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Li J, Zheng X. Morphology, Histology, and Transcriptome Analysis of Gonadal Development in Octopus minor (Sasaki, 1920). MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2023; 25:1043-1056. [PMID: 37878213 DOI: 10.1007/s10126-023-10258-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/14/2023] [Accepted: 10/09/2023] [Indexed: 10/26/2023]
Abstract
Octopus minor is an economically important species, but little is known about the histological pattern and regulatory mechanisms during gonadal development. In this study, we investigated the annual changes in total body weight (TW), gonad somatic index (GSI), gonadal histological features, and transcriptome of O. minor. The results indicated that both females and males showed a similar TW trend. The GSI peaked in June in females, while it remained constant at around 3% in males. Nine and four histological stages were observed in ovaries and testes, respectively. Our field sampling results implied that O. minor might have overwintering periods for both eggs and larvae. Transcriptome analysis revealed that a total of 1095 and 2468 genes were significantly expressed during ovarian and testicular development, separately. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis displayed that 126 GO terms and 5 KEGG pathways were significantly enriched in the ovarian group of advanced vitellogenic oocytes vs vitellogenic oocytes (AVO vs VO). The pathways "Ribosomal", "Cell cycle", and "Progesterone-mediated oocyte maturation" were predicted to promote yolk deposition. Additionally, the testicular comparison group of spent vs mature (Spent vs Mature) showed significant enrichment in 674 GO terms and 13 KEGG pathways, suggesting that energy metabolism and cell repair pathways may be involved in the spermatogenesis process. This work revealed the development process of the gonads and shed light on the potential regulatory pathways of O. minor, providing novel insights and laying a molecular basis for artificial breeding.
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Affiliation(s)
- Jiahua Li
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao, 266003, China
- Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, 266003, China
| | - Xiaodong Zheng
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao, 266003, China.
- Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, 266003, China.
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2
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Ren J, Hu Z, Li Q, Gu S, Lan F, Wang X, Li J, Li J, Shao L, Yang N, Sun C. Temperature-induced embryonic diapause in chickens is mediated by PKC-NF-κB-IRF1 signaling. BMC Biol 2023; 21:52. [PMID: 36882743 PMCID: PMC9993608 DOI: 10.1186/s12915-023-01550-0] [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: 08/19/2022] [Accepted: 02/22/2023] [Indexed: 03/09/2023] Open
Abstract
BACKGROUND Embryonic diapause (dormancy) is a state of temporary arrest of embryonic development that is triggered by unfavorable conditions and serves as an evolutionary strategy to ensure reproductive survival. Unlike maternally-controlled embryonic diapause in mammals, chicken embryonic diapause is critically dependent on the environmental temperature. However, the molecular control of diapause in avian species remains largely uncharacterized. In this study, we evaluated the dynamic transcriptomic and phosphoproteomic profiles of chicken embryos in pre-diapause, diapause, and reactivated states. RESULTS Our data demonstrated a characteristic gene expression pattern in effects on cell survival-associated and stress response signaling pathways. Unlike mammalian diapause, mTOR signaling is not responsible for chicken diapause. However, cold stress responsive genes, such as IRF1, were identified as key regulators of diapause. Further in vitro investigation showed that cold stress-induced transcription of IRF1 was dependent on the PKC-NF-κB signaling pathway, providing a mechanism for proliferation arrest during diapause. Consistently, in vivo overexpression of IRF1 in diapause embryos blocked reactivation after restoration of developmental temperatures. CONCLUSIONS We concluded that embryonic diapause in chicken is characterized by proliferation arrest, which is the same with other spices. However, chicken embryonic diapause is strictly correlated with the cold stress signal and mediated by PKC-NF-κB-IRF1 signaling, which distinguish chicken diapause from the mTOR based diapause in mammals.
