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Zhang Z, Shi Q, Zhu X, Jin L, Lang L, Lyu S, Xin X, Huang Y, Yu X, Li Z, Chen S, Xu Z, Zhang W, Wang E. Identification and Functional Analysis of Transcriptome Profiles, Long Non-Coding RNAs, Single-Nucleotide Polymorphisms, and Alternative Splicing from the Oocyte to the Preimplantation Stage of Sheep by Single-Cell RNA Sequencing. Genes (Basel) 2023; 14:1145. [PMID: 37372325 DOI: 10.3390/genes14061145] [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: 04/03/2023] [Revised: 05/16/2023] [Accepted: 05/18/2023] [Indexed: 06/29/2023] Open
Abstract
Numerous dynamic and complicated processes characterize development from the oocyte to the embryo. However, given the importance of functional transcriptome profiles, long non-coding RNAs, single-nucleotide polymorphisms, and alternative splicing during embryonic development, the effect that these features have on the blastomeres of 2-, 4-, 8-, 16-cell, and morula stages of development has not been studied. Here, we carried out experiments to identify and functionally analyze the transcriptome profiles, long non-coding RNAs, single-nucleotide polymorphisms (SNPs), and alternative splicing (AS) of cells from sheep from the oocyte to the blastocyst developmental stages. We found between the oocyte and zygote groups significantly down-regulated genes and the second-largest change in gene expression occurred between the 8- and 16-cell stages. We used various methods to construct a profile to characterize cellular and molecular features and systematically analyze the related GO and KEGG profile of cells of all stages from the oocyte to the blastocyst. This large-scale, single-cell atlas provides key cellular information and will likely assist clinical studies in improving preimplantation genetic diagnosis.
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Affiliation(s)
- Zijing Zhang
- Institute of Animal Husbandry and Veterinary Science, Henan Academy of Agricultural Sciences, No. 116 Hua Yuan Road, Zhengzhou 450002, China
| | - Qiaoting Shi
- Institute of Animal Husbandry and Veterinary Science, Henan Academy of Agricultural Sciences, No. 116 Hua Yuan Road, Zhengzhou 450002, China
| | - Xiaoting Zhu
- Institute of Animal Husbandry and Veterinary Science, Henan Academy of Agricultural Sciences, No. 116 Hua Yuan Road, Zhengzhou 450002, China
| | - Lei Jin
- Institute of Animal Husbandry and Veterinary Science, Henan Academy of Agricultural Sciences, No. 116 Hua Yuan Road, Zhengzhou 450002, China
| | - Limin Lang
- Institute of Animal Husbandry and Veterinary Science, Henan Academy of Agricultural Sciences, No. 116 Hua Yuan Road, Zhengzhou 450002, China
| | - Shijie Lyu
- Institute of Animal Husbandry and Veterinary Science, Henan Academy of Agricultural Sciences, No. 116 Hua Yuan Road, Zhengzhou 450002, China
| | - Xiaoling Xin
- Institute of Animal Husbandry and Veterinary Science, Henan Academy of Agricultural Sciences, No. 116 Hua Yuan Road, Zhengzhou 450002, China
| | - Yongzhen Huang
- College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China
| | - Xiang Yu
- Henan Animal Health Supervision Institute, Zhengzhou 450003, China
| | - Zhiming Li
- Henan Provincial Animal Husbandry General Station, Zhengzhou 450008, China
| | - Sujuan Chen
- Synthetic Biology Engineering Lab of Henan Province, School of Sciences and Technology, Xinxiang Medical University, Xinxiang 453003, China
| | - Zhaoxue Xu
- Institute of Animal Husbandry and Veterinary Science, Henan Academy of Agricultural Sciences, No. 116 Hua Yuan Road, Zhengzhou 450002, China
| | - Wei Zhang
- College of Animal Science and Veterinary Medicine, Henan Institute of Science and Technology, Xinxiang 453003, China
| | - Eryao Wang
- Institute of Animal Husbandry and Veterinary Science, Henan Academy of Agricultural Sciences, No. 116 Hua Yuan Road, Zhengzhou 450002, China
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Wang Z, Wang Y, Hui T, Chen R, Xu Y, Zhang Y, Tian H, Wang W, Cong Y, Guo S, Zhu Y, Zhang X, Guo D, Bai M, Fan Y, Yue C, Bai Z, Sun J, Cai W, Zhang X, Gu M, Qin Y, Sun Y, Wu Y, Wu R, Dou X, Bai W, Zheng Y. Single-Cell Sequencing Reveals Differential Cell Types in Skin Tissues of Liaoning Cashmere Goats and Key Genes Related Potentially to the Fineness of Cashmere Fiber. Front Genet 2021; 12:726670. [PMID: 34858469 PMCID: PMC8631524 DOI: 10.3389/fgene.2021.726670] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2021] [Accepted: 08/25/2021] [Indexed: 11/17/2022] Open
Abstract
