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Zhao X, Yang X, Lv P, Xu Y, Wang X, Zhao Z, Du J. Polycomb regulates circadian rhythms in Drosophila in clock neurons. Life Sci Alliance 2024; 7:e202302140. [PMID: 37914396 PMCID: PMC10620068 DOI: 10.26508/lsa.202302140] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Revised: 10/15/2023] [Accepted: 10/17/2023] [Indexed: 11/03/2023] Open
Abstract
Circadian rhythms are essential physiological feature for most living organisms. Previous studies have shown that epigenetic regulation plays a crucial role. There is a knowledge gap in the chromatin state of some key clock neuron clusters. In this study, we show that circadian rhythm is affected by the epigenetic regulator Polycomb (Pc) within the Drosophila clock neurons. To investigate the molecular mechanisms underlying the roles of Pc in these clock neuron clusters, we use targeted DamID (TaDa) to identify genes significantly bound by Pc in the neurons marked by C929-Gal4 (including l-LNvs cluster), R6-Gal4 (including s-LNvs cluster), R18H11-Gal4 (including DN1 cluster), and DVpdf-Gal4, pdf-Gal80 (including LNds cluster). It shows that Pc binds to the genes involved in the circadian rhythm pathways, arguing a direct role for Pc in regulating circadian rhythms through specific clock genes. This study shows the identification of Pc targets in the clock neuron clusters, providing potential resource for understanding the regulatory mechanisms of circadian rhythms by the PcG complex. Thus, this study provided an example for epigenetic regulation of adult behavior.
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Affiliation(s)
- Xianguo Zhao
- https://ror.org/04v3ywz14 Department of Entomology and MOA Key Lab of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Beijing, China
| | - Xingzhuo Yang
- https://ror.org/04v3ywz14 Department of Entomology and MOA Key Lab of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Beijing, China
| | - Pengfei Lv
- https://ror.org/04v3ywz14 Department of Entomology and MOA Key Lab of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Beijing, China
| | - Yuetong Xu
- https://ror.org/04v3ywz14 Department of Crop Genomics and Bioinformatics, College of Agronomy and Biotechnology, National Maize Improvement Center of China, China Agricultural University, Beijing, China
| | - Xiangfeng Wang
- https://ror.org/04v3ywz14 Department of Crop Genomics and Bioinformatics, College of Agronomy and Biotechnology, National Maize Improvement Center of China, China Agricultural University, Beijing, China
| | - Zhangwu Zhao
- https://ror.org/04v3ywz14 Department of Entomology and MOA Key Lab of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Beijing, China
| | - Juan Du
- https://ror.org/04v3ywz14 Department of Entomology and MOA Key Lab of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Beijing, China
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2
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Gruhn WH, Tang WW, Dietmann S, Alves-Lopes JP, Penfold CA, Wong FC, Ramakrishna NB, Surani MA. Epigenetic resetting in the human germ line entails histone modification remodeling. SCIENCE ADVANCES 2023; 9:eade1257. [PMID: 36652508 PMCID: PMC9848478 DOI: 10.1126/sciadv.ade1257] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Accepted: 12/20/2022] [Indexed: 06/17/2023]
Abstract
Epigenetic resetting in the mammalian germ line entails acute DNA demethylation, which lays the foundation for gametogenesis, totipotency, and embryonic development. We characterize the epigenome of hypomethylated human primordial germ cells (hPGCs) to reveal mechanisms preventing the widespread derepression of genes and transposable elements (TEs). Along with the loss of DNA methylation, we show that hPGCs exhibit a profound reduction of repressive histone modifications resulting in diminished heterochromatic signatures at most genes and TEs and the acquisition of a neutral or paused epigenetic state without transcriptional activation. Efficient maintenance of a heterochromatic state is limited to a subset of genomic loci, such as evolutionarily young TEs and some developmental genes, which require H3K9me3 and H3K27me3, respectively, for efficient transcriptional repression. Accordingly, transcriptional repression in hPGCs presents an exemplary balanced system relying on local maintenance of heterochromatic features and a lack of inductive cues.
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Affiliation(s)
- Wolfram H. Gruhn
- Wellcome Trust/Cancer Research UK Gurdon Institute, Henry Wellcome Building of Cancer and Developmental Biology, Cambridge CB2 1QN, UK
- Physiology, Development and Neuroscience Department, University of Cambridge, Cambridge CB2 3EL, UK
| | - Walfred W.C. Tang
- Wellcome Trust/Cancer Research UK Gurdon Institute, Henry Wellcome Building of Cancer and Developmental Biology, Cambridge CB2 1QN, UK
- Physiology, Development and Neuroscience Department, University of Cambridge, Cambridge CB2 3EL, UK
| | - Sabine Dietmann
- Wellcome Trust/Cancer Research UK Gurdon Institute, Henry Wellcome Building of Cancer and Developmental Biology, Cambridge CB2 1QN, UK
- Physiology, Development and Neuroscience Department, University of Cambridge, Cambridge CB2 3EL, UK
- Wellcome–MRC Cambridge Stem Cell Institute, Jeffrey Cheah Biomedical Centre, Puddicombe Way, Cambridge Biomedical Campus, Cambridge CB2 0AW, UK
- Institute for Informatics, Washington University School of Medicine, St. Louis, MO, USA
| | - João P. Alves-Lopes
- Wellcome Trust/Cancer Research UK Gurdon Institute, Henry Wellcome Building of Cancer and Developmental Biology, Cambridge CB2 1QN, UK
- Physiology, Development and Neuroscience Department, University of Cambridge, Cambridge CB2 3EL, UK
- NORDFERTIL Research Lab Stockholm, Childhood Cancer Research Unit, J9:30, Department of Women’s and Children’s Health, Karolinska Institutet and Karolinska University Hospital, Visionsgatan 4, 17164, Solna, Stockholm, Sweden
| | - Christopher A. Penfold
- Wellcome Trust/Cancer Research UK Gurdon Institute, Henry Wellcome Building of Cancer and Developmental Biology, Cambridge CB2 1QN, UK
- Physiology, Development and Neuroscience Department, University of Cambridge, Cambridge CB2 3EL, UK
- Centre for Trophoblast Research, University of Cambridge, Cambridge, UK
| | - Frederick C. K. Wong
- Wellcome Trust/Cancer Research UK Gurdon Institute, Henry Wellcome Building of Cancer and Developmental Biology, Cambridge CB2 1QN, UK
- Physiology, Development and Neuroscience Department, University of Cambridge, Cambridge CB2 3EL, UK
| | - Navin B. Ramakrishna
- Wellcome Trust/Cancer Research UK Gurdon Institute, Henry Wellcome Building of Cancer and Developmental Biology, Cambridge CB2 1QN, UK
- Genome Institute of Singapore, A*STAR, Biopolis, Singapore 138672, Singapore
| | - M. Azim Surani
- Wellcome Trust/Cancer Research UK Gurdon Institute, Henry Wellcome Building of Cancer and Developmental Biology, Cambridge CB2 1QN, UK
- Physiology, Development and Neuroscience Department, University of Cambridge, Cambridge CB2 3EL, UK
- Wellcome–MRC Cambridge Stem Cell Institute, Jeffrey Cheah Biomedical Centre, Puddicombe Way, Cambridge Biomedical Campus, Cambridge CB2 0AW, UK
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3
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Ramakrishna NB, Battistoni G, Surani MA, Hannon GJ, Miska EA. Mouse primordial germ-cell-like cells lack piRNAs. Dev Cell 2022; 57:2661-2668.e5. [PMID: 36473462 DOI: 10.1016/j.devcel.2022.11.004] [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: 02/24/2022] [Revised: 08/03/2022] [Accepted: 11/03/2022] [Indexed: 12/12/2022]
Abstract
PIWI-interacting RNAs (piRNAs) are small RNAs bound by PIWI-clade Argonaute proteins that function to silence transposable elements (TEs). Following mouse primordial germ cell (mPGC) specification around E6.25, fetal piRNAs emerge in male gonocytes from E13.5 onward. The in vitro differentiation of mPGC-like cells (mPGCLCs) has raised the possibility of studying the fetal piRNA pathway in greater depth. However, using single-cell RNA-seq and RT-qPCR along mPGCLC differentiation, we find that piRNA pathway factors are not fully expressed in Day 6 mPGCLCs. Moreover, we do not detect piRNAs across a panel of Day 6 mPGCLC lines using small RNA-seq. Our combined efforts highlight that in vitro differentiated Day 6 mPGCLCs do not yet resemble E13.5 or later mouse gonocytes where the piRNA pathway is active. This Matters Arising paper is in response to von Meyenn et al. (2016), published in Developmental Cell. See also the correction by von Meyenn et al. published in this issue.
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Affiliation(s)
- Navin B Ramakrishna
- Wellcome/CRUK Gurdon Institute, University of Cambridge, Cambridge CB2 1QN, UK; Department of Genetics, University of Cambridge, Cambridge CB2 3EH, UK; Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge CB2 3EL, UK
| | - Giorgia Battistoni
- CRUK Cambridge Institute, Li Ka Shing Centre, University of Cambridge, Cambridge CB2 0RE, UK
| | - M Azim Surani
- Wellcome/CRUK Gurdon Institute, University of Cambridge, Cambridge CB2 1QN, UK; Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge CB2 3EL, UK; Wellcome/MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge CB2 0AW, UK.
| | - Gregory J Hannon
- CRUK Cambridge Institute, Li Ka Shing Centre, University of Cambridge, Cambridge CB2 0RE, UK.
| | - Eric A Miska
- Wellcome/CRUK Gurdon Institute, University of Cambridge, Cambridge CB2 1QN, UK; Department of Genetics, University of Cambridge, Cambridge CB2 3EH, UK; Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge CB10 1SA, UK.
