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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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Wang T, Leng D, Cai Z, Chen B, Li J, Kui H, Li D, Li Z. Insights into left-right asymmetric development of chicken ovary at the single-cell level. J Genet Genomics 2024:S1673-8527(24)00210-8. [PMID: 39147128 DOI: 10.1016/j.jgg.2024.08.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2024] [Revised: 07/29/2024] [Accepted: 08/02/2024] [Indexed: 08/17/2024]
Abstract
Avian ovaries develop asymmetrically apart from prey birds, with only the left ovary growing more towards functional organs. Here, we analyze over 135,000 cells from chick's left and right ovaries at six distinct embryonic developmental stages utilizing single-cell transcriptome sequencing. We delineate gene expression patterns across 15 cell types within these embryo ovaries, revealing side-specific development. The left ovaries exhibit cortex cells, zygotene germ cells, and transcriptional changes unique to the left side. Differential gene expression analysis further identifies specific markers and pathways active in these cell types, highlighting the asymmetry in ovarian development. A fine-scale analysis of the germ cell meiotic transcriptome reveals seven distinct clusters with gene expression patterns specific to various meiotic stages. The study also identifies signaling pathways and intercellular communications, particularly between pre-granulosa and germ cells. Spatial transcriptome analysis shows the asymmetry, demonstrating cortex cells exclusively in the left ovary, modulating neighboring cell types through putative secreted signaling molecules. Overall, this single-cell analysis provides insights into the molecular mechanisms of the asymmetric development of avian ovaries, particularly the significant role of cortex cells in the left ovary.
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Affiliation(s)
- Tao Wang
- School of Pharmacy, Chengdu University, Chengdu, Sichuan 610106, China
| | - Dong Leng
- School of Pharmacy, Chengdu University, Chengdu, Sichuan 610106, China
| | - Zhongkun Cai
- School of Pharmacy, Chengdu University, Chengdu, Sichuan 610106, China
| | - Binlong Chen
- College of Animal Science, Xichang University, Xichang, Sichuan 615000, China
| | - Jing Li
- School of Agriculture and Life Sciences, Kunming University, Kunming, Yunnan 650214, China
| | - Hua Kui
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, Sichuan 611130, China
| | - Diyan Li
- School of Pharmacy, Chengdu University, Chengdu, Sichuan 610106, China.
| | - Zhuanjian Li
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou, Henan 450046, China.
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Kress C, Jouneau L, Pain B. Reinforcement of repressive marks in the chicken primordial germ cell epigenetic signature: divergence from basal state resetting in mammals. Epigenetics Chromatin 2024; 17:11. [PMID: 38671530 PMCID: PMC11046797 DOI: 10.1186/s13072-024-00537-7] [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: 12/12/2023] [Accepted: 04/17/2024] [Indexed: 04/28/2024] Open
Abstract
BACKGROUND In mammals, primordial germ cells (PGCs), the embryonic precursors of the germline, arise from embryonic or extra-embryonic cells upon induction by the surrounding tissues during gastrulation, according to mechanisms which are elucidated in mice but remain controversial in primates. They undergo genome-wide epigenetic reprogramming, consisting of extensive DNA demethylation and histone post-translational modification (PTM) changes, toward a basal, euchromatinized state. In contrast, chicken PGCs are specified by preformation before gastrulation based on maternally-inherited factors. They can be isolated from the bloodstream during their migration to the genital ridges. Our prior research highlighted differences in the global epigenetic profile of cultured chicken PGCs compared with chicken somatic cells and mammalian PGCs. This study investigates the acquisition and evolution of this profile during development. RESULTS Quantitative analysis of global DNA methylation and histone PTMs, including their distribution, during key stages of chicken early development revealed divergent PGC epigenetic changes compared with mammals. Unlike mammalian PGCs, chicken PGCs do not undergo genome-wide DNA demethylation or exhibit a decrease in histone H3 lysine 9 dimethylation. However, chicken PGCs show 5‑hydroxymethylcytosine loss, macroH2A redistribution, and chromatin decompaction, mirroring mammalian processes. Chicken PGCs initiate their epigenetic signature during migration, progressively accumulating high global levels of H3K9me3, with preferential enrichment in inactive genome regions. Despite apparent global chromatin decompaction, abundant heterochromatin marks, including repressive histone PTMs, HP1 variants, and DNA methylation, persists in chicken PGCs, contrasting with mammalian PGCs. CONCLUSIONS Chicken PGCs' epigenetic signature does not align with the basal chromatin state observed in mammals, suggesting a departure from extensive epigenetic reprogramming. Despite disparities in early PGC development, the persistence of several epigenetic features shared with mammals implies their involvement in chromatin-regulated germ cell properties, with the distinctive elevation of chicken-specific H3K9me3 potentially participating in these processes.
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Affiliation(s)
- Clémence Kress
- Univ Lyon, Université Lyon 1, INSERM, INRAE, U1208, USC1361, Stem Cell and Brain Research Institute, Bron, France.
| | - Luc Jouneau
- Université Paris-Saclay, UVSQ, INRAE, BREED, Jouy-en-Josas, 78350, France
- Ecole Nationale Vétérinaire d'Alfort, BREED, Maisons-Alfort, 94700, France
| | - Bertrand Pain
- Univ Lyon, Université Lyon 1, INSERM, INRAE, U1208, USC1361, Stem Cell and Brain Research Institute, Bron, France
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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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Female Germ Cell Development in Chickens and Humans: The Chicken Oocyte Enriched Genes Convergent and Divergent with the Human Oocyte. Int J Mol Sci 2022; 23:ijms231911412. [PMID: 36232712 PMCID: PMC9570461 DOI: 10.3390/ijms231911412] [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: 08/17/2022] [Revised: 09/17/2022] [Accepted: 09/21/2022] [Indexed: 11/16/2022] Open
Abstract
The development of germ cells and other physiological events in the differentiated ovary of humans are highly conserved with several mammalian species, except for the differences in timing. However, comparative knowledge on this topic is very scarce with respect to humans and lower vertebrates, such as chickens. In chickens, female germ cells enter into meiosis around embryonic day (E) 15.5 and are arrested in meiotic prophase I as primary oocytes. The oocytes arrested in meiosis I are accumulated in germ-cell cysts; shortly after hatching, they are enclosed by flattened granulosa cells in order to form primordial follicles. In humans, the process of meiotic recombination in female germ cells begins in the 10–11th week of gestation, and primordial follicles are formed at around week 20. In this review, we comprehensively elucidate both the conservation and the species-specific differences between chickens and humans with respect to germ cell, oocyte, and follicle development. Importantly, we provide functional insights into a set of chicken oocyte enriched genes (from E16 to 1 week post-hatch) that show convergent and divergent expression patterns with respect to the human oocyte (from week 11 to 26).