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Affiliation(s)
- Junxiao Ren
- Department of Animal Genetics and Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Zhengzheng Hu
- Department of Animal Genetics and Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Quanlin Li
- Department of Animal Genetics and Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Shuang Gu
- Department of Animal Genetics and Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Fangren Lan
- Department of Animal Genetics and Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Xiqiong Wang
- Department of Animal Genetics and Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Jianbo Li
- Department of Animal Genetics and Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Junying Li
- Department of Animal Genetics and Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Liwa Shao
- Department of Animal Genetics and Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Ning Yang
- Department of Animal Genetics and Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China.
| | - Congjiao Sun
- Department of Animal Genetics and Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China.
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3
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Osipova E, Barsacchi R, Brown T, Sadanandan K, Gaede AH, Monte A, Jarrells J, Moebius C, Pippel M, Altshuler DL, Winkler S, Bickle M, Baldwin MW, Hiller M. Loss of a gluconeogenic muscle enzyme contributed to adaptive metabolic traits in hummingbirds. Science 2023; 379:185-190. [PMID: 36634192 DOI: 10.1126/science.abn7050] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Hummingbirds possess distinct metabolic adaptations to fuel their energy-demanding hovering flight, but the underlying genomic changes are largely unknown. Here, we generated a chromosome-level genome assembly of the long-tailed hermit and screened for genes that have been specifically inactivated in the ancestral hummingbird lineage. We discovered that FBP2 (fructose-bisphosphatase 2), which encodes a gluconeogenic muscle enzyme, was lost during a time period when hovering flight evolved. We show that FBP2 knockdown in an avian muscle cell line up-regulates glycolysis and enhances mitochondrial respiration, coincident with an increased mitochondria number. Furthermore, genes involved in mitochondrial respiration and organization have up-regulated expression in hummingbird flight muscle. Together, these results suggest that FBP2 loss was likely a key step in the evolution of metabolic muscle adaptations required for true hovering flight.
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Affiliation(s)
- Ekaterina Osipova
- Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstr. 108, 01307 Dresden, Germany.,Max Planck Institute for the Physics of Complex Systems, Nöthnitzer Str. 38, 01187 Dresden, Germany.,Center for Systems Biology Dresden, Pfotenhauerstr. 108, 01307 Dresden, Germany.,LOEWE Centre for Translational Biodiversity Genomics, Senckenberganlage 25, 60325 Frankfurt, Germany.,Senckenberg Research Institute, Senckenberganlage 25, 60325 Frankfurt, Germany.,Goethe-University, Faculty of Biosciences, Max-von-Laue-Str. 9, 60438 Frankfurt, Germany
| | - Rico Barsacchi
- Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstr. 108, 01307 Dresden, Germany
| | - Tom Brown
- Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstr. 108, 01307 Dresden, Germany.,Center for Systems Biology Dresden, Pfotenhauerstr. 108, 01307 Dresden, Germany.,DRESDEN concept Genome Center, Technische Universität Dresden, 01062 Dresden, Germany
| | - Keren Sadanandan
- Evolution of Sensory Systems Research Group, Max Planck Institute for Ornithology, Seewiesen, Germany
| | - Andrea H Gaede
- University of British Columbia, Vancouver, Vancouver, BC V6T 1Z4, Canada.,Structure and Motion Laboratory, Royal Veterinary College, University of London, London, UK
| | - Amanda Monte
- Department of Behavioural Neurobiology, Max Planck Institute for Ornithology, Seewiesen, Germany
| | - Julia Jarrells
- Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstr. 108, 01307 Dresden, Germany
| | - Claudia Moebius
- Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstr. 108, 01307 Dresden, Germany
| | - Martin Pippel
- Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstr. 108, 01307 Dresden, Germany.,Center for Systems Biology Dresden, Pfotenhauerstr. 108, 01307 Dresden, Germany
| | | | - Sylke Winkler
- Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstr. 108, 01307 Dresden, Germany.,DRESDEN concept Genome Center, Technische Universität Dresden, 01062 Dresden, Germany
| | - Marc Bickle
- Roche Institute for Translational Bioengineering, Grenzacherstrasse 124, 4070 Basel, Switzerland
| | - Maude W Baldwin
- Evolution of Sensory Systems Research Group, Max Planck Institute for Ornithology, Seewiesen, Germany
| | - Michael Hiller
- Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstr. 108, 01307 Dresden, Germany.,Max Planck Institute for the Physics of Complex Systems, Nöthnitzer Str. 38, 01187 Dresden, Germany.,Center for Systems Biology Dresden, Pfotenhauerstr. 108, 01307 Dresden, Germany.,LOEWE Centre for Translational Biodiversity Genomics, Senckenberganlage 25, 60325 Frankfurt, Germany.,Senckenberg Research Institute, Senckenberganlage 25, 60325 Frankfurt, Germany.,Goethe-University, Faculty of Biosciences, Max-von-Laue-Str. 9, 60438 Frankfurt, Germany
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4
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Prado-Álvarez M, Dios S, García-Fernández P, Tur R, Hachero-Cruzado I, Domingues P, Almansa E, Varó I, Gestal C. De novo transcriptome reconstruction in aquacultured early life stages of the cephalopod Octopus vulgaris. Sci Data 2022; 9:609. [PMID: 36209315 PMCID: PMC9547907 DOI: 10.1038/s41597-022-01735-2] [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: 09/29/2021] [Accepted: 09/29/2022] [Indexed: 11/16/2022] Open
Abstract
Cephalopods have been considered enigmatic animals that have attracted the attention of scientists from different areas of expertise. However, there are still many questions to elucidate the way of life of these invertebrates. The aim of this study is to construct a reference transcriptome in Octopus vulgaris early life stages to enrich existing databases and provide a new dataset that can be reused by other researchers in the field. For that, samples from different developmental stages were combined including embryos, newly-hatched paralarvae, and paralarvae of 10, 20 and 40 days post-hatching. Additionally, different dietary and rearing conditions and pathogenic infections were tested. At least three biological replicates were analysed per condition and submitted to RNA-seq analysis. All sequencing reads from experimental conditions were combined in a single dataset to generate a reference transcriptome assembly that was functionally annotated. The number of reads aligned to this reference was counted to estimate the transcript abundance in each sample. This dataset compiled a complete reference for future transcriptomic studies in O. vulgaris. Measurement(s) | Transcriptome sequencing assay | Technology Type(s) | RNA-seq assay (Illumina) | Sample Characteristic - Organism | Octopus vulgaris | Sample Characteristic - Environment | Ocean | Sample Characteristic - Location | NW Spain (Ría de Vigo, Galicia) |
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Affiliation(s)
- María Prado-Álvarez
- Instituto de Investigaciones Marinas (IIM), CSIC, Eduardo Cabello 6, 36208, Vigo, Spain
| | - Sonia Dios
- Instituto de Investigaciones Marinas (IIM), CSIC, Eduardo Cabello 6, 36208, Vigo, Spain
| | - Pablo García-Fernández
- Instituto de Investigaciones Marinas (IIM), CSIC, Eduardo Cabello 6, 36208, Vigo, Spain.,Pescanova Biomarine Center, Lugar Ardia 172, 36980, O Grove, Spain
| | - Ricardo Tur
- Centro Oceanográfico de Vigo (COV-IEO), CSIC, Subida a Radio Faro 50-52, 36390, Vigo, Spain.,Pescanova Biomarine Center, Lugar Ardia 172, 36980, O Grove, Spain
| | - Ismael Hachero-Cruzado
- Centro Oceanográfico de Vigo (COV-IEO), CSIC, Subida a Radio Faro 50-52, 36390, Vigo, Spain
| | - Pedro Domingues
- Centro Oceanográfico de Vigo (COV-IEO), CSIC, Subida a Radio Faro 50-52, 36390, Vigo, Spain
| | - Eduardo Almansa
- Centro Oceanográfico de Canarias (COC-IEO), CSIC. Calle La Farola del Mar n° 22, Dársena Pesquera, 38180, Santa Cruz de Tenerife, Spain
| | - Inmaculada Varó
- Instituto de Acuicultura de Torre de la Sal (IATS), CSIC. Torre de la Sal s/n, 12595, Ribera de Cabanes, Spain
| | - Camino Gestal
- Instituto de Investigaciones Marinas (IIM), CSIC, Eduardo Cabello 6, 36208, Vigo, Spain.