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4
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Sun D, Llora Batlle O, van den Ameele J, Thomas JC, He P, Lim K, Tang W, Xu C, Meyer KB, Teichmann SA, Marioni JC, Jackson SP, Brand AH, Rawlins EL. SOX9 maintains human foetal lung tip progenitor state by enhancing WNT and RTK signalling. EMBO J 2022; 41:e111338. [PMID: 36121125 PMCID: PMC9627674 DOI: 10.15252/embj.2022111338] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2022] [Revised: 08/11/2022] [Accepted: 08/16/2022] [Indexed: 12/01/2022] Open
Abstract
The balance between self-renewal and differentiation in human foetal lung epithelial progenitors controls the size and function of the adult organ. Moreover, progenitor cell gene regulation networks are employed by both regenerating and malignant lung cells, where modulators of their effects could potentially be of therapeutic value. Details of the molecular networks controlling human lung progenitor self-renewal remain unknown. We performed the first CRISPRi screen in primary human lung organoids to identify transcription factors controlling progenitor self-renewal. We show that SOX9 promotes proliferation of lung progenitors and inhibits precocious airway differentiation. Moreover, by identifying direct transcriptional targets using Targeted DamID, we place SOX9 at the centre of a transcriptional network, which amplifies WNT and RTK signalling to stabilise the progenitor cell state. In addition, the proof-of-principle CRISPRi screen and Targeted DamID tools establish a new workflow for using primary human organoids to elucidate detailed functional mechanisms underlying normal development and disease.
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Affiliation(s)
- Dawei Sun
- Wellcome Trust/CRUK Gurdon InstituteUniversity of CambridgeCambridgeUK
- Department of Physiology, Development and NeuroscienceUniversity of CambridgeCambridgeUK
| | - Oriol Llora Batlle
- Wellcome Trust/CRUK Gurdon InstituteUniversity of CambridgeCambridgeUK
- Department of Physiology, Development and NeuroscienceUniversity of CambridgeCambridgeUK
| | - Jelle van den Ameele
- Wellcome Trust/CRUK Gurdon InstituteUniversity of CambridgeCambridgeUK
- Department of Physiology, Development and NeuroscienceUniversity of CambridgeCambridgeUK
- Present address:
Department of Clinical Neurosciences and MRC Mitochondrial Biology UnitUniversity of CambridgeCambridgeUK
| | - John C Thomas
- Wellcome Trust/CRUK Gurdon InstituteUniversity of CambridgeCambridgeUK
- Department of BiochemistryUniversity of CambridgeCambridgeUK
| | - Peng He
- Wellcome Sanger InstituteCambridgeUK
- European Molecular Biology LaboratoryEuropean Bioinformatics Institute (EMBL‐EBI)CambridgeUK
| | - Kyungtae Lim
- Wellcome Trust/CRUK Gurdon InstituteUniversity of CambridgeCambridgeUK
- Department of Physiology, Development and NeuroscienceUniversity of CambridgeCambridgeUK
| | - Walfred Tang
- Wellcome Trust/CRUK Gurdon InstituteUniversity of CambridgeCambridgeUK
- Department of Physiology, Development and NeuroscienceUniversity of CambridgeCambridgeUK
| | - Chufan Xu
- Wellcome Trust/CRUK Gurdon InstituteUniversity of CambridgeCambridgeUK
- Present address:
Department of Anaesthesiology and Surgical Intensive Care Unit, Xinhua HospitalShanghai Jiaotong University School of MedicineShanghaiChina
| | | | - Sarah A Teichmann
- Wellcome Sanger InstituteCambridgeUK
- Department of Physics/Cavendish LaboratoryUniversity of CambridgeCambridgeUK
| | - John C Marioni
- Wellcome Sanger InstituteCambridgeUK
- European Molecular Biology LaboratoryEuropean Bioinformatics Institute (EMBL‐EBI)CambridgeUK
- Cancer Research UK Cambridge InstituteUniversity of CambridgeCambridgeUK
| | - Stephen P Jackson
- Wellcome Trust/CRUK Gurdon InstituteUniversity of CambridgeCambridgeUK
- Department of BiochemistryUniversity of CambridgeCambridgeUK
| | - Andrea H Brand
- Wellcome Trust/CRUK Gurdon InstituteUniversity of CambridgeCambridgeUK
- Department of Physiology, Development and NeuroscienceUniversity of CambridgeCambridgeUK
| | - Emma L Rawlins
- Wellcome Trust/CRUK Gurdon InstituteUniversity of CambridgeCambridgeUK
- Department of Physiology, Development and NeuroscienceUniversity of CambridgeCambridgeUK
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5
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Tang JLY, Hakes AE, Krautz R, Suzuki T, Contreras EG, Fox PM, Brand AH. NanoDam identifies Homeobrain (ARX) and Scarecrow (NKX2.1) as conserved temporal factors in the Drosophila central brain and visual system. Dev Cell 2022; 57:1193-1207.e7. [PMID: 35483359 PMCID: PMC9616798 DOI: 10.1016/j.devcel.2022.04.008] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Revised: 02/08/2022] [Accepted: 04/05/2022] [Indexed: 11/24/2022]
Abstract
Temporal patterning of neural progenitors is an evolutionarily conserved strategy for generating neuronal diversity. Type II neural stem cells in the Drosophila central brain produce transit-amplifying intermediate neural progenitors (INPs) that exhibit temporal patterning. However, the known temporal factors cannot account for the neuronal diversity in the adult brain. To search for missing factors, we developed NanoDam, which enables rapid genome-wide profiling of endogenously tagged proteins in vivo with a single genetic cross. Mapping the targets of known temporal transcription factors with NanoDam revealed that Homeobrain and Scarecrow (ARX and NKX2.1 orthologs) are also temporal factors. We show that Homeobrain and Scarecrow define middle-aged and late INP temporal windows and play a role in cellular longevity. Strikingly, Homeobrain and Scarecrow have conserved functions as temporal factors in the developing visual system. NanoDam enables rapid cell-type-specific genome-wide profiling with temporal resolution and is easily adapted for use in higher organisms.
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Affiliation(s)
- Jocelyn L Y Tang
- Gurdon Institute and Department of Physiology, Development and Neuroscience, University of Cambridge, Tennis Court Road, Cambridge CB2 1QN, UK
| | - Anna E Hakes
- Gurdon Institute and Department of Physiology, Development and Neuroscience, University of Cambridge, Tennis Court Road, Cambridge CB2 1QN, UK
| | - Robert Krautz
- Gurdon Institute and Department of Physiology, Development and Neuroscience, University of Cambridge, Tennis Court Road, Cambridge CB2 1QN, UK
| | - Takumi Suzuki
- Gurdon Institute and Department of Physiology, Development and Neuroscience, University of Cambridge, Tennis Court Road, Cambridge CB2 1QN, UK
| | - Esteban G Contreras
- Gurdon Institute and Department of Physiology, Development and Neuroscience, University of Cambridge, Tennis Court Road, Cambridge CB2 1QN, UK
| | - Paul M Fox
- Gurdon Institute and Department of Physiology, Development and Neuroscience, University of Cambridge, Tennis Court Road, Cambridge CB2 1QN, UK
| | - Andrea H Brand
- Gurdon Institute and Department of Physiology, Development and Neuroscience, University of Cambridge, Tennis Court Road, Cambridge CB2 1QN, UK.
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6
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Reduced chromatin accessibility correlates with resistance to Notch activation. Nat Commun 2022; 13:2210. [PMID: 35468895 PMCID: PMC9039071 DOI: 10.1038/s41467-022-29834-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2020] [Accepted: 03/18/2022] [Indexed: 11/08/2022] Open
Abstract
The Notch signalling pathway is a master regulator of cell fate transitions in development and disease. In the brain, Notch promotes neural stem cell (NSC) proliferation, regulates neuronal migration and maturation and can act as an oncogene or tumour suppressor. How NOTCH and its transcription factor RBPJ activate distinct gene regulatory networks in closely related cell types in vivo remains to be determined. Here we use Targeted DamID (TaDa), requiring only thousands of cells, to identify NOTCH and RBPJ binding in NSCs and their progeny in the mouse embryonic cerebral cortex in vivo. We find that NOTCH and RBPJ associate with a broad network of NSC genes. Repression of NSC-specific Notch target genes in intermediate progenitors and neurons correlates with decreased chromatin accessibility, suggesting that chromatin compaction may contribute to restricting NOTCH-mediated transactivation.
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7
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Katsanos D, Barkoulas M. Targeted DamID in C. elegans reveals a direct role for LIN-22 and NHR-25 in antagonizing the epidermal stem cell fate. SCIENCE ADVANCES 2022; 8:eabk3141. [PMID: 35119932 PMCID: PMC8816332 DOI: 10.1126/sciadv.abk3141] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Accepted: 12/13/2021] [Indexed: 05/13/2023]
Abstract
Transcription factors are key players in gene networks controlling cell fate specification during development. In multicellular organisms, they display complex patterns of expression and binding to their targets, hence, tissue specificity is required in the characterization of transcription factor-target interactions. We introduce here targeted DamID (TaDa) as a method for tissue-specific transcription factor target identification in intact Caenorhabditis elegans animals. We use TaDa to recover targets in the epidermis for two factors, the HES1 homolog LIN-22, and the NR5A1/2 nuclear hormone receptor NHR-25. We demonstrate a direct link between LIN-22 and the Wnt signaling pathway through repression of the Frizzled receptor lin-17. We report a direct role for NHR-25 in promoting cell differentiation via repressing the expression of stem cell-promoting GATA factors. Our results expand our understanding of the epidermal gene network and highlight the potential of TaDa to dissect the architecture of tissue-specific gene regulatory networks.