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Choi HJ, Jung KM, Rengaraj D, Lee KY, Yoo E, Kim TH, Han JY. Single-cell RNA sequencing of mitotic-arrested prospermatogonia with DAZL::GFP chickens and revealing unique epigenetic reprogramming of chickens. J Anim Sci Biotechnol 2022; 13:64. [PMID: 35659766 PMCID: PMC9169296 DOI: 10.1186/s40104-022-00712-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Accepted: 04/01/2022] [Indexed: 11/21/2022] Open
Abstract
Background Germ cell mitotic arrest is conserved in many vertebrates, including birds, although the time of entry or exit into quiescence phase differs. Mitotic arrest is essential for the normal differentiation of male germ cells into spermatogonia and accompanies epigenetic reprogramming and meiosis inhibition from embryonic development to post-hatch. However, mitotic arrest was not well studied in chickens because of the difficulty in obtaining pure germ cells from relevant developmental stage. Results We performed single-cell RNA sequencing to investigate transcriptional dynamics of male germ cells during mitotic arrest in DAZL::GFP chickens. Using differentially expressed gene analysis and K-means clustering to analyze cells at different developmental stages (E12, E16, and hatch), we found that metabolic and signaling pathways were regulated, and that the epigenome was reprogrammed during mitotic arrest. In particular, we found that histone H3K9 and H3K14 acetylation (by HDAC2) and DNA demethylation (by DNMT3B and HELLS) led to a transcriptionally permissive chromatin state. Furthermore, we found that global DNA demethylation occurred gradually after the onset of mitotic arrest, indicating that the epigenetic-reprogramming schedule of the chicken genome differs from that of the mammalian genome. DNA hypomethylation persisted after hatching, and methylation was slowly re-established 3 weeks later. Conclusions We found a unique epigenetic-reprogramming schedule of mitotic-arrested chicken prospermatogonia and prolonged hypomethylation after hatching. This will provide a foundation for understanding the process of germ-cell epigenetic regulation in several species for which this process is not clearly described. Our findings on the biological processes related to sex-specific differentiation of prospermatogonia could help studying germline development in vitro more elaborately. Supplementary Information The online version contains supplementary material available at 10.1186/s40104-022-00712-4.
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Affiliation(s)
- Hyeon Jeong Choi
- Department of Agricultural Biotechnology and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, 08826, South Korea
| | - Kyung Min Jung
- Department of Agricultural Biotechnology and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, 08826, South Korea
| | - Deivendran Rengaraj
- Department of Agricultural Biotechnology and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, 08826, South Korea
| | - Kyung Youn Lee
- Department of Agricultural Biotechnology and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, 08826, South Korea
| | - Eunhui Yoo
- Department of Agricultural Biotechnology and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, 08826, South Korea
| | - Tae Hyun Kim
- Department of Animal Science, Pennsylvania State University, State College, PA, 16801, USA
| | - 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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Rengaraj D, Cha DG, Lee HJ, Lee KY, Choi YH, Jung KM, Kim YM, Choi HJ, Choi HJ, Yoo E, Woo SJ, Park JS, Park KJ, Kim JK, Han JY. Dissecting chicken germ cell dynamics by combining a germ cell tracing transgenic chicken model with single-cell RNA sequencing. Comput Struct Biotechnol J 2022; 20:1654-1669. [PMID: 35465157 PMCID: PMC9010679 DOI: 10.1016/j.csbj.2022.03.040] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Revised: 03/30/2022] [Accepted: 03/31/2022] [Indexed: 02/02/2023] Open
Abstract
Avian germ cells can be distinguished by certain characteristics during development. On the basis of these characteristics, germ cells can be used for germline transmission. However, the dynamic transcriptional landscape of avian germ cells during development is unknown. Here, we used a novel germ-cell-tracing method to monitor and isolate chicken germ cells at different stages of development. We targeted the deleted in azoospermia like (DAZL) gene, a germ-cell-specific marker, to integrate a green fluorescent protein (GFP) reporter gene without affecting endogenous DAZL expression. The resulting transgenic chickens (DAZL::GFP) were used to uncover the dynamic transcriptional landscape of avian germ cells. Single-cell RNA sequencing of 4,752 male and 13,028 female DAZL::GFP germ cells isolated from embryonic day E2.5 to 1 week post-hatch identified sex-specific developmental stages (4 stages in male and 5 stages in female) and trajectories (apoptosis and meiosis paths in female) of chicken germ cells. The male and female trajectories were characterized by a gradual acquisition of stage-specific transcription factor activities. We also identified evolutionary conserved and species-specific gene expression programs during both chicken and human germ-cell development. Collectively, these novel analyses provide mechanistic insights into chicken germ-cell development.
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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
| | - Dong Gon Cha
- Department of New Biology, DGIST, Daegu 42988, South Korea
| | - Hong Jo Lee
- Department of Agricultural Biotechnology, and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul 08826, South Korea
| | - Kyung Youn Lee
- Department of Agricultural Biotechnology, and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul 08826, South Korea
| | - Yoon Ha Choi
- Department of New Biology, DGIST, Daegu 42988, South Korea
- Department of Life Sciences, Pohang University of Science and Technology (POSTECH), Pohang 37673, South Korea
| | - Kyung Min Jung
- Department of Agricultural Biotechnology, and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul 08826, South Korea
| | - Young Min Kim
- Department of Agricultural Biotechnology, and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul 08826, South Korea
| | - Hee Jung Choi
- Department of Agricultural Biotechnology, and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul 08826, South Korea
| | - Hyeon Jeong Choi
- Department of Agricultural Biotechnology, and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul 08826, South Korea
| | - Eunhui Yoo
- Department of Agricultural Biotechnology, and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul 08826, South Korea
| | - Seung Je Woo
- Department of Agricultural Biotechnology, and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul 08826, South Korea
| | - Jin Se Park
- Department of Agricultural Biotechnology, and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul 08826, South Korea
| | - Kyung Je Park
- Department of Agricultural Biotechnology, and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul 08826, South Korea
| | - Jong Kyoung Kim
- Department of New Biology, DGIST, Daegu 42988, South Korea
- Department of Life Sciences, Pohang University of Science and Technology (POSTECH), Pohang 37673, South Korea
- Corresponding authors at: POSTECH, 77 Cheongam-ro, Nam-gu, Pohang-si, Gyeongsangbuk-do 37673, South Korea (J.K. Kim). Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul 08826, South Korea (J.Y. Han).
| | - Jae Yong Han
- Department of Agricultural Biotechnology, and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul 08826, South Korea
- Corresponding authors at: POSTECH, 77 Cheongam-ro, Nam-gu, Pohang-si, Gyeongsangbuk-do 37673, South Korea (J.K. Kim). Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul 08826, South Korea (J.Y. Han).
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8
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Yi Q, Xie W, Sun W, Sun W, Liao Y. A Concise Review of MicroRNA-383: Exploring the Insights of Its Function in Tumorigenesis. J Cancer 2022; 13:313-324. [PMID: 34976192 PMCID: PMC8692686 DOI: 10.7150/jca.64846] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Accepted: 11/10/2021] [Indexed: 12/15/2022] Open
Abstract
MicroRNAs (miRNAs) are small noncoding RNAs that commonly have 18-22 nucleotides and play important roles in the regulation of gene expression via directly binding to the 3'-UTR of target mRNAs. Approximately 50% of human genes are regulated by miRNAs and they are involved in many human diseases, including various types of cancers. Recently, microRNA-383 (miR-383) has been identified as being aberrantly expressed in multiple cancers, such as malignant melanoma, colorectal cancer, hepatocellular cancer, and glioma. Increasing evidence suggests that miR-383 participates in tumorigenic events including proliferation, apoptosis, invasion, and metastasis as well as drug resistance. Although downstream targets including CCND1, LDHA, VEGF, and IGF are illustrated to be regulated by miR-383, its roles in carcinogenesis are still ambiguous and the underlying mechanisms are still unclear. Herein, we review the latest studies on miR-383 and summarize its functions in human cancers and other diseases. The goal of this review is to provide new strategies for targeted therapy and further investigations.
