1
|
Guo G, Wang W, Tu M, Zhao B, Han J, Li J, Pan Y, Zhou J, Ma W, Liu Y, Sun T, Han X, An Y. Deciphering adipose development: Function, differentiation and regulation. Dev Dyn 2024. [PMID: 38516819 DOI: 10.1002/dvdy.708] [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: 11/07/2023] [Revised: 03/02/2024] [Accepted: 03/10/2024] [Indexed: 03/23/2024] Open
Abstract
The overdevelopment of adipose tissues, accompanied by excess lipid accumulation and energy storage, leads to adipose deposition and obesity. With the increasing incidence of obesity in recent years, obesity is becoming a major risk factor for human health, causing various relevant diseases (including hypertension, diabetes, osteoarthritis and cancers). Therefore, it is of significance to antagonize obesity to reduce the risk of obesity-related diseases. Excess lipid accumulation in adipose tissues is mediated by adipocyte hypertrophy (expansion of pre-existing adipocytes) or hyperplasia (increase of newly-formed adipocytes). It is necessary to prevent excessive accumulation of adipose tissues by controlling adipose development. Adipogenesis is exquisitely regulated by many factors in vivo and in vitro, including hormones, cytokines, gender and dietary components. The present review has concluded a comprehensive understanding of adipose development including its origin, classification, distribution, function, differentiation and molecular mechanisms underlying adipogenesis, which may provide potential therapeutic strategies for harnessing obesity without impairing adipose tissue function.
Collapse
Affiliation(s)
- Ge Guo
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Henan University, Kaifeng, China
- Henan Provincial Engineering Center for Tumor Molecular Medicine, Kaifeng Key Laboratory of Cell Signal Transduction, Henan University, Kaifeng, China
| | - Wanli Wang
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Henan University, Kaifeng, China
- Henan Provincial Engineering Center for Tumor Molecular Medicine, Kaifeng Key Laboratory of Cell Signal Transduction, Henan University, Kaifeng, China
| | - Mengjie Tu
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Henan University, Kaifeng, China
- Henan Provincial Engineering Center for Tumor Molecular Medicine, Kaifeng Key Laboratory of Cell Signal Transduction, Henan University, Kaifeng, China
| | - Binbin Zhao
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Henan University, Kaifeng, China
- Henan Provincial Engineering Center for Tumor Molecular Medicine, Kaifeng Key Laboratory of Cell Signal Transduction, Henan University, Kaifeng, China
| | - Jiayang Han
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Henan University, Kaifeng, China
- Henan Provincial Engineering Center for Tumor Molecular Medicine, Kaifeng Key Laboratory of Cell Signal Transduction, Henan University, Kaifeng, China
| | - Jiali Li
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Henan University, Kaifeng, China
- Henan Provincial Engineering Center for Tumor Molecular Medicine, Kaifeng Key Laboratory of Cell Signal Transduction, Henan University, Kaifeng, China
| | - Yanbing Pan
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Henan University, Kaifeng, China
- Henan Provincial Engineering Center for Tumor Molecular Medicine, Kaifeng Key Laboratory of Cell Signal Transduction, Henan University, Kaifeng, China
| | - Jie Zhou
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Henan University, Kaifeng, China
- Henan Provincial Engineering Center for Tumor Molecular Medicine, Kaifeng Key Laboratory of Cell Signal Transduction, Henan University, Kaifeng, China
| | - Wen Ma
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Henan University, Kaifeng, China
- Henan Provincial Engineering Center for Tumor Molecular Medicine, Kaifeng Key Laboratory of Cell Signal Transduction, Henan University, Kaifeng, China
| | - Yi Liu
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Henan University, Kaifeng, China
- Henan Provincial Engineering Center for Tumor Molecular Medicine, Kaifeng Key Laboratory of Cell Signal Transduction, Henan University, Kaifeng, China
| | - Tiantian Sun
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Henan University, Kaifeng, China
- Henan Provincial Engineering Center for Tumor Molecular Medicine, Kaifeng Key Laboratory of Cell Signal Transduction, Henan University, Kaifeng, China
| | - Xu Han
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Henan University, Kaifeng, China
- Henan Provincial Engineering Center for Tumor Molecular Medicine, Kaifeng Key Laboratory of Cell Signal Transduction, Henan University, Kaifeng, China
| | - Yang An
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Henan University, Kaifeng, China
- Henan Provincial Engineering Center for Tumor Molecular Medicine, Kaifeng Key Laboratory of Cell Signal Transduction, Henan University, Kaifeng, China
| |
Collapse
|
2
|
Meng M, Cao Y, Qiu J, Shan G, Wang Y, Zheng Y, Guo M, Yu J, Ma Y, Xie C, Hu C, Xu L, Mueller E, Ma X. Zinc finger protein ZNF638 regulates triglyceride metabolism via ANGPTL8 in an estrogen dependent manner. Metabolism 2024; 152:155784. [PMID: 38211696 DOI: 10.1016/j.metabol.2024.155784] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/21/2023] [Revised: 12/12/2023] [Accepted: 01/03/2024] [Indexed: 01/13/2024]
Abstract
BACKGROUND AND AIM Triglyceride (TG) levels are closely related to obesity, fatty liver and cardiovascular diseases, while the regulatory factors and mechanism for triglyceride homeostasis are still largely unknown. Zinc Finger Protein 638 (ZNF638) is a newly discovered member of zinc finger protein family for adipocyte function in vitro. The aim of the present work was to investigate the role of ZNF638 in regulating triglyceride metabolism in mice. METHODS We generated ZNF638 adipose tissue specific knockout mice (ZNF638 FKO) by cross-breeding ZNF638 flox to Adiponectin-Cre mice and achieved adipose tissue ZNF638 overexpression via adenoviral mediated ZNF638 delivery in inguinal adipose tissue (iWAT) to examined the role and mechanisms of ZNF638 in fat biology and whole-body TG homeostasis. RESULTS Although ZNF638 FKO mice showed similar body weights, body composition, glucose metabolism and serum parameters compared to wild-type mice under chow diet, serum TG levels in ZNF638 FKO mice were increased dramatically after refeeding compared to wild-type mice, accompanied with decreased endothelial lipoprotein lipase (LPL) activity and increased lipid absorption of the small intestine. Conversely, ZNF638 overexpression in iWAT reduced serum TG levels while enhanced LPL activity after refeeding in female C57BL/6J mice and obese ob/ob mice. Specifically, only female mice exhibited altered TG metabolism upon ZNF638 expression changes in fat. Mechanistically, RNA-sequencing analysis revealed that the TG regulator angiopoietin-like protein 8 (Angptl8) was highly expressed in iWAT of female ZNF638 FKO mice. Neutralizing circulating ANGPTL8 in female ZNF638 FKO mice abolished refeeding-induced TG elevation. Furthermore, we demonstrated that ZNF638 functions as a transcriptional repressor by recruiting HDAC1 for histone deacetylation and broad lipid metabolic gene suppression, including Angptl8 transcription inhibition. Moreover, we showed that the sexual dimorphism is possibly due to estrogen dependent regulation on ZNF638-ANGPTL8 axis. CONCLUSION We revealed a role of ZNF638 in the regulation of triglyceride metabolism by affecting Angptl8 transcriptional level in adipose tissue with sexual dimorphism.