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8
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Heng JIT, Viti L, Pugh K, Marshall OJ, Agostino M. Understanding the impact of ZBTB18 missense variation on transcription factor function in neurodevelopment and disease. J Neurochem 2022; 161:219-235. [PMID: 35083747 PMCID: PMC9302683 DOI: 10.1111/jnc.15572] [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: 09/28/2021] [Revised: 12/13/2021] [Accepted: 01/07/2022] [Indexed: 12/01/2022]
Abstract
Mutations to genes that encode DNA‐binding transcription factors (TFs) underlie a broad spectrum of human neurodevelopmental disorders. Here, we highlight the pathological mechanisms arising from mutations to TF genes that influence the development of mammalian cerebral cortex neurons. Drawing on recent findings for TF genes including ZBTB18, we discuss how functional missense mutations to such genes confer non‐native gene regulatory actions in developing neurons, leading to cell‐morphological defects, neuroanatomical abnormalities during foetal brain development and functional impairment. Further, we discuss how missense variation to human TF genes documented in the general population endow quantifiable changes to transcriptional regulation, with potential cell biological effects on the temporal progression of cerebral cortex neuron development and homeostasis. We offer a systematic approach to investigate the functional impact of missense variation in brain TFs and define their direct molecular and cellular actions in foetal neurodevelopment, tissue homeostasis and disease states.![]()
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Affiliation(s)
- Julian I-T Heng
- Curtin Health Innovation Research Institute, Bentley, WA, Australia.,Curtin Neuroscience Laboratories, Sarich Neuroscience Institute, Crawley, WA, Australia.,Curtin Medical School, Curtin University, Bentley, WA, Australia
| | - Leon Viti
- Curtin Health Innovation Research Institute, Bentley, WA, Australia.,Curtin Medical School, Curtin University, Bentley, WA, Australia
| | - Kye Pugh
- Curtin Health Innovation Research Institute, Bentley, WA, Australia.,Curtin Medical School, Curtin University, Bentley, WA, Australia
| | - Owen J Marshall
- Menzies Institute for Medical Research, The University of Tasmania, Hobart, Australia
| | - Mark Agostino
- Curtin Health Innovation Research Institute, Bentley, WA, Australia.,Curtin Institute for Computation, Curtin University, Bentley, Western Australia, Australia
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9
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Marshall OJ, Delandre C. Profiling Protein-DNA Interactions Cell-Type-Specifically with Targeted DamID. Methods Mol Biol 2022; 2458:195-213. [PMID: 35103969 DOI: 10.1007/978-1-0716-2140-0_11] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Targeted DamID (TaDa) is a means of profiling the binding of any DNA-associated protein cell-type specifically, including transcription factors, RNA polymerase, and chromatin-modifying proteins. The technique is highly sensitive, highly reproducible, requires no mechanical disruption, cell isolation or antibody purification, and can be performed by anyone with basic molecular biology knowledge. Here, we describe the TaDa method and downstream bioinformatics data processing.
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Affiliation(s)
- Owen J Marshall
- Menzies Institute for Medical Research, University of Tasmania, Hobart, TAS, Australia.
| | - Caroline Delandre
- Menzies Institute for Medical Research, University of Tasmania, Hobart, TAS, Australia
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10
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Sánchez-López A, Espinós-Estévez C, González-Gómez C, Gonzalo P, Andrés-Manzano MJ, Fanjul V, Riquelme-Borja R, Hamczyk MR, Macías Á, Del Campo L, Camafeita E, Vázquez J, Barkaway A, Rolas L, Nourshargh S, Dorado B, Benedicto I, Andrés V. Cardiovascular Progerin Suppression and Lamin A Restoration Rescue Hutchinson-Gilford Progeria Syndrome. Circulation 2021; 144:1777-1794. [PMID: 34694158 PMCID: PMC8614561 DOI: 10.1161/circulationaha.121.055313] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
BACKGROUND Hutchinson-Gilford progeria syndrome (HGPS) is a rare disorder characterized by premature aging and death mainly because of myocardial infarction, stroke, or heart failure. The disease is provoked by progerin, a variant of lamin A expressed in most differentiated cells. Patients look healthy at birth, and symptoms typically emerge in the first or second year of life. Assessing the reversibility of progerin-induced damage and the relative contribution of specific cell types is critical to determining the potential benefits of late treatment and to developing new therapies. METHODS We used CRISPR-Cas9 technology to generate LmnaHGPSrev/HGPSrev (HGPSrev) mice engineered to ubiquitously express progerin while lacking lamin A and allowing progerin suppression and lamin A restoration in a time- and cell type-specific manner on Cre recombinase activation. We characterized the phenotype of HGPSrev mice and crossed them with Cre transgenic lines to assess the effects of suppressing progerin and restoring lamin A ubiquitously at different disease stages as well as specifically in vascular smooth muscle cells and cardiomyocytes. RESULTS Like patients with HGPS, HGPSrev mice appear healthy at birth and progressively develop HGPS symptoms, including failure to thrive, lipodystrophy, vascular smooth muscle cell loss, vascular fibrosis, electrocardiographic anomalies, and precocious death (median lifespan of 15 months versus 26 months in wild-type controls, P<0.0001). Ubiquitous progerin suppression and lamin A restoration significantly extended lifespan when induced in 6-month-old mildly symptomatic mice and even in severely ill animals aged 13 months, although the benefit was much more pronounced on early intervention (84.5% lifespan extension in mildly symptomatic mice, P<0.0001, and 6.7% in severely ill mice, P<0.01). It is remarkable that major vascular alterations were prevented and lifespan normalized in HGPSrev mice when progerin suppression and lamin A restoration were restricted to vascular smooth muscle cells and cardiomyocytes. CONCLUSIONS HGPSrev mice constitute a new experimental model for advancing knowledge of HGPS. Our findings suggest that it is never too late to treat HGPS, although benefit is much more pronounced when progerin is targeted in mice with mild symptoms. Despite the broad expression pattern of progerin and its deleterious effects in many organs, restricting its suppression to vascular smooth muscle cells and cardiomyocytes is sufficient to prevent vascular disease and normalize lifespan.
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Affiliation(s)
- Amanda Sánchez-López
- Centro Nacional de Investigaciones Cardiovasculares Carlos III, Madrid, Spain (A.S.-L., C.E.-E., C.G.-G., P.G., M.J.A.-M., V.F., R.R.-B., M.R.H., A.M., L.d.C., E.C., J.V., B.D., I.B., V.A.).,Centro de Investigación Biomédica en Red de Enfermedades Cardiovasculares, Madrid, Spain (A.S.-L., C.G.-G., P.G., M.J.A.-M., V.F., M.R.H., A.M., L.d.C., E.C., J.V., B.D., V.A.)
| | - Carla Espinós-Estévez
- Centro Nacional de Investigaciones Cardiovasculares Carlos III, Madrid, Spain (A.S.-L., C.E.-E., C.G.-G., P.G., M.J.A.-M., V.F., R.R.-B., M.R.H., A.M., L.d.C., E.C., J.V., B.D., I.B., V.A.)
| | - Cristina González-Gómez
- Centro Nacional de Investigaciones Cardiovasculares Carlos III, Madrid, Spain (A.S.-L., C.E.-E., C.G.-G., P.G., M.J.A.-M., V.F., R.R.-B., M.R.H., A.M., L.d.C., E.C., J.V., B.D., I.B., V.A.).,Centro de Investigación Biomédica en Red de Enfermedades Cardiovasculares, Madrid, Spain (A.S.-L., C.G.-G., P.G., M.J.A.-M., V.F., M.R.H., A.M., L.d.C., E.C., J.V., B.D., V.A.)
| | - Pilar Gonzalo
- Centro Nacional de Investigaciones Cardiovasculares Carlos III, Madrid, Spain (A.S.-L., C.E.-E., C.G.-G., P.G., M.J.A.-M., V.F., R.R.-B., M.R.H., A.M., L.d.C., E.C., J.V., B.D., I.B., V.A.).,Centro de Investigación Biomédica en Red de Enfermedades Cardiovasculares, Madrid, Spain (A.S.-L., C.G.-G., P.G., M.J.A.-M., V.F., M.R.H., A.M., L.d.C., E.C., J.V., B.D., V.A.)
| | - María J Andrés-Manzano
- Centro de Investigación Biomédica en Red de Enfermedades Cardiovasculares, Madrid, Spain (A.S.-L., C.G.-G., P.G., M.J.A.-M., V.F., M.R.H., A.M., L.d.C., E.C., J.V., B.D., V.A.)
| | - Víctor Fanjul
- Centro Nacional de Investigaciones Cardiovasculares Carlos III, Madrid, Spain (A.S.-L., C.E.-E., C.G.-G., P.G., M.J.A.-M., V.F., R.R.-B., M.R.H., A.M., L.d.C., E.C., J.V., B.D., I.B., V.A.).,Centro de Investigación Biomédica en Red de Enfermedades Cardiovasculares, Madrid, Spain (A.S.-L., C.G.-G., P.G., M.J.A.-M., V.F., M.R.H., A.M., L.d.C., E.C., J.V., B.D., V.A.)
| | - Raquel Riquelme-Borja
- Centro Nacional de Investigaciones Cardiovasculares Carlos III, Madrid, Spain (A.S.-L., C.E.-E., C.G.-G., P.G., M.J.A.-M., V.F., R.R.-B., M.R.H., A.M., L.d.C., E.C., J.V., B.D., I.B., V.A.)
