1
|
Fang F, Chen D, Basharat AR, Poulos W, Wang Q, Cibelli JB, Liu X, Sun L. Quantitative proteomics reveals the dynamic proteome landscape of zebrafish embryos during the maternal-to-zygotic transition. iScience 2024; 27:109944. [PMID: 38784018 PMCID: PMC11111832 DOI: 10.1016/j.isci.2024.109944] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Revised: 08/23/2023] [Accepted: 05/06/2024] [Indexed: 05/25/2024] Open
Abstract
Maternal-to-zygotic transition (MZT) is central to early embryogenesis. However, its underlying molecular mechanisms are still not well described. Here, we revealed the expression dynamics of 5,000 proteins across four stages of zebrafish embryos during MZT, representing one of the most systematic surveys of proteome landscape of the zebrafish embryos during MZT. Nearly 700 proteins were differentially expressed and were divided into six clusters according to their expression patterns. The proteome expression profiles accurately reflect the main events that happen during the MZT, i.e., zygotic genome activation (ZGA), clearance of maternal mRNAs, and initiation of cellular differentiation and organogenesis. MZT is modulated by many proteins at multiple levels in a collaborative fashion, i.e., transcription factors, histones, histone-modifying enzymes, RNA helicases, and P-body proteins. Significant discrepancies were discovered between zebrafish proteome and transcriptome profiles during the MZT. The proteome dynamics database will be a valuable resource for bettering our understanding of MZT.
Collapse
Affiliation(s)
- Fei Fang
- Department of Chemistry, Michigan State University, 578 S Shaw Lane, East Lansing, MI 48824, USA
| | - Daoyang Chen
- Department of Chemistry, Michigan State University, 578 S Shaw Lane, East Lansing, MI 48824, USA
| | - Abdul Rehman Basharat
- Department of BioHealth Informatics, Indiana University-Purdue University Indianapolis, Indianapolis, IN 46202, USA
| | - William Poulos
- Department of Animal Science, Michigan State University, East Lansing, MI 48824, USA
| | - Qianyi Wang
- Department of Chemistry, Michigan State University, 578 S Shaw Lane, East Lansing, MI 48824, USA
| | - Jose B. Cibelli
- Department of Animal Science, Michigan State University, East Lansing, MI 48824, USA
- Department of Large Animal Clinical Sciences, Michigan State University, East Lansing, MI 48824, USA
| | - Xiaowen Liu
- Deming Department of Medicine, School of Medicine, Tulane University, 1441 Canal Street, New Orleans, LA 70112, USA
| | - Liangliang Sun
- Department of Chemistry, Michigan State University, 578 S Shaw Lane, East Lansing, MI 48824, USA
| |
Collapse
|
2
|
Riemondy K, Henriksen JC, Rissland OS. Intron dynamics reveal principles of gene regulation during the maternal-to-zygotic transition. RNA (NEW YORK, N.Y.) 2023; 29:596-608. [PMID: 36764816 PMCID: PMC10158999 DOI: 10.1261/rna.079168.122] [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: 03/17/2022] [Accepted: 01/29/2023] [Indexed: 05/06/2023]
Abstract
The maternal-to-zygotic transition (MZT) is a conserved embryonic process in animals where developmental control shifts from the maternal to zygotic genome. A key step in this transition is zygotic transcription, and deciphering the MZT requires classifying newly transcribed genes. However, due to current technological limitations, this starting point remains a challenge for studying many species. Here, we present an alternative approach that characterizes transcriptome changes based solely on RNA-seq data. By combining intron-mapping reads and transcript-level quantification, we characterized transcriptome dynamics during the Drosophila melanogaster MZT. Our approach provides an accessible platform to investigate transcriptome dynamics that can be applied to the MZT in nonmodel organisms. In addition to classifying zygotically transcribed genes, our analysis revealed that over 300 genes express different maternal and zygotic transcript isoforms due to alternative splicing, polyadenylation, and promoter usage. The vast majority of these zygotic isoforms have the potential to be subject to different regulatory control, and over two-thirds encode different proteins. Thus, our analysis reveals an additional layer of regulation during the MZT, where new zygotic transcripts can generate additional proteome diversity.
