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Abstract
Chromatin immunoprecipitation, commonly referred to as ChIP, is a powerful technique for the evaluation of in vivo interactions of proteins with specific regions of genomic DNA. Formaldehyde is used in this technique to cross-link proteins to DNA in vivo, followed by the extraction of chromatin from cross-linked cells and tissues. Harvested chromatin is sheared and subsequently used in an immunoprecipitation incorporating antibodies specific to protein(s) of interest and thus coprecipitating and enriching the cross-linked, protein-associated DNA. The cross-linking process can be reversed, and protein-bound DNA fragments of optimal length ranging from 200 to 1000 base pairs (bp) can subsequently be purified and measured or sequenced by numerous analytical methods. In this protocol, two different fixation methods are described in detail. The first involves the standard fixation of cells and tissue by formaldehyde if the target antigen is highly abundant. The dual cross-linking procedure presented at the end includes an additional preformaldehyde cross-linking step and can be especially useful when the target protein is in low abundance or if it is indirectly associated with chromatin DNA through another protein.
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Manca M, Pessoa V, Myers P, Pickles A, Hill J, Sharp H, Murgatroyd C, Bubb VJ, Quinn JP. Distinct chromatin structures at the monoamine oxidase-A promoter correlate with allele-specific expression in SH-SY5Y cells. GENES, BRAIN, AND BEHAVIOR 2019; 18:e12483. [PMID: 29667298 PMCID: PMC6617726 DOI: 10.1111/gbb.12483] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/02/2017] [Revised: 02/19/2018] [Accepted: 04/13/2018] [Indexed: 11/30/2022]
Abstract
Monoamine oxidase-A (MAOA) metabolises monoamines and is implicated in the pathophysiology of psychiatric disorders. A polymorphic repetitive DNA domain, termed the uVNTR (upstream variable number tandem repeat), located at the promoter of the MAOA gene is a risk factor for many of these disorders. MAOA is on the X chromosome suggesting gender could play a role in regulation. We analysed MAOA regulation in the human female cell line, SH-SY5Y, which is polymorphic for the uVNTR. This heterozygosity allowed us to correlate allele-specific gene expression with allele-specific transcription factor binding and epigenetic marks for MAOA. Gene regulation was analysed under basal conditions and in response to the mood stabiliser sodium valproate. Both alleles were transcriptionally active under basal growth conditions; however, the alleles showed distinct transcription factor binding and epigenetic marks at their respective promoters. Exposure of the cells to sodium valproate resulted in differential allelic expression which correlated with allele-specific changes in distinct transcription factor binding and epigenetic marks at the region encompassing the uVNTR. Biochemically our model for MAOA promoter function has implications for gender differences in gene × environment responses in which the uVNTR has been implicated as a genetic risk.
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Affiliation(s)
- M. Manca
- Department of Molecular and Clinical Pharmacology, Institute of Translational MedicineUniversity of LiverpoolLiverpoolUK
- Institute of Psychology, Health and SocietyUniversity of LiverpoolLiverpoolUK
| | - V. Pessoa
- Department of Molecular and Clinical Pharmacology, Institute of Translational MedicineUniversity of LiverpoolLiverpoolUK
- Institute of Psychology, Health and SocietyUniversity of LiverpoolLiverpoolUK
| | - P. Myers
- Department of Molecular and Clinical Pharmacology, Institute of Translational MedicineUniversity of LiverpoolLiverpoolUK
| | - A. Pickles
- King's College London, MRC Social Genetic and Developmental Psychiatry Research CentreInstitute of PsychiatryLondonUK
| | - J. Hill
- School for Psychology and Clinical Language SciencesUniversity of ReadingReadingUK
| | - H. Sharp
- Institute of Psychology, Health and SocietyUniversity of LiverpoolLiverpoolUK
| | - C. Murgatroyd
- School of Healthcare ScienceManchester Metropolitan UniversityManchesterUK
| | - V. J. Bubb
- Department of Molecular and Clinical Pharmacology, Institute of Translational MedicineUniversity of LiverpoolLiverpoolUK
| | - J. P. Quinn
- Department of Molecular and Clinical Pharmacology, Institute of Translational MedicineUniversity of LiverpoolLiverpoolUK
