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Prodani C, Irvine EE, Sardini A, Gleneadie HJ, Dimond A, Van de Pette M, John R, Kokkinou M, Howes O, Withers DJ, Ungless MA, Merkenschlager M, Fisher AG. Protein restriction during pregnancy alters Cdkn1c silencing, dopamine circuitry and offspring behaviour without changing expression of key neuronal marker genes. Sci Rep 2024; 14:8528. [PMID: 38609446 PMCID: PMC11014953 DOI: 10.1038/s41598-024-59083-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2023] [Accepted: 04/07/2024] [Indexed: 04/14/2024] Open
Abstract
We tracked the consequences of in utero protein restriction in mice throughout their development and life course using a luciferase-based allelic reporter of imprinted Cdkn1c. Exposure to gestational low-protein diet (LPD) results in the inappropriate expression of paternally inherited Cdkn1c in the brains of embryonic and juvenile mice. These animals were characterised by a developmental delay in motor skills, and by behavioural alterations indicative of reduced anxiety. Exposure to LPD in utero resulted in significantly more tyrosine hydroxylase positive (dopaminergic) neurons in the midbrain of adult offspring as compared to age-matched, control-diet equivalents. Positron emission tomography (PET) imaging revealed an increase in striatal dopamine synthesis capacity in LPD-exposed offspring, where elevated levels of dopamine correlated with an enhanced sensitivity to cocaine. These data highlight a profound sensitivity of the developing epigenome to gestational protein restriction. Our data also suggest that loss of Cdkn1c imprinting and p57KIP2 upregulation alters the cellular composition of the developing midbrain, compromises dopamine circuitry, and thereby provokes behavioural abnormalities in early postnatal life. Molecular analyses showed that despite this phenotype, exposure to LPD solely during pregnancy did not significantly change the expression of key neuronal- or dopamine-associated marker genes in adult offspring.
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Affiliation(s)
- Chiara Prodani
- Epigenetic Memory Group, MRC LMS, Imperial College London, Hammersmith Hospital Campus, Du Cane Road, London, W12 0NN, UK
| | - Elaine E Irvine
- Metabolic Signalling Group, MRC LMS, Imperial College London, Hammersmith Hospital Campus, Du Cane Road, London, W12 0NN, UK
| | - Alessandro Sardini
- Whole Animal Physiology and Imaging, MRC LMS, Imperial College London, Hammersmith Hospital Campus, Du Cane Road, London, W12 0NN, UK
| | - Hannah J Gleneadie
- Epigenetic Memory Group, MRC LMS, Imperial College London, Hammersmith Hospital Campus, Du Cane Road, London, W12 0NN, UK
| | - Andrew Dimond
- Epigenetic Memory Group, MRC LMS, Imperial College London, Hammersmith Hospital Campus, Du Cane Road, London, W12 0NN, UK
| | - Mathew Van de Pette
- MRC Toxicology Unit, University of Cambridge, Tennis Court Rd, Cambridge, CB2 1QR, UK
| | - Rosalind John
- Cardiff School of Biosciences, Cardiff University, Sir Martin Evans Building, Museum Avenue, Cardiff, CF10 3AX, UK
| | - Michelle Kokkinou
- Psychiatric Imaging Group, MRC LMS, Imperial College London, Hammersmith Hospital Campus, Du Cane Road, London, W12 0NN, UK
| | - Oliver Howes
- Psychiatric Imaging Group, MRC LMS, Imperial College London, Hammersmith Hospital Campus, Du Cane Road, London, W12 0NN, UK
| | - Dominic J Withers
- Metabolic Signalling Group, MRC LMS, Imperial College London, Hammersmith Hospital Campus, Du Cane Road, London, W12 0NN, UK
| | - Mark A Ungless
- MRC LMS, Imperial College London, Hammersmith Hospital Campus, Du Cane Road, London, W12 0NN, UK
| | - Matthias Merkenschlager
- Lymphocyte Development Group, MRC LMS, Imperial College London, Hammersmith Hospital Campus, Du Cane Road, London, W12 0NN, UK
| | - Amanda G Fisher
- Epigenetic Memory Group, MRC LMS, Imperial College London, Hammersmith Hospital Campus, Du Cane Road, London, W12 0NN, UK.
- Department of Biochemistry, University of Oxford, Oxford, OX1 3QU, UK.
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Veland N, Gleneadie HJ, Brown KE, Sardini A, Pombo J, Dimond A, Burns V, Sarkisyan K, Schiering C, Webster Z, Merkenschlager M, Fisher AG. Bioluminescence imaging of Cyp1a1-luciferase reporter mice demonstrates prolonged activation of the aryl hydrocarbon receptor in the lung. Commun Biol 2024; 7:442. [PMID: 38600349 PMCID: PMC11006662 DOI: 10.1038/s42003-024-06089-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Accepted: 03/21/2024] [Indexed: 04/12/2024] Open
Abstract
Aryl hydrocarbon receptor (AHR) signalling integrates biological processes that sense and respond to environmental, dietary, and metabolic challenges to ensure tissue homeostasis. AHR is a transcription factor that is inactive in the cytosol but upon encounter with ligand translocates to the nucleus and drives the expression of AHR targets, including genes of the cytochrome P4501 family of enzymes such as Cyp1a1. To dynamically visualise AHR activity in vivo, we generated reporter mice in which firefly luciferase (Fluc) was non-disruptively targeted into the endogenous Cyp1a1 locus. Exposure of these animals to FICZ, 3-MC or to dietary I3C induced strong bioluminescence signal and Cyp1a1 expression in many organs including liver, lung and intestine. Longitudinal studies revealed that AHR activity was surprisingly long-lived in the lung, with sustained Cyp1a1 expression evident in discrete populations of cells including columnar epithelia around bronchioles. Our data link diet to lung physiology and also reveal the power of bespoke Cyp1a1-Fluc reporters to longitudinally monitor AHR activity in vivo.
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Affiliation(s)
- Nicolas Veland
- Epigenetic Memory Group, MRC Laboratory of Medical Sciences, Imperial College London Hammersmith Hospital Campus, Du Cane Road, London, W12 OHS, UK
| | - Hannah J Gleneadie
- Epigenetic Memory Group, MRC Laboratory of Medical Sciences, Imperial College London Hammersmith Hospital Campus, Du Cane Road, London, W12 OHS, UK
| | - Karen E Brown
- Epigenetic Memory Group, MRC Laboratory of Medical Sciences, Imperial College London Hammersmith Hospital Campus, Du Cane Road, London, W12 OHS, UK
| | - Alessandro Sardini
- Whole Animal Physiology and Imaging, MRC Laboratory of Medical Sciences, Imperial College London, Hammersmith Hospital Campus, Du Cane Road, London, W12 0HS, UK
| | - Joaquim Pombo
- Senescence Group, MRC Laboratory of Medical Sciences, Imperial College London Hammersmith Hospital Campus, Du Cane Road, London, W12 0HS, UK
| | - Andrew Dimond
- Epigenetic Memory Group, MRC Laboratory of Medical Sciences, Imperial College London Hammersmith Hospital Campus, Du Cane Road, London, W12 OHS, UK
- Department of Biochemistry, University of Oxford, Oxford, OX1 3QU, UK
| | - Vanessa Burns
- Epigenetic Memory Group, MRC Laboratory of Medical Sciences, Imperial College London Hammersmith Hospital Campus, Du Cane Road, London, W12 OHS, UK
| | - Karen Sarkisyan
- Synthetic Biology Group, MRC Laboratory of Medical Sciences, Imperial College London Hammersmith Hospital Campus, Du Cane Road, London, W12 0HS, UK
| | - Chris Schiering
- Inflammation and Obesity Group, MRC Laboratory of Medical Sciences, Imperial College London Hammersmith Hospital Campus, Du Cane Road, London, W12 0HS, UK
| | - Zoe Webster
- Transgenics & Embryonic Stem Cell Facility, MRC Laboratory of Medical Sciences, Imperial College London Hammersmith Hospital Campus, Du Cane Road, London, W12 0HS, UK
| | - Matthias Merkenschlager
- Lymphocyte Development Group, MRC Laboratory of Medical Sciences, Imperial College London Hammersmith Hospital Campus, Du Cane Road, London, W12 0HS, UK
| | - Amanda G Fisher
- Epigenetic Memory Group, MRC Laboratory of Medical Sciences, Imperial College London Hammersmith Hospital Campus, Du Cane Road, London, W12 OHS, UK.
- Department of Biochemistry, University of Oxford, Oxford, OX1 3QU, UK.