Collapse
Affiliation(s)
- Kent Riemondy
- RNA Bioscience Initiative, University of Colorado School of Medicine, Aurora, Colorado 80045, USA
| | - Jesslyn C Henriksen
- RNA Bioscience Initiative, University of Colorado School of Medicine, Aurora, Colorado 80045, USA
- Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, Aurora, Colorado 80045, USA
| | - Olivia S Rissland
- RNA Bioscience Initiative, University of Colorado School of Medicine, Aurora, Colorado 80045, USA
- Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, Aurora, Colorado 80045, USA
| |
Collapse
|
3
|
Mohanty G, Jena SR, Kar S, Samanta L. Paternal factors in recurrent pregnancy loss: an insight through analysis of non-synonymous single-nucleotide polymorphism in human testis-specific chaperone HSPA2 gene. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2022; 29:62219-62234. [PMID: 34845642 DOI: 10.1007/s11356-021-17799-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/08/2021] [Accepted: 11/23/2021] [Indexed: 06/13/2023]
Abstract
Heat shock protein A2 (HSPA2) is a testis-specific molecular chaperone of the 70 kDa heat shock protein (HSP70) family and reported to play a key role in spermatogenesis as well as in the remodelling of the sperm surface during capacitation. It is established that mice lacking HSPA2 gene are infertile and spermatozoa that fail to interact with the zona pellucida of the oocyte consistently lack HSPA2 protein expression. However, its role in post fertilization events is not fully understood. Owing to the importance of HSPA2 in male reproduction, the present study is undertaken to reveal the association between genetic mutation and phenotypic variation in recurrent pregnancy loss (RPL) patients through an in silico prediction analysis. In this study, we used different computational tools and servers such as SIFT, PolyPhen2, PROVEAN, nsSNPAnalyzer, and SNPs & GO to analyse the functional consequences of the nsSNPs in human HSPA2 gene. The most damaging amino acid variants generated were subjected to I-Mutant 2.0 and ConSurf. Post-translational modifications such as phosphorylation mediated by these deleterious nsSNPs were analysed using NetPhos 2.0, and gene-gene interaction study was conducted using GeneMANIA. Finally, in-depth studies of the nsSNPs were studied through Project HOPE. The findings of the study revealed 18 nsSNPs to be deleterious using a combinatorial bioinformatic approach. Further functional analysis suggests that screening of nsSNP variants of HSPA2 that tend to be conserved and has potential to undergo phosphorylation at critical positions (rs764410231, rs200951589, rs756852956) may be useful for predicting outcome in altered reproductive outcome. The physicochemical alterations and its impact on the structural and functional conformity were determined by Project HOPE. Gene-gene interaction depicts its close association with antioxidant enzyme (SOD1) strongly supporting an inefficient oxidative scavenging regulatory mechanism in the spermatozoa of RPL patients as reported earlier. The present study has thus identified high-risk deleterious nsSNPs of HSPA2 gene and would be beneficial in the diagnosis and prognosis of the paternal effects in RPL patients.
Collapse
Affiliation(s)
- Gayatri Mohanty
- Redox Biology & Proteomics Laboratory, Department of Zoology, School of Life Sciences, Ravenshaw University, Cuttack, Odisha, India
- Centre for Excellence in Environment and Public Health, Ravenshaw University, Cuttack, Odisha, India
| | - Soumya Ranjan Jena
- Redox Biology & Proteomics Laboratory, Department of Zoology, School of Life Sciences, Ravenshaw University, Cuttack, Odisha, India
- Centre for Excellence in Environment and Public Health, Ravenshaw University, Cuttack, Odisha, India
| | - Sujata Kar
- Department of Obstetrics & Gynaecology, Kar Clinic and Hospital Pvt. Ltd., Bhubaneswar, Odisha, India
| | - Luna Samanta
- Redox Biology & Proteomics Laboratory, Department of Zoology, School of Life Sciences, Ravenshaw University, Cuttack, Odisha, India.
- Centre for Excellence in Environment and Public Health, Ravenshaw University, Cuttack, Odisha, India.