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5
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Chicken blastoderms and primordial germ cells possess a higher expression of DNA repair genes and lower expression of apoptosis genes to preserve their genome stability. Sci Rep 2022; 12:49. [PMID: 34997179 PMCID: PMC8741993 DOI: 10.1038/s41598-021-04417-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Accepted: 12/21/2021] [Indexed: 12/13/2022] Open
Abstract
DNA is susceptible to damage by various sources. When the DNA is damaged, the cell repairs the damage through an appropriate DNA repair pathway. When the cell fails to repair DNA damage, apoptosis is initiated. Although several genes are involved in five major DNA repair pathways and two major apoptosis pathways, a comprehensive understanding of those gene expression is not well-understood in chicken tissues. We performed whole-transcriptome sequencing (WTS) analysis in the chicken embryonic fibroblasts (CEFs), stage X blastoderms, and primordial germ cells (PGCs) to uncover this deficiency. Stage X blastoderms mostly consist of undifferentiated progenitor (pluripotent) cells that have the potency to differentiate into all cell types. PGCs are also undifferentiated progenitor cells that later differentiate into male and female germ cells. CEFs are differentiated and abundant somatic cells. Through WTS analysis, we identified that the DNA repair pathway genes were expressed more highly in blastoderms and high in PGCs than CEFs. Besides, the apoptosis pathway genes were expressed low in blastoderms and PGCs than CEFs. We have also examined the WTS-based expression profiling of candidate pluripotency regulating genes due to the conserved properties of blastoderms and PGCs. In the results, a limited number of pluripotency genes, especially the core transcriptional network, were detected higher in both blastoderms and PGCs than CEFs. Next, we treated the CEFs, blastoderm cells, and PGCs with hydrogen peroxide (H2O2) for 1 h to induce DNA damage. Then, the H2O2 treated cells were incubated in fresh media for 3–12 h to observe DNA repair. Subsequent analyses in treated cells found that blastoderm cells and PGCs were more likely to undergo apoptosis along with the loss of pluripotency and less likely to undergo DNA repair, contrasting with CEFs. These properties of blastoderms and PGCs should be necessary to preserve genome stability during the development of early embryos and germ cells, respectively.
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6
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Ren J, Li Q, Zhang Q, Clinton M, Sun C, Yang N. Systematic screening of long intergenic noncoding RNAs expressed during chicken embryogenesis. Poult Sci 2021; 100:101160. [PMID: 34058566 PMCID: PMC8170422 DOI: 10.1016/j.psj.2021.101160] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2020] [Revised: 03/05/2021] [Accepted: 03/22/2021] [Indexed: 11/29/2022] Open
Abstract
Long noncoding RNAs (lncRNAs) have emerged as important regulators of many biological processes, including embryogenesis and development. To provide a systematic analysis of lncRNAs expressed during chicken embryogenesis, we used Iso-Seq and RNA-Seq to identify potential lncRNAs at embryonic stages from d 1 to d 8 of incubation: sequential stages covering gastrulation, somitogenesis, and organogenesis. The data characterized an expanded landscape of lncRNAs, yielding 45,410 distinct lncRNAs (31,282 genes). Amongst these, a set of 13,141 filtered intergenic lncRNAs (lincRNAs) transcribed from 9803 lincRNA gene loci, of which, 66.5% were novel, were further analyzed. These lincRNAs were found to share many characteristics with mammalian lincRNAs, including relatively short lengths, fewer exons, lower expression levels, and stage-specific expression patterns. Functional studies motivated by "guilt-by-association" associated individual lincRNAs with specific GO functions, providing an important resource for future studies of lincRNA function. Most importantly, a weighted gene co-expression network analysis suggested that genes of the brown module were specifically associated with the day 2 stage. LincRNAs within this module were co-expressed with proteins involved in hematopoiesis and lipid metabolism. This study presents the systematic identification of lincRNAs in developing chicken embryos and will serve as a powerful resource for the study of lincRNA functions.
