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Analysis of amplification and association polymorphisms in the bovine beta-defensin 129 (BBD129) gene revealed its function in bull fertility. Sci Rep 2022; 12:19042. [PMID: 36352091 PMCID: PMC9646896 DOI: 10.1038/s41598-022-23654-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2022] [Accepted: 11/03/2022] [Indexed: 11/10/2022] Open
Abstract
β-defensins are adsorbable on the sperm surface in the male reproductive tract (MRT) and enhance sperm functional characteristics. The beta-defensin 129 (DEFB129) antimicrobial peptide is involved in sperm maturation, motility, and fertilization. However, its role in bovine fertility has not been well investigated. This study examines the relationship between the bovine BBD129 gene and Bos indicus x Bos taurus bull fertility. The complete coding sequence of BBD129 mRNA was identified by RNA Ligase Mediated-Rapid Amplification of cDNA End (RLM-RACE) and Sanger sequencing methodologies. It consisted of 582 nucleotides (nts) including 5' untranslated region (UTR) (46nts) and 3'UTR (23nts). It conserves all beta-defensin-like features. The expression level of BBD129 was checked by RT-qPCR and maximal expression was detected in the corpus-epididymis region compared to other parts of MRT. Polymorphism in BBD129 was also confirmed by Sanger sequencing of 254 clones from 5 high fertile (HF) and 6 low fertile (LF) bulls at two positions, 169 T > G and 329A > G, which change the S57A and N110S in the protein sequence respectively. These two mutations give rise to four types of BBD129 haplotypes. The non-mutated TA-BBD129 (169 T/329A) haplotype was substantially more prevalent among high-fertile bulls (P < 0.005), while the double-site mutated GG-BBD129 (169 T > G/329A > G) haplotype was significantly more prevalent among low-fertile bulls (P < 0.005). The in silico analysis confirmed that the polymorphism in BBD129 results in changes in mRNA secondary structure, protein conformations, protein stability, extracellular-surface availability, post-translational modifications (O-glycosylation and phosphorylation), and affects antibacterial and immunomodulatory capabilities. In conclusion, the mRNA expression of BBD129 in the MRT indicates its region-specific dynamics in sperm maturation. BBD129 polymorphisms were identified as the deciding elements accountable for the changed proteins with impaired functionality, contributing to cross-bred bulls' poor fertility.
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Dholpuria S, Kumar S, Kumar M, Sarwalia P, Kumar R, Datta TK. A novel lincRNA identified in buffalo oocytes with protein binding characteristics could hold the key for oocyte competence. Mol Biol Rep 2021; 48:3925-3934. [PMID: 34014469 DOI: 10.1007/s11033-021-06388-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2020] [Accepted: 04/29/2021] [Indexed: 12/23/2022]
Abstract
Studying the maternal oocyte-specific genes, in farm animals is a significant step towards delineating the underlying mechanisms that regulate oocyte quality, early embryonic development and survival. With the creation of buffalo oocyte-specific subtracted cDNA library, it has raised new questions which need to be answered. The present study has characterized one of the ESTs selected from the library and highlighted its importance in the oocyte quality. The selected EST was made full length by RLM-RACE and four transcript variants were identified. Bioinformatics analysis indicated the novelty of full-length transcript along with conserved intergenic nature. The largest transcript was identified as long intergenic noncoding RNA based upon coding potential calculator output. The expression analysis at different hours of oocyte maturation showed a significant variation in developmentally competent oocytes to that of incompetent ones. Along with this, the transcript was also found to have protein binding ability which was confirmed by RNA electrophoretic mobility shift assay. The protein used in the experiment was isolated from oocyte and cumulus cells via sonication. A novel lincRNA has been reported here that might have an important role in maturation of oocytes, inferred from its relative gene expression study and protein binding characteristics.
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Affiliation(s)
- Sunny Dholpuria
- Department of Life Science, Sharda University, Greater Noida, India.
| | - Sandeep Kumar
- Animal Biotechnology Centre, National Dairy Research Institute, Karnal, Haryana, India
| | - Manish Kumar
- Animal Biotechnology Centre, National Dairy Research Institute, Karnal, Haryana, India
| | - Parul Sarwalia
- Animal Biotechnology Centre, National Dairy Research Institute, Karnal, Haryana, India
| | - Rakesh Kumar
- Animal Biotechnology Centre, National Dairy Research Institute, Karnal, Haryana, India
| | - Tirtha Kumar Datta
- Animal Biotechnology Centre, National Dairy Research Institute, Karnal, Haryana, India.