| |
Collapse
|
4
|
Verwoolde MB, Arts J, Jansen CA, Parmentier HK, Lammers A. Transgenerational Effects of Maternal Immune Activation on Specific Antibody Responses in Layer Chickens. Front Vet Sci 2022; 9:832130. [PMID: 35252424 PMCID: PMC8891521 DOI: 10.3389/fvets.2022.832130] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Accepted: 01/19/2022] [Indexed: 11/18/2022] Open
Abstract
Activation of the maternal immune system may affect innate and adaptive immune responses in the next generation and may therefore have implications for vaccine efficacy and dietary immune modulation by feed additives. However, transgenerational effects on immune responses in chickens have been investigated to a limited extend. The present study investigated effects of intratracheal (i.t) specific and aspecific immune activation of laying hens on specific antibody production in the next generation. In two experiments laying hens received intratracheally an immune stimulus with human serum albumin (HuSA) or lipopolysaccharide (LPS). In experiment 1, hatchlings of the immune activated hens were at 4 weeks i.t. immunized with HuSA or HuSA+LPS. Maternal immune activation with LPS increased HuSA specific IgY and IgM responses in offspring. These results suggest a transgenerational effect of the maternal immune system on the specific antibody response in the next generation. In experiment 2 hatchlings received either β-glucan-enriched feed or control feed and were i.t. immunized with HuSA. Maternal immune activation with LPS decreased IgY anti-HuSA responses after HuSA immunization within hatchlings that received β-glucan enriched feed. The results of Experiment 2 suggest a transgenerational link between the innate immune system of mother and specific antibody responses in offspring. Despite variabilities in the outcomes of the two experiments, the observations of both suggest a link between the maternal innate immune system and the immune system of the offspring. Furthermore, our results may imply that maternal activation of the innate immune system can influence immune modulating dietary interventions and vaccine strategies in the next generation.
Collapse
Affiliation(s)
- Michel B. Verwoolde
- Adaptation Physiology Group, Department of Animal Sciences, Wageningen University & Research, Wageningen, Netherlands
- Animal Nutrition Group, Department of Animal Sciences, Wageningen University & Research, Wageningen, Netherlands
| | - Joop Arts
- Adaptation Physiology Group, Department of Animal Sciences, Wageningen University & Research, Wageningen, Netherlands
| | - Christine A. Jansen
- Cell Biology and Immunology Group, Department of Animal Sciences, Wageningen University & Research, Wageningen, Netherlands
| | - Henk K. Parmentier
- Adaptation Physiology Group, Department of Animal Sciences, Wageningen University & Research, Wageningen, Netherlands
| | - Aart Lammers
- Adaptation Physiology Group, Department of Animal Sciences, Wageningen University & Research, Wageningen, Netherlands
- *Correspondence: Aart Lammers
| |
Collapse
|
5
|
The embryonic transcriptome of Parhyale hawaiensis reveals different dynamics of microRNAs and mRNAs during the maternal-zygotic transition. Sci Rep 2022; 12:174. [PMID: 34996916 PMCID: PMC8741983 DOI: 10.1038/s41598-021-03642-9] [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: 07/26/2021] [Accepted: 11/09/2021] [Indexed: 11/18/2022] Open
Abstract
Parhyale hawaiensis has emerged as the crustacean model of choice due to its tractability, ease of imaging, sequenced genome, and development of CRISPR/Cas9 genome editing tools. However, transcriptomic datasets spanning embryonic development are lacking, and there is almost no annotation of non-protein-coding RNAs, including microRNAs. We have sequenced microRNAs, together with mRNAs and long non-coding RNAs, in Parhyale using paired size-selected RNA-seq libraries at seven time-points covering important transitions in embryonic development. Focussing on microRNAs, we annotate 175 loci in Parhyale, 88 of which have no known homologs. We use these data to annotate the microRNAome of 37 crustacean genomes, and suggest a core crustacean microRNA set of around 61 sequence families. We examine the dynamic expression of microRNAs and mRNAs during the maternal-zygotic transition. Our data suggest that zygotic genome activation occurs in two waves in Parhyale with microRNAs transcribed almost exclusively in the second wave. Contrary to findings in other arthropods, we do not predict a general role for microRNAs in clearing maternal transcripts. These data significantly expand the available transcriptomics resources for Parhyale, and facilitate its use as a model organism for the study of small RNAs in processes ranging from embryonic development to regeneration.
Collapse
|
6
|
Douglas C, Maciulyte V, Zohren J, Snell DM, Mahadevaiah SK, Ojarikre OA, Ellis PJI, Turner JMA. CRISPR-Cas9 effectors facilitate generation of single-sex litters and sex-specific phenotypes. Nat Commun 2021; 12:6926. [PMID: 34862376 PMCID: PMC8642469 DOI: 10.1038/s41467-021-27227-2] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Accepted: 11/05/2021] [Indexed: 11/09/2022] Open
Abstract
Animals are essential genetic tools in scientific research and global resources in agriculture. In both arenas, a single sex is often required in surplus. The ethical and financial burden of producing and culling animals of the undesired sex is considerable. Using the mouse as a model, we develop a synthetic lethal, bicomponent CRISPR-Cas9 strategy that produces male- or female-only litters with one hundred percent efficiency. Strikingly, we observe a degree of litter size compensation relative to control matings, indicating that our system has the potential to increase the yield of the desired sex in comparison to standard breeding designs. The bicomponent system can also be repurposed to generate postnatal sex-specific phenotypes. Our approach, harnessing the technological applications of CRISPR-Cas9, may be applicable to other vertebrate species, and provides strides towards ethical improvements for laboratory research and agriculture.