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Bhattacharya A, Sun S, Wang H, Liu M, Long Q, Yin L, Kersten S, Zhang K, Qi L. Hepatic Sel1L-Hrd1 ER-associated degradation (ERAD) manages FGF21 levels and systemic metabolism via CREBH. EMBO J 2018; 37:embj.201899277. [PMID: 30389665 DOI: 10.15252/embj.201899277] [Citation(s) in RCA: 56] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2018] [Revised: 08/15/2018] [Accepted: 09/05/2018] [Indexed: 12/15/2022] Open
Abstract
Fibroblast growth factor 21 (Fgf21) is a liver-derived, fasting-induced hormone with broad effects on growth, nutrient metabolism, and insulin sensitivity. Here, we report the discovery of a novel mechanism regulating Fgf21 expression under growth and fasting-feeding. The Sel1L-Hrd1 complex is the most conserved branch of mammalian endoplasmic reticulum (ER)-associated degradation (ERAD) machinery. Mice with liver-specific deletion of Sel1L exhibit growth retardation with markedly elevated circulating Fgf21, reaching levels close to those in Fgf21 transgenic mice or pharmacological models. Mechanistically, we show that the Sel1L-Hrd1 ERAD complex controls Fgf21 transcription by regulating the ubiquitination and turnover (and thus nuclear abundance) of ER-resident transcription factor Crebh, while having no effect on the other well-known Fgf21 transcription factor Pparα. Our data reveal a physiologically regulated, inverse correlation between Sel1L-Hrd1 ERAD and Crebh-Fgf21 levels under fasting-feeding and growth. This study not only establishes the importance of Sel1L-Hrd1 ERAD in the liver in the regulation of systemic energy metabolism, but also reveals a novel hepatic "ERAD-Crebh-Fgf21" axis directly linking ER protein turnover to gene transcription and systemic metabolic regulation.
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Affiliation(s)
- Asmita Bhattacharya
- Department of Molecular and Integrative Physiology, University of Michigan Medical School, Ann Arbor, MI, USA.,Graduate Program of Genetics, Genomics and Development, Cornell University, Ithaca, NY, USA.,Division of Metabolism, Endocrinology & Diabetes, Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Shengyi Sun
- Department of Pharmacology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Heting Wang
- Department of Endocrinology and Metabolism, Tianjin Medical University General Hospital, Tianjin, China
| | - Ming Liu
- Division of Metabolism, Endocrinology & Diabetes, Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, MI, USA.,Department of Endocrinology and Metabolism, Tianjin Medical University General Hospital, Tianjin, China
| | - Qiaoming Long
- Cam-Su Mouse Genomic Resource Center, Soochow University, Suzhou, Jiangsu, China
| | - Lei Yin
- Department of Molecular and Integrative Physiology, University of Michigan Medical School, Ann Arbor, MI, USA.,Division of Metabolism, Endocrinology & Diabetes, Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Sander Kersten
- Nutrition Metabolism and Genomics Group, Wageningen University, Wageningen, The Netherlands
| | - Kezhong Zhang
- Department of Biochemistry, Microbiology, and Immunology, Center for Molecular Medicine and Genetics Wayne State University School of Medicine, Detroit, MI, USA
| | - Ling Qi
- Department of Molecular and Integrative Physiology, University of Michigan Medical School, Ann Arbor, MI, USA .,Division of Metabolism, Endocrinology & Diabetes, Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, MI, USA
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Hanson BR, Tan M. Intra-ChIP: studying gene regulation in an intracellular pathogen. Curr Genet 2016; 62:547-51. [PMID: 26886234 PMCID: PMC5139683 DOI: 10.1007/s00294-016-0580-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2016] [Accepted: 02/11/2016] [Indexed: 12/25/2022]
Abstract
Intracellular bacteria that reside within a host cell use a variety of strategies to exploit this unique niche. While these organisms are technically challenging to study in the context of an infected host cell, recent advances have led to an improved understanding of how the intracellular environment impacts bacterial gene expression. We recently demonstrated that chromatin immunoprecipitation (ChIP) can be used to quantify transcription factor binding in the obligate intracellular pathogen Chlamydia trachomatis within infected cells. Furthermore, we showed it was possible to experimentally modulate transcription factor binding while simultaneously measuring changes in transcription. Here we discuss these findings as well as other recent work that has used ChIP to study intracellular pathogens within infected cells. We also discuss technical considerations associated with this approach and its possible future applications.