Collapse
Affiliation(s)
- Meiyao Meng
- Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences, School of Life Sciences, East China Normal University, Shanghai 200241, China; Chongqing Key Laboratory of Precision Optics, Chongqing Institute of East China Normal University, Chongqing 401120, China
| | - Yuxiang Cao
- Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences, School of Life Sciences, East China Normal University, Shanghai 200241, China
| | - Jin Qiu
- Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences, School of Life Sciences, East China Normal University, Shanghai 200241, China
| | - Guangyu Shan
- Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences, School of Life Sciences, East China Normal University, Shanghai 200241, China
| | - Yingwen Wang
- Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences, School of Life Sciences, East China Normal University, Shanghai 200241, China
| | - Ying Zheng
- Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences, School of Life Sciences, East China Normal University, Shanghai 200241, China
| | - Mingwei Guo
- Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences, School of Life Sciences, East China Normal University, Shanghai 200241, China
| | - Jian Yu
- Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences, School of Life Sciences, East China Normal University, Shanghai 200241, China; Department of Endocrinology and Metabolism, Fengxian Central Hospital Affiliated to Southern Medical University, Shanghai 201499, China
| | - Yuandi Ma
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Cen Xie
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Cheng Hu
- Department of Endocrinology and Metabolism, Fengxian Central Hospital Affiliated to Southern Medical University, Shanghai 201499, China; Shanghai Diabetes Institute, Shanghai Key Laboratory of Diabetes Mellitus, Shanghai Clinical Centre for Diabetes, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, Shanghai 200233, China
| | - Lingyan Xu
- Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences, School of Life Sciences, East China Normal University, Shanghai 200241, China; Chongqing Key Laboratory of Precision Optics, Chongqing Institute of East China Normal University, Chongqing 401120, China
| | - Elisabetta Mueller
- Division of Endocrinology, Diabetes and Metabolism Department of Medicine New York University, Grossman School of Medicine, New York, NY, USA
| | - Xinran Ma
- Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences, School of Life Sciences, East China Normal University, Shanghai 200241, China; Chongqing Key Laboratory of Precision Optics, Chongqing Institute of East China Normal University, Chongqing 401120, China; Department of Endocrinology and Metabolism, Fengxian Central Hospital Affiliated to Southern Medical University, Shanghai 201499, China.
| |
Collapse
|
3
|
Ye RZ, Montastier E, Frisch F, Noll C, Allard-Chamard H, Gévry N, Tchernof A, Carpentier AC. Adipocyte hypertrophy associates with in vivo postprandial fatty acid metabolism and adipose single-cell transcriptional dynamics. iScience 2024; 27:108692. [PMID: 38226167 PMCID: PMC10788217 DOI: 10.1016/j.isci.2023.108692] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Revised: 11/07/2023] [Accepted: 12/05/2023] [Indexed: 01/17/2024] Open
Abstract
Adipocyte hypertrophy is associated with metabolic complications independent of obesity. We aimed to determine: 1) the association between adipocyte size and postprandial fatty acid metabolism; 2) the potential mechanisms driving the obesity-independent, hypertrophy-associated dysmetabolism in vivo and at a single-cell resolution. Tracers with positron emission tomography were used to measure fatty acid metabolism in 40 men and women with normal or impaired glucose tolerance (NCT02808182), and single nuclei RNA-sequencing (snRNA-seq) to determine transcriptional dynamics of subcutaneous adipose tissue (AT) between individuals with AT hypertrophy vs. hyperplasia matched for sex, ethnicity, glucose-tolerance status, BMI, total and percent body fat, and waist circumference. Adipocyte size was associated with high postprandial total cardiac fatty acid uptake and higher visceral AT dietary fatty acid uptake, but lower lean tissue dietary fatty acid uptake. We found major shifts in cell transcriptomal dynamics with AT hypertrophy that were consistent with in vivo metabolic changes.
Collapse
Affiliation(s)
- Run Zhou Ye
- Division of Endocrinology, Department of Medicine, Centre de recherche du CHUS, Université de Sherbrooke, Sherbrooke, QC J1H 5N4, Canada
| | - Emilie Montastier
- Division of Endocrinology, Department of Medicine, Centre de recherche du CHUS, Université de Sherbrooke, Sherbrooke, QC J1H 5N4, Canada
| | - Frédérique Frisch
- Division of Endocrinology, Department of Medicine, Centre de recherche du CHUS, Université de Sherbrooke, Sherbrooke, QC J1H 5N4, Canada
| | - Christophe Noll
- Division of Endocrinology, Department of Medicine, Centre de recherche du CHUS, Université de Sherbrooke, Sherbrooke, QC J1H 5N4, Canada
| | - Hugues Allard-Chamard
- Division of Endocrinology, Department of Medicine, Centre de recherche du CHUS, Université de Sherbrooke, Sherbrooke, QC J1H 5N4, Canada
| | - Nicolas Gévry
- Department of Biology, Université de Sherbrooke, Sherbrooke, QC J1K 2R1, Canada
| | - André Tchernof
- Québec Heart and Lung Research Institute, Laval University, Québec, QC G1V 4G5, Canada
| | - André C. Carpentier
- Division of Endocrinology, Department of Medicine, Centre de recherche du CHUS, Université de Sherbrooke, Sherbrooke, QC J1H 5N4, Canada
- Department of Nuclear Medicine and Radiobiology, Centre de Recherche du CHUS, Université de Sherbrooke, Sherbrooke, QC J1H 5N4, Canada
| |
Collapse
|
4
|
King SB, Singh M. Primate protein-ligand interfaces exhibit significant conservation and unveil human-specific evolutionary drivers. PLoS Comput Biol 2023; 19:e1010966. [PMID: 36952575 PMCID: PMC10035887 DOI: 10.1371/journal.pcbi.1010966] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2022] [Accepted: 02/22/2023] [Indexed: 03/25/2023] Open
Abstract
Despite the vast phenotypic differences observed across primates, their protein products are largely similar to each other at the sequence level. We hypothesized that, since proteins accomplish all their functions via interactions with other molecules, alterations in the sites that participate in these interactions may be of critical importance. To uncover the extent to which these sites evolve across primates, we built a structurally-derived dataset of ~4,200 one-to-one orthologous sequence groups across 18 primate species, consisting of ~68,000 ligand-binding sites that interact with DNA, RNA, small molecules, ions, or peptides. Using this dataset, we identify functionally important patterns of conservation and variation within the amino acid residues that facilitate protein-ligand interactions across the primate phylogeny. We uncover that interaction sites are significantly more conserved than other sites, and that sites binding DNA and RNA further exhibit the lowest levels of variation. We also show that the subset of ligand-binding sites that do vary are enriched in components of gene regulatory pathways and uncover several instances of human-specific ligand-binding site changes within transcription factors. Altogether, our results suggest that ligand-binding sites have experienced selective pressure in primates and propose that variation in these sites may have an outsized effect on phenotypic variation in primates through pleiotropic effects on gene regulation.
