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Ma Z, Yan XM, Geng J, Gao L, Du W, Li HB, Yuan LX, Zhou ZY, Zhang JS, Zhang Y, Chen L. Genome-wide identification and analysis of TMT-based proteomes in longissimus dorsi tissue from Kazakh cattle and Xinjiang brown cattle. Anim Biotechnol 2023; 34:1261-1272. [PMID: 34965845 DOI: 10.1080/10495398.2021.2019756] [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: 10/19/2022]
Abstract
With the gradual completion of the human genome project, proteomes have gained extremely important value in the fields of human disease and biological process research. In our previous research, we performed transcriptomic analyses of longissimus dorsi tissue from Kazakh cattle and Xinjiang brown cattle and conducted in-depth studies on the muscles of both species through epigenetics. However, it is unclear whether differentially expressed proteins in Kazakh cattle and Xinjiang brown cattle regulate muscle production and development. In this study, a proteomic analysis was performed on Xinjiang brown cattle and Kazakh cattle by using TMT markers, HPLC classification, LC/MS and bioinformatics analysis. A total of 13,078 peptides were identified, including 11,258 unique peptides. We identified a total of 1874 proteins, among which 1565 were quantifiable. Compared to Kazakh cattle, Xinjiang brown cattle exhibited 75 upregulated proteins and 44 downregulated proteins. These differentially expressed proteins were enriched for the functions of adrenergic signaling in cardiomyocytes, fatty acid degradation and glutathione metabolism. In our research, we found differentially expressed proteins in longissimus dorsi tissue between Kazakh cattle and Xinjiang brown cattle. We predict that these proteins regulate muscle production and development through select enriched signaling pathways. This study provides novel insights into the roles of proteomes in cattle genetics and breeding.
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Affiliation(s)
- Zhen Ma
- Institute of Animal Husbandry, Xinjiang Academy of Animal Husbandry, Urumqi, China
| | - Xiang-Min Yan
- Institute of Animal Husbandry, Xinjiang Academy of Animal Husbandry, Urumqi, China
| | - Juan Geng
- Xinjiang Animal Husbandry General Station, Urumqi, China
| | - Liang Gao
- Yili Vocational and Technical College, Yili, China
| | - Wei Du
- Institute of Animal Husbandry, Xinjiang Academy of Animal Husbandry, Urumqi, China
| | - Hong-Bo Li
- Institute of Animal Husbandry, Xinjiang Academy of Animal Husbandry, Urumqi, China
| | - Li-Xing Yuan
- Institute of Animal Husbandry, Xinjiang Academy of Animal Husbandry, Urumqi, China
| | - Zhen-Yong Zhou
- Institute of Animal Husbandry, Xinjiang Academy of Animal Husbandry, Urumqi, China
| | - Jin-Shan Zhang
- Institute of Animal Husbandry, Xinjiang Academy of Animal Husbandry, Urumqi, China
| | - Yang Zhang
- Institute of Animal Husbandry, Xinjiang Academy of Animal Husbandry, Urumqi, China
| | - Lei Chen
- School of Animal Science and Technology, Shihezi University, Shihezi, China
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Bai J, Lin Y, Zhang J, Chen Z, Wang Y, Li M, Li J. Profiling of Chromatin Accessibility in Pigs across Multiple Tissues and Developmental Stages. Int J Mol Sci 2023; 24:11076. [PMID: 37446255 DOI: 10.3390/ijms241311076] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2023] [Revised: 06/27/2023] [Accepted: 06/30/2023] [Indexed: 07/15/2023] Open
Abstract
The study of chromatin accessibility across tissues and developmental stages is essential for elucidating the transcriptional regulation of various phenotypes and biological processes. However, the chromatin accessibility profiles of multiple tissues in newborn pigs and across porcine liver development remain poorly investigated. Here, we used ATAC-seq and rRNA-depleted RNA-seq to profile open chromatin maps and transcriptional features of heart, kidney, liver, lung, skeletal muscle, and spleen in newborn pigs and porcine liver tissue in the suckling and adult stages, respectively. Specifically, by analyzing a union set of protein-coding genes (PCGs) and two types of transcripts (lncRNAs and TUCPs), we obtained a comprehensive annotation of consensus ATAC-seq peaks for each tissue and developmental stage. As expected, the PCGs with tissue-specific accessible promoters had active transcription and were relevant to tissue-specific functions. In addition, other non-coding tissue-specific peaks were involved in both physical activity and the morphogenesis of neonatal tissues. We also characterized stage-specific peaks and observed a close association between dynamic chromatin accessibility and hepatic function transition during liver postnatal development. Overall, this study expands our current understanding of epigenetic regulation in mammalian tissues and organ development, which can benefit both economic trait improvement and improve the biomedical usage of pigs.