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Affiliation(s)
- Qian Yi
- The Central Laboratory, Shenzhen Second People's Hospital/First Affiliated Hospital of Shenzhen University Health Science Center, Shenzhen, Guangdong 518035, P.R. China.,Department of Physiology, School of Basic Medical Science, Southwest Medical University, Luzhou, Sichuan province 646099, P.R. China.,Laboratory of Anesthesia and Organ Protection, Southwest Medical University, Luzhou, Sichuan province 646099, P.R. China
| | - Wei Xie
- Department of Orthopedics, Shenzhen Second People's Hospital/First Affiliated Hospital of Shenzhen University Health Science Center, Shenzhen, Guangdong 518035, P.R. China
| | - Wei Sun
- Department of Orthopedics, Shenzhen Second People's Hospital/First Affiliated Hospital of Shenzhen University Health Science Center, Shenzhen, Guangdong 518035, P.R. China
| | - Weichao Sun
- The Central Laboratory, Shenzhen Second People's Hospital/First Affiliated Hospital of Shenzhen University Health Science Center, Shenzhen, Guangdong 518035, P.R. China.,Department of Orthopedics, Shenzhen Second People's Hospital/First Affiliated Hospital of Shenzhen University Health Science Center, Shenzhen, Guangdong 518035, P.R. China
| | - Yi Liao
- The Central Laboratory, Shenzhen Second People's Hospital/First Affiliated Hospital of Shenzhen University Health Science Center, Shenzhen, Guangdong 518035, P.R. China
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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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10
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Lázár B, Szabadi NT, Anand M, Tóth R, Ecker A, Urbán M, Aponte MTS, Stepanova G, Hegyi Z, Homolya L, Várkonyi EP, Pain B, Gócza E. Effect of miR-302b MicroRNA Inhibition on Chicken Primordial Germ Cell Proliferation and Apoptosis Rate. Genes (Basel) 2021; 13:genes13010082. [PMID: 35052421 PMCID: PMC8774308 DOI: 10.3390/genes13010082] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Revised: 12/16/2021] [Accepted: 12/23/2021] [Indexed: 11/22/2022] Open
Abstract
The primordial germ cells (PGCs) are the precursors for both the oocytes and spermatogonia. Recently, a novel culture system was established for chicken PGCs, isolated from embryonic blood. The possibility of PGC long-term cultivation issues a new advance in germ cell preservation, biotechnology, and cell biology. We investigated the consequence of gga-miR-302b-5P (5P), gga-miR-302b-3P (3P) and dual inhibition (5P/3P) in two male and two female chicken PGC lines. In treated and control cell cultures, the cell number was calculated every four hours for three days by the XLS Imaging system. Comparing the cell number of control and treated lines on the first day, we found that male lines had a higher proliferation rate independently from the treatments. Compared to the untreated ones, the proliferation rate and the number of apoptotic cells were considerably reduced at gga-miR-302b-5P inhibition in all PGC lines on the third day of the cultivation. The control PGC lines showed a significantly higher proliferation rate than 3P inhibited lines on Day 3 in all PGC lines. Dual inhibition of gga-miR-302b mature miRNAs caused a slight reduction in proliferation rate, but the number of apoptotic cells increased dramatically. The information gathered by examining the factors affecting cell proliferation of PGCs can lead to new data in stem cell biology.
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Affiliation(s)
- Bence Lázár
- Animal Biotechnology Department, Institute of Genetics and Biotechnology, Hungarian University of Agriculture and Life Sciences, 2100 Godollo, Hungary; (B.L.); (N.T.S.); (M.A.); (R.T.); (A.E.); (M.U.); (M.T.S.A.)
- Institute for Farm Animal Gene Conservation, National Centre for Biodiversity and Gene Conservation, 2100 Godollo, Hungary;
| | - Nikolett Tokodyné Szabadi
- Animal Biotechnology Department, Institute of Genetics and Biotechnology, Hungarian University of Agriculture and Life Sciences, 2100 Godollo, Hungary; (B.L.); (N.T.S.); (M.A.); (R.T.); (A.E.); (M.U.); (M.T.S.A.)
| | - Mahek Anand
- Animal Biotechnology Department, Institute of Genetics and Biotechnology, Hungarian University of Agriculture and Life Sciences, 2100 Godollo, Hungary; (B.L.); (N.T.S.); (M.A.); (R.T.); (A.E.); (M.U.); (M.T.S.A.)
| | - Roland Tóth
- Animal Biotechnology Department, Institute of Genetics and Biotechnology, Hungarian University of Agriculture and Life Sciences, 2100 Godollo, Hungary; (B.L.); (N.T.S.); (M.A.); (R.T.); (A.E.); (M.U.); (M.T.S.A.)
| | - András Ecker
- Animal Biotechnology Department, Institute of Genetics and Biotechnology, Hungarian University of Agriculture and Life Sciences, 2100 Godollo, Hungary; (B.L.); (N.T.S.); (M.A.); (R.T.); (A.E.); (M.U.); (M.T.S.A.)
| | - Martin Urbán
- Animal Biotechnology Department, Institute of Genetics and Biotechnology, Hungarian University of Agriculture and Life Sciences, 2100 Godollo, Hungary; (B.L.); (N.T.S.); (M.A.); (R.T.); (A.E.); (M.U.); (M.T.S.A.)
| | - Maria Teresa Salinas Aponte
- Animal Biotechnology Department, Institute of Genetics and Biotechnology, Hungarian University of Agriculture and Life Sciences, 2100 Godollo, Hungary; (B.L.); (N.T.S.); (M.A.); (R.T.); (A.E.); (M.U.); (M.T.S.A.)
| | - Ganna Stepanova
- Faculty of Medicine, Institute of Translational Medicine, Semmelweis University, 1089 Budapest, Hungary;
| | - Zoltán Hegyi
- Institute of Enzymology, Research Centre for Natural Sciences, 1117 Budapest, Hungary; (Z.H.); (L.H.)
| | - László Homolya
- Institute of Enzymology, Research Centre for Natural Sciences, 1117 Budapest, Hungary; (Z.H.); (L.H.)
| | - Eszter Patakiné Várkonyi
- Institute for Farm Animal Gene Conservation, National Centre for Biodiversity and Gene Conservation, 2100 Godollo, Hungary;
| | - Bertrand Pain
- Stem-Cell and Brain Research Institute, USC1361 INRA, U1208 INSERM, 69675 Bron, France;
| | - Elen Gócza
- Animal Biotechnology Department, Institute of Genetics and Biotechnology, Hungarian University of Agriculture and Life Sciences, 2100 Godollo, Hungary; (B.L.); (N.T.S.); (M.A.); (R.T.); (A.E.); (M.U.); (M.T.S.A.)
- Correspondence:
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11
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Xu Z, Xie Y, Zhou C, Hu Q, Gu T, Yang J, Zheng E, Huang S, Xu Z, Cai G, Liu D, Wu Z, Hong L. Expression Pattern of Seminal Plasma Extracellular Vesicle Small RNAs in Boar Semen. Front Vet Sci 2020; 7:585276. [PMID: 33263017 PMCID: PMC7685987 DOI: 10.3389/fvets.2020.585276] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2020] [Accepted: 10/14/2020] [Indexed: 12/17/2022] Open
Abstract
Extracellular vesicles (EVs) regulate multiple physiological processes. Seminal plasma contains numerous EVs that may deliver functional molecules such as small RNAs (sRNAs) to the sperm. However, the RNA profiles in the boar seminal plasma extracellular vesicles (SP-EVs) and its function have not been characterized. The aim of this study was to characterize the functions and sRNA profiles in the boar SP-EVs using deep sequencing technology. Briefly, boar SP-EVs were isolated by differential ultracentrifugation and confirmed with a transmission electron microscope (TEM), nanoparticle tracking analysis (NTA), and Western blot. The isolated boar SP-EVs contained numerous and diverse sRNA families, including microRNAs (miRNAs, 9.45% of the total reads), PIWI-interacting RNAs (piRNAs, 15.25% of the total reads), messenger RNA fragments (mRNA, 25.30% of the total reads), and tRNA-derived small RNAs (tsRNA, 0.01% of the total reads). A total of 288 known miRNAs, 37 novel miRNA, and 19,749 piRNAs were identified in boar SP-EVs. The identified ssc-miR-21-5p may confer negative effects on sperm fertility based on a dual-luciferase reporter experiment. This study therefore provides an effective method to isolate SP-EVs and characterizes the sRNA profile.
