1
|
He Z, Sun H, Zhao F, Ma L, Wang J, Liu X, Li M, Hao Z, Li S. MicroRNA expression profiles reveal wool development and fineness regulation in Gansu alpine fine-wool sheep. Genomics 2024; 116:110922. [PMID: 39178999 DOI: 10.1016/j.ygeno.2024.110922] [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: 05/28/2024] [Revised: 07/04/2024] [Accepted: 08/19/2024] [Indexed: 08/26/2024]
Abstract
The development of wool has a complex regulatory mechanism both influenced by genetic and environmental factors. MicroRNAs (miRNA) were involved in various biological processes of animals, and may play an important role in the regulation of wool development. In this study, we comprehensively analyzed and identified the histological parameters of hair follicles, as well as the miRNAs, target genes, pathways, and Gene Ontology terms related to wool fineness regulation and wool growth and development using HE staining and RNA-Seqs methods. Both coarse (group C, mean fiber diameter (MFD) = 22.26 ± 0.69 μm, n = 6) and fine (group F, MFD = 16.91 ± 0.29 μm, n = 6) of Gansu alpine fine-wool sheep with different wool fineness were used in this study. The results showed that the primary follicle diameter and secondary wool fiber diameter in group C were significantly higher than those in group F (P < 0.05). And the number of primary and secondary hair follicles in group C was significantly lower than that in group F (P < 0.05). Furthermore, a total of 67 DE miRNAs and 290 potential DE miRNAs target genes were screened in the skin tissues of sheep from groups F and C, and some potential target genes related to wool fineness regulation were screened, such as CDH2, KRT82, FOXN1, LOC101106296, KRT20, MCOLN3, KRT71, and TERT. These genes were closely related to Glutathione metabolism, epidermal cell differentiation, keratinization, and regulation of hair cycle. Moreover, the regulatory network of miRNAs-mRNAs suggested that miRNAs (miR-129-x, novel m0079-3p, miR-2484-z, novel m0025-5P, etc.) may play a key role in the wool development and wool fineness regulation of Gansu alpine fine-wool sheep. In summary, this study expands the existing miRNAs database and provides new information for studying the regulation of wool development in Gansu alpine fine wool sheep.
Collapse
Affiliation(s)
- Zhaohua He
- Gansu Key Laboratory of Herbivorous Animal Biotechnology, College of Animal Science and Technology, Gansu Agricultural University, China
| | - Hongxian Sun
- Gansu Key Laboratory of Herbivorous Animal Biotechnology, College of Animal Science and Technology, Gansu Agricultural University, China
| | - Fangfang Zhao
- Gansu Key Laboratory of Herbivorous Animal Biotechnology, College of Animal Science and Technology, Gansu Agricultural University, China
| | - Longxia Ma
- Gansu Key Laboratory of Herbivorous Animal Biotechnology, College of Animal Science and Technology, Gansu Agricultural University, China
| | - Jiqing Wang
- Gansu Key Laboratory of Herbivorous Animal Biotechnology, College of Animal Science and Technology, Gansu Agricultural University, China
| | - Xiu Liu
- Gansu Key Laboratory of Herbivorous Animal Biotechnology, College of Animal Science and Technology, Gansu Agricultural University, China
| | - Mingna Li
- Gansu Key Laboratory of Herbivorous Animal Biotechnology, College of Animal Science and Technology, Gansu Agricultural University, China
| | - Zhiyun Hao
- Gansu Key Laboratory of Herbivorous Animal Biotechnology, College of Animal Science and Technology, Gansu Agricultural University, China
| | - Shaobin Li
- Gansu Key Laboratory of Herbivorous Animal Biotechnology, College of Animal Science and Technology, Gansu Agricultural University, China.