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Affiliation(s)
- Brett R Hanson
- Department of Microbiology and Molecular Genetics, University of California, B240 Med Sci, Irvine, CA, 92697-4025, USA
| | - Ming Tan
- Department of Microbiology and Molecular Genetics, University of California, B240 Med Sci, Irvine, CA, 92697-4025, USA.
- Department of Medicine, University of California, Irvine, CA, USA.
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Xu L, Hong Q, Chen X, Xu X, Liu H, Zhou W, Duan S. H4K5 histone acetylation of BRG1 is associated with heroin administration rather than addiction. Exp Ther Med 2016; 12:1929-1933. [PMID: 27588112 DOI: 10.3892/etm.2016.3517] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2015] [Accepted: 05/19/2016] [Indexed: 11/06/2022] Open
Abstract
Diacetylmorphine hydrochloride (heroin) addiction is a chronic relapsing brain disorder that is a heavy public health burden worldwide. Brm/SWI2-related gene-1 (BRG1) is a tumor suppressor gene that can influence embryogenesis and the development of the cerebellum. The current study aimed to investigate the effect of histone H4 lysine 5 (H4K5) modifications on the BRG1 gene in brain tissue of the ventral tegmental area (VTA) of heroin-addicted rats. A total of 21 male Sprague Dawley rats were raised in a standard manner and underwent heroin self-administration training. Rats were randomly divided into three equal groups: Group A, self-administered delivery of heroin; group B, yoked delivery of heroin; and group C, yoked delivery of saline. The VTA was harvested and subjected to chromatin immunoprecipitation (ChIP) analysis. Gene expression was evaluated by quantitative polymerase chain reaction. We calculated the recovery rate, which indicated the percentage of the total input BRG1 recovered by ChIP. Our results showed that BRG1 was less associated with H4K5 histone modification in the group of rats that underwent heroin self-administration than in the other two groups (A vs. B, P=0.031; A vs. C, P=0.067). The recovery fold changes of the self-administration group and the passive-administration group were significantly different from those of the group with yoked saline (A vs. C, P=0.013; B vs. C, P=0.009; A vs. B, P=0.731). The results of the current study demonstrated that H4K5 histone acetylation of BRG1 in the VTA may be associated with heroin administration, but not addiction.
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Affiliation(s)
- Limin Xu
- Zhejiang Provincial Key Laboratory of Pathophysiology, Ningbo University School of Medicine, Ningbo, Zhejiang 315211, P.R. China; Huzhou Key Laboratory of Molecular Medicine, Huzhou Central Hospital, Huzhou, Zhejiang 313000, P.R. China
| | - Qingxiao Hong
- Zhejiang Provincial Key Laboratory of Pathophysiology, Ningbo University School of Medicine, Ningbo, Zhejiang 315211, P.R. China
| | - Xiaoying Chen
- Zhejiang Provincial Key Laboratory of Pathophysiology, Ningbo University School of Medicine, Ningbo, Zhejiang 315211, P.R. China
| | - Xuting Xu
- Zhejiang Provincial Key Laboratory of Pathophysiology, Ningbo University School of Medicine, Ningbo, Zhejiang 315211, P.R. China
| | - Huifen Liu
- Laboratory of Behavioral Neuroscience, Ningbo University, Ningbo, Zhejiang 315010, P.R. China; Ningbo Institute of Microcirculation and Henbane, Ningbo, Zhejiang 315010, P.R. China
| | - Wenhua Zhou
- Zhejiang Provincial Key Laboratory of Pathophysiology, Ningbo University School of Medicine, Ningbo, Zhejiang 315211, P.R. China; Laboratory of Behavioral Neuroscience, Ningbo University, Ningbo, Zhejiang 315010, P.R. China; Ningbo Institute of Microcirculation and Henbane, Ningbo, Zhejiang 315010, P.R. China
| | - Shiwei Duan
- Zhejiang Provincial Key Laboratory of Pathophysiology, Ningbo University School of Medicine, Ningbo, Zhejiang 315211, P.R. China
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Warburton A, Breen G, Rujescu D, Bubb VJ, Quinn JP. Characterization of a REST-Regulated Internal Promoter in the Schizophrenia Genome-Wide Associated Gene MIR137. Schizophr Bull 2015; 41:698-707. [PMID: 25154622 PMCID: PMC4393679 DOI: 10.1093/schbul/sbu117] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