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Yang CX, Wu ZW, Liu XM, Liang H, Gao ZR, Wang Y, Fang T, Liu YH, Miao YL, Du ZQ. Single-cell RNA-seq reveals mRNAs and lncRNAs important for oocytes in vitro matured in pigs. Reprod Domest Anim 2021; 56:642-657. [PMID: 33496347 DOI: 10.1111/rda.13901] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2020] [Accepted: 01/20/2021] [Indexed: 12/15/2022]
Abstract
The faithful execution of molecular programme underlying oocyte maturation and meiosis is vital to generate competent haploid gametes for efficient mammalian reproduction. However, the organization and principle of molecular circuits and modules for oocyte meiosis remain obscure. Here, we employed the recently developed single-cell RNA-seq technique to profile the transcriptomes of germinal vesicle (GV) and metaphase II (MII) oocytes, aiming to discover the dynamic changes of mRNAs and long non-coding RNAs (lncRNAs) during oocyte in vitro meiotic maturation. During the transition from GV to MII, total number of detected RNAs (mRNAs and lncRNAs) in oocytes decreased. Moreover, 1,807 (602 up- and 1,205 down-regulated) mRNAs and 313 (177 up- and 136 down-regulated) lncRNAs were significantly differentially expressed (DE), i.e., more mRNAs down-regulated, but more lncRNAs up-regulated. During maturation of pig oocytes, mitochondrial mRNAs were actively transcribed, eight of which (ND6, ND5, CYTB, ND1, ND2, COX1, COX2 and COX3) were significantly up-regulated. Both DE mRNAs and targets of DE lncRNAs were enriched in multiple biological and signal pathways potentially associated with oocyte meiosis. Highly abundantly expressed mRNAs (including DNMT1, UHRF2, PCNA, ARMC1, BTG4, ASNS and SEP11) and lncRNAs were also discovered. Weighted gene co-expression network analysis (WGCNA) revealed 20 hub mRNAs in three modules to be important for oocyte meiosis and maturation. Taken together, our findings provide insights and resources for further functional investigation of mRNAs/lncRNAs in in vitro meiotic maturation of pig oocytes.
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Affiliation(s)
- Cai-Xia Yang
- College of Animal Science, Yangtze University, Jingzhou, China.,College of Animal Science and Technology, Northeast Agricultural University, Harbin, China
| | - Zi-Wei Wu
- College of Animal Science, Yangtze University, Jingzhou, China
| | - Xiao-Man Liu
- College of Animal Science, Yangtze University, Jingzhou, China
| | - Hao Liang
- College of Animal Science, Yangtze University, Jingzhou, China
| | - Zhuo-Ran Gao
- College of Animal Science, Yangtze University, Jingzhou, China
| | - Yi Wang
- College of Animal Science, Yangtze University, Jingzhou, China
| | - Ting Fang
- College of Animal Science, Yangtze University, Jingzhou, China
| | - Yun-Hua Liu
- College of Animal Science and Technology, Northeast Agricultural University, Harbin, China
| | - Yi-Liang Miao
- Institute of Stem Cell and Regenerative Biology, College of Animal Science and Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
| | - Zhi-Qiang Du
- College of Animal Science, Yangtze University, Jingzhou, China.,College of Animal Science and Technology, Northeast Agricultural University, Harbin, China
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Li Y, Ye Y, Feng B, Qi Y. Long Noncoding RNA lncARSR Promotes Doxorubicin Resistance in Hepatocellular Carcinoma via Modulating PTEN-PI3K/Akt Pathway. J Cell Biochem 2017; 118:4498-4507. [PMID: 28464252 DOI: 10.1002/jcb.26107] [Citation(s) in RCA: 82] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2017] [Accepted: 05/01/2017] [Indexed: 12/20/2022]
Abstract
Hepatocellular carcinoma (HCC) is generally resistant to chemotherapy due to intrinsic or acquired drug resistances. Many molecules and signaling pathways are involved in chemo-resistance of HCC cells. However, the contribution of long noncoding RNA (lncRNA) to chemo-resistance of HCC cells is still largely unknown. In this study, we revealed the critical roles of long noncoding RNA lncARSR in chemo-resistance of HCC cells. lncARSR is upregulated in HCC, associated with large tumor size and advanced BCLC stage, and indicts poor prognosis. Functional assays showed that overexpression of lncARSR enhances doxorubicin resistance of HCC cells in vitro and in vivo. And while knockdown of lncARSR increases sensitivity of HCC cells to doxorubicin in vitro and in vivo. Mechanistically, we found that lncARSR physically associates with PTEN mRNA, promotes PTEN mRNA degradation, decreases PTEN expression, and activates PI3K/Akt pathway. PTEN is downregulated in HCC, and the expression of PTEN is negatively correlated with lncARSR in HCC tissues. Furthermore, the effects of lncARSR overexpression on doxorubicin resistance could be reversed by PI3K/Akt pathway inhibitor, and lncARSR knockdown-induced doxorubicin sensitivity could be reversed by PTEN depletion. Taken together, our results showed that upregulated lncARSR promotes doxorubicin resistance in HCC via modulating PTEN-PI3K/Akt pathway, and implied that lncARSR may serve as a promising prognostic biomarker and therapeutic target for HCC chemo-resistance. J. Cell. Biochem. 118: 4498-4507, 2017. © 2017 Wiley Periodicals, Inc.
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Affiliation(s)
- Yaling Li
- Department of Pharmacy, The Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan, China
| | - Yun Ye
- Department of Pharmacy, The Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan, China
| | - Bimin Feng
- Department of Pharmacy, The Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan, China
| | - Yan Qi
- Central Laboratory, Yunnan Provincial Hospital of Traditional Chinese Medicine, Kunming, Yunnan, China
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