| | - Magda R Hamczyk
- Centro Nacional de Investigaciones Cardiovasculares Carlos III, Madrid, Spain (A.S.-L., C.E.-E., C.G.-G., P.G., M.J.A.-M., V.F., R.R.-B., M.R.H., A.M., L.d.C., E.C., J.V., B.D., I.B., V.A.).,Centro de Investigación Biomédica en Red de Enfermedades Cardiovasculares, Madrid, Spain (A.S.-L., C.G.-G., P.G., M.J.A.-M., V.F., M.R.H., A.M., L.d.C., E.C., J.V., B.D., V.A.).,Now with Departamento de Bioquímica y Biología Molecular, Instituto Universitario de Oncología, Universidad de Oviedo, Spain (M.R.H.)
| | - Álvaro Macías
- Centro Nacional de Investigaciones Cardiovasculares Carlos III, Madrid, Spain (A.S.-L., C.E.-E., C.G.-G., P.G., M.J.A.-M., V.F., R.R.-B., M.R.H., A.M., L.d.C., E.C., J.V., B.D., I.B., V.A.).,Centro de Investigación Biomédica en Red de Enfermedades Cardiovasculares, Madrid, Spain (A.S.-L., C.G.-G., P.G., M.J.A.-M., V.F., M.R.H., A.M., L.d.C., E.C., J.V., B.D., V.A.)
| | - Lara Del Campo
- Centro Nacional de Investigaciones Cardiovasculares Carlos III, Madrid, Spain (A.S.-L., C.E.-E., C.G.-G., P.G., M.J.A.-M., V.F., R.R.-B., M.R.H., A.M., L.d.C., E.C., J.V., B.D., I.B., V.A.).,Centro de Investigación Biomédica en Red de Enfermedades Cardiovasculares, Madrid, Spain (A.S.-L., C.G.-G., P.G., M.J.A.-M., V.F., M.R.H., A.M., L.d.C., E.C., J.V., B.D., V.A.).,Now with Departamento de Biología Celular, Facultad de Medicina, Universidad Complutense de Madrid, 28040 Madrid, Spain (L.d.C.)
| | - Emilio Camafeita
- Centro Nacional de Investigaciones Cardiovasculares Carlos III, Madrid, Spain (A.S.-L., C.E.-E., C.G.-G., P.G., M.J.A.-M., V.F., R.R.-B., M.R.H., A.M., L.d.C., E.C., J.V., B.D., I.B., V.A.).,Centro de Investigación Biomédica en Red de Enfermedades Cardiovasculares, Madrid, Spain (A.S.-L., C.G.-G., P.G., M.J.A.-M., V.F., M.R.H., A.M., L.d.C., E.C., J.V., B.D., V.A.)
| | - Jesús Vázquez
- Centro Nacional de Investigaciones Cardiovasculares Carlos III, Madrid, Spain (A.S.-L., C.E.-E., C.G.-G., P.G., M.J.A.-M., V.F., R.R.-B., M.R.H., A.M., L.d.C., E.C., J.V., B.D., I.B., V.A.).,Centro de Investigación Biomédica en Red de Enfermedades Cardiovasculares, Madrid, Spain (A.S.-L., C.G.-G., P.G., M.J.A.-M., V.F., M.R.H., A.M., L.d.C., E.C., J.V., B.D., V.A.)
| | - Anna Barkaway
- Centre for Microvascular Research, William Harvey Research Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, United Kingdom (A.B., L.R., S.N.)
| | - Loïc Rolas
- Centre for Microvascular Research, William Harvey Research Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, United Kingdom (A.B., L.R., S.N.)
| | - Sussan Nourshargh
- Centre for Microvascular Research, William Harvey Research Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, United Kingdom (A.B., L.R., S.N.)
| | - Beatriz Dorado
- Centro Nacional de Investigaciones Cardiovasculares Carlos III, Madrid, Spain (A.S.-L., C.E.-E., C.G.-G., P.G., M.J.A.-M., V.F., R.R.-B., M.R.H., A.M., L.d.C., E.C., J.V., B.D., I.B., V.A.).,Centro de Investigación Biomédica en Red de Enfermedades Cardiovasculares, Madrid, Spain (A.S.-L., C.G.-G., P.G., M.J.A.-M., V.F., M.R.H., A.M., L.d.C., E.C., J.V., B.D., V.A.)
| | - Ignacio Benedicto
- Centro Nacional de Investigaciones Cardiovasculares Carlos III, Madrid, Spain (A.S.-L., C.E.-E., C.G.-G., P.G., M.J.A.-M., V.F., R.R.-B., M.R.H., A.M., L.d.C., E.C., J.V., B.D., I.B., V.A.)
| | - Vicente Andrés
- Centro de Investigación Biomédica en Red de Enfermedades Cardiovasculares, Madrid, Spain (A.S.-L., C.G.-G., P.G., M.J.A.-M., V.F., M.R.H., A.M., L.d.C., E.C., J.V., B.D., V.A.)
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11
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Wade AA, van den Ameele J, Cheetham SW, Yakob R, Brand AH, Nord AS. In vivo targeted DamID identifies CHD8 genomic targets in fetal mouse brain. iScience 2021; 24:103234. [PMID: 34746699 PMCID: PMC8551073 DOI: 10.1016/j.isci.2021.103234] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Revised: 08/11/2021] [Accepted: 10/04/2021] [Indexed: 01/15/2023] Open
Abstract
Genetic studies of autism have revealed causal roles for chromatin remodeling gene mutations. Chromodomain helicase DNA binding protein 8 (CHD8) encodes a chromatin remodeler with significant de novo mutation rates in sporadic autism. However, relationships between CHD8 genomic function and autism-relevant biology remain poorly elucidated. Published studies utilizing ChIP-seq to map CHD8 protein-DNA interactions have high variability, consistent with technical challenges and limitations associated with this method. Thus, complementary approaches are needed to establish CHD8 genomic targets and regulatory functions in developing brain. We used in utero CHD8 Targeted DamID followed by sequencing (TaDa-seq) to characterize CHD8 binding in embryonic mouse cortex. CHD8 TaDa-seq reproduced interaction patterns observed from ChIP-seq and further highlighted CHD8 distal interactions associated with neuronal loci. This study establishes TaDa-seq as a useful alternative for mapping protein-DNA interactions in vivo and provides insights into the regulatory targets of CHD8 and autism-relevant pathophysiology associated with CHD8 mutations.
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Affiliation(s)
- A. Ayanna Wade
- Department of Psychiatry and Behavioral Sciences, University of California, Davis, Davis, CA 95616, USA
- Department of Neurobiology, Physiology and Behavior, University of California, Davis, Davis, CA 95616, USA
| | - Jelle van den Ameele
- The Gurdon Institute and Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge, CB2 1TN, UK
| | - Seth W. Cheetham
- The Gurdon Institute and Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge, CB2 1TN, UK
| | - Rebecca Yakob
- The Gurdon Institute and Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge, CB2 1TN, UK
| | - Andrea H. Brand
- The Gurdon Institute and Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge, CB2 1TN, UK
| | - Alex S. Nord
- Department of Psychiatry and Behavioral Sciences, University of California, Davis, Davis, CA 95616, USA
- Department of Neurobiology, Physiology and Behavior, University of California, Davis, Davis, CA 95616, USA
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12
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Gómez-Saldivar G, Glauser DA, Meister P. Tissue-specific DamID protocol using nanopore sequencing. J Biol Methods 2021; 8:e152. [PMID: 34514013 PMCID: PMC8411031 DOI: 10.14440/jbm.2021.362] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2021] [Revised: 05/05/2021] [Accepted: 05/12/2021] [Indexed: 11/23/2022] Open
Abstract
DNA adenine methylation identification (DamID) is a powerful method to determine DNA binding profiles of proteins at a genomic scale. The method leverages the fusion between a protein of interest and the Dam methyltransferase of E. coli, which methylates proximal DNA in vivo. Here, we present an optimized procedure, which was developed for tissue-specific analyses in Caenorhabditis elegans and successfully used to footprint genes actively transcribed by RNA polymerases and to map transcription factor binding in gene regulatory regions. The present protocol details C. elegans-specific steps involved in the preparation of transgenic lines and genomic DNA samples, as well as broadly applicable steps for the DamID procedure, including the isolation of methylated DNA fragments, the preparation of multiplexed libraries, Nanopore sequencing, and data analysis. Two distinctive features of the approach are (i) the use of an efficient recombination-based strategy to selectively analyze rare cell types and (ii) the use of Nanopore sequencing, which streamlines the process. The method allows researchers to go from genomic DNA samples to sequencing results in less than a week, while being sensitive enough to report reliable DNA footprints in cell types as rare as 2 cells per animal.
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Affiliation(s)
| | | | - Peter Meister
- Cell Fate and Nuclear Organization, Institute of Cell Biology, University of Bern, 3012 Bern, Switzerland
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13
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Aughey GN, Delandre C, McMullen JPD, Southall TD, Marshall OJ. FlyORF-TaDa allows rapid generation of new lines for in vivo cell-type-specific profiling of protein-DNA interactions in Drosophila melanogaster. G3-GENES GENOMES GENETICS 2021; 11:6044134. [PMID: 33561239 PMCID: PMC8022459 DOI: 10.1093/g3journal/jkaa005] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/07/2020] [Accepted: 11/07/2020] [Indexed: 12/01/2022]
Abstract
Targeted DamID (TaDa) is an increasingly popular method of generating cell-type-specific DNA-binding profiles in vivo. Although sensitive and versatile, TaDa requires the generation of new transgenic fly lines for every protein that is profiled, which is both time-consuming and costly. Here, we describe the FlyORF-TaDa system for converting an existing FlyORF library of inducible open reading frames (ORFs) to TaDa lines via a genetic cross, with recombinant progeny easily identifiable by eye color. Profiling the binding of the H3K36me3-associated chromatin protein MRG15 in larval neural stem cells using both FlyORF-TaDa and conventional TaDa demonstrates that new lines generated using this system provide accurate and highly reproducible DamID-binding profiles. Our data further show that MRG15 binds to a subset of active chromatin domains in vivo. Courtesy of the large coverage of the FlyORF library, the FlyORF-TaDa system enables the easy creation of TaDa lines for 74% of all transcription factors and chromatin-modifying proteins within the Drosophila genome.
