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Ouni M, Gottmann P, Westholm E, Schwerbel K, Jähnert M, Stadion M, Rittig K, Vogel H, Schürmann A. MiR-205 is up-regulated in islets of diabetes-susceptible mice and targets the diabetes gene Tcf7l2. Acta Physiol (Oxf) 2021; 232:e13693. [PMID: 34028994 DOI: 10.1111/apha.13693] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2021] [Revised: 05/12/2021] [Accepted: 05/21/2021] [Indexed: 12/11/2022]
Abstract
AIM MicroRNAs play an important role in the maintenance of cellular functions by fine-tuning gene expression levels. The aim of the current study was to identify genetically caused changes in microRNA expression which associate with islet dysfunction in diabetic mice. METHODS To identify novel microRNAs involved in islet dysfunction, transcriptome and miRNome analyses were performed in islets of obese, diabetes-susceptible NZO and diabetes-resistant B6-ob/ob mice and results combined with quantitative trait loci (QTL) and functional in vitro analysis. RESULTS In islets of NZO and B6-ob/ob mice, 94 differentially expressed microRNAs were detected, of which 11 are located in diabetes QTL. Focusing on conserved microRNAs exhibiting the strongest expression difference and which have not been linked to islet function, miR-205-5p was selected for further analysis. According to transcriptome data and target prediction analyses, miR-205-5p affects genes involved in Wnt and calcium signalling as well as insulin secretion. Over-expression of miR-205-5p in the insulinoma cell line INS-1 increased insulin expression, left-shifted the glucose-dependence of insulin secretion and supressed the expression of the diabetes gene TCF7L2. The interaction between miR-205-5p and TCF7L2 was confirmed by luciferase reporter assay. CONCLUSION MiR-205-5p was identified as relevant microRNA involved in islet dysfunction by interacting with TCF7L2.
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Affiliation(s)
- Meriem Ouni
- Department of Experimental Diabetology German Institute of Human Nutrition Potsdam‐Rehbruecke (DIfE) Nuthetal Germany
- German Center for Diabetes Research (DZD) München‐Neuherberg Germany
| | - Pascal Gottmann
- Department of Experimental Diabetology German Institute of Human Nutrition Potsdam‐Rehbruecke (DIfE) Nuthetal Germany
- German Center for Diabetes Research (DZD) München‐Neuherberg Germany
| | - Efraim Westholm
- Department of Experimental Diabetology German Institute of Human Nutrition Potsdam‐Rehbruecke (DIfE) Nuthetal Germany
- Unit of Islet Cell Exocytosis Department of Clinical Sciences Malmö Lund University Diabetes CentreLund University Malmö Sweden
| | - Kristin Schwerbel
- Department of Experimental Diabetology German Institute of Human Nutrition Potsdam‐Rehbruecke (DIfE) Nuthetal Germany
- German Center for Diabetes Research (DZD) München‐Neuherberg Germany
| | - Markus Jähnert
- Department of Experimental Diabetology German Institute of Human Nutrition Potsdam‐Rehbruecke (DIfE) Nuthetal Germany
- German Center for Diabetes Research (DZD) München‐Neuherberg Germany
| | - Mandy Stadion
- Department of Experimental Diabetology German Institute of Human Nutrition Potsdam‐Rehbruecke (DIfE) Nuthetal Germany
- German Center for Diabetes Research (DZD) München‐Neuherberg Germany
| | - Kilian Rittig
- Clinic for Angiology and Diabetology Frankfurt (Oder) Germany
- Institute of Nutritional Science University of Potsdam Brandenburg Germany
| | - Heike Vogel
- Department of Experimental Diabetology German Institute of Human Nutrition Potsdam‐Rehbruecke (DIfE) Nuthetal Germany
- German Center for Diabetes Research (DZD) München‐Neuherberg Germany
- Research Group Genetics of Obesity German Institute of Human Nutrition Potsdam‐Rehbruecke (DIfE) Nuthetal Germany
- Research Group Molecular and Clinical Life Science of Metabolic Diseases Faculty of Health Sciences Brandenburg University of Potsdam Brandenburg Germany
| | - Annette Schürmann
- Department of Experimental Diabetology German Institute of Human Nutrition Potsdam‐Rehbruecke (DIfE) Nuthetal Germany
- German Center for Diabetes Research (DZD) München‐Neuherberg Germany
- Institute of Nutritional Science University of Potsdam Brandenburg Germany
