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Woo SJ, Han JY. Epigenetic programming of chicken germ cells: a comparative review. Poult Sci 2024; 103:103977. [PMID: 38970845 PMCID: PMC11269908 DOI: 10.1016/j.psj.2024.103977] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2024] [Revised: 05/26/2024] [Accepted: 06/10/2024] [Indexed: 07/08/2024] Open
Abstract
Chicken embryos serve as an important model for investigating germ cells due to their ease of accessibility and manipulation within the egg. Understanding the development of germ cells is particularly crucial, as they are the only cell types capable of transmitting genetic information to the next generation. Therefore, gene expression regulation in germ cells is important for genomic function. Epigenetic programming is a crucial biological process for the regulation of gene expression without altering the genome sequence. Although epigenetic programming is evolutionarily conserved, several differences between chickens and mammals have been revealed. In this review, we compared the epigenetic regulation of germ cells in chickens and mammals (mainly mice as a representative species). In mammals, migrating primordial germ cells (precursors for germ cells [PGCs]) undergo global DNA demethylation and persist until sexual differentiation, while in chickens, DNA is demethylated until reaching the gonad but remethylated when sexually differentiated. Prospermatogonia is methylated at the onset of mitotic arrest in mammals, while DNA is demethylated at mitotic arrest in chickens. Furthermore, genomic imprinting and inactivation of sex chromosomes are differentially regulated through DNA methylation in chickens and mammals. Chickens and mammals exhibit different patterns of histone modifications during germ cell development, and non-coding RNA, which is not involved in PGC differentiation in mice, plays an important role in chicken PGC development. Additionally, several chicken-specific non-coding RNAs have been identified. In conclusion, we summarized current knowledge of epigenetic gene regulation of chicken germ cells, comparing that of mammals, and highlighted notable differences between them.
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Affiliation(s)
- Seung Je Woo
- Department of Agricultural Biotechnology and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, South Korea
| | - Jae Yong Han
- Department of Agricultural Biotechnology and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, South Korea.
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2
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Ichikawa K, Horiuchi H. Fate Decisions of Chicken Primordial Germ Cells (PGCs): Development, Integrity, Sex Determination, and Self-Renewal Mechanisms. Genes (Basel) 2023; 14:genes14030612. [PMID: 36980885 PMCID: PMC10048776 DOI: 10.3390/genes14030612] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Revised: 02/24/2023] [Accepted: 02/27/2023] [Indexed: 03/05/2023] Open
Abstract
Primordial germ cells (PGCs) are precursor cells of sperm and eggs. The fate decisions of chicken PGCs in terms of their development, integrity, and sex determination have unique features, thereby providing insights into evolutionary developmental biology. Additionally, fate decisions in the context of a self-renewal mechanism have been applied to establish culture protocols for chicken PGCs, enabling the production of genome-edited chickens and the conservation of genetic resources. Thus, studies on the fate decisions of chicken PGCs have significantly contributed to both academic and industrial development. Furthermore, studies on fate decisions have rapidly advanced owing to the recent development of essential research technologies, such as genome editing and RNA sequencing. Here, we reviewed the status of fate decisions of chicken PGCs and provided insight into other important research issues that require attention.
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Affiliation(s)
- Kennosuke Ichikawa
- Genome Editing Innovation Center, Hiroshima University, 3-10-23 Kagamiyama, Higashi-Hiroshima 739-0046, Hiroshima, Japan
- Correspondence:
| | - Hiroyuki Horiuchi
- Genome Editing Innovation Center, Hiroshima University, 3-10-23 Kagamiyama, Higashi-Hiroshima 739-0046, Hiroshima, Japan
- Graduate School of Integrated Sciences for Life, Hiroshima University, 1-4-4 Kagamiyama, Higashi-Hiroshima 739-8528, Hiroshima, Japan
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3
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Ichikawa K, Nakamura Y, Bono H, Ezaki R, Matsuzaki M, Horiuchi H. Prediction of sex-determination mechanisms in avian primordial germ cells using RNA-seq analysis. Sci Rep 2022; 12:13528. [PMID: 35978076 PMCID: PMC9385715 DOI: 10.1038/s41598-022-17726-7] [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: 06/09/2022] [Accepted: 07/29/2022] [Indexed: 12/12/2022] Open
Abstract
In birds, sex is determined through cell-autonomous mechanisms and various factors, such as the dosage of DMRT1. While the sex-determination mechanism in gonads is well known, the mechanism in germ cells remains unclear. In this study, we explored the gene expression profiles of male and female primordial germ cells (PGCs) during embryogenesis in chickens to predict the mechanism underlying sex determination. Male and female PGCs were isolated from blood and gonads with a purity > 96% using flow cytometry and analyzed using RNA-seq. Prior to settlement in the gonads, female circulating PGCs (cPGCs) obtained from blood displayed sex-biased expression. Gonadal PGCs (gPGCs) also exhibited sex-biased expression, and the number of female-biased genes detected was higher than that of male-biased genes. The female-biased genes in gPGCs were enriched in some metabolic processes. To reveal the mechanisms underlying the transcriptional regulation of female-biased genes in gPGCs, we performed stimulation tests. Retinoic acid stimulation of cultured gPGCs derived from male embryos resulted in the upregulation of several female-biased genes. Overall, our results suggest that sex determination in avian PGCs involves aspects of both cell-autonomous and somatic-cell regulation. Moreover, it appears that sex determination occurs earlier in females than in males.
