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Tian Y, Lautrup S, Law PWN, Dinh ND, Fang EF, Chan WY. WRN loss accelerates abnormal adipocyte metabolism in Werner syndrome. Cell Biosci 2024; 14:7. [PMID: 38184705 PMCID: PMC10770995 DOI: 10.1186/s13578-023-01183-4] [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: 01/23/2023] [Accepted: 12/09/2023] [Indexed: 01/08/2024] Open
Abstract
BACKGROUND Metabolic dysfunction is one of the main symptoms of Werner syndrome (WS); however, the underlying mechanisms remain unclear. Here, we report that loss of WRN accelerates adipogenesis at an early stage both in vitro (stem cells) and in vivo (zebrafish). Moreover, WRN depletion causes a transient upregulation of late-stage of adipocyte-specific genes at an early stage. METHODS In an in vivo study, we generated wrn-/- mutant zebrafish and performed histological stain and Oil Red O staining to assess the fat metabolism. In an in vitro study, we used RNA-seq and ATAC-seq to profile the transcriptional features and chromatin accessibility in WRN depleted adipocytes. Moreover, we performed ChIP-seq to further study the regulatory mechanisms of metabolic dysfunction in WS. RESULTS Our findings show that mechanistically WRN deficiency causes SMARCA5 upregulation. SMARCA5 is crucial in chromatin remodeling and gene regulation. Additionally, rescuing WRN could normalize SMARCA5 expression and adipocyte differentiation. Moreover, we find that nicotinamide riboside (NR) supplementation restores adipocyte metabolism in both stem cells and zebrafish models. CONCLUSIONS Our findings unravel a new mechanism for the influence of WRN in the early stage of adipogenesis and provide a possible treatment for metabolic dysfunction in WS. These data provide promising insights into potential therapeutics for ageing and ageing-related diseases.
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Affiliation(s)
- Yuyao Tian
- Faculty of Medicine, School of Biomedical Sciences, The Chinese University of Hong Kong, Shatin, N.T., Hong Kong SAR
- Department of Biomedical Engineering, The Chinese University of Hong Kong, Shatin, N.T., Hong Kong SAR
| | - Sofie Lautrup
- Department of Clinical Molecular Biology, University of Oslo and Akershus University Hospital, 1478, Lørenskog, Norway
| | - Patrick Wai Nok Law
- Faculty of Medicine, School of Biomedical Sciences, The Chinese University of Hong Kong, Shatin, N.T., Hong Kong SAR
| | - Ngoc-Duy Dinh
- Department of Biomedical Engineering, The Chinese University of Hong Kong, Shatin, N.T., Hong Kong SAR
| | - Evandro Fei Fang
- Department of Clinical Molecular Biology, University of Oslo and Akershus University Hospital, 1478, Lørenskog, Norway
| | - Wai-Yee Chan
- Faculty of Medicine, School of Biomedical Sciences, The Chinese University of Hong Kong, Shatin, N.T., Hong Kong SAR.
- Hong Kong Branch CAS Center of Excellence for Animal Evolution and Genetics, The Chinese University of Hong Kong, Shatin, N.T., Hong Kong SAR.
- CUHK-SDU University Joint Laboratory on Reproductive Genetics, The Chinese University of Hong Kong, Shatin, N.T., Hong Kong SAR.
- MOE Key Laboratory of Regenerative Medicine (CUHK-Jinan University), The Chinese University of Hong Kong, Shatin, N.T., Hong Kong SAR.
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Li J, Chen Z, Bai Y, Wei Y, Guo D, Liu Z, Niu Y, Shi B, Zhang X, Cai Y, Zhao Z, Hu J, Wang J, Liu X, Li S, Zhao F. Integration of ATAC-Seq and RNA-Seq Analysis to Identify Key Genes in the Longissimus Dorsi Muscle Development of the Tianzhu White Yak. Int J Mol Sci 2023; 25:158. [PMID: 38203329 PMCID: PMC10779322 DOI: 10.3390/ijms25010158] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2023] [Revised: 12/18/2023] [Accepted: 12/20/2023] [Indexed: 01/12/2024] Open
Abstract
During the postnatal stages, skeletal muscle development undergoes a series of meticulously regulated alterations in gene expression. However, limited studies have employed chromatin accessibility to unravel the underlying molecular mechanisms governing muscle development in yak species. Therefore, we conducted an analysis of both gene expression levels and chromatin accessibility to comprehensively characterize the dynamic genome-wide chromatin accessibility during muscle growth and development in the Tianzhu white yak, thereby elucidating the features of accessible chromatin regions throughout this process. Initially, we compared the differences in chromatin accessibility between two groups and observed that calves exhibited higher levels of chromatin accessibility compared to adult cattle, particularly within ±2 kb of the transcription start site (TSS). In order to investigate the correlation between alterations in chromatin accessible regions and variations in gene expression levels, we employed a combination of ATAC-seq and RNA-seq techniques, leading to the identification of 18 central transcriptional factors (TFs) and 110 key genes with significant effects. Through further analysis, we successfully identified several TFs, including Sp1, YY1, MyoG, MEF2A and MEF2C, as well as a number of candidate genes (ANKRD2, ANKRD1, BTG2 and LMOD3) which may be closely associated with muscle growth and development. Moreover, we constructed an interactive network program encompassing hub TFs and key genes related to muscle growth and development. This innovative approach provided valuable insights into the molecular mechanism underlying skeletal muscle development in the postnatal stages of Tianzhu white yaks while also establishing a solid theoretical foundation for future research on yak muscle development.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | - Zhidong Zhao
- Gansu Key Laboratory of Herbivorous Animal Biotechnology, College of Animal Science and Technology, Gansu Agricultural University, Lanzhou 730070, China
| | - Jiang Hu