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Wu Q, Liu P, Wang L. Many facades of CTCF unified by its coding for three-dimensional genome architecture. J Genet Genomics 2020; 47:407-424. [PMID: 33187878 DOI: 10.1016/j.jgg.2020.06.008] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2020] [Revised: 04/15/2020] [Accepted: 06/01/2020] [Indexed: 02/06/2023]
Abstract
CCCTC-binding factor (CTCF) is a multifunctional zinc finger protein that is conserved in metazoan species. CTCF is consistently found to play an important role in many diverse biological processes. CTCF/cohesin-mediated active chromatin 'loop extrusion' architects three-dimensional (3D) genome folding. The 3D architectural role of CTCF underlies its multifarious functions, including developmental regulation of gene expression, protocadherin (Pcdh) promoter choice in the nervous system, immunoglobulin (Ig) and T-cell receptor (Tcr) V(D)J recombination in the immune system, homeobox (Hox) gene control during limb development, as well as many other aspects of biology. Here, we review the pleiotropic functions of CTCF from the perspective of its essential role in 3D genome architecture and topological promoter/enhancer selection. We envision the 3D genome as an enormous complex architecture, with tens of thousands of CTCF sites as connecting nodes and CTCF proteins as mysterious bonds that glue together genomic building parts with distinct articulation joints. In particular, we focus on the internal mechanisms by which CTCF controls higher order chromatin structures that manifest its many façades of physiological and pathological functions. We also discuss the dichotomic role of CTCF sites as intriguing 3D genome nodes for seemingly contradictory 'looping bridges' and 'topological insulators' to frame a beautiful magnificent house for a cell's nuclear home.
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Affiliation(s)
- Qiang Wu
- MOE Key Lab of Systems Biomedicine, State Key Laboratory of Oncogenes and Related Genes, Center for Comparative Biomedicine, Institute of Systems Biomedicine, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University (SJTU), Shanghai, 200240, China.
| | - Peifeng Liu
- MOE Key Lab of Systems Biomedicine, State Key Laboratory of Oncogenes and Related Genes, Center for Comparative Biomedicine, Institute of Systems Biomedicine, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University (SJTU), Shanghai, 200240, China
| | - Leyang Wang
- MOE Key Lab of Systems Biomedicine, State Key Laboratory of Oncogenes and Related Genes, Center for Comparative Biomedicine, Institute of Systems Biomedicine, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University (SJTU), Shanghai, 200240, China
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3
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Bertero A, Fields PA, Ramani V, Bonora G, Yardimci GG, Reinecke H, Pabon L, Noble WS, Shendure J, Murry CE. Dynamics of genome reorganization during human cardiogenesis reveal an RBM20-dependent splicing factory. Nat Commun 2019; 10:1538. [PMID: 30948719 PMCID: PMC6449405 DOI: 10.1038/s41467-019-09483-5] [Citation(s) in RCA: 90] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2018] [Accepted: 03/08/2019] [Indexed: 01/25/2023] Open
Abstract
Functional changes in spatial genome organization during human development are poorly understood. Here we report a comprehensive profile of nuclear dynamics during human cardiogenesis from pluripotent stem cells by integrating Hi-C, RNA-seq and ATAC-seq. While chromatin accessibility and gene expression show complex on/off dynamics, large-scale genome architecture changes are mostly unidirectional. Many large cardiac genes transition from a repressive to an active compartment during differentiation, coincident with upregulation. We identify a network of such gene loci that increase their association inter-chromosomally, and are targets of the muscle-specific splicing factor RBM20. Genome editing studies show that TTN pre-mRNA, the main RBM20-regulated transcript in the heart, nucleates RBM20 foci that drive spatial proximity between the TTN locus and other inter-chromosomal RBM20 targets such as CACNA1C and CAMK2D. This mechanism promotes RBM20-dependent alternative splicing of the resulting transcripts, indicating the existence of a cardiac-specific trans-interacting chromatin domain (TID) functioning as a splicing factory.
