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Li J, Pan X, Yuan Y, Shen HB. TFvelo: gene regulation inspired RNA velocity estimation. Nat Commun 2024; 15:1387. [PMID: 38360714 PMCID: PMC11258302 DOI: 10.1038/s41467-024-45661-w] [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: 04/15/2023] [Accepted: 01/30/2024] [Indexed: 02/17/2024] Open
Abstract
RNA velocity is closely related with cell fate and is an important indicator for the prediction of cell states with elegant physical explanation derived from single-cell RNA-seq data. Most existing RNA velocity models aim to extract dynamics from the phase delay between unspliced and spliced mRNA for each individual gene. However, unspliced/spliced mRNA abundance may not provide sufficient signal for dynamic modeling, leading to poor fit in phase portraits. Motivated by the idea that RNA velocity could be driven by the transcriptional regulation, we propose TFvelo, which expands RNA velocity concept to various single-cell datasets without relying on splicing information, by introducing gene regulatory information. Our experiments on synthetic data and multiple scRNA-Seq datasets show that TFvelo can accurately fit genes dynamics on phase portraits, and effectively infer cell pseudo-time and trajectory from RNA abundance data. TFvelo opens a robust and accurate avenue for modeling RNA velocity for single cell data.
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Affiliation(s)
- Jiachen Li
- Institute of Image Processing and Pattern Recognition, Shanghai Jiao Tong University, and Key Laboratory of System Control and Information Processing, Ministry of Education of China, Shanghai, 200240, China
| | - Xiaoyong Pan
- Institute of Image Processing and Pattern Recognition, Shanghai Jiao Tong University, and Key Laboratory of System Control and Information Processing, Ministry of Education of China, Shanghai, 200240, China
| | - Ye Yuan
- Institute of Image Processing and Pattern Recognition, Shanghai Jiao Tong University, and Key Laboratory of System Control and Information Processing, Ministry of Education of China, Shanghai, 200240, China.
| | - Hong-Bin Shen
- Institute of Image Processing and Pattern Recognition, Shanghai Jiao Tong University, and Key Laboratory of System Control and Information Processing, Ministry of Education of China, Shanghai, 200240, China.
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Zhu Y, Zhang Z, Zhang GL, Jiang MX. Effects of multi-gradient equilibration during vitrification on oocyte survival and embryo development in mice. ZYGOTE 2023; 31:612-619. [PMID: 37997743 DOI: 10.1017/s0967199423000540] [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] [Indexed: 11/25/2023]
Abstract
Vitrification has been widely used for oocyte cryopreservation, but there is still a need for optimization to improve clinical outcomes. In this study, we compared the routine droplet merge protocol with modified multi-gradient equilibration vitrification for cryopreservation of mouse oocytes at metaphase II. Subsequently, the oocytes were thawed and subjected to intracytoplasmic sperm injection (ICSI). Oocyte survival and spindle status were evaluated by morphology and immunofluorescence staining. Moreover, the fertilization rates and blastocyst development were examined in vitro. The results showed that multi-gradient equilibration vitrification outperformed droplet merge vitrification in terms of oocyte survival, spindle morphology, blastocyst formation, and embryo quality. In contrast, droplet merge vitrification exhibited decreasing survival rates, a reduced proportion of oocytes with normal spindle morphology, and lower blastocyst rates as the number of loaded oocytes increased. Notably, when more than six oocytes were loaded, reduced oocyte survival rates, abnormal oocyte spindle morphology, and poor embryo quality were observed. These findings highlight that the vitrification of mouse metaphase II oocytes by the modified multi-gradient equilibration vitrification has the advantage of maintaining oocyte survival, spindle morphology, and subsequent embryonic development.
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Affiliation(s)
- Yan Zhu
- Medical Experimental Center, Guangdong Second Provincial General Hospital, Guangzhou 510317, People's Republic of China
| | - Zhen Zhang
- Medical Experimental Center, Guangdong Second Provincial General Hospital, Guangzhou 510317, People's Republic of China
| | - Guang-Li Zhang
- Center for Reproductive Medicine, Guangdong Second Provincial General Hospital, Guangzhou 510317, People's Republic of China
| | - Man-Xi Jiang
- Center for Reproductive Medicine, Guangdong Second Provincial General Hospital, Guangzhou 510317, People's Republic of China
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Liu Y, Sun J, Su Y, Lin J, Lv C, Mo K, Xu S, Wang S. Nuclear-localized eukaryotic translation initiation factor 1A is involved in mouse preimplantation embryo development. J Mol Histol 2021; 52:965-973. [PMID: 34405343 DOI: 10.1007/s10735-021-10014-0] [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: 01/12/2021] [Accepted: 08/11/2021] [Indexed: 12/01/2022]
Abstract
Preimplantation embryo development is characterized by drastic nuclear reprogramming and dynamic stage-specific gene expression. Key regulators of this earliest developmental stage have not been revealed. In the present study, a "non-classical" nuclear-localization pattern of eIF1A was observed during early developmental stages of mouse preimplantation embryo before late-morula. In particular, eIF1A is most highly expressed in the nuclear of 2-cell embryo. Knockdown eIF1A by siRNA microinjection affected the development of mouse preimplantation embryo, resulted in decreased blastocyst formation rate. CDX2 protein expression level significantly down-regulated after eIF1A knockdown in morula stage. In addition, the mRNA expression level of Hsp70.1 was also decreased in 2-cell embryo. The results indicate an indispensable role of eIF1A in mouse preimplantation embryos.