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Affiliation(s)
- Jingyi Bai
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Yu Lin
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Jiaman Zhang
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Ziyu Chen
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Yujie Wang
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Mingzhou Li
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Jing Li
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
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Roopnarine O, Yuen SL, Thompson AR, Roelike LN, Rebbeck RT, Bidwell PA, Aldrich CC, Cornea RL, Thomas DD. Fluorescence lifetime FRET assay for live-cell high-throughput screening of the cardiac SERCA pump yields multiple classes of small-molecule allosteric modulators. Sci Rep 2023; 13:10673. [PMID: 37393380 PMCID: PMC10314922 DOI: 10.1038/s41598-023-37704-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Accepted: 06/26/2023] [Indexed: 07/03/2023] Open
Abstract
We have used FRET-based biosensors in live cells, in a robust high-throughput screening (HTS) platform, to identify small-molecules that alter the structure and activity of the cardiac sarco/endoplasmic reticulum calcium ATPase (SERCA2a). Our primary aim is to discover drug-like small-molecule activators that improve SERCA's function for the treatment of heart failure. We have previously demonstrated the use of an intramolecular FRET biosensor, based on human SERCA2a, by screening two different small validation libraries using novel microplate readers that detect the fluorescence lifetime or emission spectrum with high speed, precision, and resolution. Here we report results from FRET-HTS of 50,000 compounds using the same biosensor, with hit compounds functionally evaluated using assays for Ca2+-ATPase activity and Ca2+-transport. We focused on 18 hit compounds, from which we identified eight structurally unique scaffolds and four scaffold classes as SERCA modulators, approximately half of which are activators and half are inhibitors. Five of these compounds were identified as promising SERCA activators, one of which activates Ca2+-transport even more than Ca2+-ATPase activity thus improving SERCA efficiency. While both activators and inhibitors have therapeutic potential, the activators establish the basis for future testing in heart disease models and lead development, toward pharmaceutical therapy for heart failure.
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Affiliation(s)
- Osha Roopnarine
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN, USA.
| | - Samantha L Yuen
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN, USA
| | - Andrew R Thompson
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN, USA
| | - Lauren N Roelike
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN, USA
| | - Robyn T Rebbeck
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN, USA
| | - Philip A Bidwell
- Department of Medicine, Cardiovascular Division, University of Minnesota, Minneapolis, MN, 55455, USA
| | - Courtney C Aldrich
- Department of Medicinal Chemistry, University of Minnesota, Minneapolis, MN, 55455, USA
| | - Razvan L Cornea
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN, USA
| | - David D Thomas
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN, USA.
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Zádor E. The Meeting of Micropeptides with Major Ca 2+ Pumps in Inner Membranes-Consideration of a New Player, SERCA1b. MEMBRANES 2023; 13:274. [PMID: 36984661 PMCID: PMC10058886 DOI: 10.3390/membranes13030274] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Revised: 02/20/2023] [Accepted: 02/23/2023] [Indexed: 06/18/2023]
Abstract
Calcium is a major signalling bivalent cation within the cell. Compartmentalization is essential for regulation of calcium mediated processes. A number of players contribute to intracellular handling of calcium, among them are the sarco/endoplasmic reticulum calcium ATP-ases (SERCAs). These molecules function in the membrane of ER/SR pumping Ca2+ from cytoplasm into the lumen of the internal store. Removal of calcium from the cytoplasm is essential for signalling and for relaxation of skeletal muscle and heart. There are three genes and over a dozen isoforms of SERCA in mammals. These can be potentially influenced by small membrane peptides, also called regulins. The discovery of micropeptides has increased in recent years, mostly because of the small ORFs found in long RNAs, annotated formerly as noncoding (lncRNAs). Several excellent works have analysed the mechanism of interaction of micropeptides with each other and with the best known SERCA1a (fast muscle) and SERCA2a (heart, slow muscle) isoforms. However, the array of tissue and developmental expressions of these potential regulators raises the question of interaction with other SERCAs. For example, the most abundant calcium pump in neonatal and regenerating skeletal muscle, SERCA1b has never been looked at with scrutiny to determine whether it is influenced by micropeptides. Further details might be interesting on the interaction of these peptides with the less studied SERCA1b isoform.