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Affiliation(s)
- Alessandro Bertero
- Department of Pathology, University of Washington, 1959 NE Pacific Street, Seattle, WA, 98195, USA.,Center for Cardiovascular Biology, University of Washington, 850 Republican Street, Brotman Building, Seattle, WA, 98109, USA.,Institute for Stem Cell and Regenerative Medicine, University of Washington, 850 Republican Street, Seattle, 98109, WA, USA
| | - Paul A Fields
- Department of Pathology, University of Washington, 1959 NE Pacific Street, Seattle, WA, 98195, USA.,Center for Cardiovascular Biology, University of Washington, 850 Republican Street, Brotman Building, Seattle, WA, 98109, USA.,Institute for Stem Cell and Regenerative Medicine, University of Washington, 850 Republican Street, Seattle, 98109, WA, USA
| | - Vijay Ramani
- Department of Genome Sciences, University of Washington, William H. Foege Hall, 3720 15th Ave NE, Seattle, 98195, WA, USA
| | - Giancarlo Bonora
- Department of Genome Sciences, University of Washington, William H. Foege Hall, 3720 15th Ave NE, Seattle, 98195, WA, USA
| | - Galip G Yardimci
- Department of Genome Sciences, University of Washington, William H. Foege Hall, 3720 15th Ave NE, Seattle, 98195, WA, USA
| | - Hans Reinecke
- Department of Pathology, University of Washington, 1959 NE Pacific Street, Seattle, WA, 98195, USA.,Center for Cardiovascular Biology, University of Washington, 850 Republican Street, Brotman Building, Seattle, WA, 98109, USA.,Institute for Stem Cell and Regenerative Medicine, University of Washington, 850 Republican Street, Seattle, 98109, WA, USA
| | - Lil Pabon
- Department of Pathology, University of Washington, 1959 NE Pacific Street, Seattle, WA, 98195, USA.,Center for Cardiovascular Biology, University of Washington, 850 Republican Street, Brotman Building, Seattle, WA, 98109, USA.,Institute for Stem Cell and Regenerative Medicine, University of Washington, 850 Republican Street, Seattle, 98109, WA, USA
| | - William S Noble
- Department of Genome Sciences, University of Washington, William H. Foege Hall, 3720 15th Ave NE, Seattle, 98195, WA, USA
| | - Jay Shendure
- Department of Genome Sciences, University of Washington, William H. Foege Hall, 3720 15th Ave NE, Seattle, 98195, WA, USA.,Howard Hughes Medical Institute, Seattle, WA, USA
| | - Charles E Murry
- Department of Pathology, University of Washington, 1959 NE Pacific Street, Seattle, WA, 98195, USA. .,Center for Cardiovascular Biology, University of Washington, 850 Republican Street, Brotman Building, Seattle, WA, 98109, USA. .,Institute for Stem Cell and Regenerative Medicine, University of Washington, 850 Republican Street, Seattle, 98109, WA, USA. .,Department of Medicine/Cardiology, 1959 NE Pacific Street, University of Washington, Seattle, 98195, WA, USA. .,Department of Bioengineering, University of Washington, 3720 15th Ave NE, Seattle, WA, 98195, USA.
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Kong S, Zhang Y. Deciphering Hi-C: from 3D genome to function. Cell Biol Toxicol 2019; 35:15-32. [PMID: 30610495 DOI: 10.1007/s10565-018-09456-2] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2018] [Accepted: 12/02/2018] [Indexed: 12/11/2022]
Abstract
Hi-C is a commonly used technology in 3D genomics which can depict global chromatin interactions across eukaryotic genome. Integrating with different datasets, it can also be applied to studying various biological questions, such as nuclear organization, gene transcription regulation, spatiotemporal development, genome assembly, and cancer genomics. During the last decade, the development and application of Hi-C have dramatically changed the view of genome architecture, chromatin conformation, and gene interaction. So far, Hi-C-related studies remain vivacious and controversial; thus, a unified standard of library construction and bioinformatics analysis are urgently needed. In this review, we have summarized its history, development, methodologies, advances, applications, shortages, and future perspectives. We discuss a few limitations of the current Hi-C technologies and future directions for improvement and highlight how Hi-C can bridge 3D structure to gene function. This review will be helpful for scientists who want to engage in the 3D genomics field; it also shows some future tracks.