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Affiliation(s)
- Kennosuke Ichikawa
- Genome Editing Innovation Center, Hiroshima University, 3-10-23 Kagamiyama, Higashi-Hiroshima, Hiroshima, 739-0046, Japan.
| | - Yoshiaki Nakamura
- Graduate School of Integrated Sciences for Life, Hiroshima University, 1-4-4 Kagamiyama, Higashi-Hiroshima, Hiroshima, 739-8528, Japan
| | - Hidemasa Bono
- Graduate School of Integrated Sciences for Life, Hiroshima University, 1-4-4 Kagamiyama, Higashi-Hiroshima, Hiroshima, 739-8528, Japan
| | - Ryo Ezaki
- Graduate School of Integrated Sciences for Life, Hiroshima University, 1-4-4 Kagamiyama, Higashi-Hiroshima, Hiroshima, 739-8528, Japan
| | - Mei Matsuzaki
- Graduate School of Integrated Sciences for Life, Hiroshima University, 1-4-4 Kagamiyama, Higashi-Hiroshima, Hiroshima, 739-8528, Japan
| | - Hiroyuki Horiuchi
- Genome Editing Innovation Center, Hiroshima University, 3-10-23 Kagamiyama, Higashi-Hiroshima, Hiroshima, 739-0046, Japan.,Graduate School of Integrated Sciences for Life, Hiroshima University, 1-4-4 Kagamiyama, Higashi-Hiroshima, Hiroshima, 739-8528, Japan
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4
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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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5
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Li J, Sun C, Zheng J, Li J, Yi G, Yang N. Time-Course Transcriptional and Chromatin Accessibility Profiling Reveals Genes Associated With Asymmetrical Gonadal Development in Chicken Embryos. Front Cell Dev Biol 2022; 10:832132. [PMID: 35345851 PMCID: PMC8957256 DOI: 10.3389/fcell.2022.832132] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Accepted: 02/09/2022] [Indexed: 12/02/2022] Open
Abstract
In birds, male gonads form on both sides whereas most females develop asymmetric gonads. Multiple early lines of evidence suggested that the right gonad fails to develop into a functional ovary, mainly due to differential expression of PITX2 in the gonadal epithelium. Despite some advances in recent years, the molecular mechanisms underlying asymmetric gonadal development remain unclear. Here, using bulk analysis of whole gonads, we established a relatively detailed profile of four representative stages of chicken gonadal development at the transcriptional and chromatin levels. We revealed that many candidate genes were significantly enriched in morphogenesis, meiosis and subcellular structure formation, which may be responsible for asymmetric gonadal development. Further chromatin accessibility analysis suggested that the transcriptional activities of the candidate genes might be regulated by nearby open chromatin regions, which may act as transcription factor (TF) binding sites and potential cis-regulatory elements. We found that LHX9 was a promising TF that bound to the left-biased peaks of many cell cycle-related genes. In summary, this study provides distinctive insights into the potential molecular basis underlying the asymmetric development of chicken gonads.
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Affiliation(s)
- Jianbo Li
- National Engineering Laboratory for Animal Breeding and Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Congjiao Sun
- National Engineering Laboratory for Animal Breeding and Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Jiangxia Zheng
- National Engineering Laboratory for Animal Breeding and Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Junying Li
- National Engineering Laboratory for Animal Breeding and Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Guoqiang Yi
- 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, China
| | - Ning Yang
- National Engineering Laboratory for Animal Breeding and Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, China Agricultural University, Beijing, China
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6
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Chicken blastoderms and primordial germ cells possess a higher expression of DNA repair genes and lower expression of apoptosis genes to preserve their genome stability. Sci Rep 2022; 12:49. [PMID: 34997179 PMCID: PMC8741993 DOI: 10.1038/s41598-021-04417-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Accepted: 12/21/2021] [Indexed: 12/13/2022] Open
Abstract
DNA is susceptible to damage by various sources. When the DNA is damaged, the cell repairs the damage through an appropriate DNA repair pathway. When the cell fails to repair DNA damage, apoptosis is initiated. Although several genes are involved in five major DNA repair pathways and two major apoptosis pathways, a comprehensive understanding of those gene expression is not well-understood in chicken tissues. We performed whole-transcriptome sequencing (WTS) analysis in the chicken embryonic fibroblasts (CEFs), stage X blastoderms, and primordial germ cells (PGCs) to uncover this deficiency. Stage X blastoderms mostly consist of undifferentiated progenitor (pluripotent) cells that have the potency to differentiate into all cell types. PGCs are also undifferentiated progenitor cells that later differentiate into male and female germ cells. CEFs are differentiated and abundant somatic cells. Through WTS analysis, we identified that the DNA repair pathway genes were expressed more highly in blastoderms and high in PGCs than CEFs. Besides, the apoptosis pathway genes were expressed low in blastoderms and PGCs than CEFs. We have also examined the WTS-based expression profiling of candidate pluripotency regulating genes due to the conserved properties of blastoderms and PGCs. In the results, a limited number of pluripotency genes, especially the core transcriptional network, were detected higher in both blastoderms and PGCs than CEFs. Next, we treated the CEFs, blastoderm cells, and PGCs with hydrogen peroxide (H2O2) for 1 h to induce DNA damage. Then, the H2O2 treated cells were incubated in fresh media for 3–12 h to observe DNA repair. Subsequent analyses in treated cells found that blastoderm cells and PGCs were more likely to undergo apoptosis along with the loss of pluripotency and less likely to undergo DNA repair, contrasting with CEFs. These properties of blastoderms and PGCs should be necessary to preserve genome stability during the development of early embryos and germ cells, respectively.