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Affiliation(s)
- Yue Liu
- Key Laboratory of Stem Cell Engineering and Regenerative Medicine of Fujian Province University, Fujian Medical University, Fuzhou, 350122, People's Republic of China.,Department of Human Anatomy, Histology and Embryology, School of Basic Medical Sciences, Fujian Medical University, Fuzhou, 350122, People's Republic of China
| | - Jiandong Sun
- Key Laboratory of Stem Cell Engineering and Regenerative Medicine of Fujian Province University, Fujian Medical University, Fuzhou, 350122, People's Republic of China
| | - Yang Su
- Key Laboratory of Stem Cell Engineering and Regenerative Medicine of Fujian Province University, Fujian Medical University, Fuzhou, 350122, People's Republic of China
| | - Jianmin Lin
- Key Laboratory of Stem Cell Engineering and Regenerative Medicine of Fujian Province University, Fujian Medical University, Fuzhou, 350122, People's Republic of China
| | - Chengyu Lv
- Key Laboratory of Stem Cell Engineering and Regenerative Medicine of Fujian Province University, Fujian Medical University, Fuzhou, 350122, People's Republic of China
| | - Kaien Mo
- Key Laboratory of Stem Cell Engineering and Regenerative Medicine of Fujian Province University, Fujian Medical University, Fuzhou, 350122, People's Republic of China
| | - Songhua Xu
- Key Laboratory of Stem Cell Engineering and Regenerative Medicine of Fujian Province University, Fujian Medical University, Fuzhou, 350122, People's Republic of China.,Department of Human Anatomy, Histology and Embryology, School of Basic Medical Sciences, Fujian Medical University, Fuzhou, 350122, People's Republic of China
| | - Shie Wang
- Key Laboratory of Stem Cell Engineering and Regenerative Medicine of Fujian Province University, Fujian Medical University, Fuzhou, 350122, People's Republic of China. .,Department of Human Anatomy, Histology and Embryology, School of Basic Medical Sciences, Fujian Medical University, Fuzhou, 350122, People's Republic of China.
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Liu Y, Xu S, Lian X, Su Y, Zhong Y, Lv R, Mo K, Zhu H, Xiaojiang W, Xu L, Wang S. Atypical GATA protein TRPS1 plays indispensable roles in mouse two-cell embryo. Cell Cycle 2019; 18:437-451. [PMID: 30712485 DOI: 10.1080/15384101.2019.1577650] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Zygotic genome activation (ZGA) is one of the most critical events at the beginning of mammalian preimplantation embryo development (PED). The mechanisms underlying mouse ZGA remain unclear although it has been widely studied. In the present study, we identified that tricho-rhino-phalangeal syndrome 1 (TRPS1), an atypical GATA family member, is an important factor for ZGA in mouse PED. We found that the Trps1 mRNA level peaked at the one-cell stage while TRPS1 protein did so at the two/four-cell stage. Knockdown of Trps1 by the microinjection of Trps1 siRNA reduced the developmental rate of mouse preimplantation embryos by approximately 30%, and increased the expression of ZGA marker genes MuERV-L and Zscan4d via suppressing the expression of major histone markers H3K4me3 and H3K27me3. Furthermore, Trps1 knockdown decreased the expression of Sox2 but increased Oct4 expression. We conclude that TRPS1 may be indispensable for zygotic genome activation during mouse PED.