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Affiliation(s)
- Zhiqian Xu
- National Engineering Research Center for Breeding Swine Industry, Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou, China.,Lingnan Guangdong Laboratory of Modern Agriculture, Guangzhou, China
| | - Yanshe Xie
- National Engineering Research Center for Breeding Swine Industry, Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou, China.,Lingnan Guangdong Laboratory of Modern Agriculture, Guangzhou, China
| | - Chen Zhou
- National Engineering Research Center for Breeding Swine Industry, Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou, China.,Lingnan Guangdong Laboratory of Modern Agriculture, Guangzhou, China
| | - Qun Hu
- National Engineering Research Center for Breeding Swine Industry, Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou, China.,Lingnan Guangdong Laboratory of Modern Agriculture, Guangzhou, China
| | - Ting Gu
- National Engineering Research Center for Breeding Swine Industry, Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou, China.,Lingnan Guangdong Laboratory of Modern Agriculture, Guangzhou, China
| | - Jie Yang
- National Engineering Research Center for Breeding Swine Industry, Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou, China.,Lingnan Guangdong Laboratory of Modern Agriculture, Guangzhou, China
| | - Enqin Zheng
- National Engineering Research Center for Breeding Swine Industry, Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou, China.,Lingnan Guangdong Laboratory of Modern Agriculture, Guangzhou, China
| | - Sixiu Huang
- National Engineering Research Center for Breeding Swine Industry, Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou, China.,Lingnan Guangdong Laboratory of Modern Agriculture, Guangzhou, China
| | - Zheng Xu
- National Engineering Research Center for Breeding Swine Industry, Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou, China.,Lingnan Guangdong Laboratory of Modern Agriculture, Guangzhou, China
| | - Gengyuan Cai
- National Engineering Research Center for Breeding Swine Industry, Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou, China.,Lingnan Guangdong Laboratory of Modern Agriculture, Guangzhou, China
| | - Dewu Liu
- National Engineering Research Center for Breeding Swine Industry, Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou, China.,Lingnan Guangdong Laboratory of Modern Agriculture, Guangzhou, China
| | - Zhenfang Wu
- National Engineering Research Center for Breeding Swine Industry, Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou, China.,Lingnan Guangdong Laboratory of Modern Agriculture, Guangzhou, China
| | - Linjun Hong
- National Engineering Research Center for Breeding Swine Industry, Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou, China.,Lingnan Guangdong Laboratory of Modern Agriculture, Guangzhou, China
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12
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DNA methylation in the vertebrate germline: balancing memory and erasure. Essays Biochem 2020; 63:649-661. [PMID: 31755927 DOI: 10.1042/ebc20190038] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2019] [Revised: 10/02/2019] [Accepted: 10/03/2019] [Indexed: 02/07/2023]
Abstract
Cytosine methylation is a DNA modification that is critical for vertebrate development and provides a plastic yet stable information module in addition to the DNA code. DNA methylation memory establishment, maintenance and erasure is carefully balanced by molecular machinery highly conserved among vertebrates. In mammals, extensive erasure of epigenetic marks, including 5-methylcytosine (5mC), is a hallmark of early embryo and germline development. Conversely, global cytosine methylation patterns are preserved in at least some non-mammalian vertebrates over comparable developmental windows. The evolutionary mechanisms which drove this divergence are unknown, nevertheless a direct consequence of retaining epigenetic memory in the form of 5mC is the enhanced potential for transgenerational epigenetic inheritance (TEI). Given that DNA methylation dynamics remains underexplored in most vertebrate lineages, the extent of information transferred to offspring by epigenetic modification might be underestimated.
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13
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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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14
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Kamalidehghan B, Habibi M, Afjeh SS, Shoai M, Alidoost S, Almasi Ghale R, Eshghifar N, Pouresmaeili F. The Importance of Small Non-Coding RNAs in Human Reproduction: A Review Article. APPLICATION OF CLINICAL GENETICS 2020; 13:1-11. [PMID: 32021379 PMCID: PMC6956659 DOI: 10.2147/tacg.s207491] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/04/2019] [Accepted: 12/04/2019] [Indexed: 12/14/2022]
Abstract
Background MicroRNAs (miRNA) play a key role in the regulation of gene expression through the translational suppression and control of post-transcriptional modifications. Aim Previous studies demonstrated that miRNAs conduct the pathways involved in human reproduction including maintenance of primordial germ cells (PGCs), spermatogenesis, oocyte maturation, folliculogenesis and corpus luteum function. The association of miRNA expression with infertility, polycystic ovary syndrome (PCOS), premature ovarian failure (POF), and repeated implantation failure (RIF) was previously revealed. Furthermore, there are evidences of the importance of miRNAs in embryonic development and implantation. Piwi-interacting RNAs (piRNAs) and miRNAs play an important role in the post-transcriptional regulatory processes of germ cells. Indeed, the investigation of small RNAs including miRNAs and piRNAs increase our understanding of the mechanisms involved in fertility. In this review, the current knowledge of microRNAs in embryogenesis and fertility is discussed. Conclusion Further research is necessary to provide new insights into the application of small RNAs in the diagnosis and therapeutic approaches to infertility.
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Affiliation(s)
- Behnam Kamalidehghan
- Department of Medical Genetics, Faculty of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Mohsen Habibi
- Central Laboratory, Faculty of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Sara S Afjeh
- Department of Medical Genetics, Faculty of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Maryam Shoai
- Department of Molecular Neuroscience, UCL Institute of Neurology, London, UK
| | - Saeideh Alidoost
- Department of Biology, Science and Research Branch, Islamic Azad University, Tehran, Iran
| | - Rouzbeh Almasi Ghale
- Department of Biology, Science and Research Branch, Islamic Azad University, Tehran, Iran
| | - Nahal Eshghifar
- Department of Cellular and Molecular Biology, Faculty of Advanced Science and Technology, Tehran Medical Sciences, Islamic Azad University, Tehran, Iran and Men's Health and Reproductive Health Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Farkhondeh Pouresmaeili
- Department of Medical Genetics, Faculty of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran.,Men's Health and Reproductive Health Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran
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15
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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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16
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Abdalla BA, Li Z, Ouyang H, Jebessa E, Sun T, Yu JA, Cai B, Chen B, Nie Q, Zhang X. A Novel Dnmt3a1 Transcript Inhibits Adipogenesis. Front Physiol 2018; 9:1270. [PMID: 30333755 PMCID: PMC6176318 DOI: 10.3389/fphys.2018.01270] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2018] [Accepted: 08/21/2018] [Indexed: 12/17/2022] Open
Abstract
DNA (cytosine-5)-methyltransferase 3a (Dnmt3a) is an enzyme that catalyzes the transfer of methyl groups to specific CpG forms in DNA. In mammals, two variant transcripts of Dnmt3a have been successfully identified. To the best of our knowledge, no Dnmt3a transcripts in an avian have been successfully identified. This study was performed to detect different transcripts of Dnmt3a in chickens and to examine whether a novel Dnmt3a transcript named Dnmt3a1 may regulate adipogenesis. In addition to cloning, sequencing, transcript detection, and expression studies, a novel Dnmt3a1 transcript overexpression and knockdown were conducted to explore the potential role of Dnmt3a1 in preadipocyte proliferation and the early stage of adipocyte differentiation. In chicken abdominal fat tissue, we detected a novel Dnmt3a1 transcript that differs from Dnmt3a by lacking 23 amino acids at the exon-1/exon-2 border. Dnmt3a1 mRNA was ubiquitously expressed in a variety of tissues or cells and highly expressed in chicken adipose tissue/cells. The expression of Dnmt3a1 was regulated under different physiological conditions including aging, fasting, and high-fat diet. In addition, overexpression of Dnmt3a1 significantly decreased preadipocyte proliferation and induced cell-cycle arrest while its inhibition increased cell proliferation and S-phase cells. Furthermore, the overexpression of Dnmt3a1 significantly upregulated the mRNA level of cell-cycle-related genes, such as CDKN1A, CDKN1B, CCNB3, CCND2, CCNG2, CDKN2B, and CDK9, or the protein level of CDKN1A, CDKN1B, and CCNG2. Conversely, the knockdown of Dnmt3a1 by siRNA had the opposite effects. Moreover, during early adipocyte differentiation, the overexpression of Dnmt3a1 significantly decreased the mRNA and the protein levels of PPAR-γ, C/EBP-α, ADIPOR1, and STAT3, and the mRNA levels of FAS, LEPR, LPL, PRKAB2, and ATGL. In contrast, their expression was significantly increased after the knockdown of Dnmt3a1. Taken together, we identified a novel transcript of Dnmt3a, and it played a potential role in adipogenesis.
