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Cendron F, Rosani U, Franzoi M, Boselli C, Maggi F, De Marchi M, Penasa M. Analysis of miRNAs in milk of four livestock species. BMC Genomics 2024; 25:859. [PMID: 39277740 PMCID: PMC11401297 DOI: 10.1186/s12864-024-10783-4] [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] [Received: 06/26/2024] [Accepted: 09/09/2024] [Indexed: 09/17/2024] Open
Abstract
BACKGROUND Milk is essential for mammalian nutrition because it provides vital nutrients for growth and development. Milk composition, which is influenced by genetic and environmental factors, supports lactation, a complex process crucial for milk production and quality. Recent research has focused on noncoding RNAs, particularly microRNAs (miRNAs), which are present in body fluids and regulate gene expression post-transcriptionally. This study comprehensively characterizes miRNAs in milk of four livestock species, namely Bubalus bubalis, Capra hircus, Equus asinus, and Ovis aries and identifies potential target genes. RESULTS High-throughput sequencing of milk RNA resulted in distinct read counts across species: B. bubalis (8,790,441 reads), C. hircus (12,976,275 reads), E. asinus (9,385,067 reads), and O. aries (7,295,297 reads). E. asinus had the highest RNA mapping rate (94.6%) and O. aries the lowest (84.8%). A substantially greater proportion of miRNAs over other small RNAs was observed for the donkey milk sample (7.74%) compared to buffalo (0.87%), goat (1.57%), and sheep (1.12%). Shared miRNAs, which included miR-200a, miR-200b, miR-200c, and miR-23a among others, showed varying expression levels across species, confirmed by qPCR analysis. Functional annotation of predicted miRNA target genes highlighted diverse roles, with an enrichment in functions linked to metabolism and immunity. Pathway analysis identified immune response pathways as significant, with several miRNAs targeting specific genes across species, suggesting their regulatory function in milk. CONCLUSIONS Both conserved and species-specific miRNAs were detected in milk of the investigated species. The identified target genes of these miRNAs have important roles in neonatal development, adaptation, growth, and immune response. Furthermore, they influence milk and meat production traits in livestock.
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Affiliation(s)
- Filippo Cendron
- Department of Agronomy, Food, Natural Resources, Animals and Environment (DAFNAE), University of Padova, Viale Dell'Università 16, Legnaro (PD), 35020, Italy.
| | - Umberto Rosani
- Department of Biology (DiBio), University of Padova, Viale Giuseppe Colombo 3, Padua, 35131, Italy
| | - Marco Franzoi
- Department of Agronomy, Food, Natural Resources, Animals and Environment (DAFNAE), University of Padova, Viale Dell'Università 16, Legnaro (PD), 35020, Italy
| | - Carlo Boselli
- Istituto Zooprofilattico Sperimentale del Lazio E Della Toscana "M. Aleandri" - National Reference Centre for Ovine and Caprine Milk and Dairy Products Quality (C.Re.L.D.O.C.), Rome, 00178, Italy
| | - Flavio Maggi
- Azienda Sanitaria Locale, Roma 4, Distretto 4, Via G. Verdi 1, Rignano Flaminio, Rome, 00068, Italy
| | - Massimo De Marchi
- Department of Agronomy, Food, Natural Resources, Animals and Environment (DAFNAE), University of Padova, Viale Dell'Università 16, Legnaro (PD), 35020, Italy
| | - Mauro Penasa
- Department of Agronomy, Food, Natural Resources, Animals and Environment (DAFNAE), University of Padova, Viale Dell'Università 16, Legnaro (PD), 35020, Italy
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Almalki WH, Almujri SS. Circular RNAs and the JAK/STAT pathway: New frontiers in cancer therapeutics. Pathol Res Pract 2024; 260:155408. [PMID: 38909403 DOI: 10.1016/j.prp.2024.155408] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/01/2024] [Revised: 06/08/2024] [Accepted: 06/12/2024] [Indexed: 06/25/2024]
Abstract
Circular RNAs, known as circRNAs, have drawn more attention to cancer biology in the last few years. Novel functions of circRNAs in cancer therapy open promising prospects for personalized medicine. This review focuses on the molecular properties and potential of circRNAs as biomarkers or therapeutic targets in cancer treatment. Unique properties of circular RNAs associated with a circular form provide stability and resilience to RNA exonuclease degradation. Circular RNAs' most important characteristic is that they are involved in the JAK/STAT pathway associated with oncogenesis. Notably, their deregulation has been reported in multiple carcinomas due to involvement in JAK/STAT signaling cascade modulation. Increased knowledge about circRNAs' interaction with the JAK/STAT pathway leads to the emergence of new possibilities for targeted cancer therapy. In addition, since circRNAs demonstrate tissue-relatedness of expression, they may be a reliable biomarker for predicting and diagnosing cancer. With the development of new technologies for targeting circRNAs, novel therapeutics can be produced that offer more personalized cancer treatment options based on the nature of the patient. The present review explores the exciting prospects of circRNAs for transforming cancer treatment into personalized medicine. It describes the current understanding of circRNA biology, its relationship to tumorigenesis, and possible targeting methods.