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Affiliation(s)
- Gabriel N Aughey
- Imperial College London, Sir Ernst Chain Building, South Kensington Campus, London SW7 2AZ, UK
| | - Caroline Delandre
- Menzies Institute for Medical Research, University of Tasmania, 17 Liverpool St, Hobart 7000, Australia
| | - John P D McMullen
- Menzies Institute for Medical Research, University of Tasmania, 17 Liverpool St, Hobart 7000, Australia
| | - Tony D Southall
- Imperial College London, Sir Ernst Chain Building, South Kensington Campus, London SW7 2AZ, UK
| | - Owen J Marshall
- Menzies Institute for Medical Research, University of Tasmania, 17 Liverpool St, Hobart 7000, Australia
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14
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Van de Walle P, Muñoz-Jiménez C, Askjaer P, Schoofs L, Temmerman L. DamID identifies targets of CEH-60/PBX that are associated with neuron development and muscle structure in Caenorhabditis elegans. PLoS One 2020; 15:e0242939. [PMID: 33306687 PMCID: PMC7732058 DOI: 10.1371/journal.pone.0242939] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2020] [Accepted: 11/11/2020] [Indexed: 11/29/2022] Open
Abstract
Transcription factors govern many of the time- and tissue-specific gene expression events in living organisms. CEH-60, a homolog of the TALE transcription factor PBX in vertebrates, was recently characterized as a new regulator of intestinal lipid mobilization in Caenorhabditis elegans. Because CEH-60's orthologs and paralogs exhibit several other functions, notably in neuron and muscle development, and because ceh-60 expression is not limited to the C. elegans intestine, we sought to identify additional functions of CEH-60 through DNA adenine methyltransferase identification (DamID). DamID identifies protein-genome interaction sites through GATC-specific methylation. We here report 872 putative CEH-60 gene targets in young adult animals, and 587 in L2 larvae, many of which are associated with neuron development or muscle structure. In light of this, we investigate morphology and function of ceh-60 expressing AWC neurons, and contraction of pharyngeal muscles. We find no clear functional consequences of loss of ceh-60 in these assays, suggesting that in AWC neurons and pharyngeal muscle, CEH-60 function is likely more subtle or redundant with other factors.
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Affiliation(s)
- Pieter Van de Walle
- Animal Physiology and Neurobiology, University of Leuven (KU Leuven), Leuven, Belgium
| | - Celia Muñoz-Jiménez
- Andalusian Center for Developmental Biology (CABD), CSIC/JA/Universidad Pablo de Olavide, Seville, Spain
| | - Peter Askjaer
- Andalusian Center for Developmental Biology (CABD), CSIC/JA/Universidad Pablo de Olavide, Seville, Spain
| | - Liliane Schoofs
- Animal Physiology and Neurobiology, University of Leuven (KU Leuven), Leuven, Belgium
| | - Liesbet Temmerman
- Animal Physiology and Neurobiology, University of Leuven (KU Leuven), Leuven, Belgium
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15
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Min B, Park JS, Jeong YS, Jeon K, Kang YK. Dnmt1 binds and represses genomic retroelements via DNA methylation in mouse early embryos. Nucleic Acids Res 2020; 48:8431-8444. [PMID: 32667642 PMCID: PMC7470951 DOI: 10.1093/nar/gkaa584] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2019] [Revised: 06/10/2020] [Accepted: 07/03/2020] [Indexed: 12/12/2022] Open
Abstract
Genome-wide passive DNA demethylation in cleavage-stage mouse embryos is related to the cytoplasmic localization of the maintenance methyltransferase DNMT1. However, recent studies provided evidences of the nuclear localization of DNMT1 and its contribution to the maintenance of methylation levels of imprinted regions and other genomic loci in early embryos. Using the DNA adenine methylase identification method, we identified Dnmt1-binding regions in four- and eight-cell embryos. The unbiased distribution of Dnmt1 peaks in the genic regions (promoters and CpG islands) as well as the absence of a correlation between the Dnmt1 peaks and the expression levels of the peak-associated genes refutes the active participation of Dnmt1 in the transcriptional regulation of genes in the early developmental period. Instead, Dnmt1 was found to associate with genomic retroelements in a greatly biased fashion, particularly with the LINE1 (long interspersed nuclear elements) and ERVK (endogenous retrovirus type K) sequences. Transcriptomic analysis revealed that the transcripts of the Dnmt1-enriched retroelements were overrepresented in Dnmt1 knockdown embryos. Finally, methyl-CpG-binding domain sequencing proved that the Dnmt1-enriched retroelements, which were densely methylated in wild-type embryos, became demethylated in the Dnmt1-depleted embryos. Our results indicate that Dnmt1 is involved in the repression of retroelements through DNA methylation in early mouse development.
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Affiliation(s)
- Byungkuk Min
- Development and Differentiation Research Center, Korea Research Institute of Bioscience Biotechnology (KRIBB), 125 Gwahak-ro, Yuseong-gu, Daejeon 34141, South Korea
| | - Jung Sun Park
- Development and Differentiation Research Center, Korea Research Institute of Bioscience Biotechnology (KRIBB), 125 Gwahak-ro, Yuseong-gu, Daejeon 34141, South Korea
| | - Young Sun Jeong
- Development and Differentiation Research Center, Korea Research Institute of Bioscience Biotechnology (KRIBB), 125 Gwahak-ro, Yuseong-gu, Daejeon 34141, South Korea
| | - Kyuheum Jeon
- Development and Differentiation Research Center, Korea Research Institute of Bioscience Biotechnology (KRIBB), 125 Gwahak-ro, Yuseong-gu, Daejeon 34141, South Korea.,Department of Functional Genomics, Korea University of Science and Technology, Daejeon 34113, South Korea
| | - Yong-Kook Kang
- Development and Differentiation Research Center, Korea Research Institute of Bioscience Biotechnology (KRIBB), 125 Gwahak-ro, Yuseong-gu, Daejeon 34141, South Korea.,Department of Functional Genomics, Korea University of Science and Technology, Daejeon 34113, South Korea
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16
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van Schaik T, Vos M, Peric-Hupkes D, Hn Celie P, van Steensel B. Cell cycle dynamics of lamina-associated DNA. EMBO Rep 2020; 21:e50636. [PMID: 32893442 PMCID: PMC7645246 DOI: 10.15252/embr.202050636] [Citation(s) in RCA: 53] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2020] [Revised: 08/07/2020] [Accepted: 08/11/2020] [Indexed: 12/12/2022] Open
Abstract
In mammalian interphase nuclei, more than one thousand large genomic regions are positioned at the nuclear lamina (NL). These lamina‐associated domains (LADs) are involved in gene regulation and may provide a backbone for the folding of interphase chromosomes. Little is known about the dynamics of LADs during interphase, in particular at the onset of G1 phase and during DNA replication. We developed an antibody‐based variant of the DamID technology (named pA‐DamID) that allows us to map and visualize genome–NL interactions with high temporal resolution. Application of pA‐DamID combined with synchronization and cell sorting experiments reveals that LAD–NL contacts are generally rapidly established early in G1 phase. However, LADs on the distal ~25 Mb of most chromosomes tend to contact the NL first and then gradually detach, while centromere‐proximal LADs accumulate gradually at the NL. Furthermore, our data indicate that S‐phase chromatin shows transiently increased lamin interactions. These findings highlight a dynamic choreography of LAD–NL contacts during interphase progression and illustrate the usefulness of pA‐DamID to study the dynamics of genome compartmentalization.
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Affiliation(s)
- Tom van Schaik
- Division of Gene Regulation, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Mabel Vos
- Division of Gene Regulation, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Daan Peric-Hupkes
- Division of Gene Regulation, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Patrick Hn Celie
- Protein Facility, Oncode Institute, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Bas van Steensel
- Division of Gene Regulation, Netherlands Cancer Institute, Amsterdam, The Netherlands.,Department of Cell Biology, Erasmus University Medical Center, Rotterdam, The Netherlands
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17
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A viral toolkit for recording transcription factor-DNA interactions in live mouse tissues. Proc Natl Acad Sci U S A 2020; 117:10003-10014. [PMID: 32300008 DOI: 10.1073/pnas.1918241117] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
Transcription factors (TFs) enact precise regulation of gene expression through site-specific, genome-wide binding. Common methods for TF-occupancy profiling, such as chromatin immunoprecipitation, are limited by requirement of TF-specific antibodies and provide only end-point snapshots of TF binding. Alternatively, TF-tagging techniques, in which a TF is fused to a DNA-modifying enzyme that marks TF-binding events across the genome as they occur, do not require TF-specific antibodies and offer the potential for unique applications, such as recording of TF occupancy over time and cell type specificity through conditional expression of the TF-enzyme fusion. Here, we create a viral toolkit for one such method, calling cards, and demonstrate that these reagents can be delivered to the live mouse brain and used to report TF occupancy. Further, we establish a Cre-dependent calling cards system and, in proof-of-principle experiments, show utility in defining cell type-specific TF profiles and recording and integrating TF-binding events across time. This versatile approach will enable unique studies of TF-mediated gene regulation in live animal models.
