Qing Li

Beijing Technology and Business University

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Caihong Wei

Institute of Animal Sciences

Zengkui Lu

Lanzhou Institute of Husbandry and Pharmaceutical Sciences

Mingxing Chu

Chinese Academy of Agricultural Sciences

Lin Ma

Shenzhen Children's Hospital

Meilin Jin

Institute of Animal Sciences

Yuqiao Xu

Air Force Medical University

Xiaojuan Fei

Lanzhou Institute of Husbandry and Pharmaceutical Sciences

Xiaohui Wu

Fudan University

Kai Quan

Peking University

Jianqiang Li

First Affiliated Hospital of Harbin Medical University

Cooperative Institutions

Chinese Academy of Medical Sciences & Peking Union Medical College

Chinese Academy of Sciences

Institute of Hematology & Blood Diseases Hospital

Ministry of Agriculture and Rural Affairs

Shanghai Jiao Tong University

Air Force Medical University

Chinese Academy of Agricultural Sciences

Nanjing Medical University

Huazhong Agricultural University

University of Chinese Academy of Sciences

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Regulation of seed oil accumulation by lncRNAs in Brassica napus

Biotechnology for Biofuels and Bioproducts (2023)

Yuqing Li Zengdong Tan Chenghao Zeng Mengying Xiao Shengli Lin

Studies have indicated that long non-coding RNAs (lncRNAs) play important regulatory roles in many biological processes. However, the regulation of seed oil biosynthesis by lncRNAs remains largely unknown.We comprehensively identified and characterized the lncRNAs from seeds in three developing stages in two accessions of Brassica napus (B. napus), ZS11 (high oil content) and WH5557 (low oil content). Finally, 8094 expressed lncRNAs were identified. LncRNAs MSTRG.22563 and MSTRG.86004 were predicted to be related to seed oil accumulation. Experimental results show that the seed oil content is decreased by 3.1-3.9% in MSTRG.22563 overexpression plants, while increased about 2% in MSTRG.86004, compared to WT. Further study showed that most genes related to lipid metabolism had much lower expression, and the content of some metabolites in the processes of respiration and TCA (tricarboxylic acid) cycle was reduced in MSTRG.22563 transgenic seeds. The expression of genes involved in fatty acid synthesis and seed embryonic development (e.g., LEC1) was increased, but genes related to TAG assembly was decreased in MSTRG.86004 transgenic seeds.Our results suggest that MSTRG.22563 might impact seed oil content by affecting the respiration and TCA cycle, while MSTRG.86004 plays a role in prolonging the seed developmental time to increase seed oil accumulation.

10.1186/s13068-022-02256-1

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Citations (11)

The CIDE genes might serve as novel targets for therapeutic intervention of obesity

Medical Hypotheses (2007)

Daqing Zhao Feng Zhang Guangsheng Chen Hang Li Yu Ma

10.1016/j.mehy.2006.12.040

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Citations (4)

Whole-genome resequencing of Dulong Chicken reveal signatures of selection

Figshare (2020)

Qi Wang Dengpan Li Aihuan Guo M. Li Li Li

1. Dulong Chickens (DLCs) live at high altitude (~3000 m) and humidity (~90%), are endemic to the Yunnan province, and have gradually developed unique physiological characteristics, but their genetic basis is still unclear. Using the fixation index (F_ST) approach, based on whole-genome resequencing, DLCs were analysed to uncover the genomic architecture of the population and candidate genes involved in selection during domestication. 2. A total of 469 candidate genes were obtained to be putatively under selection in DLCs. Further investigations revealed the genic footprint for local adaptation (high-altitude and high-humidity) as the genic signatures that are involved in economic traits (related to egg production). 3. Candidate genes were identified that may be associated with disease resistance, aggressiveness, small body size and positive selection of vision in DLCs. 4. These data revealed loci of selective signals that operate during selection for production at high altitude and humidity.

10.6084/m9.figshare.12848038

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Transcriptomic Analysis Provides Novel Insights into Heat Stress Responses in Sheep

Animals (2019)

Zengkui Lu Mingxing Chu Qing Li Meilin Jin Xiaojuan Fei

With the intensified and large-scale development of sheep husbandry and global warming, sheep heat stress has become an increasingly important issue. However, little is known about the molecular mechanisms related to sheep responses to heat stress. In this study, transcriptomic analysis of liver tissues of sheep in the presence and absence of heat stress was conducted, with the goal of identifying genes and pathways related to regulation when under such stress. After a comparison with the sheep reference genome, 440,226,436 clean reads were obtained from eight libraries. A p-value ≤ 0.05 and fold change ≥ 2 were taken as thresholds for categorizing differentially expressed genes, of which 1137 were identified. The accuracy and reliability of the RNA-Seq results were confirmed by qRT-PCR. The identified differentially expressed genes were significantly associated with 419 GO terms and 51 KEGG pathways, which suggested their participation in biological processes such as response to stress, immunoreaction, and fat metabolism. This study’s results provide a comprehensive overview of sheep heat stress-induced transcriptional expression patterns, laying a foundation for further analysis of the molecular mechanisms of sheep heat stress.