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Affiliation(s)
- Waleed Hassan Almalki
- Department of Pharmacology, College of Pharmacy, Umm Al-Qura University, Makkah, Saudi Arabia.
| | - Salem Salman Almujri
- Department of Pharmacology, College of Pharmacy, King Khalid University, Abha, Aseer 61421, Saudi Arabia
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He T, Yuan Z, Chen Q, Luo J, Mao J, Tang Z, Zhao X, Yang Z. Circular RNAs Mediate the Effects of Dietary Tryptophan on the Transformation of Muscle Fiber Types in Weaned Piglets. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2024; 72:8595-8605. [PMID: 38591744 DOI: 10.1021/acs.jafc.4c00762] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/10/2024]
Abstract
The nutritional composition of the diet significantly impacts the overall growth and development of weaned piglets. The current study aimed to explore the effects and underlying mechanisms of dietary tryptophan consumption on muscle fiber type transformation during the weaning period. Thirty weaned piglets with an average body weight of 6.12 ± 0.16 kg were randomly divided into control (CON, 0.14% Trp diet) and high Trp (HT, 0.35% Trp) groups and maintained on the respective diet for 28 days. The HT group of weaned piglets exhibited highly significant improvements in growth performance and an increased proportion of fast muscle fibers. Transcriptome sequencing revealed the potential contribution of differentially expressed circular RNAs toward the transformation of myofiber types in piglets and toward the regulation of expression of related genes by targeting the microRNAs, miR-34c and miR-182, to further regulate myofiber transformation. In addition, 145 DE circRNAs were identified as potentially protein-encoding, with the encoded proteins associated with a myofiber type transformation. In conclusion, the current study greatly advances and refines our current understanding of the regulatory networks associated with piglet muscle development and myofiber type transformation and also contributes to the optimization of piglet diet formulation.
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Affiliation(s)
- Tianle He
- Laboratory for Bio-feed and Molecular Nutrition, College of Animal Science and Technology, Southwest University, Chongqing 400715, China
| | - Zhidong Yuan
- Key Laboratory of Prevention and Treatment of Cardiovascular and Cerebrovascular Diseases, Ministry of Education, School of Basic Medicine, Gannan Medical University, Ganzhou 341000, China
| | - Qingyun Chen
- Laboratory for Bio-feed and Molecular Nutrition, College of Animal Science and Technology, Southwest University, Chongqing 400715, China
| | - Ju Luo
- Laboratory for Bio-feed and Molecular Nutrition, College of Animal Science and Technology, Southwest University, Chongqing 400715, China
| | - Jiani Mao
- Laboratory for Bio-feed and Molecular Nutrition, College of Animal Science and Technology, Southwest University, Chongqing 400715, China
| | - Zhiru Tang
- Laboratory for Bio-feed and Molecular Nutrition, College of Animal Science and Technology, Southwest University, Chongqing 400715, China
| | - Xuan Zhao
- Laboratory for Bio-feed and Molecular Nutrition, College of Animal Science and Technology, Southwest University, Chongqing 400715, China
| | - Zhenguo Yang
- Laboratory for Bio-feed and Molecular Nutrition, College of Animal Science and Technology, Southwest University, Chongqing 400715, China
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He T, Li C, Chen Q, Li R, Luo J, Mao J, Yang Z. Combined analysis of lncRNA and mRNA emphasizes the potential role of tryptophan-mediated regulation of muscle development in weaned piglets by lncRNA. J Anim Sci 2024; 102:skae264. [PMID: 39276131 PMCID: PMC11465388 DOI: 10.1093/jas/skae264] [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] [Received: 06/24/2024] [Accepted: 09/13/2024] [Indexed: 09/16/2024] Open
Abstract