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Affiliation(s)
- Siyuan Kong
- Animal Functional Genomics Group, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, 7 Pengfei Road, Dapeng District, 518120, Shenzhen, People's Republic of China
| | - Yubo Zhang
- Animal Functional Genomics Group, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, 7 Pengfei Road, Dapeng District, 518120, Shenzhen, People's Republic of China.
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Tan ZW, Guarnera E, Berezovsky IN. Exploring chromatin hierarchical organization via Markov State Modelling. PLoS Comput Biol 2018; 14:e1006686. [PMID: 30596637 PMCID: PMC6355033 DOI: 10.1371/journal.pcbi.1006686] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2018] [Revised: 01/31/2019] [Accepted: 11/27/2018] [Indexed: 01/02/2023] Open
Abstract
We propose a new computational method for exploring chromatin structural organization based on Markov State Modelling of Hi-C data represented as an interaction network between genomic loci. A Markov process describes the random walk of a traveling probe in the corresponding energy landscape, mimicking the motion of a biomolecule involved in chromatin function. By studying the metastability of the associated Markov State Model upon annealing, the hierarchical structure of individual chromosomes is observed, and corresponding set of structural partitions is identified at each level of hierarchy. Then, the notion of effective interaction between partitions is derived, delineating the overall topology and architecture of chromosomes. Mapping epigenetic data on the graphs of intra-chromosomal effective interactions helps in understanding how chromosome organization facilitates its function. A sketch of whole-genome interactions obtained from the analysis of 539 partitions from all 23 chromosomes, complemented by distributions of gene expression regulators and epigenetic factors, sheds light on the structure-function relationships in chromatin, delineating chromosomal territories, as well as structural partitions analogous to topologically associating domains and active / passive epigenomic compartments. In addition to the overall genome architecture shown by effective interactions, the affinity between partitions of different chromosomes was analyzed as an indicator of the degree of association between partitions in functionally relevant genomic interactions. The overall static picture of whole-genome interactions obtained with the method presented in this work provides a foundation for chromatin structural reconstruction, for the modelling of chromatin dynamics, and for exploring the regulation of genome function. The algorithms used in this study are implemented in a freely available Python package ChromaWalker (https://bitbucket.org/ZhenWahTan/chromawalker).
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Affiliation(s)
- Zhen Wah Tan
- Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR), Matrix, Singapore
| | - Enrico Guarnera
- Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR), Matrix, Singapore
| | - Igor N. Berezovsky
- Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR), Matrix, Singapore
- Department of Biological Sciences (DBS), National University of Singapore (NUS), Singapore
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6
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Cortini R, Filion GJ. Theoretical principles of transcription factor traffic on folded chromatin. Nat Commun 2018; 9:1740. [PMID: 29712907 PMCID: PMC5928121 DOI: 10.1038/s41467-018-04130-x] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2017] [Accepted: 04/05/2018] [Indexed: 01/02/2023] Open
Abstract
All organisms regulate transcription of their genes. To understand this process, a complete understanding of how transcription factors find their targets in cellular nuclei is essential. The DNA sequence and other variables are known to influence this binding, but the distribution of transcription factor binding patterns remains mostly unexplained in metazoan genomes. Here, we investigate the role of chromosome conformation in the trajectories of transcription factors. Using molecular dynamics simulations, we uncover the principles of their diffusion on chromatin. Chromosome contacts play a conflicting role: at low density they enhance transcription factor traffic, but at high density they lower it by volume exclusion. Consistently, we observe that in human cells, highly occupied targets, where protein binding is promiscuous, are found at sites engaged in chromosome loops within uncompacted chromatin. In summary, we provide a framework for understanding the search trajectories of transcription factors, highlighting the key contribution of genome conformation. How transcription factors find their targets in vivo is still poorly understood. Here the authors use molecular dynamics simulations to investigate how transcription factors diffuse on chromatin, providing a theoretical framework for understanding the key role of genome conformation in this process.
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Affiliation(s)
- Ruggero Cortini
- Genome Architecture, Gene Regulation, Stem Cells and Cancer Programme, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, 08003, Barcelona, Spain. .,Universidad Pompeu Fabra (UPF), 08003, Barcelona, Spain.
| | - Guillaume J Filion
- Genome Architecture, Gene Regulation, Stem Cells and Cancer Programme, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, 08003, Barcelona, Spain. .,Universidad Pompeu Fabra (UPF), 08003, Barcelona, Spain.
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