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Affiliation(s)
- Junxiao Ren
- National Engineering Laboratory for Animal Breeding and MOA Key Laboratory of Animal Genetics and Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Quanlin Li
- National Engineering Laboratory for Animal Breeding and MOA Key Laboratory of Animal Genetics and Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Qinghe Zhang
- National Engineering Laboratory for Animal Breeding and MOA Key Laboratory of Animal Genetics and Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Michael Clinton
- Division of Developmental Biology, The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Roslin, Midlothian EH25 9RG, United Kingdom
| | - Congjiao Sun
- National Engineering Laboratory for Animal Breeding and MOA Key Laboratory of Animal Genetics and Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Ning Yang
- National Engineering Laboratory for Animal Breeding and MOA Key Laboratory of Animal Genetics and Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, China.
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Rengaraj D, Won S, Han JW, Yoo D, Kim H, Han JY. Whole-Transcriptome Sequencing-Based Analysis of DAZL and Its Interacting Genes during Germ Cells Specification and Zygotic Genome Activation in Chickens. Int J Mol Sci 2020; 21:ijms21218170. [PMID: 33142918 PMCID: PMC7672628 DOI: 10.3390/ijms21218170] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Revised: 10/25/2020] [Accepted: 10/28/2020] [Indexed: 11/25/2022] Open
Abstract
The deleted in azoospermia like (DAZL) is required for germ cells development and maintenance. In chickens, the mRNA and protein of DAZL, a representative maternally inherited germ plasm factor, are detected in the germ plasm of oocyte, zygote, and all stages of the intrauterine embryos. However, it is still insufficient to explain the origin and specification process of chicken germ cells, because the stage at which the zygotic transcription of DAZL occurs and the stage at which the maternal DAZL RNA/protein clears have not yet been fully identified. Moreover, a comprehensive understanding of the expression of DAZL interacting genes during the germ cells specification and development and zygotic genome activation (ZGA) is lacking in chickens. In this study, we identified a set of DAZL interacting genes in chickens using in silico prediction method. Then, we analyzed the whole-transcriptome sequencing (WTS)-based expression of DAZL and its interacting genes in the chicken oocyte, zygote, and Eyal-Giladi and Kochav (EGK) stage embryos (EGK.I to EGK.X). In the results, DAZL transcripts are increased in the zygote (onset of transcription), maintained the increased level until EGK.VI, and decreased from EGK.VIII (possible clearance of maternal RNAs). Among the DAZL interacting genes, most of them are increased either at 1st ZGA or 2nd ZGA, indicating their involvement in germ cells specification and 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, Korea; (D.R.); (J.W.H.); (H.K.)
| | - Sohyoung Won
- Interdisciplinary Program in Bioinformatics, Seoul National University, Seoul 08826, Korea; (S.W.); (D.Y.)
| | - Jong Won Han
- Department of Agricultural Biotechnology, and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul 08826, Korea; (D.R.); (J.W.H.); (H.K.)
| | - DongAhn Yoo
- Interdisciplinary Program in Bioinformatics, Seoul National University, Seoul 08826, Korea; (S.W.); (D.Y.)
| | - Heebal Kim
- Department of Agricultural Biotechnology, and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul 08826, Korea; (D.R.); (J.W.H.); (H.K.)
- Interdisciplinary Program in Bioinformatics, Seoul National University, Seoul 08826, Korea; (S.W.); (D.Y.)
- C&K Genomics, Seoul 05836, Korea
| | - Jae Yong Han
- Department of Agricultural Biotechnology, and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul 08826, Korea; (D.R.); (J.W.H.); (H.K.)
