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Du K, Bai X, Yang L, Shi Y, Chen L, Wang H, Cai M, Wang J, Chen S, Jia X, Lai S. De Novo Reconstruction of Transcriptome Identified Long Non-Coding RNA Regulator of Aging-Related Brown Adipose Tissue Whitening in Rabbits. BIOLOGY 2021; 10:biology10111176. [PMID: 34827171 PMCID: PMC8614855 DOI: 10.3390/biology10111176] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Revised: 11/10/2021] [Accepted: 11/11/2021] [Indexed: 01/16/2023]
Abstract
Simple Summary Brown adipose tissues (BATs) undergo the conversion to white adipose tissues (WATs) with age. Long non-coding RNAs (lncRNAs) were widely involved in adipose biology. Rabbit is an ideal model for studying the dynamics of the transformation from BATs to WATs. However, our knowledge of lncRNAs that mediate the transformation remains unknown in rabbits. By histological analysis and sequencing, we found rabbit interscapular adipose tissues (iATs) from BATs to WATs within two years and identified a total of 631 differentially expressed lncRNAs (DELs) during the transformation process. Several signal pathways were involved in the transformation from BAT to WAT. A novel lncRNA that was highly expressed in iATs of aged rabbits was validated to impair brown adipocyte differentiation in vitro. Our study provided a comprehensive catalog of lncRNAs involved in the transformation from BATs to WATs in rabbits, facilitating a better understanding of adipose biology. Abstract Brown adipose tissues (BATs) convert to a “white-like” phenotype with age, which is also known as “aging-related BAT whitening (ARBW)”. Emerging evidence suggested that long non-coding RNAs (lncRNAs) were widely involved in adipose biology. Rabbit is an ideal model for studying the dynamics of ARBW. In this study, we performed histological analysis and strand-specific RNA-sequencing (ssRNA-seq) of rabbit interscapular adipose tissues (iATs). Our data indicated that the rabbit iATs underwent the ARBW from 0 days to 2 years and a total of 2281 novel lncRNAs were identified in the iATs. The classical rabbit BATs showed low lncRNA transcriptional complexity compared to white adipose tissues (WATs). A total of 631 differentially expressed lncRNAs (DELs) were identified in four stages. The signal pathways of purine metabolism, Wnt signaling pathway, peroxisome proliferator-activated receptor (PPAR) signaling pathway, cyclic guanosine monophosphate (cGMP)/cGMP-dependent protein kinase (cGMP-PKG) signaling pathway and lipid and atherosclerosis were significantly enriched by the DELs with unique expression patterns. A novel lncRNA that was highly expressed in the iATs of aged rabbits was validated to impair brown adipocyte differentiation in vitro. Our study provided a comprehensive catalog of lncRNAs involved in ARBW in rabbits, which facilitates a better understanding of adipose biology.
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Affiliation(s)
- Kun Du
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, 211# Huimin Road, Chengdu 611130, China; (K.D.); (X.B.); (L.Y.); (Y.S.); (L.C.); (H.W.); (M.C.); (J.W.); (S.C.); (X.J.)
| | - Xue Bai
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, 211# Huimin Road, Chengdu 611130, China; (K.D.); (X.B.); (L.Y.); (Y.S.); (L.C.); (H.W.); (M.C.); (J.W.); (S.C.); (X.J.)
| | - Li Yang
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, 211# Huimin Road, Chengdu 611130, China; (K.D.); (X.B.); (L.Y.); (Y.S.); (L.C.); (H.W.); (M.C.); (J.W.); (S.C.); (X.J.)
| | - Yu Shi
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, 211# Huimin Road, Chengdu 611130, China; (K.D.); (X.B.); (L.Y.); (Y.S.); (L.C.); (H.W.); (M.C.); (J.W.); (S.C.); (X.J.)
| | - Li Chen
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, 211# Huimin Road, Chengdu 611130, China; (K.D.); (X.B.); (L.Y.); (Y.S.); (L.C.); (H.W.); (M.C.); (J.W.); (S.C.); (X.J.)
| | - Haoding Wang
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, 211# Huimin Road, Chengdu 611130, China; (K.D.); (X.B.); (L.Y.); (Y.S.); (L.C.); (H.W.); (M.C.); (J.W.); (S.C.); (X.J.)
| | - Mingchen Cai
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, 211# Huimin Road, Chengdu 611130, China; (K.D.); (X.B.); (L.Y.); (Y.S.); (L.C.); (H.W.); (M.C.); (J.W.); (S.C.); (X.J.)