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Dimond A, Van de Pette M, Taylor-Bateman V, Brown K, Sardini A, Whilding C, Feytout A, Prinjha RK, Merkenschlager M, Fisher AG. Drug-induced loss of imprinting revealed using bioluminescent reporters of Cdkn1c. Sci Rep 2023; 13:5626. [PMID: 37024615 PMCID: PMC10079848 DOI: 10.1038/s41598-023-32747-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Accepted: 03/31/2023] [Indexed: 04/08/2023] Open
Abstract
Genomic imprinting is an epigenetically mediated mechanism that regulates allelic expression of genes based upon parent-of-origin and provides a paradigm for studying epigenetic silencing and release. Here, bioluminescent reporters for the maternally-expressed imprinted gene Cdkn1c are used to examine the capacity of chromatin-modifying drugs to reverse paternal Cdkn1c silencing. Exposure of reporter mouse embryonic stem cells (mESCs) to 5-Azacytidine, HDAC inhibitors, BET inhibitors or GSK-J4 (KDM6A/B inhibitor) relieved repression of paternal Cdkn1c, either selectively or by inducing biallelic effects. Treatment of reporter fibroblasts with HDAC inhibitors or GSK-J4 resulted in similar paternal Cdkn1c activation, whereas BET inhibitor-induced loss of imprinting was specific to mESCs. Changes in allelic expression were generally not sustained in dividing cultures upon drug removal, indicating that the underlying epigenetic memory of silencing was maintained. In contrast, Cdkn1c de-repression by GSK-J4 was retained in both mESCs and fibroblasts following inhibitor removal, although this impact may be linked to cellular stress and DNA damage. Taken together, these data introduce bioluminescent reporter cells as tools for studying epigenetic silencing and disruption, and demonstrate that Cdkn1c imprinting requires distinct and cell-type specific chromatin features and modifying enzymes to enact and propagate a memory of silencing.
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Affiliation(s)
- Andrew Dimond
- Epigenetic Memory Group, MRC London Institute of Medical Sciences, Imperial College London, Hammersmith Hospital Campus, Du Cane Road, London, W12 0NN, UK.
| | - Mathew Van de Pette
- Epigenetic Memory Group, MRC London Institute of Medical Sciences, Imperial College London, Hammersmith Hospital Campus, Du Cane Road, London, W12 0NN, UK
- MRC Toxicology Unit, University of Cambridge, Gleeson Building, Tennis Court Road, Cambridge, CB2 1QR, UK
| | - Victoria Taylor-Bateman
- Epigenetic Memory Group, MRC London Institute of Medical Sciences, Imperial College London, Hammersmith Hospital Campus, Du Cane Road, London, W12 0NN, UK
| | - Karen Brown
- Epigenetic Memory Group, MRC London Institute of Medical Sciences, Imperial College London, Hammersmith Hospital Campus, Du Cane Road, London, W12 0NN, UK
| | - Alessandro Sardini
- Whole Animal Physiology and Imaging, MRC London Institute of Medical Sciences, Imperial College London, Hammersmith Hospital Campus, Du Cane Road, London, W12 0NN, UK
| | - Chad Whilding
- Microscopy Facility, MRC London Institute of Medical Sciences, Imperial College London, Hammersmith Hospital Campus, Du Cane Road, London, W12 0NN, UK
| | - Amelie Feytout
- Epigenetic Memory Group, MRC London Institute of Medical Sciences, Imperial College London, Hammersmith Hospital Campus, Du Cane Road, London, W12 0NN, UK
| | - Rab K Prinjha
- Immunology and Epigenetics Research Unit, Research, GlaxoSmithKline, Gunnels Wood Road, Stevenage, SG1 2NY, Herts, UK
| | - Matthias Merkenschlager
- Lymphocyte Development Group, MRC London Institute of Medical Sciences, Imperial College London, Hammersmith Hospital Campus, Du Cane Road, London, W12 0NN, UK
| | - Amanda G Fisher
- Epigenetic Memory Group, MRC London Institute of Medical Sciences, Imperial College London, Hammersmith Hospital Campus, Du Cane Road, London, W12 0NN, UK.
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Gleneadie HJ, Fernandez-Ruiz B, Sardini A, Van de Pette M, Dimond A, Prinjha RK, McGinty J, French PMW, Bagci H, Merkenschlager M, Fisher AG. Endogenous bioluminescent reporters reveal a sustained increase in utrophin gene expression upon EZH2 and ERK1/2 inhibition. Commun Biol 2023; 6:318. [PMID: 36966198 PMCID: PMC10039851 DOI: 10.1038/s42003-023-04666-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Accepted: 03/06/2023] [Indexed: 03/27/2023] Open
Abstract
Duchenne muscular dystrophy (DMD) is an X-linked disorder caused by loss of function mutations in the dystrophin gene (Dmd), resulting in progressive muscle weakening. Here we modelled the longitudinal expression of endogenous Dmd, and its paralogue Utrn, in mice and in myoblasts by generating bespoke bioluminescent gene reporters. As utrophin can partially compensate for Dmd-deficiency, these reporters were used as tools to ask whether chromatin-modifying drugs can enhance Utrn expression in developing muscle. Myoblasts treated with different PRC2 inhibitors showed significant increases in Utrn transcripts and bioluminescent signals, and these responses were independently verified by conditional Ezh2 deletion. Inhibition of ERK1/2 signalling provoked an additional increase in Utrn expression that was also seen in Dmd-mutant cells, and maintained as myoblasts differentiate. These data reveal PRC2 and ERK1/2 to be negative regulators of Utrn expression and provide specialised molecular imaging tools to monitor utrophin expression as a therapeutic strategy for DMD.
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Affiliation(s)
- Hannah J Gleneadie
- Epigenetic Memory Group, MRC London Institute of Medical Sciences (LMS), Imperial College London, Du Cane Road, London, W12 0NN, UK
| | - Beatriz Fernandez-Ruiz
- Epigenetic Memory Group, MRC London Institute of Medical Sciences (LMS), Imperial College London, Du Cane Road, London, W12 0NN, UK
| | - Alessandro Sardini
- Whole Animal Physiology and Imaging Facility, MRC LMS, Imperial College London, Du Cane Road, London, W12 0NN, UK
| | - Mathew Van de Pette
- Epigenetic Memory Group, MRC London Institute of Medical Sciences (LMS), Imperial College London, Du Cane Road, London, W12 0NN, UK
- MRC Toxicology Unit, Gleeson Building, Tennis Court Road, Cambridge, CB2 1QR, UK
| | - Andrew Dimond
- Epigenetic Memory Group, MRC London Institute of Medical Sciences (LMS), Imperial College London, Du Cane Road, London, W12 0NN, UK
| | - Rab K Prinjha
- Immunology and Epigenetics Research Unit, Research, GlaxoSmithKline, Gunnels Wood Road, Stevenage, Herts, SG1 2NY, UK
| | - James McGinty
- Photonics Group, Department of Physics, Blackett Laboratory, Imperial College London, London, SW7 2AZ, UK
| | - Paul M W French
- Photonics Group, Department of Physics, Blackett Laboratory, Imperial College London, London, SW7 2AZ, UK
| | - Hakan Bagci
- Lymphocyte Development Group, MRC LMS, Imperial College London, Du Cane Road, London, W12 0NN, UK
| | - Matthias Merkenschlager
- Lymphocyte Development Group, MRC LMS, Imperial College London, Du Cane Road, London, W12 0NN, UK
| | - Amanda G Fisher
- Epigenetic Memory Group, MRC London Institute of Medical Sciences (LMS), Imperial College London, Du Cane Road, London, W12 0NN, UK.
- Department of Biochemistry, University of Oxford, South Parks Road, OX1 3QU, Oxford, UK.
