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Tiwari S, Shahat A, Kastelic J, Thakor N, Thundathil J. Optimized total RNA isolation from bovine sperm with enhanced sperm head lysis. Biochem Cell Biol 2024; 102:194-205. [PMID: 37948675 DOI: 10.1139/bcb-2023-0231] [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: 11/12/2023] Open
Abstract
Increasing evidence of sperm RNA's role in fertilization and embryonic development has provided impetus for its isolation and thorough characterization. Sperm are considered tough-to-lyse cells due to the compact condensed DNA in sperm heads. Lack of consensus among bovine sperm RNA isolation protocols introduces experimental variability in transcriptome studies. Here, we describe an optimized method for total RNA isolation from bovine sperm using the TRIzol reagent. This study critically investigated the effects of various lysis conditions on sperm RNA isolation. Sperm suspended in TRIzol were subjected to a combination of mechanical treatments (sonication and passage through a 30G needle and syringe) and chemical treatments (supplementation with reducing agents 1,4-dithiothreitol and tris(2-carboxyethyl) phosphine hydrochloride (TCEP)). Microscopic evaluation of sperm lysis confirmed preferential sperm tail versus sperm head lysis. Interestingly, only TCEP-supplemented TRIzol (both mechanical treatments) had progressive sperm head lysis and consistently yielded total sperm RNA. Furthermore, RNA integrity was confirmed based on the electrophoresis profile and an absence of genomic DNA and somatic cells (e.g., epithelial cells, spermatids, etc.) with RT-qPCR. Our findings highlighted the importance of sperm lysis, specifically of the sperm head using TCEP with mechanical treatment, in total RNA isolation and presented a bovine-specific sperm RNA isolation method to reduce experimental variabilities.
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Affiliation(s)
- Saurabh Tiwari
- Faculty of Veterinary Medicine, University of Calgary, Calgary, AB, Canada
| | - Abdallah Shahat
- Faculty of Veterinary Medicine, University of Calgary, Calgary, AB, Canada
- Department of Theriogenology, Faculty of Veterinary Medicine, Cairo University, Giza, Egypt
| | - John Kastelic
- Faculty of Veterinary Medicine, University of Calgary, Calgary, AB, Canada
| | - Nehal Thakor
- Department of Chemistry & Biochemistry, University of Lethbridge, AB, Canada
- Arnie Charbonneau Cancer Institute, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
- Southern Alberta Genome Sciences Centre (SAGSC), University of Lethbridge, Lethbridge, AB, Canada
| | - Jacob Thundathil
- Faculty of Veterinary Medicine, University of Calgary, Calgary, AB, Canada
- Southern Alberta Genome Sciences Centre (SAGSC), University of Lethbridge, Lethbridge, AB, Canada
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Kasimanickam VR, Kasimanickam RK. Differentially Expressed Candidate miRNAs of Day 16 Bovine Embryos on the Regulation of Pregnancy Establishment in Dairy Cows. Animals (Basel) 2023; 13:3052. [PMID: 37835658 PMCID: PMC10571895 DOI: 10.3390/ani13193052] [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: 09/02/2023] [Revised: 09/25/2023] [Accepted: 09/26/2023] [Indexed: 10/15/2023] Open
Abstract
Recent advances in high-throughput in silico techniques translate experimental data into meaningful biological networks through which the role of individual proteins, interactions, and their biological functions are comprehended. The study objective was to identify differentially expressed (DE) miRNAs between the day 16 competent, elongated embryo from normal cows and the day 16 noncompetent, tubular embryos from repeat breeder cows, assimilate DE-miRNAs to their target genes, and group target genes based on biological function using in silico methods. The 84 prioritized bovine-specific miRNAs were investigated by RT-PCR, and the results showed that 19 were differentially expressed (11 up- and 8 down-regulated) in the competent embryos compared to noncompetent ones (p ≤ 0.05; fold regulation ≥ 2 magnitudes). Top-ranked integrated genes of DE-miRNAs predicted various biological and molecular functions, cellular processes, and signaling pathways. Further, analysis of the categorized groups of genes showed association with signaling pathways, turning on or off key genes and transcription factors regulating the development of embryo, placenta, and various organs. In conclusion, highly DE-miRNAs in day 16 bovine conceptus regulated the embryogenesis and pregnancy establishment. The elucidated miRNA-mRNA interactions in this study were mostly based on predictions from public databases. Therefore, the causal regulations of these interactions and mechanisms require further functional characterization.