Collapse
Affiliation(s)
- Sean B King
- Department of Molecular Biology, Princeton University, Princeton, New Jersey, United States of America
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, New Jersey, United States of America
| | - Mona Singh
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, New Jersey, United States of America
- Department of Computer Science, Princeton University, Princeton, New Jersey, United States of America
| |
Collapse
|
5
|
Arfelli VC, Chang YC, Bagnoli JW, Kerbs P, Ciamponi FE, Paz LMDS, Pankivskyi S, de Matha Salone J, Maucuer A, Massirer KB, Enard W, Kuster B, Greif PA, Archangelo LF. UHMK1 is a novel splicing regulatory kinase. J Biol Chem 2023; 299:103041. [PMID: 36803961 PMCID: PMC10033318 DOI: 10.1016/j.jbc.2023.103041] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Revised: 01/18/2023] [Accepted: 02/04/2023] [Indexed: 02/19/2023] Open
Abstract
The U2AF Homology Motif Kinase 1 (UHMK1) is the only kinase that contains the U2AF homology motif, a common protein interaction domain among splicing factors. Through this motif, UHMK1 interacts with the splicing factors SF1 and SF3B1, known to participate in the 3' splice site recognition during the early steps of spliceosome assembly. Although UHMK1 phosphorylates these splicing factors in vitro, the involvement of UHMK1 in RNA processing has not previously been demonstrated. Here, we identify novel putative substrates of this kinase and evaluate UHMK1 contribution to overall gene expression and splicing, by integrating global phosphoproteomics, RNA-seq, and bioinformatics approaches. Upon UHMK1 modulation, 163 unique phosphosites were differentially phosphorylated in 117 proteins, of which 106 are novel potential substrates of this kinase. Gene Ontology analysis showed enrichment of terms previously associated with UHMK1 function, such as mRNA splicing, cell cycle, cell division, and microtubule organization. The majority of the annotated RNA-related proteins are components of the spliceosome but are also involved in several steps of gene expression. Comprehensive analysis of splicing showed that UHMK1 affected over 270 alternative splicing events. Moreover, splicing reporter assay further supported UHMK1 function on splicing. Overall, RNA-seq data demonstrated that UHMK1 knockdown had a minor impact on transcript expression and pointed to UHMK1 function in epithelial-mesenchymal transition. Functional assays demonstrated that UHMK1 modulation affects proliferation, colony formation, and migration. Taken together, our data implicate UHMK1 as a splicing regulatory kinase, connecting protein regulation through phosphorylation and gene expression in key cellular processes.
Collapse
Affiliation(s)
- Vanessa C Arfelli
- Department of Cellular and Molecular Biology and Pathogenic Bioagents, Ribeirão Preto Medical School, University of São Paulo (FMRP-USP), Ribeirão Preto, São Paulo, Brazil
| | - Yun-Chien Chang
- Proteomics and Bioanalytics, School of Life Sciences Weihenstephan, Technical University of Munich (TUM), Freising, Germany
| | - Johannes W Bagnoli
- Anthropology & Human Genomics, Department of Biology II, Ludwig-Maximilians-University (LMU), Martinsried, Germany
| | - Paul Kerbs
- Laboratory for Experimental Leukemia and Lymphoma Research, Munich University Hospital, Ludwig-Maximilians University (LMU), Munich, Germany; German Cancer Consortium (DKTK), partner site Munich, Munich, Germany; German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Felipe E Ciamponi
- Center for Medicinal Chemistry (CQMED), Center for Molecular Biology and Genetic Engineering (CBMEG), University of Campinas (UNICAMP), Campinas, São Paulo, Brazil
| | - Laissa M da S Paz
- Department of Cellular and Molecular Biology and Pathogenic Bioagents, Ribeirão Preto Medical School, University of São Paulo (FMRP-USP), Ribeirão Preto, São Paulo, Brazil
| | - Serhii Pankivskyi
- SABNP, Univ Evry, INSERM U1204, Université Paris-Saclay, Evry, France
| | | | - Alexandre Maucuer
- SABNP, Univ Evry, INSERM U1204, Université Paris-Saclay, Evry, France
| | - Katlin B Massirer
- Center for Medicinal Chemistry (CQMED), Center for Molecular Biology and Genetic Engineering (CBMEG), University of Campinas (UNICAMP), Campinas, São Paulo, Brazil
| | - Wolfgang Enard
- Anthropology & Human Genomics, Department of Biology II, Ludwig-Maximilians-University (LMU), Martinsried, Germany
| | - Bernhard Kuster
- Proteomics and Bioanalytics, School of Life Sciences Weihenstephan, Technical University of Munich (TUM), Freising, Germany
| | - Philipp A Greif
- Laboratory for Experimental Leukemia and Lymphoma Research, Munich University Hospital, Ludwig-Maximilians University (LMU), Munich, Germany; German Cancer Consortium (DKTK), partner site Munich, Munich, Germany; German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Leticia Fröhlich Archangelo
- Department of Cellular and Molecular Biology and Pathogenic Bioagents, Ribeirão Preto Medical School, University of São Paulo (FMRP-USP), Ribeirão Preto, São Paulo, Brazil.
| |
Collapse
|
6
|
Tutanov O, Shtam T, Grigor’eva A, Tupikin A, Tsentalovich Y, Tamkovich S. Blood Plasma Exosomes Contain Circulating DNA in Their Crown. Diagnostics (Basel) 2022; 12:diagnostics12040854. [PMID: 35453902 PMCID: PMC9027845 DOI: 10.3390/diagnostics12040854] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Revised: 03/21/2022] [Accepted: 03/28/2022] [Indexed: 01/13/2023] Open
Abstract
It is known that circulating DNA (cirDNA) is protected from nuclease activity by proteins that form macromolecular complexes with DNA. In addition, it was previously shown that cirDNA can bind to the outer surface of exosomes. NTA analysis and real-time PCR show that exosomes from healthy females (HF) or breast cancer patients (BCP) plasma contain less than 1.4 × 10−8 pg of DNA. Thus, only a minor part of cirDNA is attached to the outer side of the exosome as part of the vesicle crown: the share of exosomal DNA does not exceed 0.025% HF plasma DNA and 0.004% BCP plasma DNA. Treatment of plasma exosomes with DNase I with subsequent dot immunoassay reveals that H2a, H2b, and H3 histones are not part of the exosomal membrane, but are part of the cirDNA–protein macromolecular complex associated with the surface of the exosome either through interaction with DNA-binding proteins or with histone-binding proteins. Using bioinformatics approaches after identification by MALDI-TOF mass spectrometry, 16 exosomal DNA-binding proteins were identified. It was shown that four proteins—AIFM1, IGHM, CHD5, and KCNIP3—are candidates for DNA binding on the outer membrane of exosomes; the crown of exosomes may include five DNA-binding proteins: H2a, H2b, H3, IGHM, and ALB. Of note, AIFM1, IGHM, and CHD5 proteins are found only in HF plasma exosomes; KCNIP3 protein is identified only in BCP plasma exosomes; and H2a, H2b, H3, and ALB are revealed in all samples of plasma exosomes. Two histone-binding proteins, CHD5 and KDM6B, have been found in exosomes from HF plasma. The data obtained indicate that cirDNA preferentially binds to the outer membrane of exosomes by association with DNA-binding proteins.
Collapse
Affiliation(s)
- Oleg Tutanov
- V. Zelman Institute for Medicine and Psychology, Novosibirsk State University, 630090 Novosibirsk, Russia;
| | - Tatiana Shtam
- Petersburg Nuclear Physics Institute Named by B.P. Konstantinov of National Research Center “Kurchatov Institute”, 188300 Gatchina, Russia;
| | - Alina Grigor’eva
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of Russian Academy of Sciences, 630090 Novosibirsk, Russia; (A.G.); (A.T.)
| | - Alexey Tupikin
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of Russian Academy of Sciences, 630090 Novosibirsk, Russia; (A.G.); (A.T.)
| | - Yuri Tsentalovich
- International Tomography Center, Siberian Branch of Russian Academy of Sciences, 630090 Novosibirsk, Russia;
| | - Svetlana Tamkovich
- V. Zelman Institute for Medicine and Psychology, Novosibirsk State University, 630090 Novosibirsk, Russia;
- Correspondence:
| |
Collapse
|
7
|
Al-Sayegh M, Ali H, Jamal MH, ElGindi M, Chanyong T, Al-Awadi K, Abu-Farha M. Mouse Embryonic Fibroblast Adipogenic Potential: A Comprehensive Transcriptome Analysis. Adipocyte 2021; 10:1-20. [PMID: 33345692 PMCID: PMC7757854 DOI: 10.1080/21623945.2020.1859789] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Our understanding of adipose tissue has progressed from an inert tissue for energy storage to be one of the largest endocrine organs regulating metabolic homoeostasis through its ability to synthesize and release various adipokines that regulate a myriad of pathways. The field of adipose tissue biology is growing due to this association with various chronic metabolic diseases. An important process in the regulation of adipose tissue biology is adipogenesis, which is the formation of new adipocytes. Investigating adipogenesis in vitro is currently a focus for identifying factors that might be utilized in clinically. A powerful tool for such work is high-throughput sequencing which can rapidly identify changes at gene expression level. Various cell models exist for studying adipogenesis and has been used in high-throughput studies, yet little is known about transcriptome profile that underlies adipogenesis in mouse embryonic fibroblasts. This study utilizes RNA-sequencing and computational analysis with DESeq2, gene ontology, protein–protein networks, and robust rank analysis to understand adipogenesis in mouse embryonic fibroblasts in-depth. Our analyses confirmed the requirement of mitotic clonal expansion prior to adipogenesis in this cell model and highlight the role of Cebpa and Cebpb in regulating adipogenesis through interactions of large numbers of genes.