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Djeghloul D, Dimond A, Cheriyamkunnel S, Kramer H, Patel B, Brown K, Montoya A, Whilding C, Wang YF, Futschik ME, Veland N, Montavon T, Jenuwein T, Merkenschlager M, Fisher AG. Loss of H3K9 trimethylation alters chromosome compaction and transcription factor retention during mitosis. Nat Struct Mol Biol 2023; 30:489-501. [PMID: 36941433 PMCID: PMC10113154 DOI: 10.1038/s41594-023-00943-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Accepted: 02/13/2023] [Indexed: 03/23/2023]
Abstract
Recent studies have shown that repressive chromatin machinery, including DNA methyltransferases and polycomb repressor complexes, binds to chromosomes throughout mitosis and their depletion results in increased chromosome size. In the present study, we show that enzymes that catalyze H3K9 methylation, such as Suv39h1, Suv39h2, G9a and Glp, are also retained on mitotic chromosomes. Surprisingly, however, mutants lacking histone 3 lysine 9 trimethylation (H3K9me3) have unusually small and compact mitotic chromosomes associated with increased histone H3 phospho Ser10 (H3S10ph) and H3K27me3 levels. Chromosome size and centromere compaction in these mutants were rescued by providing exogenous first protein lysine methyltransferase Suv39h1 or inhibiting Ezh2 activity. Quantitative proteomic comparisons of native mitotic chromosomes isolated from wild-type versus Suv39h1/Suv39h2 double-null mouse embryonic stem cells revealed that H3K9me3 was essential for the efficient retention of bookmarking factors such as Esrrb. These results highlight an unexpected role for repressive heterochromatin domains in preserving transcription factor binding through mitosis and underscore the importance of H3K9me3 for sustaining chromosome architecture and epigenetic memory during cell division.
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Affiliation(s)
- Dounia Djeghloul
- Epigenetic Memory Group, MRC London Institute of Medical Sciences, Imperial College London, London, UK.
| | - Andrew Dimond
- Epigenetic Memory Group, MRC London Institute of Medical Sciences, Imperial College London, London, UK
| | - Sherry Cheriyamkunnel
- Epigenetic Memory Group, MRC London Institute of Medical Sciences, Imperial College London, London, UK
| | - Holger Kramer
- Biological Mass Spectrometry and Proteomics Facility, MRC London Institute of Medical Sciences, Imperial College London, London, UK
| | - Bhavik Patel
- Flow Cytometry Facility, MRC London Institute of Medical Sciences, Imperial College London, London, UK
| | - Karen Brown
- Epigenetic Memory Group, MRC London Institute of Medical Sciences, Imperial College London, London, UK
| | - Alex Montoya
- Biological Mass Spectrometry and Proteomics Facility, MRC London Institute of Medical Sciences, Imperial College London, London, UK
| | - Chad Whilding
- Microscopy Facility, MRC London Institute of Medical Sciences, Imperial College London, London, UK
| | - Yi-Fang Wang
- Bioinformatics, MRC London Institute of Medical Sciences, Imperial College London, London, UK
| | - Matthias E Futschik
- Bioinformatics, MRC London Institute of Medical Sciences, Imperial College London, London, UK
| | - Nicolas Veland
- Epigenetic Memory Group, MRC London Institute of Medical Sciences, Imperial College London, London, UK
| | - Thomas Montavon
- Max-Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
| | - Thomas Jenuwein
- Max-Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
| | - Matthias Merkenschlager
- Lymphocyte Development Group, MRC London Institute of Medical Sciences, Imperial College London, London, UK
| | - Amanda G Fisher
- Epigenetic Memory Group, MRC London Institute of Medical Sciences, Imperial College London, London, UK.
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Van de Pette M, Dimond A, Galvão AM, Millership SJ, To W, Prodani C, McNamara G, Bruno L, Sardini A, Webster Z, McGinty J, French PMW, Uren AG, Castillo-Fernandez J, Watkinson W, Ferguson-Smith AC, Merkenschlager M, John RM, Kelsey G, Fisher AG. Epigenetic changes induced by in utero dietary challenge result in phenotypic variability in successive generations of mice. Nat Commun 2022; 13:2464. [PMID: 35513363 PMCID: PMC9072353 DOI: 10.1038/s41467-022-30022-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2020] [Accepted: 04/13/2022] [Indexed: 11/22/2022] Open
Abstract
Transmission of epigenetic information between generations occurs in nematodes, flies and plants, mediated by specialised small RNA pathways, modified histones and DNA methylation. Similar processes in mammals can also affect phenotype through intergenerational or trans-generational mechanisms. Here we generate a luciferase knock-in reporter mouse for the imprinted Dlk1 locus to visualise and track epigenetic fidelity across generations. Exposure to high-fat diet in pregnancy provokes sustained re-expression of the normally silent maternal Dlk1 in offspring (loss of imprinting) and increased DNA methylation at the somatic differentially methylated region (sDMR). In the next generation heterogeneous Dlk1 mis-expression is seen exclusively among animals born to F1-exposed females. Oocytes from these females show altered gene and microRNA expression without changes in DNA methylation, and correct imprinting is restored in subsequent generations. Our results illustrate how diet impacts the foetal epigenome, disturbing canonical and non-canonical imprinting mechanisms to modulate the properties of successive generations of offspring.
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Affiliation(s)
- Mathew Van de Pette
- Lymphocyte Development & Epigenetic Memory Groups, MRC London Institute of Medical Sciences, Imperial College London, Hammersmith Hospital Campus, Du Cane Road, London, W12 0NN, UK
| | - Andrew Dimond
- Lymphocyte Development & Epigenetic Memory Groups, MRC London Institute of Medical Sciences, Imperial College London, Hammersmith Hospital Campus, Du Cane Road, London, W12 0NN, UK
| | - António M Galvão
- Epigenetics Programme, The Babraham Institute, Cambridge, CB22 3AT, UK
- Institute of Animal Reproduction and Food Research of PAS, Department of Reproductive Immunology and Pathology, Olsztyn, Poland
- Centre for Trophoblast Research, University of Cambridge, Cambridge, CB2 3EG, UK
| | - Steven J Millership
- Department of Medicine, Imperial College London, Hammersmith Hospital Campus, Du Cane Road, London, W12 0NN, UK
| | - Wilson To
- Lymphocyte Development & Epigenetic Memory Groups, MRC London Institute of Medical Sciences, Imperial College London, Hammersmith Hospital Campus, Du Cane Road, London, W12 0NN, UK
| | - Chiara Prodani
- Lymphocyte Development & Epigenetic Memory Groups, MRC London Institute of Medical Sciences, Imperial College London, Hammersmith Hospital Campus, Du Cane Road, London, W12 0NN, UK
| | - Gráinne McNamara
- Lymphocyte Development & Epigenetic Memory Groups, MRC London Institute of Medical Sciences, Imperial College London, Hammersmith Hospital Campus, Du Cane Road, London, W12 0NN, UK
| | - Ludovica Bruno
- Lymphocyte Development & Epigenetic Memory Groups, MRC London Institute of Medical Sciences, Imperial College London, Hammersmith Hospital Campus, Du Cane Road, London, W12 0NN, UK
| | - Alessandro Sardini
- Whole Animal Physiology and Imaging, MRC London Institute of Medical Sciences, Imperial College London, Hammersmith Hospital Campus, Du Cane Road, London, W12 0NN, UK
| | - Zoe Webster
- Transgenics and Embryonic Stem Cell Laboratory, MRC London Institute of Medical Sciences, Imperial College London, Hammersmith Hospital Campus, Du Cane Road, London, W12 0NN, UK
| | - James McGinty
- Photonics Group, Department of Physics, Imperial College London, South Kensington Campus, London, SW7 2AZ, UK
| | - Paul M W French
- Photonics Group, Department of Physics, Imperial College London, South Kensington Campus, London, SW7 2AZ, UK
| | - Anthony G Uren
- Cancer Genomics Group, MRC London Institute of Medical Sciences, Imperial College London, Hammersmith Hospital Campus, Du Cane Road, London, W12 0NN, UK
| | | | - William Watkinson
- Department of Genetics, University of Cambridge, Downing Street, Cambridge, CB2 3EH, UK
| | - Anne C Ferguson-Smith
- Department of Genetics, University of Cambridge, Downing Street, Cambridge, CB2 3EH, UK
| | - Matthias Merkenschlager
- Lymphocyte Development & Epigenetic Memory Groups, MRC London Institute of Medical Sciences, Imperial College London, Hammersmith Hospital Campus, Du Cane Road, London, W12 0NN, UK
| | - Rosalind M John
- Cardiff School of Biosciences, Cardiff University, Cardiff, CF10 3AX, UK
| | - Gavin Kelsey
- Epigenetics Programme, The Babraham Institute, Cambridge, CB22 3AT, UK
- Centre for Trophoblast Research, University of Cambridge, Cambridge, CB2 3EG, UK
- Wellcome-MRC Institute of Metabolic Science-Metabolic Research Laboratories, Cambridge, CB2 0QQ, UK
| | - Amanda G Fisher
- Lymphocyte Development & Epigenetic Memory Groups, MRC London Institute of Medical Sciences, Imperial College London, Hammersmith Hospital Campus, Du Cane Road, London, W12 0NN, UK.