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7
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Zhao N, Deng Q, Zhu C, Zhang B. Mucus piRNAs profiles of Vibrio harveyi-infected Cynoglossus semilaevis: A hint for fish disease monitoring. JOURNAL OF FISH DISEASES 2022; 45:165-175. [PMID: 34741552 DOI: 10.1111/jfd.13546] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Revised: 10/18/2021] [Accepted: 10/20/2021] [Indexed: 06/13/2023]
Abstract
The half-smooth tongue sole, Cynoglossus semilaevis, is an important cultured flatfish species. Vibrio harveyi is a common pathogen to this fish, which may result in great economic loss to C. semilaevis culture industry. piRNAs, a non-coding RNAs with 26-32 nt, have been regarded as promising biomarkers for cancer diagnosis and fish diseases. Here, we extracted the RNA from mucus of C. semilaevis and constructed the differential expression profiles of piRNAs between the sick fish (MS) and healthy fish (MC). We identified 45,696 differentially expressed piRNAs including 22,735 up-regulated piRNAs and 22,961 down-regulated piRNAs in MS group compared with MC group. The GO enrichment and KEGG pathway enrichment analyses of the differential piRNAs were carried out. The result showed immunity-related target genes mainly involved in immune system process, response to stimulus, cell killing, immune system, infectious diseases and cell growth and death. The 10 most differentially expressed piRNAs were chosen to perform the qRT-PCR, while only seven piRNAs were consistent with the sequence result. Compared with MC group, the expression levels of piR-mmu-72173>piR-rno-62831>piR-xtr-704880, piR-dme-15546979, piR-mmu-49941660, piR-mmu-29283297 and piR-mmu-1758399 were significantly lower, and piR-gga-10574 and piR-gga-134812 were significantly higher in MS group. These piRNAs may be potential biomarkers during the V. harveyi infection of C. semilaevis. This study could provide a new method to identify the infection status of C. semilaevis and understand better about the innate and adaptive immune system in C. semilaevis during bacterial infection.
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Affiliation(s)
- Na Zhao
- Southern Marine science and engineering Guangdong laboratory-Zhanjiang, Guangdong Ocean University, Zhanjiang, China
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources (Shanghai Ocean University), Shanghai Ocean University, Shanghai, China
| | - Qiuxia Deng
- Southern Marine science and engineering Guangdong laboratory-Zhanjiang, Guangdong Ocean University, Zhanjiang, China
| | - Chunhua Zhu
- Southern Marine science and engineering Guangdong laboratory-Zhanjiang, Guangdong Ocean University, Zhanjiang, China
| | - Bo Zhang
- Southern Marine science and engineering Guangdong laboratory-Zhanjiang, Guangdong Ocean University, Zhanjiang, China
- Tianjin Fisheries Research Institute, Tianjin, China
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8
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Rengaraj D, Cha DG, Park KJ, Lee KY, Woo SJ, Han JY. Finer resolution analysis of transcriptional programming during the active migration of chicken primordial germ cells. Comput Struct Biotechnol J 2022; 20:5911-5924. [PMID: 36382185 PMCID: PMC9636429 DOI: 10.1016/j.csbj.2022.10.034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2022] [Revised: 10/04/2022] [Accepted: 10/21/2022] [Indexed: 12/01/2022] Open
Abstract
Primordial germ cells (PGCs) in chickens polarize and move passively toward the anterior region by the morphogenetic movement of the embryo. Further migration of PGCs towards the genital ridge via the germinal crescent region and blood vessels occurs actively through the chemoattractive signals. The mechanisms of initiation of PGCs migration, lodging the PGCs in the vascular system, and colonization of PGCs in the gonads are well-studied. However, transcriptome sequencing-based cues directing the migration of the PGCs towards gonads, some of the relevant molecules, biological processes, and transcription factors (TFs) are less studied in chickens. The current study comprehensively interprets the transcriptional programming of PGCs during their active migration (E2.5 to E8). Current results revealed several vital understandings, including a set of genes that upregulated male-specifically (XPA, GNG10, RPL17, RPS23, and NDUFS4) or female-specifically (HINTW, NIPBL, TERAL2, ATP5F1AW, and SMAD2W) in migrating PGCs, and transcriptionally distinct PGCs, particularly in the gonadal environment. We identified DNA methylation and histone modification-associated genes that are novel in chicken PGCs and show a time-dependent enrichment in migrating PGCs. We further identified a large number of differentially expressed genes (DEGs, including TFs) in blood PGCs (at E2.5) compared to gonadal PGCs (at E8) in both sexes; however, this difference was greater in males. We also revealed the enriched biological processes and signaling pathways of significant DEGs identified commonly, male-specifically, or female-specifically between the PGCs isolated at E2.5, E6, and E8. Collectively, these analyses provide molecular insights into chicken PGCs during their active migration phase.