Cashmere fineness is one of the important factors determining cashmere quality; however, our understanding of the regulation of cashmere fineness at the cellular level is limited. Here, we used single-cell RNA sequencing and computational models to identify 13 skin cell types in Liaoning cashmere goats. We also analyzed the molecular changes in the development process by cell trajectory analysis and revealed the maturation process in the gene expression profile in Liaoning cashmere goats. Weighted gene co-expression network analysis explored hub genes in cell clusters related to cashmere formation. Secondary hair follicle dermal papilla cells (SDPCs) play an important role in the growth and density of cashmere. ACTA2, a marker gene of SDPCs, was selected for immunofluorescence (IF) and Western blot (WB) verification. Our results indicate that ACTA2 is mainly expressed in SDPCs, and WB results show different expression levels. COL1A1 is a highly expressed gene in SDPCs, which was verified by IF and WB. We then selected CXCL8 of SDPCs to verify and prove the differential expression in the coarse and fine types of Liaoning cashmere goats. Therefore, the CXCL8 gene may regulate cashmere fineness. These genes may be involved in regulating the fineness of cashmere in goat SDPCs; our research provides new insights into the mechanism of cashmere growth and fineness regulation by cells.
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Affiliation(s)
- Zeying Wang
- College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang, China
- College of Food Science, Shenyang Agricultural University, Shenyang, China
| | - Yanru Wang
- College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang, China
| | - Taiyu Hui
- College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang, China
| | - Rui Chen
- College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang, China
| | - Yanan Xu
- College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang, China
| | - Yu Zhang
- College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang, China
| | - He Tian
- College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang, China
| | - Wei Wang
- College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang, China
| | - Yuyan Cong
- College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang, China
| | - Suping Guo
- College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang, China
| | - Yanxu Zhu
- Liaoning Province Modern Agricultural Production Base Construction Engineering Center, Shenyang, China
| | - Xinghui Zhang
- Liaoning Province Modern Agricultural Production Base Construction Engineering Center, Shenyang, China
| | - Dan Guo
- Liaoning Provincial Department of Science and Technology, Shenyang, China
| | - Man Bai
- College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang, China
| | - Yixing Fan
- College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang, China
| | - Chang Yue
- College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang, China
| | - Zhixian Bai
- College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang, China
| | - Jiaming Sun
- College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang, China
| | - Weidong Cai
- College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang, China
| | - Xinjiang Zhang
- College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang, China
| | - Ming Gu
- College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang, China
| | - Yuting Qin
- College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang, China
| | - Yinggang Sun
- College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang, China
| | - Yanzhi Wu
- College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang, China
| | - Rina Wu
- College of Food Science, Shenyang Agricultural University, Shenyang, China
| | - Xingtang Dou
- Liaoning Province Modern Agricultural Production Base Construction Engineering Center, Shenyang, China
| | - Wenlin Bai
- College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang, China
| | - Yuanyuan Zheng
- College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang, China
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He Y, Wang Y, Zhang H, Zhang Y, Quan F. Alpha-lipoic acid improves the maturation and the developmental potential of goat oocytes in vitro. Reprod Domest Anim 2021; 56:545-554. [PMID: 33423332 DOI: 10.1111/rda.13892] [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: 03/23/2020] [Accepted: 01/07/2021] [Indexed: 12/30/2022]
Abstract