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7
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Dimond A, Van de Pette M, Fisher AG. Illuminating Epigenetics and Inheritance in the Immune System with Bioluminescence. Trends Immunol 2020; 41:994-1005. [PMID: 33036908 DOI: 10.1016/j.it.2020.09.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2020] [Revised: 09/08/2020] [Accepted: 09/08/2020] [Indexed: 12/25/2022]
Abstract
The remarkable process of light emission by living organisms has fascinated mankind for thousands of years. A recent expansion in the repertoire of catalytic luciferase enzymes, coupled with the discovery of the genes and pathways that encode different luciferin substrates, means that bioluminescence imaging (BLI) is set to revolutionize longitudinal and dynamic studies of gene control within biomedicine, including the regulation of immune responses. In this review article, we summarize recent advances in bioluminescence-based imaging approaches that promise to enlighten our understanding of in vivo gene and epigenetic control within the immune system.
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Affiliation(s)
- Andrew Dimond
- Lymphocyte Development Group, MRC London Institute of Medical Sciences, Imperial College London, Hammersmith Hospital Campus, Du Cane Road, London, W12 0NN, UK
| | - Mathew Van de Pette
- Epigenetic Mechanisms of Toxicity, MRC Toxicology Unit, University of Cambridge, Downing Street, Cambridge, CB2 3EH, UK
| | - Amanda G Fisher
- Lymphocyte Development Group, MRC London Institute of Medical Sciences, Imperial College London, Hammersmith Hospital Campus, Du Cane Road, London, W12 0NN, UK.
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8
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Djeghloul D, Patel B, Kramer H, Dimond A, Whilding C, Brown K, Kohler AC, Feytout A, Veland N, Elliott J, Bharat TAM, Tarafder AK, Löwe J, Ng BL, Guo Y, Guy J, Huseyin MK, Klose RJ, Merkenschlager M, Fisher AG. Identifying proteins bound to native mitotic ESC chromosomes reveals chromatin repressors are important for compaction. Nat Commun 2020; 11:4118. [PMID: 32807789 PMCID: PMC7431861 DOI: 10.1038/s41467-020-17823-z] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2019] [Accepted: 07/15/2020] [Indexed: 12/14/2022] Open
Abstract
Epigenetic information is transmitted from mother to daughter cells through mitosis. Here, to identify factors that might play a role in conveying epigenetic memory through cell division, we report on the isolation of unfixed, native chromosomes from metaphase-arrested cells using flow cytometry and perform LC-MS/MS to identify chromosome-bound proteins. A quantitative proteomic comparison between metaphase-arrested cell lysates and chromosome-sorted samples reveals a cohort of proteins that were significantly enriched on mitotic ESC chromosomes. These include pluripotency-associated transcription factors, repressive chromatin-modifiers such as PRC2 and DNA methyl-transferases, and proteins governing chromosome architecture. Deletion of PRC2, Dnmt1/3a/3b or Mecp2 in ESCs leads to an increase in the size of individual mitotic chromosomes, consistent with de-condensation. Similar results were obtained by the experimental cleavage of cohesin. Thus, we identify chromosome-bound factors in pluripotent stem cells during mitosis and reveal that PRC2, DNA methylation and Mecp2 are required to maintain chromosome compaction.
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Affiliation(s)
- Dounia Djeghloul
- Lymphocyte Development Group, MRC London Institute of Medical Sciences, Imperial College London, Hammersmith Hospital Campus, Du Cane Road, London, W12 0NN, UK
| | - Bhavik Patel
- Flow Cytometry Facility, MRC London Institute of Medical Sciences, Imperial College London, Hammersmith Hospital Campus, Du Cane Road, London, W12 0NN, UK
| | - Holger Kramer
- Biological Mass Spectrometry and Proteomics Facility, MRC London Institute of Medical Sciences, Imperial College London, Hammersmith Hospital Campus, Du Cane Road, London, W12 0NN, UK
| | - Andrew Dimond
- Lymphocyte Development Group, MRC London Institute of Medical Sciences, Imperial College London, Hammersmith Hospital Campus, Du Cane Road, London, W12 0NN, UK
| | - Chad Whilding
- Microscopy Facility, MRC London Institute of Medical Sciences, Imperial College London, Hammersmith Hospital Campus, Du Cane Road, London, W12 0NN, UK
| | - Karen Brown
- Lymphocyte Development Group, MRC London Institute of Medical Sciences, Imperial College London, Hammersmith Hospital Campus, Du Cane Road, London, W12 0NN, UK
| | - Anne-Céline Kohler
- Lymphocyte Development Group, MRC London Institute of Medical Sciences, Imperial College London, Hammersmith Hospital Campus, Du Cane Road, London, W12 0NN, UK
| | - Amelie Feytout
- Lymphocyte Development Group, MRC London Institute of Medical Sciences, Imperial College London, Hammersmith Hospital Campus, Du Cane Road, London, W12 0NN, UK
| | - Nicolas Veland
- Lymphocyte Development Group, MRC London Institute of Medical Sciences, Imperial College London, Hammersmith Hospital Campus, Du Cane Road, London, W12 0NN, UK
| | - James Elliott
- Flow Cytometry Facility, MRC London Institute of Medical Sciences, Imperial College London, Hammersmith Hospital Campus, Du Cane Road, London, W12 0NN, UK
| | - Tanmay A M Bharat
- Sir William Dunn School of Pathology, University of Oxford, OX1 3RE, Oxford, UK
| | - Abul K Tarafder
- Sir William Dunn School of Pathology, University of Oxford, OX1 3RE, Oxford, UK
| | - Jan Löwe
- MRC Laboratory of Molecular Biology, Cambridge, CB2 0QH, UK
| | - Bee L Ng
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - Ya Guo
- Lymphocyte Development Group, MRC London Institute of Medical Sciences, Imperial College London, Hammersmith Hospital Campus, Du Cane Road, London, W12 0NN, UK
| | - Jacky Guy
- The Wellcome Centre for Cell Biology, University of Edinburgh, Edinburgh, EH9 3BH, UK
| | - Miles K Huseyin
- Department of Biochemistry, University of Oxford, OX1 3QU, Oxford, UK
| | - Robert J Klose
- Department of Biochemistry, University of Oxford, OX1 3QU, Oxford, UK
| | - Matthias Merkenschlager
- Lymphocyte Development Group, MRC London Institute of Medical Sciences, Imperial College London, Hammersmith Hospital Campus, Du Cane Road, London, W12 0NN, UK
| | - Amanda G Fisher
- Lymphocyte Development Group, MRC London Institute of Medical Sciences, Imperial College London, Hammersmith Hospital Campus, Du Cane Road, London, W12 0NN, UK.
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9
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Koohy H, Bolland DJ, Matheson LS, Schoenfelder S, Stellato C, Dimond A, Várnai C, Chovanec P, Chessa T, Denizot J, Manzano Garcia R, Wingett SW, Freire-Pritchett P, Nagano T, Hawkins P, Stephens L, Elderkin S, Spivakov M, Fraser P, Corcoran AE, Varga-Weisz PD. Genome organization and chromatin analysis identify transcriptional downregulation of insulin-like growth factor signaling as a hallmark of aging in developing B cells. Genome Biol 2018; 19:126. [PMID: 30180872 PMCID: PMC6124017 DOI: 10.1186/s13059-018-1489-y] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2018] [Accepted: 07/20/2018] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND Aging is characterized by loss of function of the adaptive immune system, but the underlying causes are poorly understood. To assess the molecular effects of aging on B cell development, we profiled gene expression and chromatin features genome-wide, including histone modifications and chromosome conformation, in bone marrow pro-B and pre-B cells from young and aged mice. RESULTS Our analysis reveals that the expression levels of most genes are generally preserved in B cell precursors isolated from aged compared with young mice. Nonetheless, age-specific expression changes are observed at numerous genes, including microRNA encoding genes. Importantly, these changes are underpinned by multi-layered alterations in chromatin structure, including chromatin accessibility, histone modifications, long-range promoter interactions, and nuclear compartmentalization. Previous work has shown that differentiation is linked to changes in promoter-regulatory element interactions. We find that aging in B cell precursors is accompanied by rewiring of such interactions. We identify transcriptional downregulation of components of the insulin-like growth factor signaling pathway, in particular downregulation of Irs1 and upregulation of Let-7 microRNA expression, as a signature of the aged phenotype. These changes in expression are associated with specific alterations in H3K27me3 occupancy, suggesting that Polycomb-mediated repression plays a role in precursor B cell aging. CONCLUSIONS Changes in chromatin and 3D genome organization play an important role in shaping the altered gene expression profile of aged precursor B cells. Components of the insulin-like growth factor signaling pathways are key targets of epigenetic regulation in aging in bone marrow B cell precursors.