KEGG

RNA-Seq

Fold change

Biological pathway

10.3390/ani9060387

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Citations (31)

Protective effect of 5-heptadecylresorcinol against obesity-associated skeletal muscle dysfunction by modulating mitochondrial biogenesis via the activation of SIRT3/PGC-1α signaling pathway

Journal of Functional Foods (2022)

Ziyuan Wang Qing Li Yiming Hao Zongwei Wang Haihong Yang

Obesity-associated skeletal muscle mitochondrial dysfunction contributed to exercise capacity decline. 5-heptadecylresorcinol (AR-C17) has been proven effective against obesity and insulin resistance. However, its effects on skeletal muscle performance remains unclear. In this study, we investigate whether AR-C17 could protect against high-fat diet induced C57 BL/6J mice skeletal muscle dysfunction. The results indicated that AR-C17 intervention significantly improved skeletal muscle exercise capacity according to the strength and endurance test. AR-C17 showed no effect on skeletal muscle myofiber type conversion and myogenesis, but could significantly enhance PGC-1α mediated mitochondrial biogenesis. Moreover, AR-C17 significantly attenuated PA-induced reduction of mitochondrial DNA content in C2C12 cells and promoted mitochondrial biogenesis regulator gene PGC-1α and its downstream signaling pathway protein expression. In addition, AR-C17 increased the protein levels of SIRT3, while the protective effect was abolished by SIRT3 inhibitor (3-TYP), indicating AR-C17 ameliorated obesity induced skeletal muscle dysfunction might through SIRT3/PGC-1α signaling pathway.

SIRT3

C2C12

10.1016/j.jff.2022.105178

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Expression of a Conserved Mouse Stress-Modulating Gene,Bre: Comparison with the Human Ortholog

DNA and Cell Biology (2003)

Arthur Kar Keung Ching Qing Li Pak Leong Lim John Y.H. Chan Yiu‐Loon Chui

Mouse Bre, an evolutionarily conserved stress-modulating gene, like its human counterpart, is expressed in multiple alternative transcripts. The main transcript, which is ubiquitously expressed, encodes a protein that binds tumor necrosis factor receptor 1 (TNF-R1) and downregulates TNF-induced activation of NF-κB. Alternative splicing of mouse Bre occurs only at the 5′ region of the gene, generating either nonfunctional transcripts or transcripts that can encode putative protein isoforms differ at the N-terminal sequence. In contrast, alternative splicing of human BRE occurs at either or both ends of the gene; only the 3′ alternative splicing can generate functional transcripts that encode putative protein isoforms differ at the C-terminus, occurrence of the 5′ alternative splicing only results in forming nonfunctional transcripts. Unlike the human BRE alternative transcripts which are coexpressed at considerable levels with the main transcript, the mouse counterparts are expressed in a restricted pattern and generally in low abundance except in the heart. Both species, however, share a type of Bre alternative transcripts generated by cryptic splicing at a nonstandard, noncanonical acceptor site. Thus, a highly conserved gene in two species can generate alternative transcripts different in both of the sequence structure and expression pattern, as well as a similar class of transcripts resulting from unconventional transcript processing.

Conserved sequence

Primary transcript

10.1089/10445490360708900

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Effects of Nutritionally Induced Obesity on Metabolic Pathways of Zebrafish

International Journal of Molecular Sciences (2023)

Xixi Li Guodong Ge Guili Song Qing Li Zongbin Cui

Human obesity has become a global epidemic that can lead to many metabolic diseases, including insulin resistance, type 2 diabetes, dyslipidemia, hypertension and nonalcoholic fatty liver. The development of obesity is closely associated with excess food intake and energy imbalance, family history, lifestyle, psychology and other factors, but molecular mechanisms underlying the induction and development of obesity remain to be intensively studied under a variety of internal and external pathogenesis conditions. In this study, we generated two obesity models of zebrafish that were treated with a high-fat diet (HFD) or an overfeeding diet (DIO). Both HFD and DIO zebrafish exhibited higher levels of lipid accumulation, fat distribution, microvascular steatosis and ectopic accumulation of lipid droplets in liver and muscle than normal diet (NOD) fish. The comparison of transcriptome sequencing data for the livers of HFD, DIO and NOD groups identified common and specific genes and signaling pathways that are potentially associated with zebrafish obesity induced by HFD and/or DIO. These findings provide clues for further understanding the mechanisms of obesity development and preventing nutritionally induced obesity through targeting the common signaling pathways and biological processes.