Oxidative stress inevitably occurs during oocyte maturation in vitro. α-lipoic acid (α-LA) has a strong antioxidant capacity, but the effect of α-LA on parthenogenetic activation of oocytes was rarely reported. This study aims to investigate the effect of supplementing α-LA to in vitro maturation medium on the subsequent developmental ability of goat parthenogenetic embryos during oocytes maturation. In the study, the goat cumulus-oocyte complex was divided into the experimental (with 25 μmol/L α-LA) and the control (without α-LA) groups. Oxidase expression was measured using RT-qPCR. After 18-22 hr of maturation, the oocytes were then parthenogenetic activated. The total antioxidant capacity of embryos was measured after 0, 24, 48, 72 and 96 hr of culture. Rates of oocyte maturation and the rates of development for parthenogenetic embryos in the α-LA group were significantly improved by 7.88% (p < .05) and 5.41% (p < .05) compared with those in the control group, respectively. After 24 hr, the difference in total antioxidant capacity was extremely significant in both groups. An evident decrease in the control group and a minor decrease in the α-LA group were observed (p < .01). The ratio of inner cell mass cells to the total cell number of blastocysts in the α-LA group increased compared with that in the control group (p < .05) on day 8. α-LA significantly promoted the expression of SOD and GPX4 of parthenogenetic blastocysts and maturated oocytes. α-LA (25 μmol/L) improved the maturation rate and the developmental competence of the parthenogenetic activation of oocytes, which might be mediated by maintaining the total antioxidant ability of oocytes during the culture period.
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Affiliation(s)
- Yuanyuan He
- Key Laboratory of Animal Biotechnology of the Ministry of Agriculture, College of Veterinary Medicine, Northwest A&F University, Yangling, China
| | - Yile Wang
- Key Laboratory of Animal Biotechnology of the Ministry of Agriculture, College of Veterinary Medicine, Northwest A&F University, Yangling, China
| | - Hengde Zhang
- Key Laboratory of Animal Biotechnology of the Ministry of Agriculture, College of Veterinary Medicine, Northwest A&F University, Yangling, China
| | - Yong Zhang
- Key Laboratory of Animal Biotechnology of the Ministry of Agriculture, College of Veterinary Medicine, Northwest A&F University, Yangling, China
| | - Fusheng Quan
- Key Laboratory of Animal Biotechnology of the Ministry of Agriculture, College of Veterinary Medicine, Northwest A&F University, Yangling, China
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Kimble KM, Dickinson SE, Biase FH. Extraction of total RNA from single-oocytes and single-cell mRNA sequencing of swine oocytes. BMC Res Notes 2018; 11:155. [PMID: 29482623 PMCID: PMC5828076 DOI: 10.1186/s13104-018-3264-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2018] [Accepted: 02/21/2018] [Indexed: 11/13/2022] Open
Abstract
Objective Analyses of single oocytes are essential for a fine dissection of molecular features governing developmental competence. We adapted the phenol–chloroform procedure for the purification of total RNA from single oocytes. Results Key modifications include the use of Phasemaker™ tubes, a second chloroform wash of the aqueous phase, and the precipitation of the RNA with glyclogen in a 200 μl micro-centrifuge tube. Assessment of the RNA profile from single oocytes showed distinct peaks for 18S and 28S ribosomal subunits. This approach permitted the extraction of small RNAs from single oocytes, which was evident by the presence of 5S and 5.8S rRNAs and tRNAs around 122–123 nucleotides long. The amplification of polyadenylated RNA resulted in detectable DNA products ranging from ~ 500 to ~ 5000 nucleotides. We used the amplified DNA as template for single-cell mRNA-sequencing of five swine oocytes and quantified the expression levels of 9587 genes with complete coverage of transcripts over 10,000 nucleotides in length. The coverage was similar in all oocytes sequenced, demonstrating consistent high RNA quality across samples. We isolated total RNA from single oocytes and demonstrated that the quality was appropriate for single-cell mRNA-sequencing. Electronic supplementary material The online version of this article (10.1186/s13104-018-3264-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Katelyn M Kimble
- Department of Animal Sciences, Auburn University, 559 Devall Dr, Auburn, AL, 36839, USA
| | - Sarah E Dickinson
- Department of Animal Sciences, Auburn University, 559 Devall Dr, Auburn, AL, 36839, USA
| | - Fernando H Biase
- Department of Animal Sciences, Auburn University, 559 Devall Dr, Auburn, AL, 36839, USA.
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