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Affiliation(s)
- Bahareldin A Abdalla
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science, South China Agricultural University, Guangzhou, China.,National-Local Joint Engineering Research Center for Livestock Breeding, Guangzhou, China.,Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, the Key Lab of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture, Guangzhou, China
| | - Zhenhui Li
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science, South China Agricultural University, Guangzhou, China.,National-Local Joint Engineering Research Center for Livestock Breeding, Guangzhou, China.,Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, the Key Lab of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture, Guangzhou, China
| | - Hongjia Ouyang
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science, South China Agricultural University, Guangzhou, China.,National-Local Joint Engineering Research Center for Livestock Breeding, Guangzhou, China.,Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, the Key Lab of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture, Guangzhou, China
| | - Endashaw Jebessa
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science, South China Agricultural University, Guangzhou, China.,National-Local Joint Engineering Research Center for Livestock Breeding, Guangzhou, China.,Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, the Key Lab of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture, Guangzhou, China
| | - Tianhao Sun
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science, South China Agricultural University, Guangzhou, China.,National-Local Joint Engineering Research Center for Livestock Breeding, Guangzhou, China.,Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, the Key Lab of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture, Guangzhou, China
| | - Jia-Ao Yu
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science, South China Agricultural University, Guangzhou, China.,National-Local Joint Engineering Research Center for Livestock Breeding, Guangzhou, China.,Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, the Key Lab of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture, Guangzhou, China
| | - Bolin Cai
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science, South China Agricultural University, Guangzhou, China.,National-Local Joint Engineering Research Center for Livestock Breeding, Guangzhou, China.,Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, the Key Lab of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture, Guangzhou, China
| | - Biao Chen
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science, South China Agricultural University, Guangzhou, China.,National-Local Joint Engineering Research Center for Livestock Breeding, Guangzhou, China.,Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, the Key Lab of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture, Guangzhou, China
| | - Qinghua Nie
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science, South China Agricultural University, Guangzhou, China.,National-Local Joint Engineering Research Center for Livestock Breeding, Guangzhou, China.,Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, the Key Lab of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture, Guangzhou, China
| | - Xiquan Zhang
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science, South China Agricultural University, Guangzhou, China.,National-Local Joint Engineering Research Center for Livestock Breeding, Guangzhou, China.,Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, the Key Lab of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture, Guangzhou, China
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17
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Abdalla BA, Chen J, Nie Q, Zhang X. Genomic Insights Into the Multiple Factors Controlling Abdominal Fat Deposition in a Chicken Model. Front Genet 2018; 9:262. [PMID: 30073018 PMCID: PMC6060281 DOI: 10.3389/fgene.2018.00262] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2018] [Accepted: 06/28/2018] [Indexed: 12/12/2022] Open
Abstract
Genetic selection for an increased growth rate in meat-type chickens has been accompanied by excessive fat accumulation particularly in abdominal cavity. These progressed to indirect and often unhealthy effects on meat quality properties and increased feed cost. Advances in genomics technology over recent years have led to the surprising discoveries that the genome is more complex than previously thought. Studies have identified multiple-genetic factors associated with abdominal fat deposition. Meanwhile, the obesity epidemic has focused attention on adipose tissue and the development of adipocytes. The aim of this review is to summarize the current understanding of genetic/epigenetic factors associated with abdominal fat deposition, or as it relates to the proliferation and differentiation of preadipocytes in chicken. The results discussed here have been identified by different genomic approaches, such as QTL-based studies, the candidate gene approach, epistatic interaction, copy number variation, single-nucleotide polymorphism screening, selection signature analysis, genome-wide association studies, RNA sequencing, and bisulfite sequencing. The studies mentioned in this review have described multiple-genetic factors involved in an abdominal fat deposition. Therefore, it is inevitable to further study the multiple-genetic factors in-depth to develop novel molecular markers or potential targets, which will provide promising applications for reducing abdominal fat deposition in meat-type chicken.
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Affiliation(s)
- Bahareldin A. Abdalla
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science, South China Agricultural University, Guangzhou, China
- National-Local Joint Engineering Research Center for Livestock Breeding, The Key Lab of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture, Guangzhou, China
- Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, The Key Lab of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture, Guangzhou, China
| | - Jie Chen
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science, South China Agricultural University, Guangzhou, China
- National-Local Joint Engineering Research Center for Livestock Breeding, The Key Lab of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture, Guangzhou, China
- Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, The Key Lab of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture, Guangzhou, China
| | - Qinghua Nie
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science, South China Agricultural University, Guangzhou, China
- National-Local Joint Engineering Research Center for Livestock Breeding, The Key Lab of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture, Guangzhou, China
- Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, The Key Lab of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture, Guangzhou, China
| | - Xiquan Zhang
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science, South China Agricultural University, Guangzhou, China
- National-Local Joint Engineering Research Center for Livestock Breeding, The Key Lab of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture, Guangzhou, China
- Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, The Key Lab of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture, Guangzhou, China
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18
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Guerrero-Bosagna C, Morisson M, Liaubet L, Rodenburg TB, de Haas EN, Košťál Ľ, Pitel F. Transgenerational epigenetic inheritance in birds. ENVIRONMENTAL EPIGENETICS 2018; 4:dvy008. [PMID: 29732172 PMCID: PMC5920295 DOI: 10.1093/eep/dvy008] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/08/2018] [Revised: 03/02/2018] [Accepted: 03/12/2018] [Indexed: 05/04/2023]
Abstract
While it has been shown that epigenetics accounts for a portion of the variability of complex traits linked to interactions with the environment, the real contribution of epigenetics to phenotypic variation remains to be assessed. In recent years, a growing number of studies have revealed that epigenetic modifications can be transmitted across generations in several animal species. Numerous studies have demonstrated inter- or multi-generational effects of changing environment in birds, but very few studies have been published showing epigenetic transgenerational inheritance in these species. In this review, we mention work conducted in parent-to-offspring transmission analyses in bird species, with a focus on the impact of early stressors on behaviour. We then present recent advances in transgenerational epigenetics in birds, which involve germline linked non-Mendelian inheritance, underline the advantages and drawbacks of working on birds in this field and comment on future directions of transgenerational studies in bird species.