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Affiliation(s)
- Vanmathy R. Kasimanickam
- Center for Reproductive Biology, College of Veterinary Medicine, Washington State University, Pullman, WA 99164, USA;
- AARVEE Animal Biotech LLC, Corvallis, OR 97333, USA
| | - Ramanathan K. Kasimanickam
- Department of Veterinary Clinical Sciences, College of Veterinary Medicine, Washington State University, Pullman, WA 99164, USA
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Vasisth R, Gurao A, Kumari N, Kumar G, Kumar A, Sriranga KR, Dige MS, Mukesh M, Aggarwal RAK, Singh P, Kataria RS. Development and validation of most efficient RNA isolation method from buffalo bull spermatozoa. Mol Biol Rep 2023; 50:6717-6727. [PMID: 37378747 DOI: 10.1007/s11033-023-08593-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Accepted: 06/13/2023] [Indexed: 06/29/2023]
Abstract
BACKGROUND Being highly fragmented and low in concentration, isolation of good quality RNA from sperm cells is a big challenge. Attempts have been made to evaluate various sperm RNA isolation methods from purified buffalo bull sperm cells. METHODS Both, non-membrane and membrane-based methods have been evaluated for isolating RNA from Murrah buffalo sperms and compared for their respective efficacies. The traditional TRIzol, TRIzol-heat lysed (H-TRIzol) and cocktail of TCEP-RLT lysis buffer (Qiagen RNeasy mini kit)-TRIzol (C-TRIzol) based isopropanol isolation methods have been evaluated. RESULTS H-TRIzol yielded best results among conventional methods. The combined T-RLT RNA isolation protocol yielded best quality and quantity compared to other membrane-based methods, due to high lytic property of cocktail of lysis reagents, necessary for complete breakdown of sperm membrane and RNA binding membrane for RNA isolation. Combined lysis performed by treatment with RLT-T and T-RLT differing in order of reagents used were also evaluated. T-RLT combination giving better results compared to RLT-T due to high gDNA contamination and membrane clogging in later protocol steps. CONCLUSION Overall, in terms of total RNA quantity and quality per million spermatozoa, the heat-lysed TRIzol method (H-TRIzol) performs best among RNA separation techniques employed and is also quite easy to perform. This comparative evaluation of sperm RNA isolation protocols can be useful in deciding the best protocol for isolation of good quality and high concentration sperm RNA from buffalo semen, for transcriptome and other downstream studies.
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Affiliation(s)
- Rashi Vasisth
- Animal Biotechnology Division, ICAR-National Bureau of Animal Genetic Resources, Karnal, Haryana, 132001, India
- ICAR-National Dairy Research Institute, Karnal, Haryana, 132001, India
| | - Ankita Gurao
- Animal Biotechnology Division, ICAR-National Bureau of Animal Genetic Resources, Karnal, Haryana, 132001, India
| | - Namita Kumari
- Animal Biotechnology Division, ICAR-National Bureau of Animal Genetic Resources, Karnal, Haryana, 132001, India
| | - Gautam Kumar
- Animal Biotechnology Division, ICAR-National Bureau of Animal Genetic Resources, Karnal, Haryana, 132001, India
| | - Anurag Kumar
- Animal Biotechnology Division, ICAR-National Bureau of Animal Genetic Resources, Karnal, Haryana, 132001, India
| | | | - Mahesh Shivanand Dige
- Animal Biotechnology Division, ICAR-National Bureau of Animal Genetic Resources, Karnal, Haryana, 132001, India
| | - Manishi Mukesh
- Animal Biotechnology Division, ICAR-National Bureau of Animal Genetic Resources, Karnal, Haryana, 132001, India
| | - Rajeev Anand Kumar Aggarwal
- Animal Biotechnology Division, ICAR-National Bureau of Animal Genetic Resources, Karnal, Haryana, 132001, India
| | - Pawan Singh
- ICAR-National Dairy Research Institute, Karnal, Haryana, 132001, India
| | - Ranjit Singh Kataria
- Animal Biotechnology Division, ICAR-National Bureau of Animal Genetic Resources, Karnal, Haryana, 132001, India.
