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1.
J Neurogenet ; 36(1): 32-42, 2022 Mar.
Article in English | MEDLINE | ID: mdl-35642561

ABSTRACT

It has been widely reported that dysregulated long-chain noncoding RNAs (lncRNAs) are closely associated with epilepsy. This study aimed to probe the function of lncRNA growth arrest-specific 5 (GAS5), microRNA (miR)-219 and Calmodulin-dependent protein kinase II (CaMKII)γ/N-methyl-D-aspartate receptor (NMDAR) pathway in epilepsy. Epileptic cell and animal models were constructed using magnesium deficiency treatment and diazepam injection, respectively. GAS5 and miR-219 expressions in epileptic cell and animal models were determined using qRT-PCR assay. The protein levels of CaMKIIγ, NMDAR and apoptosis-related proteins levels were assessed by western blot. Cell counting kit-8 (CCK-8) assay was employed to determine cell proliferation. Besides, TNFα, IL-1ß, IL-6 and IL-8 levels were analyzed using enzyme-linked immunosorbent assay (ELISA). Furthermore, cell apoptosis was evaluated using TUNEL staining and flow cytometric analysis. Finally, the binding relationship between GAS5 and EZH2 was verified using RIP and ChIP assay. Our results revealed that GAS5 was markedly upregulated in epileptic cell and animal models, while miR-219 was down-regulated. GAS5 knockdown dramatically increased cell proliferation of epileptic cells, whereas suppressed inflammation and the apoptosis. Furthermore, our results showed that GAS5 epigenetically suppressed transcriptional miR-219 expression via binding to EZH2. miR-219 mimics significantly enhanced cell proliferation of epileptic cells, while inhibited inflammation and the apoptosis, which was neutralized by CaMKIIγ overexpression. Finally, miR-219 inhibition reversed the effects of GAS5 silence on epileptic cells, which was eliminated by CaMKIIγ inhibition. In conclusion, GAS5 affected inflammatory response and cell apoptosis of epilepsy via inhibiting miR-219 and further regulating CaMKIIγ/NMDAR pathway (See graphic summary in Supplementary Material).


Subject(s)
Epilepsy , MicroRNAs , RNA, Long Noncoding , Animals , Apoptosis/genetics , Calcium-Calmodulin-Dependent Protein Kinase Type 2/genetics , Calcium-Calmodulin-Dependent Protein Kinase Type 2/metabolism , Epigenetic Repression , Epilepsy/genetics , Inflammation/genetics , MicroRNAs/genetics , RNA, Long Noncoding/genetics , RNA, Long Noncoding/metabolism
2.
J Exp Med ; 219(6)2022 06 06.
Article in English | MEDLINE | ID: mdl-35593887

ABSTRACT

During an immune response to microbial infection, CD8+ T cells give rise to short-lived effector cells and memory cells that provide sustained protection. Although the transcriptional programs regulating CD8+ T cell differentiation have been extensively characterized, the role of long noncoding RNAs (lncRNAs) in this process remains poorly understood. Using a functional genetic knockdown screen, we identified the lncRNA Malat1 as a regulator of terminal effector cells and the terminal effector memory (t-TEM) circulating memory subset. Evaluation of chromatin-enriched lncRNAs revealed that Malat1 grouped with trans lncRNAs that exhibit increased RNA interactions at gene promoters and gene bodies. Moreover, we observed that Malat1 was associated with increased H3K27me3 deposition at a number of memory cell-associated genes through a direct interaction with Ezh2, thereby promoting terminal effector and t-TEM cell differentiation. Our findings suggest an important functional role of Malat1 in regulating CD8+ T cell differentiation and broaden the knowledge base of lncRNAs in CD8+ T cell biology.


