basic Medical Science Research Center, Brandeis University, Waltham, Massachusetts, United States of America
| | - Yuliya A. Sytnikova
- Department of Biology and Rosenstiel Basic Medical Science Research Center, Brandeis University, Waltham, Massachusetts, United States of America
| | - Jessica A. Matts
- Department of Biology and Rosenstiel Basic Medical Science Research Center, Brandeis University, Waltham, Massachusetts, United States of America
| | - Mei Zeng
- Department of Biology and Rosenstiel Basic Medical Science Research Center, Brandeis University, Waltham, Massachusetts, United States of America
| | - Daniel Gerlach
- Research Institute of Molecular Pathology, Vienna Biocenter, Vienna, Austria
| | - Michael Yu
- Mathematics Department and Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
| | - Bonnie Berger
- Mathematics Department and Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
| | - Mayumi Naramura
- Eppley Institute, University of Nebraska Medical Center, Omaha, Nebraska, United States of America
| | - Benjamin T. Kile
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Australia
| | - Nelson C. Lau
- Department of Biology and Rosenstiel Basic Medical Science Research Center, Brandeis University, Waltham, Massachusetts, United States of America
- * E-mail:
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Rosenkranz D. piRNA cluster database: a web resource for piRNA producing loci. Nucleic Acids Res 2015; 44:D223-30. [PMID: 26582915 PMCID: PMC4702893 DOI: 10.1093/nar/gkv1265] [Citation(s) in RCA: 76] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2015] [Accepted: 11/03/2015] [Indexed: 12/14/2022] Open
Abstract
Piwi proteins and their guiding small RNAs, termed Piwi-interacting (pi-) RNAs, are essential for silencing of transposons in the germline of animals. A substantial fraction of piRNAs originates from genomic loci termed piRNA clusters and sequences encoded in these piRNA clusters determine putative targets for the Piwi/piRNA system. In the past decade, studies of piRNA transcriptomes in different species revealed additional roles for piRNAs beyond transposon silencing, reflecting the astonishing plasticity of the Piwi/piRNA system along different phylogenetic branches. Moreover, piRNA transcriptomes can change drastically during development and vary across different tissues. Since piRNA clusters crucially shape piRNA profiles, analysis of these loci is imperative for a thorough understanding of functional and evolutionary aspects of the piRNA pathway. But despite the ever-growing amount of available piRNA sequence data, we know little about the factors that determine differential regulation of piRNA clusters, nor the evolutionary events that cause their gain or loss. In order to facilitate addressing these subjects, we established a user-friendly piRNA cluster database (http://www.smallrnagroup-mainz.de/piRNAclusterDB.html) that provides comprehensive data on piRNA clusters in multiple species, tissues and developmental stages based on small RNA sequence data deposited at NCBI's Sequence Read Archive (SRA).
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Affiliation(s)
- David Rosenkranz
- Institute of Anthropology, Johannes Gutenberg University, Mainz 55099, Germany
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