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Affiliation(s)
- Deivendran Rengaraj
- Department of Agricultural Biotechnology, and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul 08826, Korea
| | - Dong Gon Cha
- Department of New Biology, DGIST, Daegu 42988, Korea
| | - Kyung Je Park
- Department of Agricultural Biotechnology, and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul 08826, Korea
| | - Kyung Youn Lee
- Department of Agricultural Biotechnology, and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul 08826, Korea
| | - Seung Je Woo
- Department of Agricultural Biotechnology, and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul 08826, Korea
| | - Jae Yong Han
- Department of Agricultural Biotechnology, and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul 08826, Korea
- Corresponding author at: Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul 08826, Korea.
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9
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Role of microRNA and long non-coding RNA in Marek's disease tumorigenesis in chicken. Res Vet Sci 2021; 135:134-142. [PMID: 33485054 DOI: 10.1016/j.rvsc.2021.01.007] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2020] [Revised: 01/03/2021] [Accepted: 01/07/2021] [Indexed: 12/11/2022]
Abstract
Marek's disease virus (MDV), the causative agent of Marek's disease (MD), results in highly infectious phymatosis, lymphatic tissue hyperplasia, and neoplasia. MD is associated with high morbidity and mortality rate. Non-coding RNAs (ncRNAs) entails long non-coding RNA (lncRNA) and microRNA (miRNA). Numerous studies have reported that specific miRNAs and lncRNAs participate in multiple cellular processes, such as proliferation, migration, and tumor cell invasion. Specialized miRNAs and lncRNAs militate a similar role in MD tumor oncogenesis. Despite its growing popularity, only a few reviews are available on ncRNA in MDV tumor oncogenes. Herein, we summarized the role of the miRNAs and lncRNAs in MD tumorigenesis. Altogether, we brought forth the research issues, such as MD prevention, screening, regulatory network formation, novel miRNAs, and lncRNAs analysis in MD that needs to be explored further. This review provides a theoretical platform for the further analysis of miRNAs and lncRNAs functions and the prevention and control of MD and malignancies in domestic animals.
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Lee KY, Lee HJ, Choi HJ, Han ST, Lee KH, Park KJ, Park JS, Jung KM, Kim YM, Han HJ, Han JY. Highly elevated base excision repair pathway in primordial germ cells causes low base editing activity in chickens. FASEB J 2020; 34:15907-15921. [PMID: 33031594 DOI: 10.1096/fj.202001065rrr] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Revised: 09/11/2020] [Accepted: 09/16/2020] [Indexed: 11/11/2022]
Abstract
Base editing technology enables the generation of precisely genome-modified animal models. In this study, we applied base editing to chicken, an important livestock animal in the fields of agriculture, nutrition, and research through primordial germ cell (PGC)-mediated germline transmission. Using this approach, we successfully produced two genome-modified chicken lines harboring mutations in the genes encoding ovotransferrin (TF) and myostatin (MSTN); however, only 55.5% and 35.7% of genome-modified chickens had the desired base substitutions in TF and MSTN, respectively. To explain the low base-editing activity, we performed molecular analysis to compare DNA repair pathways between PGCs and the chicken fibroblast cell line DF-1. The results revealed that base excision repair (BER)-related genes were significantly elevated in PGCs relative to DF-1 cells. Subsequent functional studies confirmed that the editing activity could be regulated by modulating the expression of uracil N-glycosylase (UNG), an upstream gene of the BER pathway. Collectively, our findings indicate that the distinct DNA repair property of chicken PGCs causes low editing activity during genome modification, however, modulation of BER functions could promote the production of genome-modified organisms with the desired genotypes.
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Affiliation(s)
- Kyung Youn Lee
- Department of Agricultural Biotechnology and Research Institute of Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University, Seoul, Korea
| | - Hong Jo Lee
- Department of Agricultural Biotechnology and Research Institute of Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University, Seoul, Korea
| | - Hee Jung Choi
- Department of Agricultural Biotechnology and Research Institute of Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University, Seoul, Korea
| | - Soo Taek Han
- Department of Agricultural Biotechnology and Research Institute of Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University, Seoul, Korea
| | - Kyu Hyuk Lee
- Department of Agricultural Biotechnology and Research Institute of Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University, Seoul, Korea
| | - Kyung Je Park
- Department of Agricultural Biotechnology and Research Institute of Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University, Seoul, Korea
| | - Jin Se Park
- Department of Agricultural Biotechnology and Research Institute of Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University, Seoul, Korea
| | - Kyung Min Jung
- Department of Agricultural Biotechnology and Research Institute of Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University, Seoul, Korea
| | - Young Min Kim
- Department of Agricultural Biotechnology and Research Institute of Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University, Seoul, Korea
| | - Ho Jae Han
- Department of Veterinary Physiology, College of Veterinary Medicine, Research Institute for Veterinary Science, BK21 PLUS Program for Creative Veterinary Science Research, Seoul National University, Seoul, Korea
| | - Jae Yong Han
- Department of Agricultural Biotechnology and Research Institute of Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University, Seoul, Korea
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11
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Rengaraj D, Hwang YS, Lee HC, Han JY. Zygotic genome activation in the chicken: a comparative review. Cell Mol Life Sci 2020; 77:1879-1891. [PMID: 31728579 PMCID: PMC11104987 DOI: 10.1007/s00018-019-03360-6] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2019] [Revised: 10/09/2019] [Accepted: 10/30/2019] [Indexed: 02/06/2023]
Abstract
Maternal RNAs and proteins in the oocyte contribute to early embryonic development. After fertilization, these maternal factors are cleared and embryonic development is determined by an individual's own RNAs and proteins, in a process called the maternal-to-zygotic transition. Zygotic transcription is initially inactive, but is eventually activated by maternal transcription factors. The timing and molecular mechanisms involved in zygotic genome activation (ZGA) have been well-described in many species. Among birds, a transcriptome-based understanding of ZGA has only been explored in chickens by RNA sequencing of intrauterine embryos. RNA sequencing of chicken intrauterine embryos, including oocytes, zygotes, and Eyal-Giladi and Kochav (EGK) stages I-X has enabled the identification of differentially expressed genes between consecutive stages. These studies have revealed that there are two waves of ZGA: a minor wave at the one-cell stage (shortly after fertilization) and a major wave between EGK.III and EGK.VI (during cellularization). In the chicken, the maternal genome is activated during minor ZGA and the paternal genome is quiescent until major ZGA to avoid transcription from supernumerary sperm nuclei. In this review, we provide a detailed overview of events in intrauterine embryonic development in birds (and particularly in chickens), as well as a transcriptome-based analysis of ZGA.