Collapse
Affiliation(s)
- Mohamed Al-Sayegh
- New York University Abu Dhabi, Division of Biology, Abu Dhabi, United Arab Emirates
| | - Hamad Ali
- Department of Medical Laboratory Sciences, Faculty of Allied Health Sciences, Health Sciences Center (HSC), Kuwait University, Kuwait City, State of Kuwait
- Department of Genetics and Bioinformatics, Dasman Diabetes Institute (DDI), Kuwait City, State of Kuwait
| | - Mohammad H Jamal
- Department of Surgery, Faculty of Medicine, Health Sciences Center (HSC), Kuwait University, Kuwait City, State of Kuwait
| | - Mei ElGindi
- New York University Abu Dhabi, Division of Biology, Abu Dhabi, United Arab Emirates
| | - Tina Chanyong
- New York University Abu Dhabi, Division of Biology, Abu Dhabi, United Arab Emirates
| | - Khulood Al-Awadi
- New York University Abu Dhabi, Design Studio, Abu Dhabi, United Arab Emirates
| | - Mohamed Abu-Farha
- Department of Biochemistry and Molecular Biology, Dasman Diabetes Institute (DDI), Kuwait City, State of Kuwait
| |
Collapse
|
8
|
Abstract
Since the discovery of manifest Zn deficiency in 1961, the increasing number of studies demonstrated the association between altered Zn status and multiple diseases. In this chapter, we provide a review of the most recent advances on the role of Zn in health and disease (2010-20), with a special focus on the role of Zn in neurodegenerative and neurodevelopmental disorders, diabetes and obesity, male and female reproduction, as well as COVID-19. In parallel with the revealed tight association between ASD risk and severity and Zn status, the particular mechanisms linking Zn2+ and ASD pathogenesis like modulation of synaptic plasticity through ProSAP/Shank scaffold, neurotransmitter metabolism, and gut microbiota, have been elucidated. The increasing body of data indicate the potential involvement of Zn2+ metabolism in neurodegeneration. Systemic Zn levels in Alzheimer's and Parkinson's disease were found to be reduced, whereas its sequestration in brain may result in modulation of amyloid β and α-synuclein processing with subsequent toxic effects. Zn2+ was shown to possess adipotropic effects through the role of zinc transporters, zinc finger proteins, and Zn-α2-glycoprotein in adipose tissue physiology, underlying its particular role in pathogenesis of obesity and diabetes mellitus type 2. Recent findings also contribute to further understanding of the role of Zn2+ in spermatogenesis and sperm functioning, as well as oocyte development and fertilization. Finally, Zn2+ was shown to be the potential adjuvant therapy in management of novel coronavirus infection (COVID-19), underlining the perspectives of zinc in management of old and new threats.
Collapse
Affiliation(s)
- Anatoly V Skalny
- IM Sechenov First Moscow State Medical University (Sechenov University), Moscow, Russia; Yaroslavl State University, Yaroslavl, Russia
| | - Michael Aschner
- IM Sechenov First Moscow State Medical University (Sechenov University), Moscow, Russia; Department of Molecular Pharmacology, Albert Einstein College of Medicine, Bronx, NY, United States
| | - Alexey A Tinkov
- IM Sechenov First Moscow State Medical University (Sechenov University), Moscow, Russia; Yaroslavl State University, Yaroslavl, Russia.
| |
Collapse
|
9
|
Chao Y, Jiang Y, Zhong M, Wei K, Hu C, Qin Y, Zuo Y, Yang L, Shen Z, Zou C. Regulatory roles and mechanisms of alternative RNA splicing in adipogenesis and human metabolic health. Cell Biosci 2021; 11:66. [PMID: 33795017 PMCID: PMC8017860 DOI: 10.1186/s13578-021-00581-w] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2021] [Accepted: 03/24/2021] [Indexed: 12/15/2022] Open
Abstract
Alternative splicing (AS) regulates gene expression patterns at the post-transcriptional level and generates a striking expansion of coding capacities of genomes and cellular protein diversity. RNA splicing could undergo modulation and close interaction with genetic and epigenetic machinery. Notably, during the adipogenesis processes of white, brown and beige adipocytes, AS tightly interplays with the differentiation gene program networks. Here, we integrate the available findings on specific splicing events and distinct functions of different splicing regulators as examples to highlight the directive biological contribution of AS mechanism in adipogenesis and adipocyte biology. Furthermore, accumulating evidence has suggested that mutations and/or altered expression in splicing regulators and aberrant splicing alterations in the obesity-associated genes are often linked to humans’ diet-induced obesity and metabolic dysregulation phenotypes. Therefore, significant attempts have been finally made to overview novel detailed discussion on the prospects of splicing machinery with obesity and metabolic disorders to supply featured potential management mechanisms in clinical applicability for obesity treatment strategies.
Collapse
Affiliation(s)
- Yunqi Chao
- Department of Endocrinology, The Children's Hospital, School of Medicine, Zhejiang University, Hangzhou, 310052, Zhejiang, China
| | - Yonghui Jiang
- Department of Genetics, Yale University School of Medicine, New Haven, CT, 06520, USA
| | - Mianling Zhong
- Department of Endocrinology, The Children's Hospital, School of Medicine, Zhejiang University, Hangzhou, 310052, Zhejiang, China
| | - Kaiyan Wei
- Department of Endocrinology, The Children's Hospital, School of Medicine, Zhejiang University, Hangzhou, 310052, Zhejiang, China
| | - Chenxi Hu
- Department of Endocrinology, The Children's Hospital, School of Medicine, Zhejiang University, Hangzhou, 310052, Zhejiang, China
| | - Yifang Qin
- Department of Endocrinology, The Children's Hospital, School of Medicine, Zhejiang University, Hangzhou, 310052, Zhejiang, China
| | - Yiming Zuo
- Department of Endocrinology, The Children's Hospital, School of Medicine, Zhejiang University, Hangzhou, 310052, Zhejiang, China
| | - Lili Yang
- Department of Endocrinology, The Children's Hospital, School of Medicine, Zhejiang University, Hangzhou, 310052, Zhejiang, China
| | - Zheng Shen
- Department of Endocrinology, The Children's Hospital, School of Medicine, Zhejiang University, Hangzhou, 310052, Zhejiang, China
| | - Chaochun Zou
- Department of Endocrinology, The Children's Hospital, School of Medicine, Zhejiang University, Hangzhou, 310052, Zhejiang, China.