MIR137 has been identified as a candidate gene for schizophrenia from genome-wide association studies via association with an intronic single nucleotide polymorphism (SNP), rs1625579. The location of the SNP suggests one mechanism in which transcriptional or posttranscriptional regulation of miR-137 expression could underlie schizophrenia. We identified and validated a novel promoter of the MIR137 gene adjacent to miR-137 itself which can direct the expression of distinct mRNA isoforms encoding miR-137. Analysis of both endogenous gene expression and reporter gene assays determined that this internal promoter is regulated by repressor element-1 silencing transcription factor (REST), which has previously been associated with pathways linked to schizophrenia. Distinct isoforms of REST mediate differential expression at this locus, suggesting the relative levels of these isoforms are important for miR-137 expression profiles. The internal promoter contains a variable number tandem repeat (VNTR) domain adjacent to the pre-miR-137 sequence. The reporter gene activity directed by this promoter was modified by the genotype of the VNTR. Differential expression was also observed in response to cocaine, which is known to regulate the REST pathway in SH-SY5Y cells. Our data support the hypothesis that a "gene × environment" interaction could modify the level of miR-137 expression via this internal promoter and that the genotype of the VNTR could modulate transcriptional responses. We demonstrate that this promoter region is not in disequilibrium with rs1625579 and therefore would supply a distinct pathway to potentially alter miR-137 levels in response to environmental cues.
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Affiliation(s)
- Alix Warburton
- Department of Molecular and Clinical Pharmacology, Institute of Translational Medicine, University of Liverpool, Liverpool L69 3BX, UK;
| | - Gerome Breen
- King’s College London, MRC Social Genetic and Developmental Psychiatry Research Centre, Institute of Psychiatry, London, UK; ,National Institute for Health Research (NIHR), Biomedical Research Centre for Mental Health, South London and Maudsley NHS Foundation Trust and Institute of Psychiatry, King’s College London SE5 8DF, UK;
| | - Dan Rujescu
- Department of Psychiatry, University of Halle-Wittenberg, Halle, Germany
| | - Vivien J. Bubb
- Department of Molecular and Clinical Pharmacology, Institute of Translational Medicine, University of Liverpool, Liverpool L69 3BX, UK;
| | - John P. Quinn
- Department of Molecular and Clinical Pharmacology, Institute of Translational Medicine, University of Liverpool, Liverpool L69 3BX, UK; ,*To whom correspondence should be addressed; Department of Molecular and Clinical Pharmacology, University of Liverpool, Crown Street, Liverpool L69 3BX, UK; tel: +44-151-794-5498, fax: +44-151-794-5517, e-mail:
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Schmidt-Edelkraut U, Hoffmann A, Daniel G, Spengler D. Zac1 regulates astroglial differentiation of neural stem cells through Socs3. Stem Cells 2014; 31:1621-32. [PMID: 23630160 DOI: 10.1002/stem.1405] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2012] [Accepted: 03/29/2013] [Indexed: 12/21/2022]
Abstract
Cell-fate decisions and differentiation of embryonic and adult neural stem cells (NSC) are tightly controlled by lineage-restricted and temporal factors that interact with cell-intrinsic programs and extracellular signals through multiple regulatory loops. Imprinted genes are important players in neurodevelopment and mental health although their molecular and cellular functions remain poorly understood. Here, we show that the paternally expressed transcriptional regulator Zac1 (zinc finger protein regulating apoptosis and cell cycle arrest) is transiently induced during astroglial and neuronal differentiation of embryonic and adult NSC lines. Thereby, Zac1 transactivates Socs3 (suppressor of cytokine signaling 3), a potent inhibitor of prodifferentiative Jak/Stat3 signaling, in a lineage-specific manner to prevent precocious astroglial differentiation. In vivo, Zac1 and Socs3 colocalize in the neocortical ventricular zone during incipient astrogliogenesis. Zac1 overexpression in primary NSCs delays astroglial differentiation whereas knockdown of Zac1 or Socs3 facilitates formation of astroglial cells. This negative feedback loop is unrelated to Zac1's cell cycle arrest function and specific to the Jak/Stat3 pathway. Hence, reinstating Jak/Stat3 signaling in the presence of increased Zac1 expression allows for timely astroglial differentiation. Overall, we suggest that the imprinted gene Zac1 curtails astroglial differentiation of NSCs in the developing and adult brain.