| |
Collapse
|
2
|
Yao Y, Liu P, Li Y, Wang W, Jia H, Bai Y, Yuan Z, Yang Z. Regulatory role of m 6A epitranscriptomic modifications in normal development and congenital malformations during embryogenesis. Biomed Pharmacother 2024; 173:116171. [PMID: 38394844 DOI: 10.1016/j.biopha.2024.116171] [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: 10/18/2023] [Revised: 01/08/2024] [Accepted: 01/13/2024] [Indexed: 02/25/2024] Open
Abstract
The discovery of N6-methyladenosine (m6A) methylation and its role in translation has led to the emergence of a new field of research. Despite accumulating evidence suggesting that m6A methylation is essential for the pathogenesis of cancers and aging diseases by influencing RNA stability, localization, transformation, and translation efficiency, its role in normal and abnormal embryonic development remains unclear. An increasing number of studies are addressing the development of the nervous and gonadal systems during embryonic development, but only few are assessing that of the immune, hematopoietic, urinary, and respiratory systems. Additionally, these studies are limited by the requirement for reliable embryonic animal models and the difficulty in collecting tissue samples of fetuses during development. Multiple studies on the function of m6A methylation have used suitable cell lines to mimic the complex biological processes of fetal development or the early postnatal phase; hence, the research is still in the primary stage. Herein, we discuss current advances in the extensive biological functions of m6A methylation in the development and maldevelopment of embryos/fetuses and conclude that m6A modification occurs extensively during fetal development. Aberrant expression of m6A regulators is probably correlated with single or multiple defects in organogenesis during the intrauterine life. This comprehensive review will enhance our understanding of the pivotal role of m6A modifications involved in fetal development and examine future research directions in embryogenesis.
Collapse
Affiliation(s)
- Yifan Yao
- Department of Pediatric Surgery, Shengjing Hospital of China Medical University, Shenyang, Liaoning, China; Key Laboratory of Health Ministry for Congenital Malformation, Shengjing Hospital of China Medical University, Shenyang, Liaoning, China
| | - Peiqi Liu
- Department of Pediatric Surgery, Shengjing Hospital of China Medical University, Shenyang, Liaoning, China
| | - Yue Li
- Department of Pediatric Surgery, Shengjing Hospital of China Medical University, Shenyang, Liaoning, China
| | - Weilin Wang
- Department of Pediatric Surgery, Shengjing Hospital of China Medical University, Shenyang, Liaoning, China
| | - Huimin Jia
- Department of Pediatric Surgery, Shengjing Hospital of China Medical University, Shenyang, Liaoning, China
| | - Yuzuo Bai
- Department of Pediatric Surgery, Shengjing Hospital of China Medical University, Shenyang, Liaoning, China.
| | - Zhengwei Yuan
- Key Laboratory of Health Ministry for Congenital Malformation, Shengjing Hospital of China Medical University, Shenyang, Liaoning, China.
| | - Zhonghua Yang
- Department of Pediatric Surgery, Shengjing Hospital of China Medical University, Shenyang, Liaoning, China; Key Laboratory of Health Ministry for Congenital Malformation, Shengjing Hospital of China Medical University, Shenyang, Liaoning, China.
| |
Collapse
|
3
|
Yang C, Wu D, Lin H, Ma D, Fu W, Yao Y, Pan X, Wang S, Zhuang Z. Role of RNA Modifications, Especially m6A, in Aflatoxin Biosynthesis of Aspergillus flavus. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2024; 72:726-741. [PMID: 38112282 DOI: 10.1021/acs.jafc.3c05926] [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: 12/21/2023]
Abstract
RNA modifications play key roles in eukaryotes, but the functions in Aspergillus flavus are still unknown. Temperature has been reported previously to be a critical environmental factor that regulates the aflatoxin production of A. flavus, but much remains to be learned about the molecular networks. Here, we demonstrated that 12 kinds of RNA modifications in A. flavus were significantly changed under 29 °C compared to 37 °C incubation; among them, m6A was further verified by a colorimetric method. Then, the transcriptome-wide m6A methylome and m6A-altered genes were comprehensively illuminated through methylated RNA immunoprecipitation sequencing and RNA sequencing, from which 22 differentially methylated and expressed transcripts under 29 °C were screened out. It is especially notable that AFCA_009549, an aflatoxin biosynthetic pathway gene (aflQ), and the m6A methylation of its 332nd adenine in the mRNA significantly affect aflatoxin biosynthesis in A. flavus both on media and crop kernels. The content of sterigmatocystin in both ΔaflQ and aflQA332C strains was significantly higher than that in the WT strain. Together, these findings reveal that RNA modifications are associated with secondary metabolite biosynthesis of A. flavus.