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Affiliation(s)
- Hashem Koohy
- Nuclear Dynamics Programme, Babraham Institute, Cambridge, UK
- Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Daniel J Bolland
- Nuclear Dynamics Programme, Babraham Institute, Cambridge, UK
- Laboratory of Lymphocyte Signalling and Development, Babraham Institute, Cambridge, UK
| | - Louise S Matheson
- Nuclear Dynamics Programme, Babraham Institute, Cambridge, UK
- Laboratory of Lymphocyte Signalling and Development, Babraham Institute, Cambridge, UK
| | | | | | - Andrew Dimond
- Nuclear Dynamics Programme, Babraham Institute, Cambridge, UK
| | - Csilla Várnai
- Nuclear Dynamics Programme, Babraham Institute, Cambridge, UK
| | - Peter Chovanec
- Nuclear Dynamics Programme, Babraham Institute, Cambridge, UK
- Laboratory of Lymphocyte Signalling and Development, Babraham Institute, Cambridge, UK
| | | | - Jeremy Denizot
- Nuclear Dynamics Programme, Babraham Institute, Cambridge, UK
- Present address: Université Clermont Auvergne, Inserm U1071, M2iSH, USC-INRA 2018, F-, 63000, Clermont-Ferrand, France
| | | | - Steven W Wingett
- Nuclear Dynamics Programme, Babraham Institute, Cambridge, UK
- Bioinformatics, Babraham Institute, Cambridge, UK
| | - Paula Freire-Pritchett
- Nuclear Dynamics Programme, Babraham Institute, Cambridge, UK
- Division of Cell Biology, Medical Research Council Laboratory of Molecular Biology, Cambridge, CB2 0QH, UK
| | - Takashi Nagano
- Nuclear Dynamics Programme, Babraham Institute, Cambridge, UK
| | | | | | - Sarah Elderkin
- Nuclear Dynamics Programme, Babraham Institute, Cambridge, UK
| | - Mikhail Spivakov
- Nuclear Dynamics Programme, Babraham Institute, Cambridge, UK
- Functional Gene Control Group, MRC London Institute of Medical Sciences (LMS), Du Cane Road, London, W12 0NN, UK
| | - Peter Fraser
- Nuclear Dynamics Programme, Babraham Institute, Cambridge, UK
- Department of Biological Science, Florida State University, Tallahassee, FL, USA
| | - Anne E Corcoran
- Nuclear Dynamics Programme, Babraham Institute, Cambridge, UK.
- Laboratory of Lymphocyte Signalling and Development, Babraham Institute, Cambridge, UK.
| | - Patrick D Varga-Weisz
- Nuclear Dynamics Programme, Babraham Institute, Cambridge, UK.
- School of Biological Sciences, University of Essex, Colchester, UK.
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10
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Rivera-Mulia JC, Dimond A, Vera D, Trevilla-Garcia C, Sasaki T, Zimmerman J, Dupont C, Gribnau J, Fraser P, Gilbert DM. Allele-specific control of replication timing and genome organization during development. Genome Res 2018; 28:800-811. [PMID: 29735606 PMCID: PMC5991511 DOI: 10.1101/gr.232561.117] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2017] [Accepted: 04/26/2018] [Indexed: 12/14/2022]
Abstract
DNA replication occurs in a defined temporal order known as the replication-timing (RT) program. RT is regulated during development in discrete chromosomal units, coordinated with transcriptional activity and 3D genome organization. Here, we derived distinct cell types from F1 hybrid musculus × castaneus mouse crosses and exploited the high single-nucleotide polymorphism (SNP) density to characterize allelic differences in RT (Repli-seq), genome organization (Hi-C and promoter-capture Hi-C), gene expression (total nuclear RNA-seq), and chromatin accessibility (ATAC-seq). We also present HARP, a new computational tool for sorting SNPs in phased genomes to efficiently measure allele-specific genome-wide data. Analysis of six different hybrid mESC clones with different genomes (C57BL/6, 129/sv, and CAST/Ei), parental configurations, and gender revealed significant RT asynchrony between alleles across ∼12% of the autosomal genome linked to subspecies genomes but not to parental origin, growth conditions, or gender. RT asynchrony in mESCs strongly correlated with changes in Hi-C compartments between alleles but not as strongly with SNP density, gene expression, imprinting, or chromatin accessibility. We then tracked mESC RT asynchronous regions during development by analyzing differentiated cell types, including extraembryonic endoderm stem (XEN) cells, four male and female primary mouse embryonic fibroblasts (MEFs), and neural precursor cells (NPCs) differentiated in vitro from mESCs with opposite parental configurations. We found that RT asynchrony and allelic discordance in Hi-C compartments seen in mESCs were largely lost in all differentiated cell types, accompanied by novel sites of allelic asynchrony at a considerably smaller proportion of the genome, suggesting that genome organization of homologs converges to similar folding patterns during cell fate commitment.
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Affiliation(s)
- Juan Carlos Rivera-Mulia
- Department of Biological Science, Florida State University, Tallahassee, Florida 32306-4295, USA
| | - Andrew Dimond
- The Babraham Institute, Babraham Research Campus, Cambridge CB22 3AT, United Kingdom
| | - Daniel Vera
- Center for Genomics and Personalized Medicine, Florida State University, Tallahassee, Florida 32306, USA
| | - Claudia Trevilla-Garcia
- Department of Biological Science, Florida State University, Tallahassee, Florida 32306-4295, USA
| | - Takayo Sasaki
- Department of Biological Science, Florida State University, Tallahassee, Florida 32306-4295, USA
| | - Jared Zimmerman
- Department of Biological Science, Florida State University, Tallahassee, Florida 32306-4295, USA
| | - Catherine Dupont
- Department of Reproduction and Development, Erasmus MC, University Medical Center, 3015GE Rotterdam, The Netherlands
| | - Joost Gribnau
- Department of Reproduction and Development, Erasmus MC, University Medical Center, 3015GE Rotterdam, The Netherlands
| | - Peter Fraser
- Department of Biological Science, Florida State University, Tallahassee, Florida 32306-4295, USA
- The Babraham Institute, Babraham Research Campus, Cambridge CB22 3AT, United Kingdom
- Center for Genomics and Personalized Medicine, Florida State University, Tallahassee, Florida 32306, USA
| | - David M Gilbert
- Department of Biological Science, Florida State University, Tallahassee, Florida 32306-4295, USA
- Center for Genomics and Personalized Medicine, Florida State University, Tallahassee, Florida 32306, USA
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11
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Van de Pette M, Abbas A, Feytout A, McNamara G, Bruno L, To WK, Dimond A, Sardini A, Webster Z, McGinty J, Paul EJ, Ungless MA, French PMW, Withers DJ, Uren A, Ferguson-Smith AC, Merkenschlager M, John RM, Fisher AG. Visualizing Changes in Cdkn1c Expression Links Early-Life Adversity to Imprint Mis-regulation in Adults. Cell Rep 2017; 18:1090-1099. [PMID: 28147266 PMCID: PMC5300902 DOI: 10.1016/j.celrep.2017.01.010] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2016] [Revised: 12/22/2016] [Accepted: 01/07/2017] [Indexed: 12/13/2022] Open
Abstract