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Affiliation(s)
- Deivendran Rengaraj
- Department of Agricultural Biotechnology, and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, 08826, South Korea
| | - Young Sun Hwang
- Department of Agricultural Biotechnology, and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, 08826, South Korea
- Department of Biomedical Sciences, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Hyung Chul Lee
- Department of Agricultural Biotechnology, and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, 08826, South Korea
- Department of Cell and Developmental Biology, University College London, London, WC1E 6BT, UK
| | - Jae Yong Han
- Department of Agricultural Biotechnology, and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, 08826, South Korea.
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12
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Abstract
Transposons are major genome constituents that can mobilize and trigger mutations, DNA breaks and chromosome rearrangements. Transposon silencing is particularly important in the germline, which is dedicated to transmission of the inherited genome. Piwi-interacting RNAs (piRNAs) guide a host defence system that transcriptionally and post-transcriptionally silences transposons during germline development. While germline control of transposons by the piRNA pathway is conserved, many piRNA pathway genes are evolving rapidly under positive selection, and the piRNA biogenesis machinery shows remarkable phylogenetic diversity. Conservation of core function combined with rapid gene evolution is characteristic of a host–pathogen arms race, suggesting that transposons and the piRNA pathway are engaged in an evolutionary tug of war that is driving divergence of the biogenesis machinery. Recent studies suggest that this process may produce biochemical incompatibilities that contribute to reproductive isolation and species divergence.
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Affiliation(s)
- Swapnil S Parhad
- Program in Molecular Medicine, University of Massachusetts Medical School , 373 Plantation Street, Worcester, MA 01605 , USA
| | - William E Theurkauf
- Program in Molecular Medicine, University of Massachusetts Medical School , 373 Plantation Street, Worcester, MA 01605 , USA
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13
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Li XZ. What can PIWI-interacting RNA research learn from chickens, and vice versa? CANADIAN JOURNAL OF ANIMAL SCIENCE 2019. [DOI: 10.1139/cjas-2018-0252] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
P-element induced wimpy testis (PIWI) interacting RNA (piRNA) are essential for fertility, by protecting the integrity of the germ-line genome via silencing of transposable elements (TE). Because new TE are constantly invading the host genome, piRNA-producing loci are under continuous pressure to undergo rapid evolution. This arms race between TE and piRNA is a prime example of the genome being more plastic than previously thought. Historically, the study of piRNA and TE has benefited from the use of diverse model organisms, including worms, fruit fly, zebrafish, frogs, and mice. In domestic chickens, we recently identified a new mode of piRNA acquisition in which the host hijacks and converts a pre-existing provirus into a piRNA-producing locus to defend against Avian leukosis virus, an adaptive immune strategy similar to the prokaryotic CRISPR–Cas [clustered regularly interspaced short palindromic repeats (CRISPR) and CRISPR-associated (Cas)] system. This finding reveals a previously unrecognized mechanism of the host piRNA repertoire to rapidly evolve and target TE specifically. In this review, we will focus on both the unique and common features of chicken piRNA, as well as the advantages of using chickens as a model system, to address fundamental questions regarding piRNA acquisition in hosts. We will also comment on the potential application of piRNA for improving poultry health and reproductive efficiency.