- College of Landscape Architecture and Life Science/Institute of Special Plants, Chongqing University of Arts and Sciences, Chongqing 402160, China
| | - Jie Wang
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, 211# Huimin Road, Chengdu 611130, China; (K.D.); (X.B.); (L.Y.); (Y.S.); (L.C.); (H.W.); (M.C.); (J.W.); (S.C.); (X.J.)
| | - Shiyi Chen
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, 211# Huimin Road, Chengdu 611130, China; (K.D.); (X.B.); (L.Y.); (Y.S.); (L.C.); (H.W.); (M.C.); (J.W.); (S.C.); (X.J.)
| | - Xianbo Jia
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, 211# Huimin Road, Chengdu 611130, China; (K.D.); (X.B.); (L.Y.); (Y.S.); (L.C.); (H.W.); (M.C.); (J.W.); (S.C.); (X.J.)
| | - Songjia Lai
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, 211# Huimin Road, Chengdu 611130, China; (K.D.); (X.B.); (L.Y.); (Y.S.); (L.C.); (H.W.); (M.C.); (J.W.); (S.C.); (X.J.)
- Correspondence: or
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Fu X, Zhao B, Tian K, Wu Y, Suo L, Ba G, Ciren D, De J, Awang C, Gun S, Yang B. Integrated analysis of lncRNA and mRNA reveals novel insights into cashmere fineness in Tibetan cashmere goats. PeerJ 2020; 8:e10217. [PMID: 33240606 PMCID: PMC7659624 DOI: 10.7717/peerj.10217] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2020] [Accepted: 09/29/2020] [Indexed: 12/15/2022] Open
Abstract
Tibetan cashmere goats are famous for producing the finest, softest and lightest cashmere fiber in China. The growth and development of skin are closely related to fineness and are the key factors affecting the quality of cashmere. To investigate the specific role of long noncoding RNAs (lncRNAs) and messenger RNAs (mRNAs) in regulating cashmere fineness of Tibetan Cashmere goats in the anagen phase, we conducted high-throughput RNA sequencing of fine-type and coarse-type skin tissues. We identified 2,059 lncRNA candidates (1,589 lncRNAs annotated, 470 lncRNAs novel), and 80 differentially expressed (DE) lncRNAs and their potential targets were predicted. We also identified 384 DE messenger RNAs (mRNAs) out of 29,119 mRNAs. Several key genes in KRT26, KRT28, KRT39, IFT88, JAK3, NOTCH2 and NOTCH3 and a series of lncRNAs, including ENSCHIT00000009853, MSTRG.16794.17, MSTRG.17532.2, were shown to be potentially important for regulating cashmere fineness. GO and KEGG enrichment analyses of DE mRNAs and DE lncRNAs targets significantly enriched in positive regulation of the canonical Wnt signaling pathway, regulation of protein processing and metabolism processes. The mRNA-mRNA and lncRNA-mRNA regulatory networks further revealed potential transcripts involved in cashmere fineness. We further validated the expression patterns of DE mRNAs and DE lncRNAs by quantitative real-time PCR (qRT-PCR), and the results were consistent with the sequencing data. This study will shed new light on selective cashmere goat breeding, and these lncRNAs and mRNAs that were found to be enriched in Capra hircus RNA database.
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Affiliation(s)
- Xuefeng Fu
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China.,Key Laboratory of Genetics Breeding and Reproduction of Xinjiang Wool-sheep & Cashmere-goat, Institute of Animal Science, Xinjiang Academy of Animal Sciences, Urumqi, China.,Lanzhou Institute of Husbandry and Pharmaceutical Sciences of Chinese Academy of Agricultural Sciences, Lanzhou, China
| | - Bingru Zhao
- College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Kechuan Tian
- Key Laboratory of Genetics Breeding and Reproduction of Xinjiang Wool-sheep & Cashmere-goat, Institute of Animal Science, Xinjiang Academy of Animal Sciences, Urumqi, China
| | - Yujiang Wu
- Institute of Animal Science, Tibet Academy of Agricultural and Animal Husbandry Sciences, Lhasa, China
| | - Langda Suo
- Institute of Animal Science, Tibet Academy of Agricultural and Animal Husbandry Sciences, Lhasa, China
| | - Gui Ba
- Institute of Animal Science, Tibet Academy of Agricultural and Animal Husbandry Sciences, Lhasa, China
| | - Deji Ciren
- Institute of Animal Science, Tibet Academy of Agricultural and Animal Husbandry Sciences, Lhasa, China
| | - Ji De
- Institute of Animal Science, Tibet Academy of Agricultural and Animal Husbandry Sciences, Lhasa, China
| | - Cuoji Awang
- Institute of Animal Science, Tibet Academy of Agricultural and Animal Husbandry Sciences, Lhasa, China
| | - Shuangbao Gun
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Bohui Yang
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China.,Lanzhou Institute of Husbandry and Pharmaceutical Sciences of Chinese Academy of Agricultural Sciences, Lanzhou, China
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