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Affiliation(s)
- Carlos Guerrero-Bosagna
- Avian Behavioural Genomics and Physiology Group, IFM Biology, Linköping University, Linköping 58 183, Sweden
| | - Mireille Morisson
- GenPhySE, Université de Toulouse, INRA, ENVT, F-31326 Castanet-Tolosan, France
| | - Laurence Liaubet
- GenPhySE, Université de Toulouse, INRA, ENVT, F-31326 Castanet-Tolosan, France
| | - T Bas Rodenburg
- Behavioural Ecology Group, Wageningen University, 6700 AH Wageningen, The Netherlands
| | - Elske N de Haas
- Behavioural Ecology Group, Wageningen University, 6700 AH Wageningen, The Netherlands
| | - Ľubor Košťál
- Centre of Biosciences, Slovak Academy of Sciences, 840 05 Bratislava, Slovakia
| | - Frédérique Pitel
- GenPhySE, Université de Toulouse, INRA, ENVT, F-31326 Castanet-Tolosan, France
- Correspondence address. GenPhySE, INRA, 31326 Castanet-Tolosan, France. Tel:+33 561 28 54 35. E-mail:
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19
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Li G, Luo W, Abdalla BA, Ouyang H, Yu J, Hu F, Nie Q, Zhang X. miRNA-223 upregulated by MYOD inhibits myoblast proliferation by repressing IGF2 and facilitates myoblast differentiation by inhibiting ZEB1. Cell Death Dis 2017; 8:e3094. [PMID: 28981085 PMCID: PMC5682648 DOI: 10.1038/cddis.2017.479] [Citation(s) in RCA: 51] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2017] [Revised: 08/23/2017] [Accepted: 08/24/2017] [Indexed: 12/24/2022]
Abstract
Skeletal muscle differentiation can be regulated by various transcription factors and non-coding RNAs. In our previous work, miR-223 is differentially expressed in the skeletal muscle of chicken with different growth rates, but its role, expression and action mechanism in muscle development still remains unknown. Here, we found that MYOD transcription factor can upregulate miR-223 expression by binding to an E-box region of the gga-miR-223 gene promoter during avian myoblast differentiation. IGF2 and ZEB1 are two target genes of miR-223. The target inhibition of miR-223 on IGF2 and ZEB1 are dynamic from proliferation to differentiation of myoblast. miR-223 inhibits IGF2 expression only in the proliferating myoblast, whereas it inhibits ZEB1 mainly in the differentiating myoblast. The inhibition of IGF2 by miR-223 resulted in the repression of myoblast proliferation. During myoblast differentiation, miR-223 would be upregulated owing to the promoting effect of MYOD, and the upregulation of miR-223 would inhibit ZEB1 to promote myoblast differentiation. These results not only demonstrated that the well-known muscle determination factor MYOD can promote myoblast differentiation by upregulate miR-223 transcription, but also identified that miR-223 can influence myoblast proliferation and differentiation by a dynamic manner regulates the expression of its target genes.
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Affiliation(s)
- Guihuan Li
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science, South China Agricultural University, Guangzhou 510642, Guangdong Province, China.,Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, and Key Lab of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture, South China Agricultural University, Guangzhou 510642, Guangdong Province, China.,Department of Cell Biology, School of Basic Medical Sciences, Southern Medical University, Guangzhou 510515, China
| | - Wen Luo
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science, South China Agricultural University, Guangzhou 510642, Guangdong Province, China.,Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, and Key Lab of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture, South China Agricultural University, Guangzhou 510642, Guangdong Province, China
| | - Bahareldin A Abdalla
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science, South China Agricultural University, Guangzhou 510642, Guangdong Province, China.,Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, and Key Lab of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture, South China Agricultural University, Guangzhou 510642, Guangdong Province, China
| | - Hongjia Ouyang
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science, South China Agricultural University, Guangzhou 510642, Guangdong Province, China.,Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, and Key Lab of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture, South China Agricultural University, Guangzhou 510642, Guangdong Province, China
| | - Jiao Yu
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science, South China Agricultural University, Guangzhou 510642, Guangdong Province, China.,Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, and Key Lab of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture, South China Agricultural University, Guangzhou 510642, Guangdong Province, China
| | - Fan Hu
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science, South China Agricultural University, Guangzhou 510642, Guangdong Province, China.,Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, and Key Lab of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture, South China Agricultural University, Guangzhou 510642, Guangdong Province, China
| | - Qinghua Nie
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science, South China Agricultural University, Guangzhou 510642, Guangdong Province, China.,Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, and Key Lab of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture, South China Agricultural University, Guangzhou 510642, Guangdong Province, China
| | - Xiquan Zhang
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science, South China Agricultural University, Guangzhou 510642, Guangdong Province, China.,Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, and Key Lab of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture, South China Agricultural University, Guangzhou 510642, Guangdong Province, China
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Rengaraj D, Lee BR, Han JY, Pang MG. Comprehensive analysis on the homology, interaction, and miRNA regulators of human deleted in azoospermia proteins: updated evolutionary relationships with primates. Genes Genomics 2017. [DOI: 10.1007/s13258-017-0598-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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21
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Analysis of JAK-STAT signaling pathway genes and their microRNAs in the intestinal mucosa of genetically disparate chicken lines induced with necrotic enteritis. Vet Immunol Immunopathol 2017; 187:1-9. [DOI: 10.1016/j.vetimm.2017.03.001] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2016] [Revised: 01/14/2017] [Accepted: 03/09/2017] [Indexed: 01/03/2023]
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22
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Dynamics of miRNA transcriptome during gonadal development of zebrafish. Sci Rep 2017; 7:43850. [PMID: 28262836 PMCID: PMC5338332 DOI: 10.1038/srep43850] [Citation(s) in RCA: 50] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2016] [Accepted: 01/31/2017] [Indexed: 12/28/2022] Open
Abstract
Studies in non-teleost vertebrates have found microRNAs (miRNAs) to be essential for proper gonadal development. However, comparatively little is known about their role during gonadal development in teleost fishes. So far in zebrafish, a model teleost, transcript profiling throughout gonadal development has not been established because of a tiny size of an organ in juvenile stages and its poor distinguishability from surrounding tissues. We performed small RNA sequencing on isolated gonads of See-Thru-Gonad line, from the undifferentiated state at 3 weeks post fertilization (wpf) to fully mature adults at 24 wpf. We identified 520 gonadal mature miRNAs; 111 of them had significant changes in abundance over time, while 50 miRNAs were either testis- or ovary-enriched significantly in at least one developmental stage. We characterized patterns of miRNA abundance over time including isomiR variants. We identified putative germline versus gonadal somatic miRNAs through differential small RNA sequencing of isolated gametes versus the whole gonads. This report is the most comprehensive analysis of the miRNA repertoire in zebrafish gonads during the sexual development to date and provides an important database from which functional studies can be performed.
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23
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Miao N, Wang X, Hou Y, Feng Y, Gong Y. Identification of male-biased microRNA-107 as a direct regulator for nuclear receptor subfamily 5 group A member 1 based on sexually dimorphic microRNA expression profiling from chicken embryonic gonads. Mol Cell Endocrinol 2016; 429:29-40. [PMID: 27036932 DOI: 10.1016/j.mce.2016.03.033] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/25/2016] [Revised: 03/08/2016] [Accepted: 03/27/2016] [Indexed: 12/15/2022]
Abstract
Several studies indicate that sexual dimorphic microRNAs (miRNAs) in chicken gonads are likely to have important roles in sexual development, but a more global understanding of the roles of miRNAs in sexual differentiation is still needed. To this end, we performed miRNA expression profiling in chicken gonads at embryonic day 5.5 (E5.5). Among the sex-biased miRNAs validated by qRT-PCR, twelve male-biased and six female-biased miRNAs were consistent with the sequencing results. Bioinformatics analysis revealed that some sex-biased miRNAs were potentially involved in gonadal development. Further functional analysis found that over-expression of miR-107 directly inhibited nuclear receptor subfamily 5 group A member 1 (NR5a1), and its downstream cytochrome P450 family 19 subfamily A, polypeptide 1 (CYP19A1). However, anti-Mullerian hormone (AMH) was not directly or indirectly regulated by miR-107. Overall results indicate that miR-107 may specifically mediate avian ovary-development by post-transcriptional regulation of NR5a1 and CYP19A1 in estrogen signaling pathways.