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18
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Kribelbauer JF, Loker RE, Feng S, Rastogi C, Abe N, Rube HT, Bussemaker HJ, Mann RS. Context-Dependent Gene Regulation by Homeodomain Transcription Factor Complexes Revealed by Shape-Readout Deficient Proteins. Mol Cell 2020; 78:152-167.e11. [PMID: 32053778 DOI: 10.1016/j.molcel.2020.01.027] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2019] [Revised: 12/01/2019] [Accepted: 01/27/2020] [Indexed: 01/09/2023]
Abstract
Eukaryotic transcription factors (TFs) form complexes with various partner proteins to recognize their genomic target sites. Yet, how the DNA sequence determines which TF complex forms at any given site is poorly understood. Here, we demonstrate that high-throughput in vitro DNA binding assays coupled with unbiased computational analysis provide unprecedented insight into how different DNA sequences select distinct compositions and configurations of homeodomain TF complexes. Using inferred knowledge about minor groove width readout, we design targeted protein mutations that destabilize homeodomain binding both in vitro and in vivo in a complex-specific manner. By performing parallel systematic evolution of ligands by exponential enrichment sequencing (SELEX-seq), chromatin immunoprecipitation sequencing (ChIP-seq), RNA sequencing (RNA-seq), and Hi-C assays, we not only classify the majority of in vivo binding events in terms of complex composition but also infer complex-specific functions by perturbing the gene regulatory network controlled by a single complex.
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Affiliation(s)
- Judith F Kribelbauer
- Department of Biological Sciences, Columbia University, New York, NY 10025, USA; Department of Systems Biology, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Ryan E Loker
- Department of Biochemistry and Molecular Biophysics, Mortimer B. Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY 10027, USA
| | - Siqian Feng
- Department of Biochemistry and Molecular Biophysics, Mortimer B. Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY 10027, USA
| | - Chaitanya Rastogi
- Department of Biological Sciences, Columbia University, New York, NY 10025, USA; Department of Systems Biology, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Namiko Abe
- Department of Biochemistry and Molecular Biophysics, Mortimer B. Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY 10027, USA
| | - H Tomas Rube
- Department of Biological Sciences, Columbia University, New York, NY 10025, USA; Department of Systems Biology, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Harmen J Bussemaker
- Department of Biological Sciences, Columbia University, New York, NY 10025, USA; Department of Systems Biology, Columbia University Irving Medical Center, New York, NY 10032, USA.
| | - Richard S Mann
- Department of Systems Biology, Columbia University Irving Medical Center, New York, NY 10032, USA; Department of Biochemistry and Molecular Biophysics, Mortimer B. Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY 10027, USA; Department of Neuroscience, Columbia University, New York, NY 10027, USA.
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19
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Kobayashi T, Kobayashi H, Goto T, Takashima T, Oikawa M, Ikeda H, Terada R, Yoshida F, Sanbo M, Nakauchi H, Kurimoto K, Hirabayashi M. Germline development in rat revealed by visualization and deletion of Prdm14. Development 2020; 147:dev.183798. [PMID: 32001439 DOI: 10.1242/dev.183798] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2019] [Accepted: 01/15/2020] [Indexed: 12/22/2022]
Abstract
Primordial germ cells (PGCs), the founder cells of the germline, are specified in pre-gastrulating embryos in mammals, and subsequently migrate towards gonads to mature into functional gametes. Here, we investigated PGC development in rats, by genetically modifying Prdm14, a unique marker and an essential PGC transcriptional regulator. We trace PGC development in rats, for the first time, from specification until the sex determination stage in fetal gonads using Prdm14 H2BVenus knock-in rats. We uncover that the crucial role of Prdm14 in PGC specification is conserved between rat and mice, by analyzing Prdm14-deficient rat embryos. Notably, loss of Prdm14 completely abrogates the PGC program, as demonstrated by failure of the maintenance and/or activation of germ cell markers and pluripotency genes. Finally, we profile the transcriptome of the post-implantation epiblast and all PGC stages in rat to reveal enrichment of distinct gene sets at each transition point, thereby providing an accurate transcriptional timeline for rat PGC development. Thus, the novel genetically modified rats and data sets obtained in this study will advance our knowledge on conserved versus species-specific features for germline development in mammals.
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Affiliation(s)
- Toshihiro Kobayashi
- Section of Mammalian Transgenesis, Center for Genetic Analysis of Behavior, National Institute for Physiological Sciences, Okazaki, 444-8787 Aichi, Japan.,Department of Physiological Sciences, The Graduate University of Advanced Studies, Okazaki, 444-8787 Aichi, Japan
| | - Hisato Kobayashi
- Department of Embryology, Nara Medical University, Kashihara, 634-0813 Nara, Japan
| | - Teppei Goto
- Section of Mammalian Transgenesis, Center for Genetic Analysis of Behavior, National Institute for Physiological Sciences, Okazaki, 444-8787 Aichi, Japan
| | - Tomoya Takashima
- Department of Bioscience, Tokyo University of Agriculture, Setagaya-ku, 156-8502 Tokyo, Japan
| | - Mami Oikawa
- Section of Mammalian Transgenesis, Center for Genetic Analysis of Behavior, National Institute for Physiological Sciences, Okazaki, 444-8787 Aichi, Japan
| | - Hiroki Ikeda
- Department of Embryology, Nara Medical University, Kashihara, 634-0813 Nara, Japan
| | - Reiko Terada
- Section of Mammalian Transgenesis, Center for Genetic Analysis of Behavior, National Institute for Physiological Sciences, Okazaki, 444-8787 Aichi, Japan
| | - Fumika Yoshida
- Section of Mammalian Transgenesis, Center for Genetic Analysis of Behavior, National Institute for Physiological Sciences, Okazaki, 444-8787 Aichi, Japan
| | - Makoto Sanbo
- Section of Mammalian Transgenesis, Center for Genetic Analysis of Behavior, National Institute for Physiological Sciences, Okazaki, 444-8787 Aichi, Japan
| | - Hiromitsu Nakauchi
- Division of Stem Cell Therapy, Institute of Medical Science, The University of Tokyo, Minato-ku, 108-8639 Tokyo, Japan.,Institute for Stem Cell Biology and Regenerative Medicine, Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Kazuki Kurimoto
- Department of Embryology, Nara Medical University, Kashihara, 634-0813 Nara, Japan
| | - Masumi Hirabayashi
- Section of Mammalian Transgenesis, Center for Genetic Analysis of Behavior, National Institute for Physiological Sciences, Okazaki, 444-8787 Aichi, Japan .,Department of Physiological Sciences, The Graduate University of Advanced Studies, Okazaki, 444-8787 Aichi, Japan
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20
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Aloia L, McKie MA, Vernaz G, Cordero-Espinoza L, Aleksieva N, van den Ameele J, Antonica F, Font-Cunill B, Raven A, Aiese Cigliano R, Belenguer G, Mort RL, Brand AH, Zernicka-Goetz M, Forbes SJ, Miska EA, Huch M. Epigenetic remodelling licences adult cholangiocytes for organoid formation and liver regeneration. Nat Cell Biol 2019; 21:1321-1333. [PMID: 31685987 PMCID: PMC6940196 DOI: 10.1038/s41556-019-0402-6] [Citation(s) in RCA: 89] [Impact Index Per Article: 17.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2019] [Accepted: 09/11/2019] [Indexed: 12/11/2022]
Abstract
Following severe or chronic liver injury, adult ductal cells (cholangiocytes) contribute to regeneration by restoring both hepatocytes and cholangiocytes. We recently showed that ductal cells clonally expand as self-renewing liver organoids that retain their differentiation capacity into both hepatocytes and ductal cells. However, the molecular mechanisms by which adult ductal-committed cells acquire cellular plasticity, initiate organoids and regenerate the damaged tissue remain largely unknown. Here, we describe that ductal cells undergo a transient, genome-wide, remodelling of their transcriptome and epigenome during organoid initiation and in vivo following tissue damage. TET1-mediated hydroxymethylation licences differentiated ductal cells to initiate organoids and activate the regenerative programme through the transcriptional regulation of stem-cell genes and regenerative pathways including the YAP-Hippo signalling. Our results argue in favour of the remodelling of genomic methylome/hydroxymethylome landscapes as a general mechanism by which differentiated cells exit a committed state in response to tissue damage.
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Affiliation(s)
- Luigi Aloia
- The Wellcome Trust/CRUK Gurdon Institute, University of Cambridge, Cambridge, UK
- Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge, UK
- Wellcome Trust - Medical Research Council Stem Cell Institute, University of Cambridge, Cambridge, UK
| | - Mikel Alexander McKie
- The Wellcome Trust/CRUK Gurdon Institute, University of Cambridge, Cambridge, UK
- Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge, UK
- Wellcome Trust - Medical Research Council Stem Cell Institute, University of Cambridge, Cambridge, UK
| | - Grégoire Vernaz
- The Wellcome Trust/CRUK Gurdon Institute, University of Cambridge, Cambridge, UK
- Department of Genetics, University of Cambridge, Cambridge, UK
- Wellcome Sanger Institute, Hinxton, UK
| | - Lucía Cordero-Espinoza
- The Wellcome Trust/CRUK Gurdon Institute, University of Cambridge, Cambridge, UK
- Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge, UK
- Wellcome Trust - Medical Research Council Stem Cell Institute, University of Cambridge, Cambridge, UK
| | - Niya Aleksieva
- MRC Centre for Regenerative Medicine, University of Edinburgh, Edinburgh, UK
| | - Jelle van den Ameele
- The Wellcome Trust/CRUK Gurdon Institute, University of Cambridge, Cambridge, UK
- Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge, UK
| | - Francesco Antonica
- Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge, UK
| | - Berta Font-Cunill
- The Wellcome Trust/CRUK Gurdon Institute, University of Cambridge, Cambridge, UK
- Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge, UK
- Wellcome Trust - Medical Research Council Stem Cell Institute, University of Cambridge, Cambridge, UK
| | - Alexander Raven
- MRC Centre for Regenerative Medicine, University of Edinburgh, Edinburgh, UK
| | | | - German Belenguer
- The Wellcome Trust/CRUK Gurdon Institute, University of Cambridge, Cambridge, UK
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | - Richard L Mort
- Division of Biomedical and Life Sciences, Faculty of Health and Medicine, Lancaster University, Bailrigg, Lancaster, UK
| | - Andrea H Brand
- The Wellcome Trust/CRUK Gurdon Institute, University of Cambridge, Cambridge, UK
- Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge, UK
| | - Magdalena Zernicka-Goetz
- Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge, UK
- Division of Biology and Biological Engineering, Caltech, Pasadena, CA, USA
| | - Stuart J Forbes
- MRC Centre for Regenerative Medicine, University of Edinburgh, Edinburgh, UK
| | - Eric A Miska
- The Wellcome Trust/CRUK Gurdon Institute, University of Cambridge, Cambridge, UK
- Department of Genetics, University of Cambridge, Cambridge, UK
- Wellcome Sanger Institute, Hinxton, UK
| | - Meritxell Huch
- The Wellcome Trust/CRUK Gurdon Institute, University of Cambridge, Cambridge, UK.
- Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge, UK.
- Wellcome Trust - Medical Research Council Stem Cell Institute, University of Cambridge, Cambridge, UK.
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany.
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21
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Rakow S, Pullamsetti SS, Bauer UM, Bouchard C. Assaying epigenome functions of PRMTs and their substrates. Methods 2019; 175:53-65. [PMID: 31542509 DOI: 10.1016/j.ymeth.2019.09.014] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2019] [Revised: 09/09/2019] [Accepted: 09/16/2019] [Indexed: 12/20/2022] Open
Abstract
Among the widespread and increasing number of identified post-translational modifications (PTMs), arginine methylation is catalyzed by the protein arginine methyltransferases (PRMTs) and regulates fundamental processes in cells, such as gene regulation, RNA processing, translation, and signal transduction. As epigenetic regulators, PRMTs play key roles in pluripotency, differentiation, proliferation, survival, and apoptosis, which are essential biological programs leading to development, adult homeostasis but also pathological conditions including cancer. A full understanding of the molecular mechanisms that underlie PRMT-mediated gene regulation requires the genome wide mapping of each player, i.e., PRMTs, their substrates and epigenetic marks, methyl-marks readers as well as interaction partners, in a thorough and unambiguous manner. However, despite the tremendous advances in high throughput sequencing technologies and the numerous efforts from the scientific community, the epigenomic profiling of PRMTs as well as their histone and non-histone substrates still remains a big challenge owing to obvious limitations in tools and methodologies. This review will summarize the present knowledge about the genome wide mapping of PRMTs and their substrates as well as the technical approaches currently in use. The limitations and pitfalls of the technical tools along with conventional approaches will be then discussed in detail. Finally, potential new strategies for chromatin profiling of PRMTs and histone substrates will be proposed and described.
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Affiliation(s)
- Sinja Rakow
- Institute for Molecular Biology and Tumor Research (IMT), Philipps University of Marburg, Hans-Meerwein-Str. 2, BMFZ, 35043 Marburg, Germany
| | - Soni Savai Pullamsetti
- Department of Lung Development and Remodeling, Max Planck Institute for Heart and Lung Research, Member of the German Center for Lung Research (DZL), Bad Nauheim, Germany
| | - Uta-Maria Bauer
- Institute for Molecular Biology and Tumor Research (IMT), Philipps University of Marburg, Hans-Meerwein-Str. 2, BMFZ, 35043 Marburg, Germany
| | - Caroline Bouchard
- Institute for Molecular Biology and Tumor Research (IMT), Philipps University of Marburg, Hans-Meerwein-Str. 2, BMFZ, 35043 Marburg, Germany.
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22
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Lucas T, Kohwi M. From insects to mammals: regulation of genome architecture in neural development. Curr Opin Neurobiol 2019; 59:146-156. [PMID: 31299459 DOI: 10.1016/j.conb.2019.05.006] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2019] [Accepted: 05/28/2019] [Indexed: 10/26/2022]
Abstract
One of the hallmarks of the metazoan genome is that genes are non-randomly positioned within the cell nucleus; in fact, the entire genome is packaged in a highly organized manner to orchestrate proper gene expression for each cell type. This is an especially daunting task for the development of the brain, which consists of an incredibly diverse population of neural cells. How genome architecture is established, maintained, and regulated to promote diverse cell fates and functions are fascinating questions with important implications in development and disease. The explosion in various biochemical and imaging techniques to analyze chromatin is now making it possible to interrogate the genome at an unprecedented resolution. Here we will focus on current advances in understanding genome architecture and gene regulation in the context of neural development.
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Affiliation(s)
- Tanguy Lucas
- Department of Neuroscience, Mortimer B. Zuckerman Institute for Mind Brain Behavior, Kavli Institute for Brain Sciences, Columbia University, New York, NY, United States
| | - Minoree Kohwi
- Department of Neuroscience, Mortimer B. Zuckerman Institute for Mind Brain Behavior, Kavli Institute for Brain Sciences, Columbia University, New York, NY, United States.
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23
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Kribelbauer JF, Rastogi C, Bussemaker HJ, Mann RS. Low-Affinity Binding Sites and the Transcription Factor Specificity Paradox in Eukaryotes. Annu Rev Cell Dev Biol 2019; 35:357-379. [PMID: 31283382 DOI: 10.1146/annurev-cellbio-100617-062719] [Citation(s) in RCA: 110] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Eukaryotic transcription factors (TFs) from the same structural family tend to bind similar DNA sequences, despite the ability of these TFs to execute distinct functions in vivo. The cell partly resolves this specificity paradox through combinatorial strategies and the use of low-affinity binding sites, which are better able to distinguish between similar TFs. However, because these sites have low affinity, it is challenging to understand how TFs recognize them in vivo. Here, we summarize recent findings and technological advancements that allow for the quantification and mechanistic interpretation of TF recognition across a wide range of affinities. We propose a model that integrates insights from the fields of genetics and cell biology to provide further conceptual understanding of TF binding specificity. We argue that in eukaryotes, target specificity is driven by an inhomogeneous 3D nuclear distribution of TFs and by variation in DNA binding affinity such that locally elevated TF concentration allows low-affinity binding sites to be functional.
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Affiliation(s)
- Judith F Kribelbauer
- Department of Biological Sciences, Columbia University, New York, NY 10027, USA; .,Department of Systems Biology, Columbia University Irving Medical Center, New York, NY 10031, USA;
| | - Chaitanya Rastogi
- Department of Biological Sciences, Columbia University, New York, NY 10027, USA; .,Department of Systems Biology, Columbia University Irving Medical Center, New York, NY 10031, USA;
| | - Harmen J Bussemaker
- Department of Biological Sciences, Columbia University, New York, NY 10027, USA; .,Department of Systems Biology, Columbia University Irving Medical Center, New York, NY 10031, USA;
| | - Richard S Mann
- Department of Systems Biology, Columbia University Irving Medical Center, New York, NY 10031, USA; .,Department of Biochemistry and Molecular Biophysics, Columbia University Irving Medical Center, New York, NY 10031, USA.,Mortimer B. Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY 10027, USA
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24
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Vázquez-Marín J, Gutiérrez-Triana JA, Almuedo-Castillo M, Buono L, Gómez-Skarmeta JL, Mateo JL, Wittbrodt J, Martínez-Morales JR. yap1b, a divergent Yap/Taz family member, cooperates with yap1 in survival and morphogenesis via common transcriptional targets. Development 2019; 146:dev.173286. [PMID: 31142542 DOI: 10.1242/dev.173286] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2018] [Accepted: 05/17/2019] [Indexed: 11/20/2022]
Abstract
Yap1/Taz are well-known Hippo effectors triggering complex transcriptional programs controlling growth, survival and cancer progression. Here, we describe yap1b, a new Yap1/Taz family member with a unique transcriptional activation domain that cannot be phosphorylated by Src/Yes kinases. We show that yap1b evolved specifically in euteleosts (i.e. including medaka but not zebrafish) by duplication and adaptation of yap1. Using DamID-seq, we generated maps of chromatin occupancy for Yap1, Taz (Wwtr1) and Yap1b in gastrulating zebrafish and medaka embryos. Our comparative analyses uncover the genetic programs controlled by Yap family proteins during early embryogenesis, and show largely overlapping targets for Yap1 and Yap1b. CRISPR/Cas9-induced mutation of yap1b in medaka does not result in an overt phenotype during embryogenesis or adulthood. However, yap1b mutation strongly enhances the embryonic malformations observed in yap1 mutants. Thus yap1 -/-; yap1b -/- double mutants display more severe body flattening, eye misshaping and increased apoptosis than yap1 -/- single mutants, thus revealing overlapping gene functions. Our results indicate that, despite its divergent transactivation domain, Yap1b cooperates with Yap1 to regulate cell survival and tissue morphogenesis during early development.