Steatosis

Dyslipidemia

10.3390/ijms24031850

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Citations (9)

Verification and Analysis of Sheep Tail Type-Associated PDGF-D Gene Polymorphisms

Animals (2020)

Qing Li Zengkui Lu Meilin Jin Xiaojuan Fei Kai Quan

The aim of this study was to examine the correlation between the platelet-derived growth factor-D (PDGF-D) gene and sheep tail type character and explore the potential underlying mechanism. A total of 533 sheep were included in this study. Polymorphic sites were examined by Pool-seq, and individual genotype identification and correlation analysis between tail type data were conducted using the matrix-assisted laser desorption/ionization time-of-flight mass spectrometer (MALDI-TOF-MS) method. JASPART website was used to predict transcription factor binding sites in the promoter region with and without PDGF-D gene mutation. The effect of PDGF-D on adipogenic differentiation of sheep preadipocytes was investigated. Two single nucleotide polymorphism sites were identified: g.4122606 C > G site was significantly correlated with tail length, and g.3852134 C > T site was significantly correlated with tail width. g.3852134 C > T was located in the promoter region. Six transcription factor binding sites were eliminated after promoter mutation, and three new transcription factor binding sites appeared. Expression levels of peroxisome proliferator-activated receptor gamma (PPARγ) and lipoproteinlipase (LPL) were significantly up-regulated upon PDGF-D overexpression. Oil red O staining showed increased small and large oil drops in the PDGF-D overexpression group. Together these results indicate the PDGF-D gene is an important gene controlling sheep tail shape and regulating sheep tail fat deposition to a certain degree.

10.3390/ani10010089

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Citations (22)

N6-methyladenosine modification modulate in the heat stress of sheep (Ovis aries)

Research Square (Research Square) (2019)

Zengkui Lu Huihua Wang Youji Ma Mingxing Chu Kai Quan

Abstract Background: Intensive and large-scale development of the sheep industry and increases in global temperature are increasingly exposing sheep to heat stress. N6-methyladenosine (m6A) mRNA methylation varies in response to stress, and can link external stress with complex transcriptional and post-transcriptional processes. However, no m6A mRNA methylation map has been obtained for sheep, nor is it known what effect this has on regulating heat stress in sheep. Results: A total of 8,306 and 12,958 m6A peaks were detected in heat stress and control groups, respectively, with 2,697 and 5,494 genes associated with each. Peaks were mainly enriched in coding regions and near stop codons with classical RRACH motifs. Methylation levels of heat stress and control sheep were higher near stop codons, although methylation was significantly lower in heat stress sheep. GO revealed that differential m6A-containing genes were mainly enriched in the nucleus and were involved in several stress responses and substance metabolism processes. KEGG pathway analysis found that differential m6A-containing genes were significantly enriched in Rap1, FoxO, MAPK, and other signaling pathways of the stress response, and TGF-beta, AMPK, Wnt, and other signaling pathways involved in fat metabolism. These m6A-modified genes were moderately expressed in both heat stress and control sheep, and the enrichment of m6A modification was significantly negatively correlated with gene expression. Conclusions: Our results showed that m6A mRNA methylation modifications regulate heat stress in sheep, and it also provided a new way for the study of animal response to heat stress.

10.21203/rs.2.9885/v1

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Citations (2)

Genome-Wide Integrated Analysis Revealed Functions of lncRNA–miRNA–mRNA Interaction in Growth of Intermuscular Bones in Megalobrama amblycephala

Frontiers in Cell and Developmental Biology (2021)

Yulong Chen Shi‐Ming Wan Qing Li Xiaoru Dong Jinghan Diao

Intermuscular bone (IB) occurs in the myosepta of teleosts. Its existence has an adverse influence on the edible and economic value of fish, especially for aquaculture species belonging to Cypriniformes. The growth mechanism of IBs is quite lacking. In this study, we firstly used single molecular real-time sequencing (SMRT) technology to improve the draft genome annotation and full characterization of the transcriptome for one typical aquaculture species, blunt snout bream ( Megalobrama amblycephala ). The long non-coding RNA (lncRNA), microRNA (miRNA), and messenger RNA (mRNA) expression profiles in two IB growth stages (1 and 3 years old) were compared through transcriptome and degradome analyses. A total of 126 miRNAs, 403 mRNAs, and 353 lncRNAs were found to be differentially expressed between the two stages. Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis revealed that the significantly upregulated map2k6 and cytc in the MAPK/p53 signaling pathway and the significantly downregulated lama3 and thbs4b in the extracellular matrix (ECM)–receptor pathway may play a key regulatory role in IB growth. Bioinformatics analysis subsequently revealed 14 competing endogenous RNA (ceRNA) pairs related to the growth of IBs, consisting of 10 lncRNAs, 7 miRNAs, and 10 mRNAs. Of these, dre-miR-24b-3p and dre-miR-193b-3p are core regulatory factors interacting with four lncRNAs and three mRNAs, the interaction mechanism of which was also revealed by subsequent experiments at the cellular level. In conclusion, our data showed that IBs had higher activity of cell apoptosis and lower mineralization activity in IB_III compared to IB_I via interaction of MAPK/p53 and ECM–receptor signaling pathways. The downregulated zip1 interacted with miR-24a-3p and lnc017705, decreased osteoblast differentiation and Ca 2+ deposition in the IB_III stage. Our identified functional mRNAs, lncRNAs, and miRNAs provide a data basis for in-depth elucidation of the growth mechanism of teleost IB.

Megalobrama

10.3389/fcell.2020.603815

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Citations (20)