| |
Collapse
|
10
|
Agirre E, Oldfield AJ, Bellora N, Segelle A, Luco RF. Splicing-associated chromatin signatures: a combinatorial and position-dependent role for histone marks in splicing definition. Nat Commun 2021; 12:682. [PMID: 33514745 PMCID: PMC7846797 DOI: 10.1038/s41467-021-20979-x] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2019] [Accepted: 01/05/2021] [Indexed: 12/14/2022] Open
Abstract
Alternative splicing relies on the combinatorial recruitment of splicing regulators to specific RNA binding sites. Chromatin has been shown to impact this recruitment. However, a limited number of histone marks have been studied at a global level. In this work, a machine learning approach, applied to extensive epigenomics datasets in human H1 embryonic stem cells and IMR90 foetal fibroblasts, has identified eleven chromatin modifications that differentially mark alternatively spliced exons depending on the level of exon inclusion. These marks act in a combinatorial and position-dependent way, creating characteristic splicing-associated chromatin signatures (SACS). In support of a functional role for SACS in coordinating splicing regulation, changes in the alternative splicing of SACS-marked exons between ten different cell lines correlate with changes in SACS enrichment levels and recruitment of the splicing regulators predicted by RNA motif search analysis. We propose the dynamic nature of chromatin modifications as a mechanism to rapidly fine-tune alternative splicing when necessary. Chromatin is known to regulate splicing by modulating recruitment of splicing factors. Using machine learning approaches, the authors have underlined a chromatin code for alternative splicing regulation that is conserved amongst cell lines.
Collapse
Affiliation(s)
- E Agirre
- Institute of Human Genetics, UMR9002 CNRS-University of Montpellier, 34000, Montpellier, France.,Laboratory of Molecular Neurobiology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - A J Oldfield
- Institute of Human Genetics, UMR9002 CNRS-University of Montpellier, 34000, Montpellier, France
| | - N Bellora
- Institute of Nuclear Technologies for Health (INTECNUS), National Scientific and Technical Research Council (CONICET), Bariloche, 8400, Argentina
| | - A Segelle
- Institute of Human Genetics, UMR9002 CNRS-University of Montpellier, 34000, Montpellier, France
| | - R F Luco
- Institute of Human Genetics, UMR9002 CNRS-University of Montpellier, 34000, Montpellier, France.
| |
Collapse
|
11
|
Song T, Yang Y, Jiang S, Peng J. Novel Insights into Adipogenesis from the Perspective of Transcriptional and RNA N6-Methyladenosine-Mediated Post-Transcriptional Regulation. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2020; 7:2001563. [PMID: 33173729 PMCID: PMC7610318 DOI: 10.1002/advs.202001563] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Indexed: 05/09/2023]
Abstract
Obesity is a critical risk factor causing the development of metabolic diseases and cancers. Its increasing prevalence worldwide has aroused great concerns of the researchers on adipose development and metabolic function. During adipose expansion, adipogenesis is a way to store lipids as well as to avoid lipotoxicity in other tissues, and may be an approach to offset the negative metabolic effects of obesity. In this Review, the transcriptional regulation of adipogenesis is outlined to characterize numerous biological processes in research on the determination of adipocyte fate and regulation of adipogenic differentiation. Notably, one of the post-transcriptional modifications of mRNA, namely, N6-methyladenosine (m6A), has been recently found to play a role in adipogenesis. Here, the roles of m6A-related enzymes and proteins in adipogenesis, with a particular focus on how these m6A-related proteins function at different stages of adipogenesis, are mainly discussed. The Review also highlights the coordination role of the transcriptional and post-transcriptional (RNA m6A methylation) regulation in adipogenesis and related biological processes. In this context, a better understanding of adipogenesis at both the transcriptional and post-transcriptional levels may facilitate the development of novel strategies to improve metabolic health in obesity.
Collapse
Affiliation(s)
- Tongxing Song
- Department of Animal Nutrition and Feed ScienceCollege of Animal Science and TechnologyHuazhong Agricultural UniversityWuhan430070China
- The Cooperative Innovation Center for Sustainable Pig ProductionWuhan430070China
| | - Yang Yang
- Department of Animal Nutrition and Feed ScienceCollege of Animal Science and TechnologyHuazhong Agricultural UniversityWuhan430070China
- The Cooperative Innovation Center for Sustainable Pig ProductionWuhan430070China
| | - Siwen Jiang
- The Cooperative Innovation Center for Sustainable Pig ProductionWuhan430070China
- Key Laboratory of Animal GeneticsBreeding and Reproduction Ministry of EducationCollege of Animal Science and TechnologyHuazhong Agricultural UniversityWuhan430070China
| | - Jian Peng
- Department of Animal Nutrition and Feed ScienceCollege of Animal Science and TechnologyHuazhong Agricultural UniversityWuhan430070China
- The Cooperative Innovation Center for Sustainable Pig ProductionWuhan430070China
| |
Collapse
|
12
|
Ambele MA, Dhanraj P, Giles R, Pepper MS. Adipogenesis: A Complex Interplay of Multiple Molecular Determinants and Pathways. Int J Mol Sci 2020; 21:ijms21124283. [PMID: 32560163 PMCID: PMC7349855 DOI: 10.3390/ijms21124283] [Citation(s) in RCA: 140] [Impact Index Per Article: 35.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2020] [Accepted: 06/07/2020] [Indexed: 11/24/2022] Open
Abstract
The formation of adipocytes during embryogenesis has been largely understudied. However, preadipocytes appear to originate from multipotent mesenchymal stromal/stem cells which migrate from the mesoderm to their anatomical localization. Most studies on adipocyte formation (adipogenesis) have used preadipocytes derived from adult stem/stromal cells. Adipogenesis consists of two phases, namely commitment and terminal differentiation. This review discusses the role of signalling pathways, epigenetic modifiers, and transcription factors in preadipocyte commitment and differentiation into mature adipocytes, as well as limitations in our understanding of these processes. To date, a limited number of transcription factors, genes and signalling pathways have been described to regulate preadipocyte commitment. One reason could be that most studies on adipogenesis have used preadipocytes already committed to the adipogenic lineage, which are therefore not suitable for studying preadipocyte commitment. Conversely, over a dozen molecular players including transcription factors, genes, signalling pathways, epigenetic regulators, and microRNAs have been described to be involved in the differentiation of preadipocytes to adipocytes; however, only peroxisome proliferator-activated receptor gamma has proven to be clinically relevant. A detailed understanding of how the molecular players underpinning adipogenesis relate to adipose tissue function could provide new therapeutic approaches for addressing obesity without compromising adipose tissue function.
Collapse
Affiliation(s)
- Melvin A. Ambele
- Department of Immunology, and SAMRC Extramural Unit for Stem Cell Research and Therapy, Institute for Cellular and Molecular Medicine, Faculty of Health Sciences, University of Pretoria, Pretoria 0001, South Africa; (M.A.A.); (P.D.); (R.G.)
- Department of Oral Pathology and Oral Biology, School of Dentistry, Faculty of Health Sciences, University of Pretoria, Pretoria 0001, South Africa
| | - Priyanka Dhanraj
- Department of Immunology, and SAMRC Extramural Unit for Stem Cell Research and Therapy, Institute for Cellular and Molecular Medicine, Faculty of Health Sciences, University of Pretoria, Pretoria 0001, South Africa; (M.A.A.); (P.D.); (R.G.)
| | - Rachel Giles
- Department of Immunology, and SAMRC Extramural Unit for Stem Cell Research and Therapy, Institute for Cellular and Molecular Medicine, Faculty of Health Sciences, University of Pretoria, Pretoria 0001, South Africa; (M.A.A.); (P.D.); (R.G.)
| | - Michael S. Pepper
- Department of Immunology, and SAMRC Extramural Unit for Stem Cell Research and Therapy, Institute for Cellular and Molecular Medicine, Faculty of Health Sciences, University of Pretoria, Pretoria 0001, South Africa; (M.A.A.); (P.D.); (R.G.)