Pork is an important high-value protein source that fulfills the nutritional requirements for normal growth development, repair, and metabolism. Tryptophan (Trp), a crucial amino acid for piglet growth performance and muscle development, has an essential yet unclear regulatory mechanism. To investigate the biological basis of Trp regulation of piglet muscle development and identify the related regulatory pathways, we studied 20 weaned piglets. The piglets were divided into control (CON, 0.14% Trp) and high Trp (HT, 0.35% Trp) groups. They were fed with different Trp concentrations for 28 d, after which we collected the longissimus dorsi (LD) muscle for histomorphometric analysis and RNA extraction. Our results showed that the HT diet significantly increased the average daily weight gain, myocyte number, and muscle fiber density in weaned piglets. We then analyzed the differentially expressed (DE) genes in the LD muscle through RNA sequencing (RNA-seq). We identified 253 lncRNAs and 1,055 mRNAs mainly involved in myoblast proliferation and myofiber formation, particularly through the FoxO and AMPK signaling pathways and metabolism. Further analysis of the DE lncRNA targeting relationship and construction of a protein-protein interaction network resulted in the discovery of a novel lncRNA, XLOC_021675, or FRPMD, and elucidated its role in regulating piglet muscle development. Finally, we confirmed the RNA-seq results by reverse transcription polymerase chain reaction (RT-PCR). This study provides valuable insights into the regulatory mechanism of lncRNA-mediated Trp regulation of muscle development in weaned piglets offering a theoretical basis for optimizing piglet dietary ratios and enhancing pork production.
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Affiliation(s)
- Tianle He
- Laboratory for Bio-feed and Molecular Nutrition, College of Animal Science and Technology, Southwest University, Chongqing, China
- State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, Beijing, China
- College of Animal Science and Technology, Ningxia University, Yinchuan, China
| | - Chenlei Li
- College of Animal Science and Technology, Ningxia University, Yinchuan, China
| | - Qingyun Chen
- Laboratory for Bio-feed and Molecular Nutrition, College of Animal Science and Technology, Southwest University, Chongqing, China
- State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Ruiqian Li
- College of Animal Science and Technology, Ningxia University, Yinchuan, China
| | - Ju Luo
- Laboratory for Bio-feed and Molecular Nutrition, College of Animal Science and Technology, Southwest University, Chongqing, China
| | - Jiani Mao
- Laboratory for Bio-feed and Molecular Nutrition, College of Animal Science and Technology, Southwest University, Chongqing, China
| | - Zhenguo Yang
- Laboratory for Bio-feed and Molecular Nutrition, College of Animal Science and Technology, Southwest University, Chongqing, China
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Chang C, He X, Di R, Wang X, Han M, Liang C, Chu M. Transcriptome Analysis Reveals Differentially Expressed circRNAs Associated with Fecundity in Small-Tail Han Sheep Thyroid with Different FecB Genotypes. Animals (Basel) 2023; 14:105. [PMID: 38200837 PMCID: PMC10777913 DOI: 10.3390/ani14010105] [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: 10/07/2023] [Revised: 12/20/2023] [Accepted: 12/25/2023] [Indexed: 01/12/2024] Open
Abstract
Litter size is an economically important trait in sheep, and it is a complex trait controlled by multiple genes in multiple organs. Among them, the regulation of lamb number trait by the thyroid gland is a very important part. However, the molecular mechanisms of the thyroid gland in sheep reproduction remain unclear. Here, RNA-seq was used to detect transcriptome expression patterns in the thyroid gland between follicular phase (FP) and luteal phase (LP) in FecB BB (MM) and FecB ++ (ww) STH sheep, respectively, and to identify differentially expressed circRNAs (DECs) associated with reproduction. Bioinformatic analysis of the source genes of these DECs revealed that they can be enriched in multiple signaling pathways involved in the reproductive process of animals. We found that the source genes of these DECs, such as GNAQ, VEGFC, MAPK1, STAT1, and HSD17B7, may play important roles in the reproductive process of animals. To better understand the function of these DECs, we constructed circRNA-miRNA co-expression networks. Dual luciferase reporter assays suggested that a ceRNA regulatory mechanism between circ_0003259-oar-miR-133-TXLNA and circ_0012128-oar-miR-370-3p-FGFR1 may hold. All of these DEC expression profiles in the thyroid gland provide a novel resource for elucidating the regulatory mechanisms underlying STH sheep prolificacy.