Subject(s)
RNA, Long Noncoding , CD8-Positive T-Lymphocytes , Cell Differentiation/genetics , Epigenetic Repression , Lymphocyte Activation , RNA, Long Noncoding/genetics
3.
Cancer Immunol Res ; 10(7): 829-843, 2022 07 01.
Article in English | MEDLINE | ID: mdl-35561311

ABSTRACT

The MYC oncogene is frequently amplified in triple-negative breast cancer (TNBC). Here, we show that MYC suppression induces immune-related hallmark gene set expression and tumor-infiltrating T cells in MYC-hyperactivated TNBCs. Mechanistically, MYC repressed stimulator of interferon genes (STING) expression via direct binding to the STING1 enhancer region, resulting in downregulation of the T-cell chemokines CCL5, CXCL10, and CXCL11. In primary and metastatic TNBC cohorts, tumors with high MYC expression or activity exhibited low STING expression. Using a CRISPR-mediated enhancer perturbation approach, we demonstrated that MYC-driven immune evasion is mediated by STING repression. STING repression induced resistance to PD-L1 blockade in mouse models of TNBC. Finally, a small-molecule inhibitor of MYC combined with PD-L1 blockade elicited a durable response in immune-cold TNBC with high MYC expression, suggesting a strategy to restore PD-L1 inhibitor sensitivity in MYC-overexpressing TNBC.


Subject(s)
Membrane Proteins/genetics , Proto-Oncogene Proteins c-myc/metabolism , Triple Negative Breast Neoplasms , Animals , B7-H1 Antigen , Cell Line, Tumor , Epigenetic Repression , Humans , Immune Checkpoint Inhibitors/pharmacology , Immune Checkpoint Inhibitors/therapeutic use , Immune Evasion , Mice , Triple Negative Breast Neoplasms/drug therapy , Triple Negative Breast Neoplasms/genetics , Triple Negative Breast Neoplasms/pathology
4.
Proc Natl Acad Sci U S A ; 119(22): e2120633119, 2022 05 31.
Article in English | MEDLINE | ID: mdl-35605119

ABSTRACT

Dysregulated epigenetic and transcriptional programming due to abnormalities of transcription factors (TFs) contributes to and sustains the oncogenicity of cancer cells. Here, we unveiled the role of zinc finger protein 280C (ZNF280C), a known DNA damage response protein, as a tumorigenic TF in colorectal cancer (CRC), required for colitis-associated carcinogenesis and Apc deficiency­driven intestinal tumorigenesis in mice. Consistently, ZNF280C silencing in human CRC cells inhibited proliferation, clonogenicity, migration, xenograft growth, and liver metastasis. As a C2H2 (Cys2-His2) zinc finger-containing TF, ZNF280C occupied genomic intervals with both transcriptionally active and repressive states and coincided with CCCTC-binding factor (CTCF) and cohesin binding. Notably, ZNF280C was crucial for the repression program of trimethylation of histone H3 at lysine 27 (H3K27me3)-marked genes and the maintenance of both focal and broad H3K27me3 levels. Mechanistically, ZNF280C counteracted CTCF/cohesin activities and condensed the chromatin environment at the cis elements of certain tumor suppressor genes marked by H3K27me3, at least partially through recruiting the epigenetic repressor structural maintenance of chromosomes flexible hinge domain-containing 1 (SMCHD1). In clinical relevance, ZNF280C was highly expressed in primary CRCs and distant metastases, and a higher ZNF280C level independently predicted worse prognosis of CRC patients. Thus, our study uncovered a contributor with good prognostic value to CRC pathogenesis and also elucidated the essence of DNA-binding TFs in orchestrating the epigenetic programming of gene regulation.