- Correspondence:
| |
Collapse
|
13
|
Li G, Ma X, Xu L. The roles of zinc finger proteins in non-alcoholic fatty liver disease. LIVER RESEARCH 2020. [DOI: 10.1016/j.livres.2020.01.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
|
14
|
Li Y, McGrail DJ, Xu J, Mills GB, Sahni N, Yi S. Gene Regulatory Network Perturbation by Genetic and Epigenetic Variation. Trends Biochem Sci 2018; 43:576-592. [PMID: 29941230 DOI: 10.1016/j.tibs.2018.05.002] [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] [Received: 02/04/2018] [Revised: 04/25/2018] [Accepted: 05/27/2018] [Indexed: 01/28/2023]
Abstract
Gene regulatory networks underlie biological function and cellular physiology. Alternative splicing (AS) is a fundamental step in gene regulatory networks and plays a key role in development and disease. In addition to the identification of aberrant AS events, an increasing number of studies are focusing on molecular determinants of AS, including genetic and epigenetic regulators. We review here recent efforts to identify various deregulated AS events as well as their molecular determinants that alter biological functions, and discuss clinical features of AS and their druggable potential.
Collapse
Affiliation(s)
- Yongsheng Li
- Department of Systems Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; College of Bioinformatics Science and Technology and Bio-Pharmaceutical Key Laboratory of Heilongjiang Province, Harbin Medical University, Harbin 150081, China
| | - Daniel J McGrail
- Department of Systems Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Juan Xu
- College of Bioinformatics Science and Technology and Bio-Pharmaceutical Key Laboratory of Heilongjiang Province, Harbin Medical University, Harbin 150081, China
| | - Gordon B Mills
- Department of Systems Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Nidhi Sahni
- Department of Systems Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; Program in Quantitative and Computational Biosciences (QCB), Baylor College of Medicine, Houston, TX 77030, USA; Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA; Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Smithville, TX 78957, USA.
| | - Song Yi
- Department of Oncology, Dell Medical School, The University of Texas at Austin, Austin, TX 78712, USA; Department of Biomedical Engineering, Cockrell School of Engineering, The University of Texas at Austin, Austin, TX 78712, USA.
| |
Collapse
|
15
|
Imbriano C, Molinari S. Alternative Splicing of Transcription Factors Genes in Muscle Physiology and Pathology. Genes (Basel) 2018; 9:genes9020107. [PMID: 29463057 PMCID: PMC5852603 DOI: 10.3390/genes9020107] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2018] [Revised: 02/10/2018] [Accepted: 02/13/2018] [Indexed: 12/13/2022] Open
Abstract
Skeletal muscle formation is a multi-step process that is governed by complex networks of transcription factors. The regulation of their functions is in turn multifaceted, including several mechanisms, among them alternative splicing (AS) plays a primary role. On the other hand, altered AS has a role in the pathogenesis of numerous muscular pathologies. Despite these premises, the causal role played by the altered splicing pattern of transcripts encoding myogenic transcription factors in neuromuscular diseases has been neglected so far. In this review, we systematically investigate what has been described about the AS patterns of transcription factors both in the physiology of the skeletal muscle formation process and in neuromuscular diseases, in the hope that this may be useful in re-evaluating the potential role of altered splicing of transcription factors in such diseases.
Collapse
Affiliation(s)
- Carol Imbriano
- University of Modena and Reggio Emilia, Department of Life Sciences, Modena, Italy.
| | - Susanna Molinari
- University of Modena and Reggio Emilia, Department of Life Sciences, Modena, Italy.
| |
Collapse
|
16
|
Parker Gaddis K, Megonigal J, Clay J, Wolfe C. Genome-wide association study for ketosis in US Jerseys using producer-recorded data. J Dairy Sci 2018; 101:413-424. [DOI: 10.3168/jds.2017-13383] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2017] [Accepted: 09/16/2017] [Indexed: 12/20/2022]
|
17
|
Saha A, Kim Y, Gewirtz ADH, Jo B, Gao C, McDowell IC, Engelhardt BE, Battle A. Co-expression networks reveal the tissue-specific regulation of transcription and splicing. Genome Res 2017; 27:1843-1858. [PMID: 29021288 PMCID: PMC5668942 DOI: 10.1101/gr.216721.116] [Citation(s) in RCA: 119] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2016] [Accepted: 08/22/2017] [Indexed: 11/24/2022]
Abstract
Gene co-expression networks capture biologically important patterns in gene expression data, enabling functional analyses of genes, discovery of biomarkers, and interpretation of genetic variants. Most network analyses to date have been limited to assessing correlation between total gene expression levels in a single tissue or small sets of tissues. Here, we built networks that additionally capture the regulation of relative isoform abundance and splicing, along with tissue-specific connections unique to each of a diverse set of tissues. We used the Genotype-Tissue Expression (GTEx) project v6 RNA sequencing data across 50 tissues and 449 individuals. First, we developed a framework called Transcriptome-Wide Networks (TWNs) for combining total expression and relative isoform levels into a single sparse network, capturing the interplay between the regulation of splicing and transcription. We built TWNs for 16 tissues and found that hubs in these networks were strongly enriched for splicing and RNA binding genes, demonstrating their utility in unraveling regulation of splicing in the human transcriptome. Next, we used a Bayesian biclustering model that identifies network edges unique to a single tissue to reconstruct Tissue-Specific Networks (TSNs) for 26 distinct tissues and 10 groups of related tissues. Finally, we found genetic variants associated with pairs of adjacent nodes in our networks, supporting the estimated network structures and identifying 20 genetic variants with distant regulatory impact on transcription and splicing. Our networks provide an improved understanding of the complex relationships of the human transcriptome across tissues.
Collapse
|
18
|
Lin YJ, Liao WL, Wang CH, Tsai LP, Tang CH, Chen CH, Wu JY, Liang WM, Hsieh AR, Cheng CF, Chen JH, Chien WK, Lin TH, Wu CM, Liao CC, Huang SM, Tsai FJ. Association of human height-related genetic variants with familial short stature in Han Chinese in Taiwan. Sci Rep 2017; 7:6372. [PMID: 28744006 PMCID: PMC5527114 DOI: 10.1038/s41598-017-06766-z] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2016] [Accepted: 06/19/2017] [Indexed: 12/19/2022] Open
Abstract
Human height can be described as a classical and inherited trait model. Genome-wide association studies (GWAS) have revealed susceptible loci and provided insights into the polygenic nature of human height. Familial short stature (FSS) represents a suitable trait for investigating short stature genetics because disease associations with short stature have been ruled out in this case. In addition, FSS is caused only by genetically inherited factors. In this study, we explored the correlations of FSS risk with the genetic loci associated with human height in previous GWAS, alone and cumulatively. We systematically evaluated 34 known human height single nucleotide polymorphisms (SNPs) in relation to FSS in the additive model (p < 0.00005). A cumulative effect was observed: the odds ratios gradually increased with increasing genetic risk score quartiles (p < 0.001; Cochran-Armitage trend test). Six affected genes-ZBTB38, ZNF638, LCORL, CABLES1, CDK10, and TSEN15-are located in the nucleus and have been implicated in embryonic, organismal, and tissue development. In conclusion, our study suggests that 13 human height GWAS-identified SNPs are associated with FSS risk both alone and cumulatively.