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Affiliation(s)
- Cheng Chang
- State Key Laboratory of Animal Biotech Breeding, Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100193, China; (C.C.); (X.H.); (R.D.); (X.W.)
- College of Animal Science, Shanxi Agricultural University, Taigu 030801, China;
| | - Xiaoyun He
- State Key Laboratory of Animal Biotech Breeding, Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100193, China; (C.C.); (X.H.); (R.D.); (X.W.)
| | - Ran Di
- State Key Laboratory of Animal Biotech Breeding, Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100193, China; (C.C.); (X.H.); (R.D.); (X.W.)
| | - Xiangyu Wang
- State Key Laboratory of Animal Biotech Breeding, Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100193, China; (C.C.); (X.H.); (R.D.); (X.W.)
| | - Miaoceng Han
- College of Animal Science, Shanxi Agricultural University, Taigu 030801, China;
| | - Chen Liang
- College of Animal Science, Shanxi Agricultural University, Taigu 030801, China;
| | - Mingxing Chu
- State Key Laboratory of Animal Biotech Breeding, Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100193, China; (C.C.); (X.H.); (R.D.); (X.W.)
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6
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Sun P, Chen M, Sooranna SR, Shi D, Liu Q, Li H. The emerging roles of circRNAs in traits associated with livestock breeding. WILEY INTERDISCIPLINARY REVIEWS. RNA 2023; 14:e1775. [PMID: 36631071 DOI: 10.1002/wrna.1775] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Revised: 12/22/2022] [Accepted: 12/27/2022] [Indexed: 01/13/2023]
Abstract
Many indicators can be used to evaluate the productivity and quality of livestock, such as meat and milk production as well as fat deposition. Meat and milk production are measures of livestock performance, while fat deposition affects the taste and flavor of the meat. The circRNAs, are non-coding RNAs, that are involved in the regulation of all these three traits. We review the functions and mechanisms of circRNAs in muscle and fat development as well as lactation to provide a theoretical basis for circRNA research in animal husbandry. Various phenotypic changes presented in livestock may be produced by different circRNAs. Our current concern is how to use the roles played by circRNAs to our advantage to produce the best possible livestock. Hence, we describe the advantages and disadvantages of knockout techniques for circRNAs. In addition, we also put forward our thoughts regarding the mechanism and network of circRNAs to provide researchers with novel ideas of how molecular biology can help us advance our goals in animal farming. This article is categorized under: RNA in Disease and Development > RNA in Disease RNA Interactions with Proteins and Other Molecules > Protein-RNA Interactions: Functional Implications RNA Interactions with Proteins and Other Molecules > Protein-RNA Recognition RNA Interactions with Proteins and Other Molecules > RNA-Protein Complexes.
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Affiliation(s)
- Ping Sun
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Animal Science and Technology, Guangxi University, Nanning, China
| | - Mengjie Chen
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Animal Science and Technology, Guangxi University, Nanning, China
| | - Suren R Sooranna
- Institute of Reproductive and Developmental Biology, Imperial College London, London, UK
| | - Deshun Shi
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Animal Science and Technology, Guangxi University, Nanning, China
| | - Qingyou Liu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Animal Science and Technology, Guangxi University, Nanning, China
- Guangdong Provincial Key Laboratory of Animal Molecular Design and Precise Breeding, School of Life Science and Engineering, Foshan University, Foshan, China
| | - Hui Li
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Animal Science and Technology, Guangxi University, Nanning, China
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7
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Yuan YG, Xing YT, Liu SZ, Li L, Reza AMMT, Cai HQ, Wang JL, Wu P, Zhong P, Kong IK. Identification of circular RNAs expression pattern in caprine fetal fibroblast cells exposed to a chronic non-cytotoxic dose of graphene oxide-silver nanoparticle nanocomposites. Front Bioeng Biotechnol 2023; 11:1090814. [PMID: 37020511 PMCID: PMC10069586 DOI: 10.3389/fbioe.2023.1090814] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2022] [Accepted: 02/24/2023] [Indexed: 03/18/2023] Open
Abstract
The widespread use of graphene oxide-silver nanoparticle nanocomposites (GO-AgNPs) in biomedical sciences is increasing the chances of human and animal exposure to its chronic non-toxic doses. Exposure to AgNPs-related nanomaterials may result in the negative effect on the dam, fetus and offspring. However, there are only little available information for profound understanding of the epigenetic alteration in the cells and animals caused by low-dose chronic exposure of GO-AgNPs. The present study investigated the effect of 0.5 μg/mL GO-AgNPs for 10 weeks on the differential expression of circular RNAs (circRNAs) in caprine fetal fibroblast cells (CFFCs), and this dose of GO-AgNPs did not affect cell viability and ROS level. We predicted the functions of those differentially expressed (DE) circRNAs in CFFCs by bioinformatics analysis. Furthermore, we validated the expression of ten DE circRNAs using quantitative real-time reverse transcription-polymerase chain reaction (qRT-PCR) to ensure the reliability of the sequencing data. Our results showed that the DE circRNAs may potentially regulate the GO-AgNPs-inducing epigenetic toxicity through a regulatory network consisted of circRNAs, miRNAs and messenger RNAs (mRNAs). Therefore, the epigenetics toxicity is essential to assess the biosafety level of GO-AgNPs.