Collapse
Affiliation(s)
- Charlotte Douglas
- Sex Chromosome Biology Laboratory, The Francis Crick Institute, London, UK
| | - Valdone Maciulyte
- Sex Chromosome Biology Laboratory, The Francis Crick Institute, London, UK
| | - Jasmin Zohren
- Sex Chromosome Biology Laboratory, The Francis Crick Institute, London, UK
| | - Daniel M Snell
- Sex Chromosome Biology Laboratory, The Francis Crick Institute, London, UK
| | | | - Obah A Ojarikre
- Sex Chromosome Biology Laboratory, The Francis Crick Institute, London, UK
| | | | - James M A Turner
- Sex Chromosome Biology Laboratory, The Francis Crick Institute, London, UK.
| |
Collapse
|
7
|
Mizushima S, Sasanami T, Ono T, Matsuzaki M, Kansaku N, Kuroiwa A. Cyclin D1 gene expression is essential for cell cycle progression from the maternal-to-zygotic transition during blastoderm development in Japanese quail. Dev Biol 2021; 476:249-258. [PMID: 33905721 DOI: 10.1016/j.ydbio.2021.04.005] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2020] [Revised: 03/31/2021] [Accepted: 04/20/2021] [Indexed: 12/26/2022]
Abstract
Embryogenesis proceeds by a highly regulated series of events. In animals, maternal factors that accumulate in the egg cytoplasm control cell cycle progression at the initial stage of cleavage. However, cell cycle regulation is switched to a system governed by the activated nuclear genome at a specific stage of development, referred to as maternal-to-zygotic transition (MZT). Detailed molecular analyses have been performed on maternal factors and activated zygotic genes in MZT in mammals, fishes and chicken; however, the underlying mechanisms remain unclear in quail. In the present study, we demonstrated that MZT occurred at blastoderm stage V in the Japanese quail using novel gene targeting technology in which the CRISPR/Cas9 and intracytoplasmic sperm injection (ICSI) systems were combined. At blastoderm stage V, we found that maternal retinoblastoma 1 (RB1) protein expression was down-regulated, whereas the gene expression of cyclin D1 (CCND1) was initiated. When a microinjection of sgRNA containing CCND1-targeted sequencing and Cas9 mRNA was administered at the pronuclear stage, blastoderm development stopped at stage V and the down-regulation of RB1 did not occur. This result indicates the most notable difference from mammals in which CCND-knockout embryos are capable of developing beyond MZT. We also showed that CCND1 induced the phosphorylation of the serine/threonine residues of the RB1 protein, which resulted in the degradation of this protein. These results suggest that CCND1 is one of the key factors for RB1 protein degradation at MZT, and the elimination of RB1 may contribute to cell cycle progression after MZT during blastoderm development in the Japanese quail. Our novel technology, which combined the CRISPR/Cas9 system and ICSI, has the potential to become a powerful tool for avian-targeted mutagenesis.
Collapse
Affiliation(s)
- Shusei Mizushima
- Faculty of Science, Hokkaido University, Sapporo, Hokkaido, 060-0810, Japan.
| | - Tomohiro Sasanami
- Department of Applied Life Sciences, Faculty of Agriculture, Shizuoka University, Shizuoka, Shizuoka, 422-8529, Japan
| | - Tamao Ono
- Faculty of Agriculture, Shinshu University, Kamiina, Nagano, 399-4598, Japan
| | - Mei Matsuzaki
- Program of Food and AgriLife Science, Graduate School of Integrated Sciences for Life, Hiroshima University, Kagamiyama, Higashi-Hiroshima City, Hiroshima, 739-8528, Japan
| | - Norio Kansaku
- Department of Animal Science and Biotechnology, Azabu University, Fuchinobe, Sagamihara, 229-8501, Japan
| | - Asato Kuroiwa
- Faculty of Science, Hokkaido University, Sapporo, Hokkaido, 060-0810, Japan
| |
Collapse
|
8
|
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.
Collapse
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
| |
Collapse
|
9
|
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.
Collapse
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.
| |
Collapse
|
10
|
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.
Collapse
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
| |
Collapse
|