- Correspondence: ; Tel.: +82-2-880-4810
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8
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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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9
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Ren J, Sun C, Clinton M, Yang N. Dynamic Transcriptional Landscape of the Early Chick Embryo. Front Cell Dev Biol 2019; 7:196. [PMID: 31572727 PMCID: PMC6751280 DOI: 10.3389/fcell.2019.00196] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2019] [Accepted: 08/29/2019] [Indexed: 01/22/2023] Open
Abstract
Defining the dynamic transcriptome of the early embryo at high resolution would assist greatly in understanding vertebrate development. Here, we describe the dynamic transcription landscape of early chick embryo development using advanced single-molecule long-read isoform sequencing (Iso-Seq) and RNA-Seq technology. Our transcriptomic profiling reflected the time course of chicken embryonic development from day 1 to day 8 of incubation, a period encompassing gastrulation, somitogenesis, and organogenesis. This analysis identified transcriptional isoforms, alternative splicing (AS) events, fusion transcripts, alternative polyadenylation (APA) sites, and novel genes. Our results showed that intron retention (IR) represented the most abundant AS type and displayed distinct features and dynamic modulation during development. Moreover, we constructed a high-resolution expression profile across embryonic development. Our combined expression dataset correlates distinct gene clusters with specific morphological changes, and provides the first framework for the molecular basis of early chicken embryogenesis. Analysis of gene expression in the developing chicken embryo highlighted the dynamic nature and complexity of the chicken transcriptome and demonstrated that dramatically increased IR events are associated with distinct gene sets.
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Affiliation(s)
- Junxiao Ren
- Department of Animal Genetics and Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, China.,National Engineering Laboratory for Animal Breeding, Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, China Agricultural University, Beijing, China
| | - Congjiao Sun
- Department of Animal Genetics and Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, China.,National Engineering Laboratory for Animal Breeding, Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, China Agricultural University, Beijing, China
| | - Michael Clinton
- Division of Developmental Biology, The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Midlothian, United Kingdom
| | - Ning Yang
- Department of Animal Genetics and Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, China.,National Engineering Laboratory for Animal Breeding, Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, China Agricultural University, Beijing, China
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10
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Hwang YS, Seo M, Choi HJ, Kim SK, Kim H, Han JY. The first whole transcriptomic exploration of pre-oviposited early chicken embryos using single and bulked embryonic RNA-sequencing. Gigascience 2018; 7:1-9. [PMID: 29659814 PMCID: PMC5893961 DOI: 10.1093/gigascience/giy030] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2017] [Accepted: 03/21/2018] [Indexed: 01/09/2023] Open
Abstract
Background The chicken is a valuable model organism, especially in evolutionary and embryology research because its embryonic development occurs in the egg. However, despite its scientific importance, no transcriptome data have been generated for deciphering the early developmental stages of the chicken because of practical and technical constraints in accessing pre-oviposited embryos. Findings Here, we determine the entire transcriptome of pre-oviposited avian embryos, including oocyte, zygote, and intrauterine embryos from Eyal-giladi and Kochav stage I (EGK.I) to EGK.X collected using a noninvasive approach for the first time. We also compare RNA-sequencing data obtained using a bulked embryo sequencing and single embryo/cell sequencing technique. The raw sequencing data were preprocessed with two genome builds, Galgal4 and Galgal5, and the expression of 17,108 and 26,102 genes was quantified in the respective builds. There were some differences between the two techniques, as well as between the two genome builds, and these were affected by the emergence of long intergenic noncoding RNA annotations. Conclusion The first transcriptome datasets of pre-oviposited early chicken embryos based on bulked and single embryo sequencing techniques will serve as a valuable resource for investigating early avian embryogenesis, for comparative studies among vertebrates, and for novel gene annotation in the chicken genome.