Collapse
Affiliation(s)
- Ying-Ju Lin
- Genetic Center, Department of Medical Research, China Medical University Hospital, Taichung, Taiwan.,School of Chinese Medicine, China Medical University, Taichung, Taiwan
| | - Wen-Ling Liao
- Graduate Institute of Integrated Medicine, China Medical University, Taichung, Taiwan.,Center for Personalized Medicine, China Medical University Hospital, Taichung, Taiwan
| | - Chung-Hsing Wang
- Children's Hospital of China Medical University, Taichung, Taiwan
| | - Li-Ping Tsai
- Department of Pediatrics, Buddhist Tzu Chi General Hospital, Taipei Branch, Taipei, Taiwan
| | - Chih-Hsin Tang
- Graduate Institute of Biomedical Sciences, China Medical University, Taichung, Taiwan
| | - Chien-Hsiun Chen
- School of Chinese Medicine, China Medical University, Taichung, Taiwan.,Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan
| | - Jer-Yuarn Wu
- School of Chinese Medicine, China Medical University, Taichung, Taiwan.,Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan
| | - Wen-Miin Liang
- Graduate Institute of Biostatistics, School of Public Health, China Medical University, Taichung, Taiwan
| | - Ai-Ru Hsieh
- Graduate Institute of Biostatistics, School of Public Health, China Medical University, Taichung, Taiwan
| | - Chi-Fung Cheng
- Graduate Institute of Biostatistics, School of Public Health, China Medical University, Taichung, Taiwan
| | - Jin-Hua Chen
- Biostatistics Center and School of Public Health, Taipei Medical University, Taipei, Taiwan
| | - Wen-Kuei Chien
- National Applied Research Laboratories, National Center for High-performance Computing, Hsinchu, Taiwan
| | - Ting-Hsu Lin
- Genetic Center, Department of Medical Research, China Medical University Hospital, Taichung, Taiwan
| | - Chia-Ming Wu
- Genetic Center, Department of Medical Research, China Medical University Hospital, Taichung, Taiwan
| | - Chiu-Chu Liao
- Genetic Center, Department of Medical Research, China Medical University Hospital, Taichung, Taiwan
| | - Shao-Mei Huang
- Genetic Center, Department of Medical Research, China Medical University Hospital, Taichung, Taiwan
| | - Fuu-Jen Tsai
- Genetic Center, Department of Medical Research, China Medical University Hospital, Taichung, Taiwan. .,School of Chinese Medicine, China Medical University, Taichung, Taiwan. .,Children's Hospital of China Medical University, Taichung, Taiwan. .,Department of Biotechnology and Bioinformatics, Asia University, Taichung, Taiwan.
| |
Collapse
|
19
|
Germline Chd8 haploinsufficiency alters brain development in mouse. Nat Neurosci 2017; 20:1062-1073. [PMID: 28671691 DOI: 10.1038/nn.4592] [Citation(s) in RCA: 162] [Impact Index Per Article: 23.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2016] [Accepted: 05/23/2017] [Indexed: 02/06/2023]
Abstract
The chromatin remodeling gene CHD8 represents a central node in neurodevelopmental gene networks implicated in autism. We examined the impact of germline heterozygous frameshift Chd8 mutation on neurodevelopment in mice. Chd8+/del5 mice displayed normal social interactions with no repetitive behaviors but exhibited cognitive impairment correlated with increased regional brain volume, validating that phenotypes of Chd8+/del5 mice overlap pathology reported in humans with CHD8 mutations. We applied network analysis to characterize neurodevelopmental gene expression, revealing widespread transcriptional changes in Chd8+/del5 mice across pathways disrupted in neurodevelopmental disorders, including neurogenesis, synaptic processes and neuroimmune signaling. We identified a co-expression module with peak expression in early brain development featuring dysregulation of RNA processing, chromatin remodeling and cell-cycle genes enriched for promoter binding by Chd8, and we validated increased neuronal proliferation and developmental splicing perturbation in Chd8+/del5 mice. This integrative analysis offers an initial picture of the consequences of Chd8 haploinsufficiency for brain development.
Collapse
|
20
|
Mota de Sá P, Richard AJ, Hang H, Stephens JM. Transcriptional Regulation of Adipogenesis. Compr Physiol 2017; 7:635-674. [PMID: 28333384 DOI: 10.1002/cphy.c160022] [Citation(s) in RCA: 243] [Impact Index Per Article: 34.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Adipocytes are the defining cell type of adipose tissue. Once considered a passive participant in energy storage, adipose tissue is now recognized as a dynamic organ that contributes to several important physiological processes, such as lipid metabolism, systemic energy homeostasis, and whole-body insulin sensitivity. Therefore, understanding the mechanisms involved in its development and function is of great importance. Adipocyte differentiation is a highly orchestrated process which can vary between different fat depots as well as between the sexes. While hormones, miRNAs, cytoskeletal proteins, and many other effectors can modulate adipocyte development, the best understood regulators of adipogenesis are the transcription factors that inhibit or promote this process. Ectopic expression and knockdown approaches in cultured cells have been widely used to understand the contribution of transcription factors to adipocyte development, providing a basis for more sophisticated in vivo strategies to examine adipogenesis. To date, over two dozen transcription factors have been shown to play important roles in adipocyte development. These transcription factors belong to several families with many different DNA-binding domains. While peroxisome proliferator-activated receptor gamma (PPARγ) is undoubtedly the most important transcriptional modulator of adipocyte development in all types of adipose tissue, members of the CCAAT/enhancer-binding protein, Krüppel-like transcription factor, signal transducer and activator of transcription, GATA, early B cell factor, and interferon-regulatory factor families also regulate adipogenesis. The importance of PPARγ activity is underscored by several covalent modifications that modulate its activity and its ability to modulate adipocyte development. This review will primarily focus on the transcriptional control of adipogenesis in white fat cells and on the mechanisms involved in this fine-tuned developmental process. © 2017 American Physiological Society. Compr Physiol 7:635-674, 2017.
Collapse
Affiliation(s)
- Paula Mota de Sá
- Pennington Biomedical Research Center, Louisiana State University System, Baton Rouge, LA, USA
| | - Allison J Richard
- Pennington Biomedical Research Center, Louisiana State University System, Baton Rouge, LA, USA
| | - Hardy Hang
- Pennington Biomedical Research Center, Louisiana State University System, Baton Rouge, LA, USA
| | - Jacqueline M Stephens
- Pennington Biomedical Research Center, Louisiana State University System, Baton Rouge, LA, USA
| |
Collapse
|
21
|
Martínez-Redondo V, Jannig PR, Correia JC, Ferreira DMS, Cervenka I, Lindvall JM, Sinha I, Izadi M, Pettersson-Klein AT, Agudelo LZ, Gimenez-Cassina A, Brum PC, Dahlman-Wright K, Ruas JL. Peroxisome Proliferator-activated Receptor γ Coactivator-1 α Isoforms Selectively Regulate Multiple Splicing Events on Target Genes. J Biol Chem 2016; 291:15169-84. [PMID: 27231350 DOI: 10.1074/jbc.m115.705822] [Citation(s) in RCA: 56] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2015] [Indexed: 11/06/2022] Open
Abstract
Endurance and resistance exercise training induces specific and profound changes in the skeletal muscle transcriptome. Peroxisome proliferator-activated receptor γ coactivator-1 α (PGC-1α) coactivators are not only among the genes differentially induced by distinct training methods, but they also participate in the ensuing signaling cascades that allow skeletal muscle to adapt to each type of exercise. Although endurance training preferentially induces PGC-1α1 expression, resistance exercise activates the expression of PGC-1α2, -α3, and -α4. These three alternative PGC-1α isoforms lack the arginine/serine-rich (RS) and RNA recognition motifs characteristic of PGC-1α1. Discrete functions for PGC-1α1 and -α4 have been described, but the biological role of PGC-1α2 and -α3 remains elusive. Here we show that different PGC-1α variants can affect target gene splicing through diverse mechanisms, including alternative promoter usage. By analyzing the exon structure of the target transcripts for each PGC-1α isoform, we were able to identify a large number of previously unknown PGC-1α2 and -α3 target genes and pathways in skeletal muscle. In particular, PGC-1α2 seems to mediate a decrease in the levels of cholesterol synthesis genes. Our results suggest that the conservation of the N-terminal activation and repression domains (and not the RS/RNA recognition motif) is what determines the gene programs and splicing options modulated by each PGC-1α isoform. By using skeletal muscle-specific transgenic mice for PGC-1α1 and -α4, we could validate, in vivo, splicing events observed in in vitro studies. These results show that alternative PGC-1α variants can affect target gene expression both quantitatively and qualitatively and identify novel biological pathways under the control of this system of coactivators.