Collapse
Affiliation(s)
- Chi Yang
- Key Laboratory of Pathogenic Fungi and Mycotoxins of Fujian Province, Key Laboratory of Biopesticide and Chemical Biology of Education Ministry, Proteomic Research Center, and School of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- Institute of Edible Mushroom, Fujian Academy of Agricultural Sciences, Fuzhou 350012, China
| | - Dandan Wu
- Key Laboratory of Pathogenic Fungi and Mycotoxins of Fujian Province, Key Laboratory of Biopesticide and Chemical Biology of Education Ministry, Proteomic Research Center, and School of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Hong Lin
- Key Laboratory of Pathogenic Fungi and Mycotoxins of Fujian Province, Key Laboratory of Biopesticide and Chemical Biology of Education Ministry, Proteomic Research Center, and School of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Dongmei Ma
- Key Laboratory of Pathogenic Fungi and Mycotoxins of Fujian Province, Key Laboratory of Biopesticide and Chemical Biology of Education Ministry, Proteomic Research Center, and School of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- College of Animal Sciences (College of Bee Science), Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Wangzhuo Fu
- Key Laboratory of Pathogenic Fungi and Mycotoxins of Fujian Province, Key Laboratory of Biopesticide and Chemical Biology of Education Ministry, Proteomic Research Center, and School of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Yanfang Yao
- Key Laboratory of Pathogenic Fungi and Mycotoxins of Fujian Province, Key Laboratory of Biopesticide and Chemical Biology of Education Ministry, Proteomic Research Center, and School of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Xiaohua Pan
- Key Laboratory of Pathogenic Fungi and Mycotoxins of Fujian Province, Key Laboratory of Biopesticide and Chemical Biology of Education Ministry, Proteomic Research Center, and School of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Shihua Wang
- Key Laboratory of Pathogenic Fungi and Mycotoxins of Fujian Province, Key Laboratory of Biopesticide and Chemical Biology of Education Ministry, Proteomic Research Center, and School of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Zhenhong Zhuang
- Key Laboratory of Pathogenic Fungi and Mycotoxins of Fujian Province, Key Laboratory of Biopesticide and Chemical Biology of Education Ministry, Proteomic Research Center, and School of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| |
Collapse
|
4
|
Wang J, Hua G, Cai G, Ma Y, Yang X, Zhang L, Li R, Liu J, Ma Q, Wu K, Zhao Y, Deng X. Genome-wide DNA methylation and transcriptome analyses reveal the key gene for wool type variation in sheep. J Anim Sci Biotechnol 2023; 14:88. [PMID: 37420295 DOI: 10.1186/s40104-023-00893-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Accepted: 05/07/2023] [Indexed: 07/09/2023] Open
Abstract
BACKGROUND Wool fibers are valuable materials for textile industry. Typical wool fibers are divided into medullated and non-medullated types, with the former generated from primary wool follicles and the latter by either primary or secondary wool follicles. The medullated wool is a common wool type in the ancestors of fine wool sheep before breeding. The fine wool sheep have a non-medullated coat. However, the critical period determining the type of wool follicles is the embryonic stage, which limits the phenotypic observation and variant contrast, making both selection and studies of wool type variation fairly difficult. RESULTS During the breeding of a modern fine (MF) wool sheep population with multiple-ovulation and embryo transfer technique, we serendipitously discovered lambs with ancestral-like coarse (ALC) wool. Whole-genome resequencing confirmed ALC wool lambs as a variant type from the MF wool population. We mapped the significantly