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Affiliation(s)
- Yue Liu
- a Key Laboratory of Stem Cell Engineering and Regenerative Medicine , Fujian Province University
| | - Songhua Xu
- b Department of Human Anatomy, Histology and Embryology , Fujian Medical University , Fuzhou , P. R. China
| | - Xiuli Lian
- b Department of Human Anatomy, Histology and Embryology , Fujian Medical University , Fuzhou , P. R. China
| | - Yang Su
- b Department of Human Anatomy, Histology and Embryology , Fujian Medical University , Fuzhou , P. R. China
| | - Yuhuan Zhong
- b Department of Human Anatomy, Histology and Embryology , Fujian Medical University , Fuzhou , P. R. China
| | - Ruimin Lv
- b Department of Human Anatomy, Histology and Embryology , Fujian Medical University , Fuzhou , P. R. China
| | - Kaien Mo
- b Department of Human Anatomy, Histology and Embryology , Fujian Medical University , Fuzhou , P. R. China
| | - Huimin Zhu
- c Fujian Key Laboratory of Medical Bioinformatics, School of Basic Medical Sciences , Fujian Medical University , Fuzhou , P. R. China.,d Key Laboratory of Ministry of Education for Gastrointestinal Cancer, School of Basic Medical Sciences , Fujian Medical University , Fuzhou , P. R. China
| | - Wang Xiaojiang
- b Department of Human Anatomy, Histology and Embryology , Fujian Medical University , Fuzhou , P. R. China
| | - Lixuan Xu
- b Department of Human Anatomy, Histology and Embryology , Fujian Medical University , Fuzhou , P. R. China
| | - Shie Wang
- a Key Laboratory of Stem Cell Engineering and Regenerative Medicine , Fujian Province University.,b Department of Human Anatomy, Histology and Embryology , Fujian Medical University , Fuzhou , P. R. China
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Jiang M, Hu L, Wang B, Chen D, Li Y, Zhang Z, Zhu Y. Uterine RGS2 expression is regulated by exogenous estrogen and progesterone in ovariectomized mice, and downregulation of RGS2 expression in artificial decidualized ESCs inhibits trophoblast spreading in vitro. Mol Reprod Dev 2018; 86:88-99. [PMID: 30412338 DOI: 10.1002/mrd.23087] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2018] [Accepted: 10/29/2018] [Indexed: 12/12/2022]
Affiliation(s)
- Manxi Jiang
- The Reproductive Medical Center, Guangdong Second Provincial General Hospital; Guangzhou China
| | - Liangshan Hu
- Department of Laboratory Medicine and Central Laboratories; Guangdong Second Provincial General Hospital; Guangzhou China
| | - Baoping Wang
- The Reproductive Medical Center, Guangdong Second Provincial General Hospital; Guangzhou China
| | - Danxia Chen
- Department of Laboratory Medicine and Central Laboratories; Guangdong Second Provincial General Hospital; Guangzhou China
| | - Yahong Li
- Department of Laboratory Medicine and Central Laboratories; Guangdong Second Provincial General Hospital; Guangzhou China
| | - Zhen Zhang
- Department of Laboratory Medicine and Central Laboratories; Guangdong Second Provincial General Hospital; Guangzhou China
| | - Yan Zhu
- Department of Laboratory Medicine and Central Laboratories; Guangdong Second Provincial General Hospital; Guangzhou China
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Menchero S, Rayon T, Andreu MJ, Manzanares M. Signaling pathways in mammalian preimplantation development: Linking cellular phenotypes to lineage decisions. Dev Dyn 2016; 246:245-261. [DOI: 10.1002/dvdy.24471] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2016] [Revised: 11/16/2016] [Accepted: 11/16/2016] [Indexed: 12/20/2022] Open
Affiliation(s)
- Sergio Menchero
- Centro Nacional de Investigaciones Cardiovasculares (CNIC); Madrid Spain
| | - Teresa Rayon
- Centro Nacional de Investigaciones Cardiovasculares (CNIC); Madrid Spain
| | - Maria Jose Andreu
- Centro Nacional de Investigaciones Cardiovasculares (CNIC); Madrid Spain
| | - Miguel Manzanares
- Centro Nacional de Investigaciones Cardiovasculares (CNIC); Madrid Spain
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Jiang MX, Shi Y, Sun ZG, Zhang Z, Zhu Y. Inhibition of the Binding between RGS2 and β-Tubulin Interferes with Spindle Formation and Chromosome Segregation during Mouse Oocyte Maturation In Vitro. PLoS One 2016; 11:e0159535. [PMID: 27463806 PMCID: PMC4963123 DOI: 10.1371/journal.pone.0159535] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2016] [Accepted: 07/04/2016] [Indexed: 11/18/2022] Open
Abstract
RGS2 is a negative regulator of G protein signaling that contains a GTPase-activating domain and a β-tubulin binding region. This study aimed to determine the localization and function of RGS2 during mouse oocyte maturation in vitro. Immunofluorescent staining revealed that RGS2 was widely expressed in the cytoplasm with a greater abundance on both meiotic spindles and first/second polar bodies from the fully-grown germinal vesicle (GV) stage to the MII stages. Co-expression of RGS2 and β-tubulin could also be detected in the spindle and polar body of mouse oocytes at the MI, AI, and MII stages. Inhibition of the binding site between RGS2 and β-tubulin was accomplished by injecting anti-RGS2 antibody into GV-stage oocytes, which could result in oocytes arrest at the MI or AI stage during in vitro maturation, but it did not affect germinal vesicle breakdown. Moreover, injecting anti-RGS2 antibody into oocytes resulted in a significant reduction in the rate of first polar body extrusion and abnormal spindle formation. Additionally, levels of phosphorylated MEK1/2 were significantly reduced in anti-RGS2 antibody injected oocytes compared with control oocytes. These findings suggest that RGS2 might play a critical role in mouse oocyte meiotic maturation by affecting β-tubulin polymerization and chromosome segregation.