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Investigation of Sperm and Seminal Plasma Candidate MicroRNAs of Bulls with Differing Fertility and In Silico Prediction of miRNA-mRNA Interaction Network of Reproductive Function. Animals (Basel) 2022; 12:ani12182360. [PMID: 36139221 PMCID: PMC9495167 DOI: 10.3390/ani12182360] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Revised: 09/02/2022] [Accepted: 09/02/2022] [Indexed: 11/17/2022] Open
Abstract
Simple Summary The objective of this study was to identify differentially expressed (DE) sperm and seminal plasma microRNAs (miRNAs) in high- and low-fertile Holstein bulls (four bulls per group), integrate miRNAs to their target genes, and categorize target genes based on predicted biological processes. Out of 84 bovine-specific, prioritized miRNAs analyzed by RT-PCR, 30 were differentially expressed in high-fertile sperm and seminal plasma compared to low-fertile sperm and seminal plasma, respectively (p ≤ 0.05, fold regulation ≥5 magnitudes). Interestingly, expression levels of DE-miRNAs in sperm and seminal plasma followed a similar pattern. Highly scored integrated genes of DE-miRNAs predicted various biological and molecular functions, cellular process, and pathways. Further in silico analysis revealed categorized genes may have a plausible association with pathways regulating sperm structure and function, fertilization, and embryo and placental development. In conclusion, highly DE-miRNAs in bovine sperm and seminal plasma could be used as a tool for predicting reproductive functions. Since the identified miRNA-mRNA interactions were mostly based on predictions from public databases, the causal regulations of miRNA-mRNA and the underlying mechanisms require further functional characterization in future studies. Abstract Recent advances in high-throughput in silico techniques portray experimental data as exemplified biological networks and help us understand the role of individual proteins, interactions, and their biological functions. The objective of this study was to identify differentially expressed (DE) sperm and seminal plasma microRNAs (miRNAs) in high- and low-fertile Holstein bulls (four bulls per group), integrate miRNAs to their target genes, and categorize the target genes based on biological process predictions. Out of 84 bovine-specific, prioritized miRNAs analyzed by RT-PCR, 30 were differentially expressed in high-fertile sperm and seminal plasma compared to low-fertile sperm and seminal plasma, respectively (p ≤ 0.05, fold regulation ≥ 5 magnitudes). The expression levels of DE-miRNAs in sperm and seminal plasma followed a similar pattern. Highly scored integrated genes of DE-miRNAs predicted various biological and molecular functions, cellular process, and pathways. Further, analysis of the categorized genes showed association with pathways regulating sperm structure and function, fertilization, and embryo and placental development. In conclusion, highly DE-miRNAs in bovine sperm and seminal plasma could be used as a tool for predicting reproductive functions. Since the identified miRNA-mRNA interactions were mostly based on predictions from public databases, the causal regulations of miRNA-mRNA and the underlying mechanisms require further functional characterization in future studies.
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Hodge MJ, de las Heras-Saldana S, Rindfleish SJ, Stephen CP, Pant SD. Characterization of Breed Specific Differences in Spermatozoal Transcriptomes of Sheep in Australia. Genes (Basel) 2021; 12:genes12020203. [PMID: 33573244 PMCID: PMC7912062 DOI: 10.3390/genes12020203] [Citation(s) in RCA: 3] [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: 12/14/2020] [Revised: 01/10/2021] [Accepted: 01/22/2021] [Indexed: 01/27/2023] Open
Abstract
Reduced reproductive efficiency results in economic losses to the Australian sheep industry. Reproductive success, particularly after artificial insemination, is dependent on a number of contributing factors on both ewe and ram sides. Despite considerable emphasis placed on characterising ewe side contributions, little emphasis has been placed on characterising ram side contributions to conception success. Over 14,000 transcripts are in spermatozoa of other species, which are transferred to the ova on fertilisation. These transcripts conceivably influence early embryonic development and whether conception is successful. Semen was collected (n = 45) across three breeds; Merino, Dohne, and Poll Dorset. Following collection, each ejaculate was split in two; an aliquot was assessed utilising Computer Assisted Semen Analysis (CASA) and the remaining was utilised for RNA extraction and subsequent next-generation sequencing. Overall, 754 differentially expressed genes were identified in breed contrasts and contrast between ejaculates of different quality. Downstream analysis indicated that these genes could play significant roles in a broad range of physiological functions, including maintenance of spermatogenesis, fertilisation, conception, embryonic development, and offspring production performance. Overall results provide evidence that the spermatozoal transcriptome could be a crucial contributing factor in improving reproductive performance as well as in the overall productivity and profitability of sheep industries.
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Affiliation(s)
- Marnie J. Hodge
- Graham Centre for Agricultural Innovation (Charles Sturt University and NSW Department of Primary Industries), Charles Sturt University, Wagga Wagga, NSW 2678, Australia; (M.J.H.); (C.P.S.)
- Apiam Animal Health, Apiam Genetic Services, Dubbo, NSW 2830, Australia;
| | - Sara de las Heras-Saldana
- School of Environmental and Rural Science, University of New England, Armidale, NSW 2351, Australia;
| | | | - Cyril P. Stephen
- Graham Centre for Agricultural Innovation (Charles Sturt University and NSW Department of Primary Industries), Charles Sturt University, Wagga Wagga, NSW 2678, Australia; (M.J.H.); (C.P.S.)
| | - Sameer D. Pant
- Graham Centre for Agricultural Innovation (Charles Sturt University and NSW Department of Primary Industries), Charles Sturt University, Wagga Wagga, NSW 2678, Australia; (M.J.H.); (C.P.S.)
- Correspondence:
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