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Affiliation(s)
- Yu-Guo Yuan
- College of Veterinary Medicine, Yangzhou University, Yangzhou, China
- Jiangsu Co-Innovation Center of Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, China
- *Correspondence: Yu-Guo Yuan, ; Ping Zhong, ; Il-Keun Kong,
| | - Yi-Tian Xing
- College of Veterinary Medicine, Yangzhou University, Yangzhou, China
| | - Song-Zi Liu
- College of Veterinary Medicine, Yangzhou University, Yangzhou, China
| | - Ling Li
- College of Veterinary Medicine, Yangzhou University, Yangzhou, China
- Jiangsu Co-Innovation Center of Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, China
| | - Abu Musa Md Talimur Reza
- Department of Molecular Biology and Genetics, Faculty of Basic Sciences, Gebze Technical University, Gebze, Kocaeli, Türkiye
| | - He-Qing Cai
- College of Veterinary Medicine, Yangzhou University, Yangzhou, China
- Jiangsu Co-Innovation Center of Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, China
| | - Jia-Lin Wang
- College of Veterinary Medicine, Yangzhou University, Yangzhou, China
- Jiangsu Co-Innovation Center of Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, China
| | - Pengfei Wu
- College of Veterinary Medicine, Yangzhou University, Yangzhou, China
| | - Ping Zhong
- College of Veterinary Medicine, Yangzhou University, Yangzhou, China
- *Correspondence: Yu-Guo Yuan, ; Ping Zhong, ; Il-Keun Kong,
| | - Il-Keun Kong
- Division of Applied Life Science (BK21 Four), Institute of Agriculture and Life Science, Gyeongsang National University, Jinju, Gyeongnam, Republic of Korea
- *Correspondence: Yu-Guo Yuan, ; Ping Zhong, ; Il-Keun Kong,
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Gao L, Tan J, Han C, Fan J, He J, Luo T, Yu S, Che X, Zhang L, Wang X. Identification and characterization of differentially expressed circRNA in 2,3,7,8-tetrachlorodibenzo-p-dioxin-induced cleft palate. Hum Exp Toxicol 2023; 42:9603271231183359. [PMID: 37303070 DOI: 10.1177/09603271231183359] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Various circular RNAs (circRNAs) are novel class of non-coding RNAs, which are pervasively transcribed in the genome. CircRNAs play important roles in human, animals and plants. Up to now, there was no report regarding circRNAs of cleft palate by 2,3,7,8-tetrachlorodibenzo-pdioxin (TCDD) induce. The present study screened identification and characterization of differential expressed-circRNAs in TCDD-induced cleft palate. 6903 circRNAs candidates came from cleft palates. Among them, 3525 circRNAs are up-regulation, and 3378 circRNAs are down-regulation by TCDD induce. The cluster and GO analysis found that circRNAs involved in biological process, cellular component, and molecular function. Through the analysis of KEGG Pathway, circRNAs made functions via classical signaling pathway in cleft palate, such as TGF-beta signaling pathway, BMP signal pathway, MAPK signaling pathway. In addition, we found down-regulated circRNA224, circRNA3302 and up-regulated circRNA5021 targeted tgfbr3, but up-regulated circRNA4451 targeted tgfbr2. circRNA4451 may make functions through TGF-beta signaling pathway. These results suggested that many different circRNAs may make important role in TCDD-induced cleft palate, which provided a theoretical basis for further research.