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Affiliation(s)
- Xin Zhiguo Li
- Center for RNA Biology: From Genome to Therapeutics, Department of Biochemistry and Biophysics, University of Rochester Medical Center, Rochester, NY 14642, USA
- Center for RNA Biology: From Genome to Therapeutics, Department of Biochemistry and Biophysics, University of Rochester Medical Center, Rochester, NY 14642, USA
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14
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Lee BR, Rengaraj D, Choi HJ, Han JY. A novel F-box domain containing cyclin F like gene is required for maintaining the genome stability and survival of chicken primordial germ cells. FASEB J 2019; 34:1001-1017. [PMID: 31914591 DOI: 10.1096/fj.201901294r] [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: 05/23/2019] [Revised: 10/25/2019] [Accepted: 11/07/2019] [Indexed: 12/13/2022]
Abstract
The stability and survival of germ cells are controlled by the germline-specific genes, however, such genes are less known in the avian species. Using a microarray-based the National Center for Biotechnology Information Gene Expression Omnibus dataset, we found an unigene (Gga.9721) that upregulated in the chicken primordial germ cells (PGCs). The unigene showed 97% identities with an uncharacterized chicken cyclin F like gene. The predicted chicken cyclin F like gene was further characterized through expression and regulation in the chicken PGCs. The sequence analysis revealed that the gene shows identities with cyclin F gene and contains an F-box domain. The expression of chicken cyclin F like was detected specifically in the gonads, PGCs, and germline cells. The knockdown of cyclin F like gene resulted in DNA damage and apoptosis in the PGCs. The genes related to stemness and germness were downregulated, whereas, genes related to apoptosis and DNA damage response were increased in the PGCs after the knockdown of chicken cyclin F like. We further observed that the Nanog homeobox controlled the transcriptional activity of chicken cyclin F like gene in PGCs. Collectively, the chicken cyclin F like gene, which is not reported in any other species, is required for maintaining the genome stability of germ cells.
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Affiliation(s)
- Bo Ram Lee
- Department of Agricultural Biotechnology, and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, Korea.,Animal Biotechnology Division, National Institute of Animal Science, Rural Development Administration, Wanju-gun, Korea
| | - Deivendran Rengaraj
- Department of Agricultural Biotechnology, and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, Korea
| | - Hee Jung Choi
- Department of Agricultural Biotechnology, and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, Korea
| | - Jae Yong Han
- Department of Agricultural Biotechnology, and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, Korea
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15
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Zhang QL, Wang H, Zhu QH, Wang XX, Li YM, Chen JY, Morikawa H, Yang LF, Wang YJ. Genome-Wide Identification and Transcriptomic Analysis of MicroRNAs Across Various Amphioxus Organs Using Deep Sequencing. Front Genet 2019; 10:877. [PMID: 31616471 PMCID: PMC6775235 DOI: 10.3389/fgene.2019.00877] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2019] [Accepted: 08/21/2019] [Indexed: 01/28/2023] Open
Abstract
Amphioxus is the closest living invertebrate proxy of the vertebrate ancestor. Systematic gene identification and expression profile analysis of amphioxus organs are thus important for clarifying the molecular mechanisms of organ function formation and further understanding the evolutionary origin of organs and genes in vertebrates. The precise regulation of microRNAs (miRNAs) is crucial for the functional specification and differentiation of organs. In particular, those miRNAs that are expressed specifically in organs (OSMs) play key roles in organ identity, differentiation, and function. In this study, the genome-wide miRNA transcriptome was analyzed in eight organs of adult amphioxus Branchiostoma belcheri using deep sequencing. A total of 167 known miRNAs and 23 novel miRNAs (named novel_mir), including 139 conserved miRNAs, were discovered, and 79 of these were identified as OSMs. Additionally, analyses of the expression patterns of eight randomly selected known miRNAs demonstrated the accuracy of the miRNA deep sequencing that was used in this study. Furthermore, potentially OSM-regulated genes were predicted for each organ type. Functional enrichment of these predicted targets, as well as further functional analyses of known OSMs, was conducted. We found that the OSMs were potentially to be involved in organ-specific functions, such as epidermis development, gonad development, muscle cell development, proteolysis, lipid metabolism, and generation of neurons. Moreover, OSMs with non-organ-specific functions were detected and primarily include those related to innate immunity and response to stimuli. These findings provide insights into the regulatory roles of OSMs in various amphioxus organs.
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Affiliation(s)
- Qi-Lin Zhang
- Guangxi Key Laboratory of Beibu Gulf Marine Biodiversity Conservation, Ocean College, Beibu Gulf University, Qinzhou, China.,Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, China
| | - Hong Wang
- Guangxi Key Laboratory of Beibu Gulf Marine Biodiversity Conservation, Ocean College, Beibu Gulf University, Qinzhou, China
| | | | - Xiao-Xue Wang
- Guangxi Key Laboratory of Beibu Gulf Marine Biodiversity Conservation, Ocean College, Beibu Gulf University, Qinzhou, China
| | - Yi-Min Li
- Guangxi Key Laboratory of Beibu Gulf Marine Biodiversity Conservation, Ocean College, Beibu Gulf University, Qinzhou, China
| | - Jun-Yuan Chen
- Evo-devo Institute, School of Life Sciences, Nanjing University, Nanjing, China
| | - Hideaki Morikawa
- Faculty of Textile Science and Technology, Shinshu University, Ueda, Nagano, Japan
| | | | - Yu-Jun Wang
- Guangxi Key Laboratory of Beibu Gulf Marine Biodiversity Conservation, Ocean College, Beibu Gulf University, Qinzhou, China
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16
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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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Chen YC, Lin SP, Chang YY, Chang WP, Wei LY, Liu HC, Huang JF, Pain B, Wu SC. In vitro culture and characterization of duck primordial germ cells. Poult Sci 2019; 98:1820-1832. [PMID: 30462334 PMCID: PMC6414036 DOI: 10.3382/ps/pey515] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2018] [Accepted: 10/15/2018] [Indexed: 12/15/2022] Open
Abstract
This study aimed to isolate, culture, and characterize duck primordial germ cells (PGCs) and to compare these cells with chicken PGCs. We first cultured Muscovy duck (Cairina moschata) circulating PGCs and gonadal PGCs (gPGCs) in the modified serum-containing medium used to amplify chicken PGCs. gPGCs were found to proliferate better in serum-free chemically defined medium than in serum-containing medium. Thereafter, gPGCs were similarly isolated from 2 other duck breeds, the Pekin duck (Anas platyrhynchos) and the hybrid mule duck (C. moschata × A. platyrhynchos), and amplified for a limited period of time in the chemically defined culture condition, but sufficiently to be characterized and transplanted. Cultured gPGCs of all 3 duck breeds were characterized by Periodic acid-Schiff staining, immunocytochemical staining, and expression analysis of germline-specific and pluripotency genes. Cultured duck gPGCs colonized the gonads after being genetically labeled and injected into recipient embryos. Taken together, these results demonstrate that duck PGCs retain their germline characteristics after being isolated, expanded in vitro, and genetically modified. Further studies are required to establish the optimal conditions for long-term culture of duck PGCs, which may involve supplementing the culture medium with other growth factors or compounds.