Collapse
Affiliation(s)
- Vicente Martínez-Redondo
- From the Department of Physiology and Pharmacology, Molecular and Cellular Exercise Physiology Unit and
| | - Paulo R Jannig
- From the Department of Physiology and Pharmacology, Molecular and Cellular Exercise Physiology Unit and School of Physical Education and Sport, University of São Paulo, 05508-030 São Paulo, Brazil, and
| | - Jorge C Correia
- From the Department of Physiology and Pharmacology, Molecular and Cellular Exercise Physiology Unit and
| | - Duarte M S Ferreira
- From the Department of Physiology and Pharmacology, Molecular and Cellular Exercise Physiology Unit and
| | - Igor Cervenka
- From the Department of Physiology and Pharmacology, Molecular and Cellular Exercise Physiology Unit and
| | - Jessica M Lindvall
- Department of Biosciences and Nutrition, Novum, Karolinska Institutet, SE-141 83 Huddinge, Sweden
| | - Indranil Sinha
- Department of Biosciences and Nutrition, Novum, Karolinska Institutet, SE-141 83 Huddinge, Sweden
| | - Manizheh Izadi
- From the Department of Physiology and Pharmacology, Molecular and Cellular Exercise Physiology Unit and
| | - Amanda T Pettersson-Klein
- From the Department of Physiology and Pharmacology, Molecular and Cellular Exercise Physiology Unit and
| | - Leandro Z Agudelo
- From the Department of Physiology and Pharmacology, Molecular and Cellular Exercise Physiology Unit and
| | - Alfredo Gimenez-Cassina
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, SE-171 77 Stockholm, Sweden
| | - Patricia C Brum
- School of Physical Education and Sport, University of São Paulo, 05508-030 São Paulo, Brazil, and
| | - Karin Dahlman-Wright
- Department of Biosciences and Nutrition, Novum, Karolinska Institutet, SE-141 83 Huddinge, Sweden
| | - Jorge L Ruas
- From the Department of Physiology and Pharmacology, Molecular and Cellular Exercise Physiology Unit and
| |
Collapse
|
22
|
Coelho MB, Attig J, Ule J, Smith CWJ. Matrin3: connecting gene expression with the nuclear matrix. WILEY INTERDISCIPLINARY REVIEWS-RNA 2016; 7:303-15. [PMID: 26813864 DOI: 10.1002/wrna.1336] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2015] [Revised: 12/18/2015] [Accepted: 12/18/2015] [Indexed: 01/06/2023]
Abstract
As indicated by its name, Matrin3 was discovered as a component of the nuclear matrix, an insoluble fibrogranular network that structurally organizes the nucleus. Matrin3 possesses both DNA- and RNA-binding domains and, consistent with this, has been shown to function at a number of stages in the life cycle of messenger RNAs. These numerous activities indicate that Matrin3, and indeed the nuclear matrix, do not just provide a structural framework for nuclear activities but also play direct functional roles in these activities. Here, we review the structure, functions, and molecular interactions of Matrin3 and of Matrin3-related proteins, and the pathologies that can arise upon mutation of Matrin3. WIREs RNA 2016, 7:303-315. doi: 10.1002/wrna.1336 For further resources related to this article, please visit the WIREs website.
Collapse
Affiliation(s)
- Miguel B Coelho
- Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - Jan Attig
- Department of Molecular Neuroscience, UCL Institute of Neurology, London, UK
| | - Jernej Ule
- Department of Molecular Neuroscience, UCL Institute of Neurology, London, UK
| | | |
Collapse
|
23
|
Snyder CA, Goodson ML, Schroeder AC, Privalsky ML. Regulation of corepressor alternative mRNA splicing by hormonal and metabolic signaling. Mol Cell Endocrinol 2015; 413:228-35. [PMID: 26166430 PMCID: PMC4556269 DOI: 10.1016/j.mce.2015.06.036] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/13/2015] [Revised: 06/24/2015] [Accepted: 06/29/2015] [Indexed: 12/14/2022]
Abstract
Alternative mRNA splicing diversifies the products encoded by the NCoR and SMRT corepressor loci. There is a programmed alteration in NCoR mRNA splicing during adipocyte differentiation from an NCoRω isoform, which contains three nuclear receptor interaction domains, to an NCoRδ isoform that contains two nuclear receptor interaction domains. This alternative mRNA splicing of NCoR has profound effects on adiposity and on diabetes in mouse models. We report here that dexamethasone, a powerful regulator of metabolism and of adipocyte differentiation, confers this change in NCoR mRNA splicing in cultured adipocytes. We also demonstrate that changes in dietary components can consistently, if moderately, modulate the total transcript levels and the mRNA splicing of NCoR and SMRT in both cultured cells and intact mice. This ability of alternative corepressor mRNA splicing to respond to nutritional changes confirms its importance in regulating glucose and lipid metabolism, and its promise as a therapeutic candidate for metabolic disorders such as type 2 diabetes.
Collapse
Affiliation(s)
- Chelsea A Snyder
- Department of Microbiology and Molecular Genetics, College of Biological Sciences, University of California at Davis, USA.
| | - Michael L Goodson
- Department of Microbiology and Molecular Genetics, College of Biological Sciences, University of California at Davis, USA.
| | - Amy C Schroeder
- Department of Microbiology and Molecular Genetics, College of Biological Sciences, University of California at Davis, USA.
| | - Martin L Privalsky
- Department of Microbiology and Molecular Genetics, College of Biological Sciences, University of California at Davis, USA.
| |
Collapse
|
24
|
Lin JC. Impacts of Alternative Splicing Events on the Differentiation of Adipocytes. Int J Mol Sci 2015; 16:22169-89. [PMID: 26389882 PMCID: PMC4613302 DOI: 10.3390/ijms160922169] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2015] [Revised: 09/07/2015] [Accepted: 09/07/2015] [Indexed: 02/07/2023] Open
Abstract
Alternative splicing was found to be a common phenomenon after the advent of whole transcriptome analyses or next generation sequencing. Over 90% of human genes were demonstrated to undergo at least one alternative splicing event. Alternative splicing is an effective mechanism to spatiotemporally expand protein diversity, which influences the cell fate and tissue development. The first focus of this review is to highlight recent studies, which demonstrated effects of alternative splicing on the differentiation of adipocytes. Moreover, use of evolving high-throughput approaches, such as transcriptome analyses (RNA sequencing), to profile adipogenic transcriptomes, is also addressed.
Collapse
Affiliation(s)
- Jung-Chun Lin
- School of Medical Laboratory Science and Biotechnology, College of Medical Science and Technology, Taipei Medical University, 250 Wu-Hsing Street, Taipei 11031, Taiwan.
| |
Collapse
|
25
|
Ridaifen G, tamoxifen analog, is a potent anticancer drug working through a combinatorial association with multiple cellular factors. Bioorg Med Chem 2015; 23:6118-24. [DOI: 10.1016/j.bmc.2015.08.001] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2015] [Revised: 07/31/2015] [Accepted: 08/01/2015] [Indexed: 12/31/2022]
|