associated methylation locus on chromosome 4 by using whole genome bisulfite sequencing signals, and in turn identified the SOSTDC1 gene as exons hypermethylated in ALC wool lambs compare to their half/full sibling MF wool lambs. Transcriptome sequencing found that SOSTDC1 was expressed dozens of times more in ALC wool lamb skin than that of MF and was at the top of all differentially expressed genes. An analogy with the transcriptome of coarse/fine wool breeds revealed that differentially expressed genes and enriched pathways at postnatal lamb stage in ALC/MF were highly similar to those at the embryonic stage in the former. Further experiments validated that the SOSTDC1 gene was specifically highly expressed in the nucleus of the dermal papilla of primary wool follicles. CONCLUSION In this study, we conducted genome-wide differential methylation site association analysis on differential wool type trait, and located the only CpG locus that strongly associated with primary wool follicle development. Combined with transcriptome analysis, SOSTDC1 was identified as the only gene at this locus that was specifically overexpressed in the primary wool follicle stem cells of ALC wool lamb skin. The discovery of this key gene and its epigenetic regulation contributes to understanding the domestication and breeding of fine wool sheep.
Collapse
Affiliation(s)
- Jiankui Wang
- State Key Laboratory of Animal Biotech Breeding, China Agricultural University, No. 2 Yuanmingyuan West Rd, Beijing, 100193, People's Republic of China
- Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture & Beijing Key Laboratory for Animal Genetic Improvement, China Agricultural University, No. 2 Yuanmingyuan West Rd, Beijing, 100193, People's Republic of China
| | - Guoying Hua
- State Key Laboratory of Animal Biotech Breeding, China Agricultural University, No. 2 Yuanmingyuan West Rd, Beijing, 100193, People's Republic of China
| | - Ganxian Cai
- State Key Laboratory of Animal Biotech Breeding, China Agricultural University, No. 2 Yuanmingyuan West Rd, Beijing, 100193, People's Republic of China
| | - Yuhao Ma
- State Key Laboratory of Animal Biotech Breeding, China Agricultural University, No. 2 Yuanmingyuan West Rd, Beijing, 100193, People's Republic of China
| | - Xue Yang
- State Key Laboratory of Animal Biotech Breeding, China Agricultural University, No. 2 Yuanmingyuan West Rd, Beijing, 100193, People's Republic of China
| | - Letian Zhang
- State Key Laboratory of Animal Biotech Breeding, China Agricultural University, No. 2 Yuanmingyuan West Rd, Beijing, 100193, People's Republic of China
| | - Rui Li
- Jinfeng Animal Husbandry Group Co., Ltd., Chifeng, 024000, China
| | - Jianbin Liu
- Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou, 730050, China
| | - Qing Ma
- Animal Science Institute of Ningxia Agriculture and Forestry Academy, Yinchuan, 750002, China
| | - Keliang Wu
- State Key Laboratory of Animal Biotech Breeding, China Agricultural University, No. 2 Yuanmingyuan West Rd, Beijing, 100193, People's Republic of China
| | - Yaofeng Zhao
- State Key Laboratory of Animal Biotech Breeding, China Agricultural University, No. 2 Yuanmingyuan West Rd, Beijing, 100193, People's Republic of China
- Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture & Beijing Key Laboratory for Animal Genetic Improvement, China Agricultural University, No. 2 Yuanmingyuan West Rd, Beijing, 100193, People's Republic of China
| | - Xuemei Deng
- State Key Laboratory of Animal Biotech Breeding, China Agricultural University, No. 2 Yuanmingyuan West Rd, Beijing, 100193, People's Republic of China.
- Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture & Beijing Key Laboratory for Animal Genetic Improvement, China Agricultural University, No. 2 Yuanmingyuan West Rd, Beijing, 100193, People's Republic of China.
| |
Collapse
|