- Gansu Key Laboratory of Herbivorous Animal Biotechnology, College of Animal Science and Technology, Gansu Agricultural University, Lanzhou 730070, China
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Li Q, Wang X, Xu S, Chen B, Wu T, Liu J, Zhao G, Wu L. Remodeling of Chromatin Accessibility Regulates the Radiological Responses of NSCLC A549 Cells to High-LET Carbon Ions. Radiat Res 2023; 200:474-488. [PMID: 37815204 DOI: 10.1667/rade-23-00097.1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2023] [Accepted: 09/19/2023] [Indexed: 10/11/2023]
Abstract
Carbon-ion radiation therapy (CIRT) may offer remarkable advantages in cancer treatment with its unique physical and biological characteristics. However, the underlying epigenetic regulatory mechanisms of cancer response to CIRT remain to be identified. In this study, we showed consistent but different degrees of biological effects induced in NSCLC A549 cells by carbon ions of different LET. The genome-wide chromatin accessibility and transcriptional profiles of carbon ion-treated A549 cells were performed using transposase-accessible chromatin sequencing (ATAC-seq) and RNA-seq, respectively, and further gene regulatory network analysis was performed by integrating the two sets of genomic data. Alterations in chromatin accessibility by carbon ions of different LET predominantly occurred in intron, distal intergenic and promoter regions of differential chromatin accessibility regions. The transcriptional changes were mainly regulated by proximal chromatin accessibility. Notably, CCCTC-binding factor (CTCF) was identified as a key transcription factor in the cellular response to carbon ions. The target genes regulated by CTCF in response to carbon ions were found to be closely associated with the LET of carbon ions, particularly in the regulation of gene transcription within the DNA replication- and metabolism-related signaling pathways. This study provides a regulatory profile of genes involved in key signaling pathways and highlighted key regulatory elements in NSCLC A549 cells during CIRT, which expands our understanding of the epigenetic mechanisms of carbon ion-induced biological effects and reveals an important role for LET in the regulation of changes in chromatin accessibility, although further research is needed.
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Affiliation(s)
- Qian Li
- School of Environmental Science and Optoelectronic Technology, University of Science and Technology of China, Hefei, Anhui, 230026, PR China
| | - Xiaofei Wang
- School of Biology, Food and Environment, Hefei University, Hefei 230601, P. R. China
| | - Shengmin Xu
- Information Materials and Intelligent Sensing Laboratory of Anhui Province, Institutes of Physical Science and Information Technology, Anhui University, Hefei, Anhui, 230601, PR China
| | - Biao Chen
- Information Materials and Intelligent Sensing Laboratory of Anhui Province, Institutes of Physical Science and Information Technology, Anhui University, Hefei, Anhui, 230601, PR China
| | - Tao Wu
- School of Environmental Science and Optoelectronic Technology, University of Science and Technology of China, Hefei, Anhui, 230026, PR China
| | - Jie Liu
- Information Materials and Intelligent Sensing Laboratory of Anhui Province, Institutes of Physical Science and Information Technology, Anhui University, Hefei, Anhui, 230601, PR China
| | - Guoping Zhao
- School of Environmental Science and Optoelectronic Technology, University of Science and Technology of China, Hefei, Anhui, 230026, PR China
| | - Lijun Wu
- School of Environmental Science and Optoelectronic Technology, University of Science and Technology of China, Hefei, Anhui, 230026, PR China
- Information Materials and Intelligent Sensing Laboratory of Anhui Province, Institutes of Physical Science and Information Technology, Anhui University, Hefei, Anhui, 230601, PR China
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Analysis of Chromatin Openness in Testicle Tissue of Yak and Cattle-Yak. Int J Mol Sci 2022; 23:ijms232415810. [PMID: 36555451 PMCID: PMC9785434 DOI: 10.3390/ijms232415810] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Revised: 12/07/2022] [Accepted: 12/09/2022] [Indexed: 12/15/2022] Open
Abstract
Cattle-yak, a crossbreed of yak and cattle, which can exhibit obvious heterosis and can adapt to the harsh environmental conditions of the Qinghai Tibet Plateau (QTP). However, F1 cattle-yak were found to be sterile because they were unable to produce sperm, which adversely restricted the fixation of heterosis. Many prior attempts have been made to decipher the mechanism underlying the spermatogenesis stagnation of cattle-yak. However, the open chromatin region (OCR) map of yak and cattle-yak testes has not been generated yet. Here, we have analyzed the OCRs landscape of testicular tissues of cattle-yak and yaks by performing ATAC-seq technology. The OCRs of cattle-yak and yak testes displayed similar genome distribution and showed priority in intergenic regions, introns and promoters. The pathway enrichment analysis indicated that the differential OCRs-related genes were involved in spermatogenesis, involving the cell cycle, as well as Hippo, mTOR, MAPK, Notch, and Wnt signaling pathways. The integration of ATAC-seq and mRNA-seq indicated that the majority of the gene expression levels were positively correlated with chromatin openness. At the same time, we have identified a number of transcription factors (TFs) related to spermatogenesis and the differential expression of these TFs may contribute to the spermatogenesis stagnation of the cattle-yak. Overall, the findings of this study provide valuable information for advancing the research related to yak crossbreeding improvement and sperm production stagnation of cattle-yak.
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