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Affiliation(s)
- Yi-Chen Chen
- Institute of Biotechnology, National Taiwan University, Taipei 10672, Taiwan.,Univ Lyon, Université Lyon 1, Stem Cell and Brain Research Institute, U1208, USC1361, INSERM, INRA, Bron 69500, France
| | - Shau-Ping Lin
- Institute of Biotechnology, National Taiwan University, Taipei 10672, Taiwan.,Agricultural Biotechnology Research Center, Academia Sinica, Taipei 11529, Taiwan
| | - Yi-Ying Chang
- Ilan Branch, Livestock Research Institute, Council of Agriculture, Executive Yuan, Ilan 26846, Taiwan
| | - Wei-Peng Chang
- Ilan Branch, Livestock Research Institute, Council of Agriculture, Executive Yuan, Ilan 26846, Taiwan
| | - Liang-Yuan Wei
- Ilan Branch, Livestock Research Institute, Council of Agriculture, Executive Yuan, Ilan 26846, Taiwan
| | - Hsiu-Chou Liu
- Ilan Branch, Livestock Research Institute, Council of Agriculture, Executive Yuan, Ilan 26846, Taiwan
| | - Jeng-Fang Huang
- Ilan Branch, Livestock Research Institute, Council of Agriculture, Executive Yuan, Ilan 26846, Taiwan.,Livestock Research Institute, Council of Agriculture, Executive Yuan, Tainan 71246, Taiwan
| | - Bertrand Pain
- Univ Lyon, Université Lyon 1, Stem Cell and Brain Research Institute, U1208, USC1361, INSERM, INRA, Bron 69500, France
| | - Shinn-Chih Wu
- Institute of Biotechnology, National Taiwan University, Taipei 10672, Taiwan.,Department of Animal Science and Technology, National Taiwan University, Taipei 10672, Taiwan
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18
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Chang KW, Tseng YT, Chen YC, Yu CY, Liao HF, Chen YC, Tu YFE, Wu SC, Liu IH, Pinskaya M, Morillon A, Pain B, Lin SP. Stage-dependent piRNAs in chicken implicated roles in modulating male germ cell development. BMC Genomics 2018; 19:425. [PMID: 29859049 PMCID: PMC5984780 DOI: 10.1186/s12864-018-4820-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2018] [Accepted: 05/23/2018] [Indexed: 02/06/2023] Open
Abstract
Background The PIWI/piRNA pathway is a conserved machinery important for germ cell development and fertility. This piRNA-guided molecular machinery is best known for repressing derepressed transposable elements (TE) during epigenomic reprogramming. The extent to which piRNAs are involved in modulating transcripts beyond TEs still need to be clarified, and it may be a stage-dependent event. We chose chicken germline as a study model because of the significantly lower TE complexity in the chicken genome compared to mammalian species. Results We generated high-confidence piRNA candidates in various stages across chicken germline development by 3′-end-methylation-enriched small RNA sequencing and in-house bioinformatics analysis. We observed a significant developmental stage-dependent loss of TE association and a shifting of the ping-pong cycle signatures. Moreover, the stage-dependent reciprocal abundance of LINE retrotransposons, CR1-C, and its associated piRNAs implicated the developmental stage-dependent role of piRNA machinery. The stage dependency of piRNA expression and its potential functions can be better addressed by analyzing the piRNA precursors/clusters. Interestingly, the new piRNA clusters identified from embryonic chicken testes revealed evolutionary conservation between chickens and mammals, which was previously thought to not exist. Conclusions In this report, we provided an original chicken RNA resource and proposed an analytical methodology that can be used to investigate stage-dependent changes in piRNA compositions and their potential roles in TE regulation and beyond, and also revealed possible conserved functions of piRNAs in developing germ cells. Electronic supplementary material The online version of this article (10.1186/s12864-018-4820-9) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Kai-Wei Chang
- Genome and Systems Biology Degree Program, National Taiwan University, Taipei, 106, Taiwan.,Present Address: Graduate Institute of Brain and Mind Sciences, College of Medicine, National Taiwan University, Taipei, 10051, Taiwan
| | - Yen-Tzu Tseng
- Institute of Biotechnology, National Taiwan University, Taipei, 106, Taiwan.,Department of Animal Science and Technology, National Taiwan University, Taipei, 106, Taiwan
| | - Yi-Chen Chen
- Institute of Biotechnology, National Taiwan University, Taipei, 106, Taiwan.,Department of Animal Science and Technology, National Taiwan University, Taipei, 106, Taiwan.,Univ Lyon, Université Lyon 1, INSERM, INRA, Stem Cell and Brain Research Institute, U1208, USC1361, F-69500, Bron, France
| | - Chih-Yun Yu
- Institute of Biotechnology, National Taiwan University, Taipei, 106, Taiwan
| | - Hung-Fu Liao
- Institute of Biotechnology, National Taiwan University, Taipei, 106, Taiwan
| | - Yi-Chun Chen
- Institute of Biotechnology, National Taiwan University, Taipei, 106, Taiwan