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Affiliation(s)
- Young Sun Hwang
- Department of Agricultural Biotechnology and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul 08826, Korea
| | - Minseok Seo
- CHO&KIM genomics, SNU Research Park, Seoul National University Mt.4-2, Seoul 08826, Korea.,Channing Division of Network Medicine, Harvard Medical School and Brigham and Women's Hospital, Boston, Massachusetts, USA
| | - Hee Jung Choi
- Department of Agricultural Biotechnology and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul 08826, Korea
| | - Sang Kyung Kim
- Department of Agricultural Biotechnology and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul 08826, Korea
| | - Heebal Kim
- Department of Agricultural Biotechnology and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul 08826, Korea.,CHO&KIM genomics, SNU Research Park, Seoul National University Mt.4-2, Seoul 08826, Korea.,Institute for Biomedical Sciences, Shinshu University, Minamiminowa, Nagano 399-4598, Japan
| | - Jae Yong Han
- Department of Agricultural Biotechnology and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul 08826, Korea.,Institute for Biomedical Sciences, Shinshu University, Minamiminowa, Nagano 399-4598, Japan
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Hwang YS, Seo M, Kim SK, Bang S, Kim H, Han JY. Zygotic gene activation in the chicken occurs in two waves, the first involving only maternally derived genes. eLife 2018; 7:39381. [PMID: 30375976 PMCID: PMC6242549 DOI: 10.7554/elife.39381] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2018] [Accepted: 10/29/2018] [Indexed: 12/11/2022] Open
Abstract
The first wave of transcriptional activation occurs after fertilisation in a species-specific pattern. Despite its importance to initial embryonic development, the characteristics of transcription following fertilisation are poorly understood in Aves. Here, we report detailed insights into the onset of genome activation in chickens. We established that two waves of transcriptional activation occurred, one shortly after fertilisation and another at Eyal-Giladi and Kochav Stage V. We found 1544 single nucleotide polymorphisms across 424 transcripts derived from parents that were expressed in offspring during the early embryonic stages. Surprisingly, only the maternal genome was activated in the zygote, and the paternal genome remained silent until the second-wave, regardless of the presence of a paternal pronucleus or supernumerary sperm in the egg. The identified maternal genes involved in cleavage that were replaced by bi-allelic expression. The results demonstrate that only maternal alleles are activated in the chicken zygote upon fertilisation, which could be essential for early embryogenesis and evolutionary outcomes in birds. The early stages of animal development involve a handover of genetic control. Initially, the egg cell is maintained by genetic information inherited from the mother, but soon after fertilization it starts to depend on its own genes instead. Activating genes inside the fertilized egg cell (zygote) so that they can take control of development is known as zygotic genome activation. Despite the fact that birds are often used to study how embryos develop, zygotic genome activation in birds is not well understood. Fertilization in birds, including chickens, is different to mammals in that it requires multiple sperm to fertilize an egg cell. As such, zygotic genome activation in birds is likely to differ from that in mammals. By examining gene expression in embryos from mixed-breed chickens, Hwang, Seo et al. showed that there are two stages of zygotic genome activation in chickens. The genes derived from the mother become active in the first stage, while genes from the father become active in the second stage. Genome activation in birds is therefore very different to the same process in mammals, which involves genome activation of both parents from the first stage. This extra level of control may help to prevent genetic complications resulting from the presence of multiple sperm, each of which carries a different set of genes from the father.
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Affiliation(s)
- Young Sun Hwang
- Department of Agricultural Biotechnology, Seoul National University, Seoul, Republic of Korea.,Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, Republic of Korea
| | - Minseok Seo
- C&K Genomics, Seoul, Republic of Korea.,Channing Division of Network Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, United States
| | - Sang Kyung Kim
- Department of Agricultural Biotechnology, Seoul National University, Seoul, Republic of Korea.,Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, Republic of Korea
| | | | - Heebal Kim
- Department of Agricultural Biotechnology, Seoul National University, Seoul, Republic of Korea.,Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, Republic of Korea.,C&K Genomics, Seoul, Republic of Korea
| | - Jae Yong Han
- Department of Agricultural Biotechnology, Seoul National University, Seoul, Republic of Korea.,Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, Republic of Korea
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