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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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Abstract
DIO3 and DIO3OS are two imprinted genes identified in mouse and humans. The DIO3 gene, which encodes for the type 3 deiodinase, is preferentially expressed from the paternal allele, while the DIO3OS transcript is transcribed in opposite orientation to DIO3, multiple noncoding and alternatively splicing isoforms from maternal allele. In this study, the five splice variants of DIO3OS were identified in Holstein cattle and had complex, tissue-specific expression patterns observed in eight tissues, including heart, liver, spleen, lung, kidney, muscle, fat and brain. In the G+C rich region, upstream from the cattle DIO3 gene, there were three small conserved regions and some promoter elements similar to those observed in mouse and humans. An allele-specific expression analysis-based SNP method revealed that DIO3 and DIO3OS genes exhibited monoallelic expression in the eight tissues, indicating that DIO3 and DIO3OS are imprinted in cattle.
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Yan M, Tian HF, Hu QM, Xiao HB. Molecular Cloning of Cathelicidin-like cDNA from Andrias davidianus. RUSS J GENET+ 2018. [DOI: 10.1134/s102279541801012x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Yang W, Li D, Wang G, Zhang C, Zhang M, Zhang W, Li S. Three intronic lncRNAs with monoallelic expression derived from the MEG8 gene in cattle. Anim Genet 2016; 48:272-277. [PMID: 27925264 DOI: 10.1111/age.12527] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/18/2016] [Indexed: 12/13/2022]
Abstract
The field of long noncoding RNA (lncRNA) research has been rapidly advancing in recent years. Antisense lncRNAs, intergenetic lncRNAs and enhancer lncRNAs can regulate genomic imprinting, which leads to parent-origin-specific monoalletic expression of genes. However, the function of intronic ncRNAs in genomic imprinting remains unclear. Previously, we obtained the cDNA sequence of cattle MEG8 gene, which is located in the DLK1-DIO3 imprinted clusters of cattle chromosome 21. In this study, we undertook a systematic search for transcripts mapping to the MEG8 intronic region and identified three novel lncRNAs, named MEG8 intronic RNA 1 (MEG8-IT1), MEG8 intronic RNA 2 (MEG8-IT2) and MEG8 intronic RNA 3 (MEG8-IT3) according to the GENCODE annotated bibliography. We characterized the expression pattern of these lncRNAs using RT-PCR in adult cattle tissues, and they were expressed in all tested eight tissues, similar to the expression pattern of MEG8. The allele-specific expression of three novel lncRNAs was assessed using a polymorphism-based sequencing approach. Three single nucleotide polymorphism sites were identified in these three lncRNAs. We found that the three lncRNAs showed monoallelic expression in the analyzed tissues, suggesting that they may be imprinted in cattle. These results expand the number of known monoallelically expressed lncRNAs from the DLK1-DIO3 domain and contribute to further investigation of lncRNA regulatory mechanisms and function.
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Affiliation(s)
- W Yang
- Department of Biochemistry and Molecular Biology, College of Life Science, Hebei Agriculture University, Baoding, 071001, China
| | - D Li
- College of Life Science and Life Engineering, Hebei Science and Technology University, Shijiazhuang, 050018, China
| | - G Wang
- Department of Biochemistry and Molecular Biology, College of Life Science, Hebei Agriculture University, Baoding, 071001, China
| | - C Zhang
- Department of Biochemistry and Molecular Biology, College of Life Science, Hebei Agriculture University, Baoding, 071001, China
| | - M Zhang
- Department of Biochemistry and Molecular Biology, College of Life Science, Hebei Agriculture University, Baoding, 071001, China
| | - W Zhang
- Department of Biochemistry and Molecular Biology, College of Life Science, Hebei Agriculture University, Baoding, 071001, China
| | - S Li
- Department of Biochemistry and Molecular Biology, College of Life Science, Hebei Agriculture University, Baoding, 071001, China
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Zhang M, Zhao Y, Wang G, Li D, Chen W, Zhang C, Li S. An imprinted long noncoding RNA located between genes Meg8 and Meg9 in the cattle Dlk1-Dio3 domain. Genetica 2016; 145:1-7. [PMID: 27858207 DOI: 10.1007/s10709-016-9939-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2016] [Accepted: 11/14/2016] [Indexed: 11/24/2022]
Abstract
The Dlk1-Dio3 imprinted domain is located on the cattle chromosome 21 and contains three paternally expressed protein-coding genes and a number of maternally expressed short or long noncoding RNA genes. We have previously obtained two maternally expressed long noncoding RNA genes, Meg8 and Meg9, from the cattle. In this study, we identified a novel noncoding RNA located between Meg8 and Meg9 known as LINC24061 according to the GENCODE annotated bibliography. Two alternatively spliced transcripts (LINC24061-v1 and LINC24061-v2) were obtained using RT-PCR and RACE, and the expression pattern of LINC24061-v1 and LINC24061-v2 was shown to be tissue-specific. The LINC24061-v1 splice variant was expressed in only three types of tissues: heart, kidney and muscle; in contrast, LINC24061-v2 was expressed in all eight tissues examined, including heart, liver, spleen, lung, kidney, skeletal muscle, subcutaneous fat, and brain of adult cattle. The allele-specific expression of LINC24061 was identified based on a single nucleotide polymorphism (SNP) in exon 2 of LINC24061. The results showed that LINC24061 exhibited monoallelic expression in all the examined cattle tissues.
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Affiliation(s)
- Mingyue Zhang
- Department of Biochemistry and Molecular Biology, College of Life Science, Agriculture University of Hebei, Baoding, China
| | | | - Guannan Wang
- Department of Biochemistry and Molecular Biology, College of Life Science, Agriculture University of Hebei, Baoding, China
| | - Dongjie Li
- College of Life Science and Life Engineering, Hebei University of Science and Technology, Shijiazhuang, China
| | - Weina Chen
- College of Medical Science, Hebei University, Baoding, China
| | - Cui Zhang
- Department of Biochemistry and Molecular Biology, College of Life Science, Agriculture University of Hebei, Baoding, China
| | - Shijie Li
- Department of Biochemistry and Molecular Biology, College of Life Science, Agriculture University of Hebei, Baoding, China.
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Zhang K, Li D, Wang M, Wu G, Shi Y, Li S. The differential expression of alternatively spliced transcripts and imprinting status ofMEG9gene in cows. Anim Genet 2014; 45:660-4. [DOI: 10.1111/age.12195] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/20/2014] [Indexed: 01/08/2023]
Affiliation(s)
- Kun Zhang
- Department of Biochemistry and Molecular Biology; College of Life Science; Hebei Agriculture University; Baoding 071001 China
| | - Dongjie Li
- College of Life Science and Life Engineering; Hebei Science and Technology University; Shijiazhuang 050018 China
| | - Mengnan Wang
- Department of Biochemistry and Molecular Biology; College of Life Science; Hebei Agriculture University; Baoding 071001 China
| | - Guojiang Wu
- Department of Biochemistry and Molecular Biology; College of Life Science; Hebei Agriculture University; Baoding 071001 China
| | - Yunjiao Shi
- Department of Biochemistry and Molecular Biology; College of Life Science; Hebei Agriculture University; Baoding 071001 China
| | - Shijie Li
- Department of Biochemistry and Molecular Biology; College of Life Science; Hebei Agriculture University; Baoding 071001 China
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