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Affiliation(s)
- Liyun Gao
- School of Basic Medicine, Jiujiang University, Jiujiang, China
| | - Jingwen Tan
- School of Pharmacy and Life Sciences, Jiujiang University, Jiujiang, China
| | - Chunhua Han
- Internal Medicine, First People's Hospital of Jiujiang City, Jiujiang, China
| | - Junfei Fan
- School of Humanities, Shangluo University, Shangluo, China
| | - Jiayin He
- School of Literature and Journalism, South-Central Minzu University, Wuhan, China
| | - Ting Luo
- School of Public Health, Nanchang University, Nanchang, China
| | - Shiqun Yu
- School of Public Health, Nanchang University, Nanchang, China
| | - Xiangxin Che
- School of Basic Medicine, Jiujiang University, Jiujiang, China
| | - Lin Zhang
- Yangze river fisheries research institute, Chinese academy of fisheries sciences, Wuhan, China
| | - Xin Wang
- School of Basic Medicine, Jiujiang University, Jiujiang, China
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Solodneva EV, Kuznetsov SB, Velieva AE, Stolpovsky YA. Molecular-Genetic Bases of Mammary Gland Development Using the Example of Cattle and Other Animal Species: I. Embryonic and Pubertal Developmental Stage. RUSS J GENET+ 2022. [DOI: 10.1134/s1022795422080087] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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10
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Khan A, Singh K, Jaiswal S, Raza M, Jasrotia RS, Kumar A, Gurjar AKS, Kumari J, Nayan V, Iquebal MA, Angadi UB, Rai A, Datta TK, Kumar D. Whole-Genome-Based Web Genomic Resource for Water Buffalo (Bubalus bubalis). Front Genet 2022; 13:809741. [PMID: 35480326 PMCID: PMC9035531 DOI: 10.3389/fgene.2022.809741] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Accepted: 02/14/2022] [Indexed: 11/13/2022] Open
Abstract
Water buffalo (Bubalus bubalis), belonging to the Bovidae family, is an economically important animal as it is the major source of milk, meat, and drought in numerous countries. It is mainly distributed in tropical and subtropical regions with a global population of approximately 202 million. The advent of low cost and rapid sequencing technologies has opened a new vista for global buffalo researchers. In this study, we utilized the genomic data of five commercially important buffalo breeds, distributed globally, namely, Mediterranean, Egyptian, Bangladesh, Jaffrarabadi, and Murrah. Since there is no whole-genome sequence analysis of these five distinct buffalo breeds, which represent a highly diverse ecosystem, we made an attempt for the same. We report the first comprehensive, holistic, and user-friendly web genomic resource of buffalo (BuffGR) accessible at http://backlin.cabgrid.res.in/buffgr/, that catalogues 6028881 SNPs and 613403 InDels extracted from a set of 31 buffalo tissues. We found a total of 7727122 SNPs and 634124 InDels distributed in four breeds of buffalo (Murrah, Bangladesh, Jaffarabadi, and Egyptian) with reference to the Mediterranean breed. It also houses 4504691 SSR markers from all the breeds along with 1458 unique circRNAs, 37712 lncRNAs, and 938 miRNAs. This comprehensive web resource can be widely used by buffalo researchers across the globe for use of markers in marker trait association, genetic diversity among the different breeds of buffalo, use of ncRNAs as regulatory molecules, post-transcriptional regulations, and role in various diseases/stresses. These SNPs and InDelscan also be used as biomarkers to address adulteration and traceability. This resource can also be useful in buffalo improvement programs and disease/breed management.
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Affiliation(s)
- Aamir Khan
- Centre for Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, New Delhi, India
| | - Kalpana Singh
- Centre for Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, New Delhi, India
| | - Sarika Jaiswal
- Centre for Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, New Delhi, India
| | - Mustafa Raza
- Centre for Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, New Delhi, India
| | - Rahul Singh Jasrotia
- Centre for Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, New Delhi, India
| | - Animesh Kumar
- Centre for Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, New Delhi, India
| | - Anoop Kishor Singh Gurjar
- Centre for Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, New Delhi, India
| | - Juli Kumari
- Centre for Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, New Delhi, India
| | - Varij Nayan
- ICAR-Central Institute for Research on Buffaloes, Hisar, India
| | - Mir Asif Iquebal
- Centre for Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, New Delhi, India
- *Correspondence: Mir Asif Iquebal,
| | - U. B. Angadi
- Centre for Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, New Delhi, India
| | - Anil Rai
- Centre for Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, New Delhi, India
| | | | - Dinesh Kumar
- Centre for Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, New Delhi, India
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