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Affiliation(s)
| | - José Arturo Gutiérrez-Triana
- Centre for Organismal Studies (COS), University of Heidelberg, 69120 Heidelberg, Germany.,Escuela de Microbiología, Facultad de la Salud, Universidad Industrial de Santander, Bucaramanga, 680002, Colombia
| | | | - Lorena Buono
- Centro Andaluz de Biología del Desarrollo (CSIC/UPO/JA), 41013 Seville, Spain
| | | | - Juan Luis Mateo
- Centre for Organismal Studies (COS), University of Heidelberg, 69120 Heidelberg, Germany.,Departamento de Informática, Universidad de Oviedo, Oviedo 33005, Spain
| | - Joachim Wittbrodt
- Centre for Organismal Studies (COS), University of Heidelberg, 69120 Heidelberg, Germany
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25
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PRDM14 controls X-chromosomal and global epigenetic reprogramming of H3K27me3 in migrating mouse primordial germ cells. Epigenetics Chromatin 2019; 12:38. [PMID: 31221220 PMCID: PMC6585054 DOI: 10.1186/s13072-019-0284-7] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2019] [Accepted: 06/12/2019] [Indexed: 01/18/2023] Open
Abstract
Background In order to prepare the genome for gametogenesis, primordial germ cells (PGCs) undergo extensive epigenetic reprogramming during migration toward the gonads in mammalian embryos. This includes changes on a genome-wide scale and additionally in females the remodeling of the inactive X-chromosome to enable X-chromosome reactivation (XCR). However, if global remodeling and X-chromosomal remodeling are related, how they occur in PGCs in vivo in relation to their migration progress and which factors are important are unknown. Results Here we identify the germ cell determinant PR-domain containing protein 14 (PRDM14) as the first known factor that is instrumental for both global reprogramming and X-chromosomal reprogramming in migrating mouse PGCs. We find that global upregulation of the repressive histone H3 lysine 27 trimethylation (H3K27me3) mark is PRDM14 dosage dependent in PGCs of both sexes. When focusing on XCR, we observed that PRDM14 is required for removal of H3K27me3 from the inactive X-chromosome, which, in contrast to global upregulation, takes place progressively along the PGC migration path. Furthermore, we show that global and X-chromosomal reprogramming of H3K27me3 are functionally separable, despite their common regulation by PRDM14. Conclusions In summary, here we provide new insight and spatiotemporal resolution to the progression and regulation of epigenome remodeling along mouse PGC migration in vivo and link epigenetic reprogramming to its developmental context. Electronic supplementary material The online version of this article (10.1186/s13072-019-0284-7) contains supplementary material, which is available to authorized users.
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26
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Szczesnik T, Ho JWK, Sherwood R. Dam mutants provide improved sensitivity and spatial resolution for profiling transcription factor binding. Epigenetics Chromatin 2019; 12:36. [PMID: 31196130 PMCID: PMC6567924 DOI: 10.1186/s13072-019-0273-x] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2019] [Accepted: 04/23/2019] [Indexed: 11/17/2022] Open
Abstract
DamID, in which a protein of interest is fused to Dam methylase, enables mapping of protein-DNA binding through readout of adenine methylation in genomic DNA.
DamID offers a compelling alternative to chromatin immunoprecipitation sequencing (ChIP-Seq), particularly in cases where cell number or antibody availability is limiting. This comes at a cost, however, of high non-specific signal and a lowered spatial resolution of several kb, limiting its application to transcription factor-DNA binding. Here we show that mutations in Dam, when fused to the transcription factor Tcf7l2, greatly reduce non-specific methylation. Combined with a simplified DamID sequencing protocol, we find that these Dam mutants allow for accurate detection of transcription factor binding at a sensitivity and spatial resolution closely matching that seen in ChIP-seq.
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Affiliation(s)
- Tomasz Szczesnik
- Victor Chang Cardiac Research Institute, Darlinghurst, NSW, 2010, Australia.,St Vincent's Clinical School, University of New South Wales, Darlinghurst, NSW, 2010, Australia
| | - Joshua W K Ho
- Victor Chang Cardiac Research Institute, Darlinghurst, NSW, 2010, Australia.,St Vincent's Clinical School, University of New South Wales, Darlinghurst, NSW, 2010, Australia.,School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong, SAR, China
| | - Richard Sherwood
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, 02115, USA. .,Hubrecht Institute, 3584 CT, Utrecht, The Netherlands.
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27
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Aughey GN, Cheetham SW, Southall TD. DamID as a versatile tool for understanding gene regulation. Development 2019; 146:146/6/dev173666. [PMID: 30877125 PMCID: PMC6451315 DOI: 10.1242/dev.173666] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2018] [Accepted: 02/18/2019] [Indexed: 12/22/2022]
Abstract
The interaction of proteins and RNA with chromatin underlies the regulation of gene expression. The ability to profile easily these interactions is fundamental for understanding chromatin biology in vivo. DNA adenine methyltransferase identification (DamID) profiles genome-wide protein-DNA interactions without antibodies, fixation or protein pull-downs. Recently, DamID has been adapted for applications beyond simple assaying of protein-DNA interactions, such as for studying RNA-chromatin interactions, chromatin accessibility and long-range chromosome interactions. Here, we provide an overview of DamID and introduce improvements to the technology, discuss their applications and compare alternative methodologies. Summary: This Primer provides an overview of DNA adenine methyltransferase identification (DamID), which is used to profile genome-wide chromatin interactions, and introduces recent improvements to the technology.
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Affiliation(s)
- Gabriel N Aughey
- Department of Life Sciences, Imperial College London, Sir Ernst Chain Building, London, SW7 2AZ, UK
| | - Seth W Cheetham
- Mater Research Institute-University of Queensland, TRI Building, Woolloongabba, QLD 4102, Australia
| | - Tony D Southall
- Department of Life Sciences, Imperial College London, Sir Ernst Chain Building, London, SW7 2AZ, UK
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28
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TaDa! Analysing cell type-specific chromatin in vivo with Targeted DamID. Curr Opin Neurobiol 2019; 56:160-166. [PMID: 30844670 DOI: 10.1016/j.conb.2019.01.021] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2019] [Accepted: 01/23/2019] [Indexed: 01/16/2023]
Abstract
The emergence of neuronal diversity during development of the nervous system relies on dynamic changes in the epigenetic landscape of neural stem cells and their progeny. Targeted DamID (TaDa) is proving invaluable in identifying the genome-wide binding sites of chromatin-associated proteins in vivo, without fixation, cell isolation, or immunoprecipitation. The simplicity and efficiency of the technique have led to an ever-expanding TaDa toolbox. These tools enable profiling of gene expression and chromatin accessibility, as well as the identification of the genome-wide binding sites of chromatin complexes, transcription factors and RNAs. Here, we review these new developments, with particular emphasis on the use of TaDa in studying neuronal specification.
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29
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Sen SQ, Chanchani S, Southall TD, Doe CQ. Neuroblast-specific open chromatin allows the temporal transcription factor, Hunchback, to bind neuroblast-specific loci. eLife 2019; 8:44036. [PMID: 30694180 PMCID: PMC6377230 DOI: 10.7554/elife.44036] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2018] [Accepted: 01/24/2019] [Indexed: 12/12/2022] Open
Abstract
Spatial and temporal cues are required to specify neuronal diversity, but how these cues are integrated in neural progenitors remains unknown. Drosophila progenitors (neuroblasts) are a good model: they are individually identifiable with relevant spatial and temporal transcription factors known. Here we test whether spatial/temporal factors act independently or sequentially in neuroblasts. We used Targeted DamID to identify genomic binding sites of the Hunchback temporal factor in two neuroblasts (NB5-6 and NB7-4) that make different progeny. Hunchback targets were different in each neuroblast, ruling out the independent specification model. Moreover, each neuroblast had distinct open chromatin domains, which correlated with differential Hb-bound loci in each neuroblast. Importantly, the Gsb/Pax3 spatial factor, expressed in NB5-6 but not NB7-4, had genomic binding sites correlated with open chromatin in NB5-6, but not NB7-4. Our data support a model in which early-acting spatial factors like Gsb establish neuroblast-specific open chromatin domains, leading to neuroblast-specific temporal factor binding and the production of different neurons in each neuroblast lineage. The human brain is considered to be the most complicated object in the universe, but it only takes a handful of stem cells to make one. The process depends on two types of information: signals separated across space and time. Spatial cues tell a stem cell what type of cell it is going to be, while temporal cues work as molecular clocks to generate a sequence of different neurons over time. Together, these cues generate the large array of cell types in the nervous system. Each stem cell occupies its own space in the developing body and receives its own spatial cues, but they all follow the same timeline. For example, proteins called transcription factors act as molecular clocks and interact with specific genes, telling the cell when to turn them on or off. The same series of transcription factors operates in different stem cells, but they have different effects. So far, it has been unclear whether spatial and temporal signals work independently or sequentially to generate new cell types. To find out, Sen et al. studied two distinct, developing stem cells in fruit flies, which receive different spatial signals. Transcription factors only work if they are able to get to their target genes. Cells can open or close access to different genes by changing the structure of the chromatin wrapping that surrounds the genes. In the experiments, a marker was used to reveal the areas of open chromatin in each of the cells. Another marker was used to track the transcription factors. The results showed that the areas of open chromatin varied between stem cells. Moreover, although both cells used the same transcription factor called Hunchback, it targeted different genes in each stem cell. This was due to changes in the chromatin wrapping: Hunchback only acted in areas where the chromatin was open. This suggests that the spatial cues first sculpt the chromatin, making some genes easier to get to than others. Then, the same transcription factors go to the accessible gene, which will differ from one stem cell to another. These findings help us to understand how different types of brain cells develop, which may also aid us in finding a way how to engineer specific cell types. If we could turn stem cells into different types of brain cells, it might help us to treat brain diseases. This may involve giving the right spatial signal before starting the temporal cues.
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Affiliation(s)
- Sonia Q Sen
- Institute of Neuroscience, Institute of Molecular Biology, Howard Hughes Medical Institute, University of Oregon, Eugene, United States
| | - Sachin Chanchani
- Institute of Neuroscience, Institute of Molecular Biology, Howard Hughes Medical Institute, University of Oregon, Eugene, United States
| | - Tony D Southall
- Department of Life Sciences, Imperial College London, London, United Kingdom
| | - Chris Q Doe
- Institute of Neuroscience, Institute of Molecular Biology, Howard Hughes Medical Institute, University of Oregon, Eugene, United States
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