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Affiliation(s)
- Man-Xi Jiang
- Guangdong No.2 Provincial People’s Hospital, Guangzhou 510317, China
| | - Yan Shi
- NPFPC Key Lab of Contraceptives and Devices, Shanghai Institute of Planned Parenthood Research, Shanghai 200032, China
| | - Zhao-Gui Sun
- NPFPC Key Lab of Contraceptives and Devices, Shanghai Institute of Planned Parenthood Research, Shanghai 200032, China
| | - Zhi Zhang
- Guangdong No.2 Provincial People’s Hospital, Guangzhou 510317, China
- * E-mail: (YZ); (ZZ)
| | - Yan Zhu
- Guangdong No.2 Provincial People’s Hospital, Guangzhou 510317, China
- * E-mail: (YZ); (ZZ)
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Zhang Q, Dan J, Wang H, Guo R, Mao J, Fu H, Wei X, Liu L. Tcstv1 and Tcstv3 elongate telomeres of mouse ES cells. Sci Rep 2016; 6:19852. [PMID: 26816107 PMCID: PMC4728397 DOI: 10.1038/srep19852] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2015] [Accepted: 12/18/2015] [Indexed: 02/05/2023] Open
Abstract
Mouse embryonic stem cell (ESC) cultures exhibit a heterogeneous mixture of metastable cells sporadically entering the 2-cell (2C)-embryo-like state, critical for ESC potency. One of 2-cell genes, Zscan4, has been shown to be responsible for telomere maintenance, genomic stability and pluripotency of mouse ESCs. Functions of other 2C-genes in ESCs remain elusive. Here we show that 2C-genes Tcstv1 and Tcstv3 play a role in regulation of telomere lengths. Overexpression or knockdown Tcstv1 and Tcstv3 does not immediately affect proliferation, pluripotency and differentiation in vitro of ESCs. However, ectopic expression of Tcstv1 or Tcstv3 results in telomere elongation, whereas Tcstv1/3 knockdown shortens telomeres of ESCs. Overexpression of Tcstv1 or Tcstv3 does not alter telomere stability. Furthermore, Tcstv1 can increase Zscan4 protein levels and telomere recombination by telomere sister chromatid exchange (T-SCE). Depletion of Tcstv1/3 reduces Zscan4 protein levels. Together, Tcstv1 and Tcstv3 are involved in telomere maintenance that is required for long-term self-renewal of mouse ESCs. Our data also suggests that Tcstv1/3 may co-operate and stabilize Zscan4 protein but the molecular bases remain to be determined.
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Affiliation(s)
- Qian Zhang
- State Key Laboratory of Medicinal Chemical Biology; 2011 Collaborative Innovation Center for Biotherapy, Department of Cell Biology and Genetics, College of Life Sciences, Nankai University, Tianjin 300071, China
| | - Jiameng Dan
- State Key Laboratory of Medicinal Chemical Biology; 2011 Collaborative Innovation Center for Biotherapy, Department of Cell Biology and Genetics, College of Life Sciences, Nankai University, Tianjin 300071, China
| | - Hua Wang
- State Key Laboratory of Medicinal Chemical Biology; 2011 Collaborative Innovation Center for Biotherapy, Department of Cell Biology and Genetics, College of Life Sciences, Nankai University, Tianjin 300071, China
| | - Renpeng Guo
- State Key Laboratory of Medicinal Chemical Biology; 2011 Collaborative Innovation Center for Biotherapy, Department of Cell Biology and Genetics, College of Life Sciences, Nankai University, Tianjin 300071, China
| | - Jian Mao
- State Key Laboratory of Medicinal Chemical Biology; 2011 Collaborative Innovation Center for Biotherapy, Department of Cell Biology and Genetics, College of Life Sciences, Nankai University, Tianjin 300071, China
| | - Haifeng Fu
- State Key Laboratory of Medicinal Chemical Biology; 2011 Collaborative Innovation Center for Biotherapy, Department of Cell Biology and Genetics, College of Life Sciences, Nankai University, Tianjin 300071, China
| | - Xiawei Wei
- State Key Laboratory of Biotherapy/Collaborative Innovation Center for Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China
| | - Lin Liu
- State Key Laboratory of Medicinal Chemical Biology; 2011 Collaborative Innovation Center for Biotherapy, Department of Cell Biology and Genetics, College of Life Sciences, Nankai University, Tianjin 300071, China
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