Imprinted genes are regulated according to parental origin and can influence embryonic growth and metabolism and confer disease susceptibility. Here, we designed sensitive allele-specific reporters to non-invasively monitor imprinted Cdkn1c expression in mice and showed that expression was modulated by environmental factors encountered in utero. Acute exposure to chromatin-modifying drugs resulted in de-repression of paternally inherited (silent) Cdkn1c alleles in embryos that was temporary and resolved after birth. In contrast, deprivation of maternal dietary protein in utero provoked permanent de-repression of imprinted Cdkn1c expression that was sustained into adulthood and occurred through a folate-dependent mechanism of DNA methylation loss. Given the function of imprinted genes in regulating behavior and metabolic processes in adults, these results establish imprinting deregulation as a credible mechanism linking early-life adversity to later-life outcomes. Furthermore, Cdkn1c-luciferase mice offer non-invasive tools to identify factors that disrupt epigenetic processes and strategies to limit their long-term impact. Allele-specific expression of imprinted Cdkn1c imaged in vivo using bioluminescence Chromatin-modifying drugs applied in utero transiently de-repress Cdkn1c imprinting In utero exposure to low-protein diet permanently disrupts the Cdkn1c imprint Folate supplements during gestation protect against loss of Cdkn1c imprinting
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Affiliation(s)
- Mathew Van de Pette
- MRC London Institute of Medical Sciences, Imperial College London, Hammersmith Hospital Campus, Du Cane Road, London W12 0NN, UK
| | - Allifia Abbas
- MRC London Institute of Medical Sciences, Imperial College London, Hammersmith Hospital Campus, Du Cane Road, London W12 0NN, UK
| | - Amelie Feytout
- MRC London Institute of Medical Sciences, Imperial College London, Hammersmith Hospital Campus, Du Cane Road, London W12 0NN, UK
| | - Gráinne McNamara
- MRC London Institute of Medical Sciences, Imperial College London, Hammersmith Hospital Campus, Du Cane Road, London W12 0NN, UK
| | - Ludovica Bruno
- MRC London Institute of Medical Sciences, Imperial College London, Hammersmith Hospital Campus, Du Cane Road, London W12 0NN, UK
| | - Wilson K To
- MRC London Institute of Medical Sciences, Imperial College London, Hammersmith Hospital Campus, Du Cane Road, London W12 0NN, UK
| | - Andrew Dimond
- MRC London Institute of Medical Sciences, Imperial College London, Hammersmith Hospital Campus, Du Cane Road, London W12 0NN, UK
| | - Alessandro Sardini
- MRC London Institute of Medical Sciences, Imperial College London, Hammersmith Hospital Campus, Du Cane Road, London W12 0NN, UK
| | - Zoe Webster
- MRC London Institute of Medical Sciences, Imperial College London, Hammersmith Hospital Campus, Du Cane Road, London W12 0NN, UK
| | - James McGinty
- Photonics Group, Department of Physics, Blackett Laboratory, Imperial College London, London SW7 2AZ, UK
| | - Eleanor J Paul
- MRC London Institute of Medical Sciences, Imperial College London, Hammersmith Hospital Campus, Du Cane Road, London W12 0NN, UK
| | - Mark A Ungless
- MRC London Institute of Medical Sciences, Imperial College London, Hammersmith Hospital Campus, Du Cane Road, London W12 0NN, UK
| | - Paul M W French
- Photonics Group, Department of Physics, Blackett Laboratory, Imperial College London, London SW7 2AZ, UK
| | - Dominic J Withers
- MRC London Institute of Medical Sciences, Imperial College London, Hammersmith Hospital Campus, Du Cane Road, London W12 0NN, UK
| | - Anthony Uren
- MRC London Institute of Medical Sciences, Imperial College London, Hammersmith Hospital Campus, Du Cane Road, London W12 0NN, UK
| | - Anne C Ferguson-Smith
- Department of Genetics, University of Cambridge, Downing Street, Cambridge CB2 3EH, UK
| | - Matthias Merkenschlager
- MRC London Institute of Medical Sciences, Imperial College London, Hammersmith Hospital Campus, Du Cane Road, London W12 0NN, UK
| | - Rosalind M John
- Cardiff School of Biosciences, Cardiff University, Cardiff CF10 3AX, UK
| | - Amanda G Fisher
- MRC London Institute of Medical Sciences, Imperial College London, Hammersmith Hospital Campus, Du Cane Road, London W12 0NN, UK.
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12
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Cairns J, Freire-Pritchett P, Wingett SW, Várnai C, Dimond A, Plagnol V, Zerbino D, Schoenfelder S, Javierre BM, Osborne C, Fraser P, Spivakov M. CHiCAGO: robust detection of DNA looping interactions in Capture Hi-C data. Genome Biol 2016; 17:127. [PMID: 27306882 PMCID: PMC4908757 DOI: 10.1186/s13059-016-0992-2] [Citation(s) in RCA: 242] [Impact Index Per Article: 30.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2016] [Accepted: 05/25/2016] [Indexed: 12/14/2022] Open
Abstract
Capture Hi-C (CHi-C) is a method for profiling chromosomal interactions involving targeted regions of interest, such as gene promoters, globally and at high resolution. Signal detection in CHi-C data involves a number of statistical challenges that are not observed when using other Hi-C-like techniques. We present a background model and algorithms for normalisation and multiple testing that are specifically adapted to CHi-C experiments. We implement these procedures in CHiCAGO ( http://regulatorygenomicsgroup.org/chicago ), an open-source package for robust interaction detection in CHi-C. We validate CHiCAGO by showing that promoter-interacting regions detected with this method are enriched for regulatory features and disease-associated SNPs.
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Affiliation(s)
- Jonathan Cairns
- Nuclear Dynamics Programme, Babraham Institute, Cambridge, UK
| | | | - Steven W Wingett
- Nuclear Dynamics Programme, Babraham Institute, Cambridge, UK
- Bioinformatics Group, Babraham Institute, Cambridge, UK
| | - Csilla Várnai
- Nuclear Dynamics Programme, Babraham Institute, Cambridge, UK
| | - Andrew Dimond
- Nuclear Dynamics Programme, Babraham Institute, Cambridge, UK
| | | | - Daniel Zerbino
- European Molecular Biology Laboratory, European Bioinformatics Institute, Cambridge, UK
| | | | | | - Cameron Osborne
- Department of Medical and Molecular Genetics, King's College, London, UK
| | - Peter Fraser
- Nuclear Dynamics Programme, Babraham Institute, Cambridge, UK
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13
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Schoenfelder S, Sugar R, Dimond A, Javierre BM, Armstrong H, Mifsud B, Dimitrova E, Matheson L, Tavares-Cadete F, Furlan-Magaril M, Segonds-Pichon A, Jurkowski W, Wingett SW, Tabbada K, Andrews S, Herman B, LeProust E, Osborne CS, Koseki H, Fraser P, Luscombe NM, Elderkin S. Polycomb repressive complex PRC1 spatially constrains the mouse embryonic stem cell genome. Nat Genet 2015; 47:1179-1186. [PMID: 26323060 PMCID: PMC4847639 DOI: 10.1038/ng.3393] [Citation(s) in RCA: 255] [Impact Index Per Article: 28.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2014] [Accepted: 08/05/2015] [Indexed: 02/08/2023]
Abstract
The Polycomb repressive complexes PRC1 and PRC2 maintain embryonic stem cell (ESC) pluripotency by silencing lineage-specifying developmental regulator genes. Emerging evidence suggests that Polycomb complexes act through controlling spatial genome organization. We show that PRC1 functions as a master regulator of mouse ESC genome architecture by organizing genes in three-dimensional interaction networks. The strongest spatial network is composed of the four Hox gene clusters and early developmental transcription factor genes, the majority of which contact poised enhancers. Removal of Polycomb repression leads to disruption of promoter-promoter contacts in the Hox gene network. In contrast, promoter-enhancer contacts are maintained in the absence of Polycomb repression, with accompanying widespread acquisition of active chromatin signatures at network enhancers and pronounced transcriptional upregulation of network genes. Thus, PRC1 physically constrains developmental transcription factor genes and their enhancers in a silenced but poised spatial network. We propose that the selective release of genes from this spatial network underlies cell fate specification during early embryonic development.