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Affiliation(s)
- Ernő Zádor
- Institute of Biochemistry, Albert Szent-Györgyi Faculty of Medicine, University of Szeged, Dóm tér 9, H-6720 Szeged, Hungary
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Dang W, Lu H, Wu Q, Gao Y, Qi Q, Fan H. Comparative transcriptional profiling analysis of the effect of heat waves during embryo incubation on the hatchlings of the Chinese soft-shelled turtle ( Pelodiscus sinensis). Ecol Evol 2018; 8:3763-3773. [PMID: 29686856 PMCID: PMC5901165 DOI: 10.1002/ece3.3850] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2017] [Revised: 12/19/2017] [Accepted: 12/28/2017] [Indexed: 12/02/2022] Open
Abstract
Temperature is one of most the important environmental factors that affect the ontogenesis of organisms. In this study, we incubated Chinese soft‐shelled turtle eggs at 28°C (control temperature, C treatment), a temperature with a 16°C cold shock and a 36°C heat shock twice per week (S treatment) or a ramp‐programmed temperature of 29 ± 9°C (with 12 hr (+) and 12 hr (−) every day) (F treatment). The incubation period, hatching success, hatchling weight, and locomotor performance were significantly different between the controls and the different heat treatment groups. The pathogen challenge results illustrated that hatchlings from the S treatment group were more resistant to bacterial infection, whereas hatchlings from the F treatment group were more vulnerable. We used RNA‐seq quantification analysis to identify differentially expressed genes (DEGs) of hatchlings in the S treatment group. Based on the functional annotation results for the DEGs, 9 genes were chosen to verify the RNA‐seq results. The background expression of DEGs was also analyzed for the three treatments, as was the regulation of the pathogen challenge. The results showed that 8 DEGs were related to the immune response after pathogen challenge and that temperature was an important factor in differential regulation of the immunity pathways.
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Affiliation(s)
- Wei Dang
- Hangzhou Key Laboratory of Animal Adaptation and Evolution Hangzhou Key Laboratory of Ecosystem Protection and Restoration School of Life and Environmental Sciences Hangzhou Normal University Hangzhou China
| | - Hongliang Lu
- Hangzhou Key Laboratory of Animal Adaptation and Evolution Hangzhou Key Laboratory of Ecosystem Protection and Restoration School of Life and Environmental Sciences Hangzhou Normal University Hangzhou China
| | - Qiong Wu
- Hangzhou Key Laboratory of Animal Adaptation and Evolution Hangzhou Key Laboratory of Ecosystem Protection and Restoration School of Life and Environmental Sciences Hangzhou Normal University Hangzhou China
| | - Yuan Gao
- Hangzhou Key Laboratory of Animal Adaptation and Evolution Hangzhou Key Laboratory of Ecosystem Protection and Restoration School of Life and Environmental Sciences Hangzhou Normal University Hangzhou China
| | - Qinqin Qi
- Hangzhou Key Laboratory of Animal Adaptation and Evolution Hangzhou Key Laboratory of Ecosystem Protection and Restoration School of Life and Environmental Sciences Hangzhou Normal University Hangzhou China.,School of Food Science and Biotechnology Zhejiang Gongshang University Hangzhou China
| | - Handong Fan
- Hangzhou Key Laboratory of Animal Adaptation and Evolution Hangzhou Key Laboratory of Ecosystem Protection and Restoration School of Life and Environmental Sciences Hangzhou Normal University Hangzhou China
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