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Affiliation(s)
- Nan Miao
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, 430070, People's Republic of China
| | - Xin Wang
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, 430070, People's Republic of China
| | - Yue Hou
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, 430070, People's Republic of China
| | - Yanping Feng
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, 430070, People's Republic of China.
| | - Yanzhang Gong
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, 430070, People's Republic of China.
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24
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Kress C, Montillet G, Jean C, Fuet A, Pain B. Chicken embryonic stem cells and primordial germ cells display different heterochromatic histone marks than their mammalian counterparts. Epigenetics Chromatin 2016; 9:5. [PMID: 26865862 PMCID: PMC4748481 DOI: 10.1186/s13072-016-0056-6] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2015] [Accepted: 01/27/2016] [Indexed: 12/17/2022] Open
Abstract
Background Chromatin epigenetics participate in control of gene expression during metazoan development. DNA methylation and post-translational modifications (PTMs) of histones have been extensively characterised in cell types present in, or derived from, mouse embryos. In embryonic stem cells (ESCs) derived from blastocysts, factors involved in deposition of epigenetic marks regulate properties related to self-renewal and pluripotency. In the germ lineage, changes in histone PTMs and DNA demethylation occur during formation of the primordial germ cells (PGCs) to reset the epigenome of the future gametes. Trimethylation of histone H3 on lysine 27 (H3K27me3) by Polycomb group proteins is involved in several epigenome-remodelling steps, but it remains unclear whether these epigenetic features are conserved in non-mammalian vertebrates. To investigate this question, we compared the abundance and nuclear distribution of the main histone PTMs, 5-methylcytosine (5mC) and 5-hydroxymethylcytosine (5hmC) in chicken ESCs, PGCs and blastodermal cells (BCs) with differentiated chicken ESCs and embryonic fibroblasts. In addition, we analysed the expression of chromatin modifier genes to better understand the establishment and dynamics of chromatin epigenetic profiles. Results The nuclear distributions of most PTMs and 5hmC in chicken stem cells were similar to what has been described for mammalian cells. However, unlike mouse pericentric heterochromatin (PCH), chicken ESC PCH contained high levels of trimethylated histone H3 on lysine 27 (H3K27me3). In differentiated chicken cells, PCH was less enriched in H3K27me3 relative to chromatin overall. In PGCs, the H3K27me3 global level was greatly reduced, whereas the H3K9me3 level was elevated. Most chromatin modifier genes known in mammals were expressed in chicken ESCs, PGCs and BCs. Genes presumably involved in de novo DNA methylation were very highly expressed. DNMT3B and HELLS/SMARCA6 were highly expressed in chicken ESCs, PGCs and BCs compared to differentiated chicken ESCs and embryonic fibroblasts, and DNMT3A was strongly expressed in ESCs, differentiated ESCs and BCs. Conclusions Chicken ESCs and PGCs differ from their mammalian counterparts with respect to H3K27 methylation. High enrichment of H3K27me3 at PCH is specific to pluripotent cells in chicken. Our results demonstrate that the dynamics in chromatin constitution described during mouse development is not universal to all vertebrate species. Electronic supplementary material The online version of this article (doi:10.1186/s13072-016-0056-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Clémence Kress
- Inserm, U1208, INRA, USC1361, Stem Cell and Brain Research Institute, 18 avenue du Doyen Lépine, 69500 Bron, France ; Université de Lyon, Université Lyon 1, Lyon, France
| | - Guillaume Montillet
- Inserm, U1208, INRA, USC1361, Stem Cell and Brain Research Institute, 18 avenue du Doyen Lépine, 69500 Bron, France ; Université de Lyon, Université Lyon 1, Lyon, France
| | - Christian Jean
- Inserm, U1208, INRA, USC1361, Stem Cell and Brain Research Institute, 18 avenue du Doyen Lépine, 69500 Bron, France ; Université de Lyon, Université Lyon 1, Lyon, France
| | - Aurélie Fuet
- Inserm, U1208, INRA, USC1361, Stem Cell and Brain Research Institute, 18 avenue du Doyen Lépine, 69500 Bron, France ; Université de Lyon, Université Lyon 1, Lyon, France
| | - Bertrand Pain
- Inserm, U1208, INRA, USC1361, Stem Cell and Brain Research Institute, 18 avenue du Doyen Lépine, 69500 Bron, France ; Université de Lyon, Université Lyon 1, Lyon, France
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25
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MicroRNAs: From Female Fertility, Germ Cells, and Stem Cells to Cancer in Humans. Stem Cells Int 2015; 2016:3984937. [PMID: 26664407 PMCID: PMC4655303 DOI: 10.1155/2016/3984937] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2015] [Accepted: 08/19/2015] [Indexed: 12/14/2022] Open
Abstract
MicroRNAs are a family of naturally occurring small noncoding RNA molecules that play an important regulatory role in gene expression. They are suggested to regulate a large proportion of protein encoding genes by mediating the translational suppression and posttranscriptional control of gene expression. Recent findings show that microRNAs are emerging as important regulators of cellular differentiation and dedifferentiation, and are deeply involved in developmental processes including human preimplantation development. They keep a balance between pluripotency and differentiation in the embryo and embryonic stem cells. Moreover, it became evident that dysregulation of microRNA expression may play a fundamental role in progression and dissemination of different cancers including ovarian cancer. The interest is still increased by the discovery of exosomes, that is, cell-derived vesicles, which can carry different proteins but also microRNAs between different cells and are involved in cell-to-cell communication. MicroRNAs, together with exosomes, have a great potential to be used for prognosis, therapy, and biomarkers of different diseases including infertility. The aim of this review paper is to summarize the existent knowledge on microRNAs related to female fertility and cancer: from primordial germ cells and ovarian function, germinal stem cells, oocytes, and embryos to embryonic stem cells.
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26
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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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27
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Bosch PJ, Benton MC, Macartney-Coxson D, Kivell BM. mRNA and microRNA analysis reveals modulation of biochemical pathways related to addiction in the ventral tegmental area of methamphetamine self-administering rats. BMC Neurosci 2015; 16:43. [PMID: 26188473 PMCID: PMC4506769 DOI: 10.1186/s12868-015-0186-y] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2015] [Accepted: 07/14/2015] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND Methamphetamine is a highly addictive central nervous system stimulant with increasing levels of abuse worldwide. Alterations to mRNA and miRNA expression within the mesolimbic system can affect addiction-like behaviors and thus play a role in the development of drug addiction. While many studies have investigated the effects of high-dose methamphetamine, and identified neurotoxic effects, few have looked at the role that persistent changes in gene regulation play following methamphetamine self-administration. Therefore, the aim of this study was to identify RNA changes in the ventral tegmental area following methamphetamine self-administration. We performed microarray analyses on RNA extracted from the ventral tegmental area of Sprague-Dawley rats following methamphetamine self-administration training (2 h/day) and 14 days of abstinence. RESULTS We identified 78 miRNA and 150 mRNA transcripts that were differentially expressed (fdr adjusted p < 0.05, absolute log2 fold change >0.5); these included genes not previously associated with addiction (miR-125a-5p, miR-145 and Foxa1), loci encoding receptors related to drug addiction behaviors and genes with previously recognized roles in addiction such as miR-124, miR-181a, DAT and Ret. CONCLUSION This study provides insight into the effects of methamphetamine on RNA expression in a key brain region associated with addiction, highlighting the possibility that persistent changes in the expression of genes with both known and previously unknown roles in addiction occur.
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Affiliation(s)
- P J Bosch
- Centre for Biodiscovery, School of Biological Sciences, Victoria University of Wellington, Kelburn Parade, PO Box 600, Wellington, 6140, New Zealand.
| | - M C Benton
- Institute of Environmental Science and Research, Wellington, New Zealand.