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Affiliation(s)
| | - Robert Sugar
- EMBL European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
| | - Andrew Dimond
- Nuclear Dynamics Programme, The Babraham Institute, Cambridge, UK
| | | | - Harry Armstrong
- Nuclear Dynamics Programme, The Babraham Institute, Cambridge, UK
| | - Borbala Mifsud
- Cancer Research UK London Research Institute, London, UK
- Department of Genetics, Evolution & Environment, University College London, London, UK
| | - Emilia Dimitrova
- Nuclear Dynamics Programme, The Babraham Institute, Cambridge, UK
- Department of Biochemistry, Oxford University, Oxford, UK
| | - Louise Matheson
- Nuclear Dynamics Programme, The Babraham Institute, Cambridge, UK
| | - Filipe Tavares-Cadete
- Cancer Research UK London Research Institute, London, UK
- present address: Okinawa Institute for Science and Technology Graduate University, Okinawa, Japan
| | | | | | - Wiktor Jurkowski
- Nuclear Dynamics Programme, The Babraham Institute, Cambridge, UK
| | - Steven W Wingett
- Nuclear Dynamics Programme, The Babraham Institute, Cambridge, UK
- Bioinformatics, The Babraham Institute, Cambridge, UK
| | - Kristina Tabbada
- Nuclear Dynamics Programme, The Babraham Institute, Cambridge, UK
| | - Simon Andrews
- Bioinformatics, The Babraham Institute, Cambridge, UK
| | - Bram Herman
- Agilent Technologies Inc., Santa Clara, California, USA
| | | | | | - Haruhiko Koseki
- Laboratory for Developmental Genetics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Peter Fraser
- Nuclear Dynamics Programme, The Babraham Institute, Cambridge, UK
| | - Nicholas M Luscombe
- EMBL European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
- Cancer Research UK London Research Institute, London, UK
- Department of Genetics, Evolution & Environment, University College London, London, UK
- Okinawa Institute for Science and Technology Graduate University, Okinawa, Japan
| | - Sarah Elderkin
- Nuclear Dynamics Programme, The Babraham Institute, Cambridge, UK
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14
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Knock E, Pereira J, Lombard PD, Dimond A, Leaford D, Livesey FJ, Hendrich B. The methyl binding domain 3/nucleosome remodelling and deacetylase complex regulates neural cell fate determination and terminal differentiation in the cerebral cortex. Neural Dev 2015; 10:13. [PMID: 25934499 PMCID: PMC4432814 DOI: 10.1186/s13064-015-0040-z] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2014] [Accepted: 04/17/2015] [Indexed: 12/28/2022] Open
Abstract
BACKGROUND Chromatin-modifying complexes have key roles in regulating various aspects of neural stem cell biology, including self-renewal and neurogenesis. The methyl binding domain 3/nucleosome remodelling and deacetylation (MBD3/NuRD) co-repressor complex facilitates lineage commitment of pluripotent cells in early mouse embryos and is important for stem cell homeostasis in blood and skin, but its function in neurogenesis had not been described. Here, we show for the first time that MBD3/NuRD function is essential for normal neurogenesis in mice. RESULTS Deletion of MBD3, a structural component of the NuRD complex, in the developing mouse central nervous system resulted in reduced cortical thickness, defects in the proper specification of cortical projection neuron subtypes and neonatal lethality. These phenotypes are due to alterations in PAX6+ apical progenitor cell outputs, as well as aberrant terminal neuronal differentiation programmes of cortical plate neurons. Normal numbers of PAX6+ apical neural progenitor cells were generated in the MBD3/NuRD-mutant cortex; however, the PAX6+ apical progenitor cells generate EOMES+ basal progenitor cells in reduced numbers. Cortical progenitor cells lacking MBD3/NuRD activity generate neurons that express both deep- and upper-layer markers. Using laser capture microdissection, gene expression profiling and chromatin immunoprecipitation, we provide evidence that MBD3/NuRD functions to control gene expression patterns during neural development. CONCLUSIONS Our data suggest that although MBD3/NuRD is not required for neural stem cell lineage commitment, it is required to repress inappropriate transcription in both progenitor cells and neurons to facilitate appropriate cell lineage choice and differentiation programmes.
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Affiliation(s)
- Erin Knock
- Wellcome Trust - Medical Research Council Stem Cell Institute, University of Cambridge, Cambridge, CB2 1QR, UK.
- Tanz Centre for Research in Neurodegenerative Diseases, Krembil Discovery Tower, 6KD-404, 60 Leonard Avenue, Toronto, ON, Canada.
| | - João Pereira
- Gurdon Institute, University of Cambridge, Cambridge, CB2 1QW, UK.
- Department of Biochemistry, University of Cambridge, Cambridge, CB2 1QN, UK.
| | - Patrick D Lombard
- Wellcome Trust - Medical Research Council Stem Cell Institute, University of Cambridge, Cambridge, CB2 1QR, UK.
| | - Andrew Dimond
- Department of Biochemistry, University of Cambridge, Cambridge, CB2 1QN, UK.
| | - Donna Leaford
- Wellcome Trust - Medical Research Council Stem Cell Institute, University of Cambridge, Cambridge, CB2 1QR, UK.
| | - Frederick J Livesey
- Wellcome Trust - Medical Research Council Stem Cell Institute, University of Cambridge, Cambridge, CB2 1QR, UK.
- Gurdon Institute, University of Cambridge, Cambridge, CB2 1QW, UK.
- Department of Biochemistry, University of Cambridge, Cambridge, CB2 1QN, UK.
| | - Brian Hendrich
- Wellcome Trust - Medical Research Council Stem Cell Institute, University of Cambridge, Cambridge, CB2 1QR, UK.
- Department of Biochemistry, University of Cambridge, Cambridge, CB2 1QN, UK.
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15
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Schoenfelder S, Furlan-Magaril M, Mifsud B, Tavares-Cadete F, Sugar R, Javierre BM, Nagano T, Katsman Y, Sakthidevi M, Wingett SW, Dimitrova E, Dimond A, Edelman LB, Elderkin S, Tabbada K, Darbo E, Andrews S, Herman B, Higgs A, LeProust E, Osborne CS, Mitchell JA, Luscombe NM, Fraser P. The pluripotent regulatory circuitry connecting promoters to their long-range interacting elements. Genome Res 2015; 25:582-97. [PMID: 25752748 PMCID: PMC4381529 DOI: 10.1101/gr.185272.114] [Citation(s) in RCA: 308] [Impact Index Per Article: 34.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2014] [Accepted: 02/11/2015] [Indexed: 12/17/2022]
Abstract
The mammalian genome harbors up to one million regulatory elements often located at great distances from their target genes. Long-range elements control genes through physical contact with promoters and can be recognized by the presence of specific histone modifications and transcription factor binding. Linking regulatory elements to specific promoters genome-wide is currently impeded by the limited resolution of high-throughput chromatin interaction assays. Here we apply a sequence capture approach to enrich Hi-C libraries for >22,000 annotated mouse promoters to identify statistically significant, long-range interactions at restriction fragment resolution, assigning long-range interacting elements to their target genes genome-wide in embryonic stem cells and fetal liver cells. The distal sites contacting active genes are enriched in active histone modifications and transcription factor occupancy, whereas inactive genes contact distal sites with repressive histone marks, demonstrating the regulatory potential of the distal elements identified. Furthermore, we find that coregulated genes cluster nonrandomly in spatial interaction networks correlated with their biological function and expression level. Interestingly, we find the strongest gene clustering in ES cells between transcription factor genes that control key developmental processes in embryogenesis. The results provide the first genome-wide catalog linking gene promoters to their long-range interacting elements and highlight the complex spatial regulatory circuitry controlling mammalian gene expression.