| | - Yu-Fan Evan Tu
- Institute of Biotechnology, National Taiwan University, Taipei, 106, Taiwan
| | - Shinn-Chih Wu
- Department of Animal Science and Technology, National Taiwan University, Taipei, 106, Taiwan
| | - I-Hsuan Liu
- Department of Animal Science and Technology, National Taiwan University, Taipei, 106, Taiwan
| | - Marina Pinskaya
- ncRNA, epigenetic and genome fluidity, Institut Curie, Centre de Recherche, CNRS UMR 3244, PSL Research University, Université Pierre et Marie Curie, F-75005, Paris, France
| | - Antonin Morillon
- ncRNA, epigenetic and genome fluidity, Institut Curie, Centre de Recherche, CNRS UMR 3244, PSL Research University, Université Pierre et Marie Curie, F-75005, Paris, France
| | - Bertrand Pain
- Univ Lyon, Université Lyon 1, INSERM, INRA, Stem Cell and Brain Research Institute, U1208, USC1361, F-69500, Bron, France
| | - Shau-Ping Lin
- Genome and Systems Biology Degree Program, National Taiwan University, Taipei, 106, Taiwan. .,Institute of Biotechnology, National Taiwan University, Taipei, 106, Taiwan. .,Research Center for Developmental Biology and Regenerative Medicine, National Taiwan University, Taipei, 106, Taiwan. .,Agricultural Biotechnology Research Centre, Academia Sinica, Taipei, 106, Taiwan. .,Center for Systems Biology, National Taiwan University, Taipei, 106, Taiwan.
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Hwang YS, Seo M, Bang S, Kim H, Han JY. Transcriptional and translational dynamics during maternal‐to‐zygotic transition in early chicken development. FASEB J 2018; 32:2004-2011. [DOI: 10.1096/fj.201700955r] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Affiliation(s)
- Young Sun Hwang
- Department of Agricultural BiotechnologyResearch Institute of Agriculture and Life SciencesSeoul National UniversitySeoulKorea
| | - Minseok Seo
- C& K Genomics, SNU Research ParkSeoul National UniversitySeoulKorea
- Channing Division of Network MedicineHarvard Medical School and Brigham and Women's HospitalBostonMassachusettsUSA
| | - Sohyun Bang
- C& K Genomics, SNU Research ParkSeoul National UniversitySeoulKorea
| | - Heebal Kim
- Department of Agricultural BiotechnologyResearch Institute of Agriculture and Life SciencesSeoul National UniversitySeoulKorea
- C& K Genomics, SNU Research ParkSeoul National UniversitySeoulKorea
- Institute for Biomedical SciencesShinshu UniversityMinamiminowaJapan
| | - Jae Yong Han
- Department of Agricultural BiotechnologyResearch Institute of Agriculture and Life SciencesSeoul National UniversitySeoulKorea
- Institute for Biomedical SciencesShinshu UniversityMinamiminowaJapan
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20
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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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21
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Lee HJ, Lee HC, Han JY. Germline Modification and Engineering in Avian Species. Mol Cells 2015; 38:743-9. [PMID: 26333275 PMCID: PMC4588716 DOI: 10.14348/molcells.2015.0225] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2015] [Revised: 08/26/2015] [Accepted: 08/27/2015] [Indexed: 12/21/2022] Open
Abstract
Production of genome-edited animals using germline-competent cells and genetic modification tools has provided opportunities for investigation of biological mechanisms in various organisms. The recently reported programmed genome editing technology that can induce gene modification at a target locus in an efficient and precise manner facilitates establishment of animal models. In this regard, the demand for genome-edited avian species, which are some of the most suitable model animals due to their unique embryonic development, has also increased. Furthermore, germline chimera production through long-term culture of chicken primordial germ cells (PGCs) has facilitated research on production of genome-edited chickens. Thus, use of avian germline modification is promising for development of novel avian models for research of disease control and various biological mechanisms. Here, we discuss recent progress in genome modification technology in avian species and its applications and future strategies.
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Affiliation(s)
- Hong Jo Lee
- Department of Agricultural Biotechnology, College of Agriculture and Life Sciences, and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul 151-921,
Korea
| | - Hyung Chul Lee
- Department of Cell and Developmental Biology, University College London, Gower Street, London WC1E 6BT,
UK
| | - Jae Yong Han
- Department of Agricultural Biotechnology, College of Agriculture and Life Sciences, and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul 151-921,
Korea
- Institute for Biomedical Sciences, Shinshu University, 8304 Minamiminowa, Kamiina, Nagano 399-4598,
Japan
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