- Genomics Research Centre, Institute of Health and Biomedical Innovation, Queensland University of Technology, Brisbane, Australia.
| | - D Macartney-Coxson
- Institute of Environmental Science and Research, Wellington, New Zealand.
| | - B M Kivell
- Centre for Biodiscovery, School of Biological Sciences, Victoria University of Wellington, Kelburn Parade, PO Box 600, Wellington, 6140, New Zealand.
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28
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Jiao F, Wang X, Yan Z, Liu C, Yue Z, Li Z, Ma Y, Li Y, Wang J. Effect of dynamic DNA methylation and histone acetylation on cPouV expression in differentiation of chick embryonic germ cells. Stem Cells Dev 2013; 22:2725-35. [PMID: 23750509 DOI: 10.1089/scd.2013.0046] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
As a crucial pluripotency-related factor, the epigenetic regulation of Oct4 has been studied intensively in mammalians. However, its dynamic changes of DNA methylation and histone modification in avians remain poorly understood. In the present study, we first described the alterations of DNA methylation and histone acetylation in the promoter of chicken PouV (cPouV; the homologue of Oct4 in avian) during chick embryonic germ (EG) cell differentiation. The epigenetic modification analysis showed that DNA methylation in the cPouV promoter increased obviously, while histone acetylation decreased dramatically detected by chromatin immunoprecipitation assay in the process of differentiation. Gene expression analysis detection indicated that the levels of DNA methyltransferase 3a (Dnmt 3a), Dnmt 3b, and histone deacetylase 3 (HDAC 3) transcripts were significantly high, whereas the relative abundance of Dnmt 1, histone acetyltransferase (HAT), and cPouV mRNA was significantly decreased during the conversion of EG to embryoid body-like structures (EBs), which was correlated with the increased level of methylation and reduced level of H3 acetylation. Moreover, in vitro methylation assay indicated that the reporter gene was remarkably inhibited by the methylated promoter of cPouV. To further understand the effect of epigenetic modifiers on cPouV expression, we performed an analysis of EB cells treated with trichostatin A (TSA), Aza-2'-deoxycytidine (Aza), or TSA plus Aza (TSA/Aza). We observed that the effect of TSA/Aza is more sensitive to the reactivation of cPouV compared with TSA or Aza, indicating that these epigenetic inhibitors can function synergistically to facilitate the reprogramming process. The present study provided evidences that a critical role for cPouV activation/repression by DNA methylation and/or histone modifications is involved in the pluripotency maintenance and differentiation process of chick EG.
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Affiliation(s)
- Fei Jiao
- 1 Department of Biochemistry and Molecular Biology, Binzhou Medical College , Yantai, Shandong Province, People's Republic of China
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Abstract
MicroRNAs (miRNAs) are a class of ~22 nucleotide-long small noncoding RNAs that target mRNAs for translational repression or degradation. miRNAs target mRNAs by base-pairing with the 3'-untranslated regions (3'-UTRs) of mRNAs. miRNAs are present in various species, from animals to plants. In this review, we summarize the identification, expression, and function of miRNAs in four important farm animal species: cattle, chicken, pig and sheep. In each of these species, hundreds of miRNAs have been identified through homology search, small RNA cloning and next generation sequencing. Real-time RT-PCR and microarray experiments reveal that many miRNAs are expressed in a tissue-specific or spatiotemporal-specific manner in farm animals. Limited functional studies suggest that miRNAs have important roles in muscle development and hypertrophy, adipose tissue growth, oocyte maturation and early embryonic development in farm animals. Increasing evidence suggests that single-nucleotide polymorphisms in miRNA target sites or miRNA gene promoters may contribute to variation in production or health traits in farm animals.
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30
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Maupetit-Méhouas S, Azzi S, Steunou V, Sakakini N, Silve C, Reynes C, Perez de Nanclares G, Keren B, Chantot S, Barlier A, Linglart A, Netchine I. Simultaneous Hyper- and Hypomethylation at Imprinted Loci in a Subset of Patients withGNASEpimutations Underlies a Complex and Different Mechanism of Multilocus Methylation Defect in Pseudohypoparathyroidism Type 1b. Hum Mutat 2013; 34:1172-80. [DOI: 10.1002/humu.22352] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2013] [Accepted: 04/29/2013] [Indexed: 12/31/2022]
Affiliation(s)
- Stéphanie Maupetit-Méhouas
- Inserm U986, Hôpital Bicêtre-Paris-Sud; Le Kremlin-Bicêtre; France
- Center of reference for rare disorders of the calcium and phosphorus metabolism; Hôpital Bicêtre-Paris-Sud; Le Kremlin-Bicêtre France
| | - Salah Azzi
- Saint Antoine research center INSERM UMR-S938 Yves Le Bouc team, Pierre & Marie Curie-Paris 6 University, Endocrine Laboratory of functional Explorations, APHP; Armand Trousseau Hospital; Paris France
| | - Virginie Steunou
- Saint Antoine research center INSERM UMR-S938 Yves Le Bouc team, Pierre & Marie Curie-Paris 6 University, Endocrine Laboratory of functional Explorations, APHP; Armand Trousseau Hospital; Paris France
| | - Nathalie Sakakini
- Laboratory of Molecular Biology; University Hospital of Marseille - AP-HM - Conception; Marseille France
- CRN2M; UMR7286-CNRS, Aix-Marseille University, Marseille Cedex 15; Marseille France
| | - Caroline Silve
- Inserm U986, Hôpital Bicêtre-Paris-Sud; Le Kremlin-Bicêtre; France
- Center of reference for rare disorders of the calcium and phosphorus metabolism; Hôpital Bicêtre-Paris-Sud; Le Kremlin-Bicêtre France
| | - Christelle Reynes
- Laboratoire de Physique Industrielle et Traitement de l'Information; EA 2415, UFR Pharmacie-Univ. Montpellier 1, Montpellier Cedex 5; France
| | | | - Boris Keren
- Department of Genetics, APHP; CRicm UPMC Inserm UMRS975/CNRS UMR7225, Pitié-Salpêtrière Hospital; Paris France
| | - Sandra Chantot
- Laboratoire de génétique moléculaire, APHP; Hôpital Armand Trousseau; Paris France
| | - Anne Barlier
- Laboratory of Molecular Biology; University Hospital of Marseille - AP-HM - Conception; Marseille France
- CRN2M; UMR7286-CNRS, Aix-Marseille University, Marseille Cedex 15; Marseille France
| | - Agnès Linglart
- Inserm U986, Hôpital Bicêtre-Paris-Sud; Le Kremlin-Bicêtre; France
- Center of reference for rare disorders of the calcium and phosphorus metabolism; Hôpital Bicêtre-Paris-Sud; Le Kremlin-Bicêtre France
- Endocrinology and Diabetology for Children; APHP, Hôpital Bicêtre-Paris-Sud, University Paris 11; Le Kremlin-Bicêtre France
| | - Irène Netchine
- Saint Antoine research center INSERM UMR-S938 Yves Le Bouc team, Pierre & Marie Curie-Paris 6 University, Endocrine Laboratory of functional Explorations, APHP; Armand Trousseau Hospital; Paris France
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Kim T, Yun T, Rengaraj D, Lee S, Lim S, Seo H, Park T, Han J. Conserved functional characteristics of the PIWI family members in chicken germ cell lineage. Theriogenology 2012; 78:1948-59. [DOI: 10.1016/j.theriogenology.2012.07.019] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2012] [Revised: 07/15/2012] [Accepted: 07/18/2012] [Indexed: 10/27/2022]
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32
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Jang HJ, Kim YM, Rengaraj D, Shin YS, Han JY. DNA methyltransferase 3a is Correlated with Transgene Expression in Transgenic Quails. JOURNAL OF ANIMAL SCIENCE AND TECHNOLOGY 2011. [DOI: 10.5187/jast.2011.53.3.269] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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