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Affiliation(s)
- Stefan Schoenfelder
- Nuclear Dynamics Programme, The Babraham Institute, Babraham Research Campus, Cambridge CB22 3AT, United Kingdom
| | - Mayra Furlan-Magaril
- Nuclear Dynamics Programme, The Babraham Institute, Babraham Research Campus, Cambridge CB22 3AT, United Kingdom
| | - Borbala Mifsud
- University College London, UCL Genetics Institute, Department of Genetics, Evolution and Environment, University College London, London WC1E 6BT, United Kingdom; Cancer Research UK London Research Institute, London WC2A 3LY, United Kingdom
| | - Filipe Tavares-Cadete
- University College London, UCL Genetics Institute, Department of Genetics, Evolution and Environment, University College London, London WC1E 6BT, United Kingdom; Cancer Research UK London Research Institute, London WC2A 3LY, United Kingdom
| | - Robert Sugar
- Cancer Research UK London Research Institute, London WC2A 3LY, United Kingdom; EMBL European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, United Kingdom
| | - Biola-Maria Javierre
- Nuclear Dynamics Programme, The Babraham Institute, Babraham Research Campus, Cambridge CB22 3AT, United Kingdom
| | - Takashi Nagano
- Nuclear Dynamics Programme, The Babraham Institute, Babraham Research Campus, Cambridge CB22 3AT, United Kingdom
| | - Yulia Katsman
- Department of Cell and Systems Biology, University of Toronto, Toronto, Ontario M5S 3G5, Canada
| | - Moorthy Sakthidevi
- Department of Cell and Systems Biology, University of Toronto, Toronto, Ontario M5S 3G5, Canada
| | - Steven W Wingett
- Nuclear Dynamics Programme, The Babraham Institute, Babraham Research Campus, Cambridge CB22 3AT, United Kingdom; Bioinformatics Group, The Babraham Institute, Babraham Research Campus, Cambridge CB22 3AT, United Kingdom
| | - Emilia Dimitrova
- Nuclear Dynamics Programme, The Babraham Institute, Babraham Research Campus, Cambridge CB22 3AT, United Kingdom
| | - Andrew Dimond
- Nuclear Dynamics Programme, The Babraham Institute, Babraham Research Campus, Cambridge CB22 3AT, United Kingdom
| | - Lucas B Edelman
- Nuclear Dynamics Programme, The Babraham Institute, Babraham Research Campus, Cambridge CB22 3AT, United Kingdom
| | - Sarah Elderkin
- Nuclear Dynamics Programme, The Babraham Institute, Babraham Research Campus, Cambridge CB22 3AT, United Kingdom
| | - Kristina Tabbada
- Nuclear Dynamics Programme, The Babraham Institute, Babraham Research Campus, Cambridge CB22 3AT, United Kingdom
| | - Elodie Darbo
- University College London, UCL Genetics Institute, Department of Genetics, Evolution and Environment, University College London, London WC1E 6BT, United Kingdom; Cancer Research UK London Research Institute, London WC2A 3LY, United Kingdom
| | - Simon Andrews
- Bioinformatics Group, The Babraham Institute, Babraham Research Campus, Cambridge CB22 3AT, United Kingdom
| | - Bram Herman
- Agilent Technologies, Inc., Santa Clara, California 95051, USA
| | - Andy Higgs
- Agilent Technologies, Inc., Santa Clara, California 95051, USA
| | - Emily LeProust
- Agilent Technologies, Inc., Santa Clara, California 95051, USA
| | - Cameron S Osborne
- Nuclear Dynamics Programme, The Babraham Institute, Babraham Research Campus, Cambridge CB22 3AT, United Kingdom
| | - Jennifer A Mitchell
- Department of Cell and Systems Biology, University of Toronto, Toronto, Ontario M5S 3G5, Canada
| | - Nicholas M Luscombe
- University College London, UCL Genetics Institute, Department of Genetics, Evolution and Environment, University College London, London WC1E 6BT, United Kingdom; Cancer Research UK London Research Institute, London WC2A 3LY, United Kingdom; Okinawa Institute for Science and Technology Graduate University, 1919-1 Tancha, Onna-son, Kunigami-gun, Okinawa 904-0495, Japan
| | - Peter Fraser
- Nuclear Dynamics Programme, The Babraham Institute, Babraham Research Campus, Cambridge CB22 3AT, United Kingdom;
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16
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Herzog VA, Lempradl A, Trupke J, Okulski H, Altmutter C, Ruge F, Boidol B, Kubicek S, Schmauss G, Aumayr K, Ruf M, Pospisilik A, Dimond A, Senergin HB, Vargas ML, Simon JA, Ringrose L. A strand-specific switch in noncoding transcription switches the function of a Polycomb/Trithorax response element. Nat Genet 2014; 46:973-981. [PMID: 25108384 DOI: 10.1038/ng.3058] [Citation(s) in RCA: 83] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2014] [Accepted: 07/14/2014] [Indexed: 12/14/2022]
Abstract
Polycomb/Trithorax response elements (PRE/TREs) can switch their function reversibly between silencing and activation by mechanisms that are poorly understood. Here we show that a switch in forward and reverse noncoding transcription from the Drosophila melanogaster vestigial (vg) PRE/TRE switches the status of the element between silencing (induced by the forward strand) and activation (induced by the reverse strand). In vitro, both noncoding RNAs inhibit PRC2 histone methyltransferase activity, but, in vivo, only the reverse strand binds PRC2. Overexpression of the reverse strand evicts PRC2 from chromatin and inhibits its enzymatic activity. We propose that the interaction of RNAs with PRC2 is differentially regulated in vivo, allowing regulated inhibition of local PRC2 activity. Genome-wide analysis shows that strand switching of noncoding RNAs occurs at several hundred Polycomb-binding sites in fly and vertebrate genomes. This work identifies a previously unreported and potentially widespread class of PRE/TREs that switch function by switching the direction of noncoding RNA transcription.
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Affiliation(s)
- Veronika A Herzog
- IMBA, Institute of Molecular Biotechnology GmBH, Dr. Bohr-Gasse 3, 1030 Vienna, Austria
| | - Adelheid Lempradl
- IMBA, Institute of Molecular Biotechnology GmBH, Dr. Bohr-Gasse 3, 1030 Vienna, Austria.,Max Planck Institute of Immunobiology and Epigenetics, Stübeweg 51, 79108 Freiburg, Germany
| | - Johanna Trupke
- IMBA, Institute of Molecular Biotechnology GmBH, Dr. Bohr-Gasse 3, 1030 Vienna, Austria
| | - Helena Okulski
- IMBA, Institute of Molecular Biotechnology GmBH, Dr. Bohr-Gasse 3, 1030 Vienna, Austria
| | - Christina Altmutter
- IMBA, Institute of Molecular Biotechnology GmBH, Dr. Bohr-Gasse 3, 1030 Vienna, Austria
| | - Frank Ruge
- IMBA, Institute of Molecular Biotechnology GmBH, Dr. Bohr-Gasse 3, 1030 Vienna, Austria
| | - Bernd Boidol
- CeMM, Research Center for Molecular Medicine, Lazarettgasse 14, 1090 Vienna, Austria
| | - Stefan Kubicek
- CeMM, Research Center for Molecular Medicine, Lazarettgasse 14, 1090 Vienna, Austria
| | - Gerald Schmauss
- IMP, Institute of Molecular Pathology, Dr. Bohr-Gasse 7, 1030 Vienna, Austria
| | - Karin Aumayr
- IMP, Institute of Molecular Pathology, Dr. Bohr-Gasse 7, 1030 Vienna, Austria
| | - Marius Ruf
- Max Planck Institute of Immunobiology and Epigenetics, Stübeweg 51, 79108 Freiburg, Germany
| | - Andrew Pospisilik
- Max Planck Institute of Immunobiology and Epigenetics, Stübeweg 51, 79108 Freiburg, Germany
| | - Andrew Dimond
- IMBA, Institute of Molecular Biotechnology GmBH, Dr. Bohr-Gasse 3, 1030 Vienna, Austria.,The Babraham Institute, Babraham Research Campus, Cambridge, CB22 3AT, United Kingdom
| | - Hasene Basak Senergin
- IMBA, Institute of Molecular Biotechnology GmBH, Dr. Bohr-Gasse 3, 1030 Vienna, Austria
| | - Marcus L Vargas
- Department of Genetics, Cell Biology and Development, University of Minnesota. Minneapolis, Minnesota, USA
| | - Jeffrey A Simon
- Department of Genetics, Cell Biology and Development, University of Minnesota. Minneapolis, Minnesota, USA
| | - Leonie Ringrose
- IMBA, Institute of Molecular Biotechnology GmBH, Dr. Bohr-Gasse 3, 1030 Vienna, Austria
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17
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Affiliation(s)
- Andrew Dimond
- Nuclear Dynamics Programme, The Babraham Institute, Cambridge, UK
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18
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Mitchell DM, Gildeh P, Rehahn M, Dimond A, Collins JV. Psychological changes and improvement in chronic airflow limitation after corticosteroid treatment. Thorax 1984; 39:924-7. [PMID: 6393417 PMCID: PMC459954 DOI: 10.1136/thx.39.12.924] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Corticosteroids may produce mood changes. This could account for improvement in patients with chronic airflow limitation following trials of oral corticosteroid treatment as mood elevation might improve performance in objective measurements. This proposition was tested in 21 patients with chronic airflow limitation, who underwent detailed psychological assessment during a randomised controlled double blind crossover trial of the effect of prednisolone 40 mg daily compared with that of a placebo. Self rating visual analogue scales for various qualities of mood were completed before the study and after each phase in addition to depression and psychological symptom questionnaires. After treatment with the placebo, patients showed increases in cheerfulness (p less than 0.01) and sociability (p less than 0.01) and a decrease in depression (p less than 0.01). After treatment with prednisolone there were increases in cheerfulness (p less than 0.01), optimism (p less than 0.01), activity (p less than 0.05), and sociability (p less than 0.02) and there was a decrease in depression (p less than 0.01). When placebo and prednisolone values were compared, however, there were no significant differences. Some patients showed improvements (greater than 20%) in peak expiratory flow, FEV1 or forced vital capacity (FVC) after prednisolone, but nearly all had improvements in at least one psychological test. There were no detectable associations between changes in objective measurements and changes in psychological test ratings. This study suggests that in patients with chronic obstructive lung disease significant psychological changes are no more likely to follow treatment with a corticosteroid than treatment with a placebo and that physiological improvement after corticosteroid treatment is not tied to psychological changes.
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19
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Affiliation(s)
- A Dimond
- Department of Botany, University of Wisconsin
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