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Polycomb binding precedes early-life stress responsive DNA methylation at the Avp enhancer. PLoS One 2014; 9:e90277. [PMID: 24599304 PMCID: PMC3943912 DOI: 10.1371/journal.pone.0090277] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2013] [Accepted: 01/28/2014] [Indexed: 01/07/2023] Open
Abstract
Early-life stress (ELS) in mice causes sustained hypomethylation at the downstream Avp enhancer, subsequent overexpression of hypothalamic Avp and increased stress responsivity. The sequence of events leading to Avp enhancer methylation is presently unknown. Here, we used an embryonic stem cell-derived model of hypothalamic-like differentiation together with in vivo experiments to show that binding of polycomb complexes (PcG) preceded the emergence of ELS-responsive DNA methylation and correlated with gene silencing. At the same time, PcG occupancy associated with the presence of Tet proteins preventing DNA methylation. Early hypothalamic-like differentiation triggered PcG eviction, DNA-methyltransferase recruitment and enhancer methylation. Concurrently, binding of the Methyl-CpG-binding and repressor protein MeCP2 increased at the enhancer although Avp expression during later stages of differentiation and the perinatal period continued to increase. Overall, we provide evidence of a new role of PcG proteins in priming ELS-responsive DNA methylation at the Avp enhancer prior to epigenetic programming consistent with the idea that PcG proteins are part of a flexible silencing system during neuronal development.
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Abstract
Imprinted genes play a critical role in brain development and mental health, although the underlying molecular and cellular mechanisms remain incompletely understood. The family of basic helix-loop-helix (bHLH) proteins directs the proliferation, differentiation, and specification of distinct neuronal progenitor populations. Here, we identified the bHLH factor gene Tcf4 as a direct target gene of Zac1/Plagl1, a maternally imprinted transcriptional regulator, during early neurogenesis. Zac1 and Tcf4 expression levels concomitantly increased during neuronal progenitor differentiation; moreover, Zac1 interacts with two cis-regulatory elements in the Tcf4 gene locus, and these elements together confer synergistic activation of the Tcf4 gene. Tcf4 upregulation enhances the expression of the cyclin-dependent kinase inhibitor gene p57(Kip2), a paternally imprinted Tcf4 target gene, and increases the number of cells in G1 phase. Overall, we show that Zac1 controls cell cycle arrest function in neuronal progenitors through induction of p57(Kip2) via Tcf4 and provide evidence for cooperation between imprinted genes and a bHLH factor in early neurodevelopment.
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Transient neonatal diabetes mellitus gene Zac1 impairs insulin secretion in mice through Rasgrf1. Mol Cell Biol 2012; 32:2549-60. [PMID: 22547676 DOI: 10.1128/mcb.06637-11] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
The biallelic expression of the imprinted gene ZAC1/PLAGL1 underlies ≈ 60% of all cases of transient neonatal diabetes mellitus (TNDM) that present with low perinatal insulin secretion. Molecular targets of ZAC1 misexpression in pancreatic β cells are unknown. Here, we identified the guanine nucleotide exchange factor Rasgrf1 as a direct Zac1/Plagl1 target gene in murine β cells. Doubling Zac1 expression reduced Rasgrf1 expression, the stimulus-induced activation of mitogen-activated protein kinase (MAPK) and phosphoinositide 3-kinase (PI3K) pathways, and, ultimately, insulin secretion. Normalizing Rasgrf1 expression reversed this phenotype. Moreover, the transplantation of Zac1-overexpressing β cells failed to reinstate euglycemia in experimental diabetic mice. In contrast, Zac1 expression did not interfere with the signaling of the glucagon-like peptide 1 receptor (GLP-1R), and the GLP-1 analog liraglutide improved hyperglycemia in transplanted experimental diabetic mice. This study unravels a mechanism contributing to insufficient perinatal insulin secretion in TNDM and raises new prospects for therapy.
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