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Fu Y, Li J, Tang Q, Zou C, Shen L, Jin L, Li C, Fang C, Liu R, Li M, Zhao S, Li C. Integrated analysis of methylome, transcriptome and miRNAome of three pig breeds. Epigenomics 2018; 10:597-612. [PMID: 29692202 DOI: 10.2217/epi-2017-0087] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
AIM Integrated analysis of methylome and transcriptome may help understand the molecular basis of the different breeds with different traits of commercial interest. MATERIALS & METHODS We obtained the first genome-wide methylome with single-base resolution, miRNAome and transcriptome from three swine breeds. RESULTS We displayed the landscape of the three omics in the whole-genome level. Integrated outcomes of methylome with genetic selection, miRNAome and transcriptome are also provided. Finally, we identified 11 candidate differentially methylated genes associated with phenotype variance in pigs. CONCLUSION DNA methylation not only suppresses transcriptome but also miRNAome. The different -omics data have complicated interaction in directly or indirectly and exhibited close relations with the distinct phenotypic traits of growth, disease resistance and energy metabolism.
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Affiliation(s)
- Yuhua Fu
- Key Lab of Agriculture Animal Genetics, Breeding, & Reproduction of Ministry of Education, College of Animal Sciences & Technology, Huazhong Agricultural University, Wuhan, 430070, PR China
| | - Jingxuan Li
- Key Lab of Agriculture Animal Genetics, Breeding, & Reproduction of Ministry of Education, College of Animal Sciences & Technology, Huazhong Agricultural University, Wuhan, 430070, PR China
| | - Qianzi Tang
- Institute of Animal Genetics & Breeding, College of Animal Science & Technology, Sichuan Agricultural University, Chengdu, 611130, PR China
| | - Cheng Zou
- Key Lab of Agriculture Animal Genetics, Breeding, & Reproduction of Ministry of Education, College of Animal Sciences & Technology, Huazhong Agricultural University, Wuhan, 430070, PR China
| | - Linyuan Shen
- Institute of Animal Genetics & Breeding, College of Animal Science & Technology, Sichuan Agricultural University, Chengdu, 611130, PR China
| | - Long Jin
- Institute of Animal Genetics & Breeding, College of Animal Science & Technology, Sichuan Agricultural University, Chengdu, 611130, PR China
| | - Cencen Li
- Key Lab of Agriculture Animal Genetics, Breeding, & Reproduction of Ministry of Education, College of Animal Sciences & Technology, Huazhong Agricultural University, Wuhan, 430070, PR China
| | - Chengchi Fang
- Key Lab of Agriculture Animal Genetics, Breeding, & Reproduction of Ministry of Education, College of Animal Sciences & Technology, Huazhong Agricultural University, Wuhan, 430070, PR China
| | - Rui Liu
- Institute of Animal Genetics & Breeding, College of Animal Science & Technology, Sichuan Agricultural University, Chengdu, 611130, PR China
| | - Mingzhou Li
- Institute of Animal Genetics & Breeding, College of Animal Science & Technology, Sichuan Agricultural University, Chengdu, 611130, PR China
| | - Shuhong Zhao
- Key Lab of Agriculture Animal Genetics, Breeding, & Reproduction of Ministry of Education, College of Animal Sciences & Technology, Huazhong Agricultural University, Wuhan, 430070, PR China
| | - Changchun Li
- Key Lab of Agriculture Animal Genetics, Breeding, & Reproduction of Ministry of Education, College of Animal Sciences & Technology, Huazhong Agricultural University, Wuhan, 430070, PR China
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Matsunaga N, Ikeda E, Kakimoto K, Watanabe M, Shindo N, Tsuruta A, Ikeyama H, Hamamura K, Higashi K, Yamashita T, Kondo H, Yoshida Y, Matsuda M, Ogino T, Tokushige K, Itcho K, Furuichi Y, Nakao T, Yasuda K, Doi A, Amamoto T, Aramaki H, Tsuda M, Inoue K, Ojida A, Koyanagi S, Ohdo S. Inhibition of G0/G1 Switch 2 Ameliorates Renal Inflammation in Chronic Kidney Disease. EBioMedicine 2016; 13:262-273. [PMID: 27745900 PMCID: PMC5264248 DOI: 10.1016/j.ebiom.2016.10.008] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2015] [Revised: 10/05/2016] [Accepted: 10/05/2016] [Indexed: 12/20/2022] Open
Abstract
Chronic kidney disease (CKD) is a global health problem, and novel therapies to treat CKD are urgently needed. Here, we show that inhibition of G0/G1 switch 2 (G0s2) ameliorates renal inflammation in a mouse model of CKD. Renal expression of chemokine (C-C motif) ligand 2 (Ccl2) was increased in response to p65 activation in the kidneys of wild-type 5/6 nephrectomy (5/6Nx) mice. Moreover, 5/6Nx Clk/Clk mice, which carry homozygous mutations in the gene encoding circadian locomotor output cycles kaput (CLOCK), did not exhibit aggravation of apoptosis or induction of F4/80-positive cells. The renal expression of G0s2 in wild-type 5/6Nx mice was important for the transactivation of Ccl2 by p65. These pathologies were ameliorated by G0s2 knockdown. Furthermore, a novel small-molecule inhibitor of G0s2 expression was identified by high-throughput chemical screening, and the inhibitor suppressed renal inflammation in 5/6Nx mice. These findings indicated that G0s2 inhibitors may have applications in the treatment of CKD.
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Affiliation(s)
- Naoya Matsunaga
- Department of Pharmaceutics, Graduate School of Pharmaceutical Sciences, Kyushu University, Higashi-ku, Fukuoka 812-8582, Japan; Department of Glocal Healthcare Science, Faculty of Pharmaceutical Sciences, Kyushu University, Fukuoka 812-8582, Japan
| | - Eriko Ikeda
- Department of Molecular Biology, Daiichi University of Pharmacy, Minami-ku, Fukuoka 815-8511, Japan
| | - Keisuke Kakimoto
- Department of Pharmaceutics, Graduate School of Pharmaceutical Sciences, Kyushu University, Higashi-ku, Fukuoka 812-8582, Japan
| | - Miyako Watanabe
- Department of Pharmaceutics, Graduate School of Pharmaceutical Sciences, Kyushu University, Higashi-ku, Fukuoka 812-8582, Japan
| | - Naoya Shindo
- Department of Bio-Analytical Chemistry, Graduate School of Pharmaceutical Sciences, Kyushu University, Higashi-ku, Fukuoka 812-8582, Japan
| | - Akito Tsuruta
- Department of Pharmaceutics, Graduate School of Pharmaceutical Sciences, Kyushu University, Higashi-ku, Fukuoka 812-8582, Japan
| | - Hisako Ikeyama
- Department of Pharmaceutics, Graduate School of Pharmaceutical Sciences, Kyushu University, Higashi-ku, Fukuoka 812-8582, Japan
| | - Kengo Hamamura
- Department of Molecular Biology, Daiichi University of Pharmacy, Minami-ku, Fukuoka 815-8511, Japan
| | - Kazuhiro Higashi
- Department of Pharmaceutics, Graduate School of Pharmaceutical Sciences, Kyushu University, Higashi-ku, Fukuoka 812-8582, Japan
| | - Tomohiro Yamashita
- Department of Molecular and System Pharmacology, Graduate School of Pharmaceutical Sciences, Kyushu University, Fukuoka 812-8582, Japan
| | - Hideaki Kondo
- Center for Sleep Medicine, Saiseikai Nagasaki Hospital, Katafuchi, Nagasaki 850-0003, Japan
| | - Yuya Yoshida
- Department of Pharmaceutics, Graduate School of Pharmaceutical Sciences, Kyushu University, Higashi-ku, Fukuoka 812-8582, Japan
| | - Masaki Matsuda
- Department of Pharmaceutics, Graduate School of Pharmaceutical Sciences, Kyushu University, Higashi-ku, Fukuoka 812-8582, Japan
| | - Takashi Ogino
- Department of Pharmaceutics, Graduate School of Pharmaceutical Sciences, Kyushu University, Higashi-ku, Fukuoka 812-8582, Japan
| | - Kazutaka Tokushige
- Department of Pharmaceutics, Graduate School of Pharmaceutical Sciences, Kyushu University, Higashi-ku, Fukuoka 812-8582, Japan
| | - Kazufumi Itcho
- Department of Pharmaceutics, Graduate School of Pharmaceutical Sciences, Kyushu University, Higashi-ku, Fukuoka 812-8582, Japan
| | - Yoko Furuichi
- Department of Pharmaceutics, Graduate School of Pharmaceutical Sciences, Kyushu University, Higashi-ku, Fukuoka 812-8582, Japan
| | - Takaharu Nakao
- Department of Pharmaceutics, Graduate School of Pharmaceutical Sciences, Kyushu University, Higashi-ku, Fukuoka 812-8582, Japan
| | - Kaori Yasuda
- Cell-Innovator Inc., EC building, Kyushu University, Higashi-ku, Fukuoka 812-8582, Japan
| | - Atsushi Doi
- Cell-Innovator Inc., EC building, Kyushu University, Higashi-ku, Fukuoka 812-8582, Japan
| | - Toshiaki Amamoto
- NMedical Co. Ouryokukai, Chuo-ku, Nihombashi-Kayabacho, Tokyo 103-0025, Japan
| | - Hironori Aramaki
- Department of Molecular Biology, Daiichi University of Pharmacy, Minami-ku, Fukuoka 815-8511, Japan
| | - Makoto Tsuda
- Department of Life Innovation, Graduate School of Pharmaceutical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka 812-8582, Japan
| | - Kazuhide Inoue
- Department of Molecular and System Pharmacology, Graduate School of Pharmaceutical Sciences, Kyushu University, Fukuoka 812-8582, Japan
| | - Akio Ojida
- Department of Bio-Analytical Chemistry, Graduate School of Pharmaceutical Sciences, Kyushu University, Higashi-ku, Fukuoka 812-8582, Japan
| | - Satoru Koyanagi
- Department of Pharmaceutics, Graduate School of Pharmaceutical Sciences, Kyushu University, Higashi-ku, Fukuoka 812-8582, Japan; Department of Glocal Healthcare Science, Faculty of Pharmaceutical Sciences, Kyushu University, Fukuoka 812-8582, Japan
| | - Shigehiro Ohdo
- Department of Pharmaceutics, Graduate School of Pharmaceutical Sciences, Kyushu University, Higashi-ku, Fukuoka 812-8582, Japan.
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