Subject(s)
Chromatin , Colorectal Neoplasms , Epigenetic Repression , CCCTC-Binding Factor/metabolism , Carcinogenesis/genetics , Chromatin/genetics , Colorectal Neoplasms/genetics , Colorectal Neoplasms/metabolism , DNA-Binding Proteins , Histones/genetics , Histones/metabolism , Humans , Prognosis , Transcription Factors , Zinc Fingers
5.
EBioMedicine ; 79: 103985, 2022 May.
Article in English | MEDLINE | ID: mdl-35429693

ABSTRACT

BACKGROUND: The multiplicity, heterogeneity, and dynamic nature of human immunodeficiency virus type-1 (HIV-1) latency mechanisms are reflected in the current lack of functional cure for HIV-1. Accordingly, all classes of latency-reversing agents (LRAs) have been reported to present variable ex vivo potencies. Here, we investigated the molecular mechanisms underlying the potency variability of one LRA: the DNA methylation inhibitor 5-aza-2'-deoxycytidine (5-AzadC). METHODS: We employed epigenetic interrogation methods (electrophoretic mobility shift assays, chromatin immunoprecipitation, Infinium array) in complementary HIV-1 infection models (latently-infected T-cell line models, primary CD4+ T-cell models and ex vivo cultures of PBMCs from HIV+ individuals). Extracellular staining of cell surface receptors and intracellular metabolic activity were measured in drug-treated cells. HIV-1 expression in reactivation studies was explored by combining the measures of capsid p24Gag protein, green fluorescence protein signal, intracellular and extracellular viral RNA and viral DNA. FINDINGS: We uncovered specific demethylation CpG signatures induced by 5-AzadC in the HIV-1 promoter. By analyzing the binding modalities to these CpG, we revealed the recruitment of the epigenetic integrator Ubiquitin-like with PHD and RING finger domain 1 (UHRF1) to the HIV-1 promoter. We showed that UHRF1 redundantly binds to the HIV-1 promoter with different binding modalities where DNA methylation was either non-essential, essential or enhancing UHRF1 binding. We further demonstrated the role of UHRF1 in the epigenetic repression of the latent viral promoter by a concerted control of DNA and histone methylations. INTERPRETATION: A better understanding of the molecular mechanisms of HIV-1 latency allows for the development of innovative antiviral strategies. As a proof-of-concept, we showed that pharmacological inhibition of UHRF1 in ex vivo HIV+ patient cell cultures resulted in potent viral reactivation from latency. Together, we identify UHRF1 as a novel actor in HIV-1 epigenetic silencing and highlight that it constitutes a new molecular target for HIV-1 cure strategies. FUNDING: Funding was provided by the Belgian National Fund for Scientific Research (F.R.S.-FNRS, Belgium), the « Fondation Roi Baudouin ¼, the NEAT (European AIDS Treatment Network) program, the Internationale Brachet Stiftung, ViiV Healthcare, the Télévie, the Walloon Region (« Fonds de Maturation ¼), « Les Amis des Instituts Pasteur à Bruxelles, asbl ¼, the University of Brussels (Action de Recherche Concertée ULB grant), the Marie Skodowska Curie COFUND action, the European Union's Horizon 2020 research and innovation program under grant agreement No 691119-EU4HIVCURE-H2020-MSCA-RISE-2015, the French Agency for Research on AIDS and Viral Hepatitis (ANRS), the Sidaction and the "Alsace contre le Cancer" Foundation. This work is supported by 1UM1AI164562-01, co-funded by National Heart, Lung and Blood Institute, National Institute of Diabetes and Digestive and Kidney Diseases, National Institute of Neurological Disorders and Stroke, National Institute on Drug Abuse and the National Institute of Allergy and Infectious Diseases.


Subject(s)
CCAAT-Enhancer-Binding Proteins , Epigenetic Repression , HIV Infections , HIV-1 , Ubiquitin-Protein Ligases , Virus Latency , Acquired Immunodeficiency Syndrome , CCAAT-Enhancer-Binding Proteins/genetics , CCAAT-Enhancer-Binding Proteins/metabolism , DNA Methylation , Decitabine/metabolism , HIV Infections/genetics , HIV-1/physiology , Humans , Ubiquitin-Protein Ligases/genetics , Ubiquitin-Protein Ligases/metabolism , Virus Latency/genetics
6.
Nat Commun ; 13(1): 1972, 2022 04 13.
Article in English | MEDLINE | ID: mdl-35418126

ABSTRACT

Hyperimmunity drives the development of Alzheimer disease (AD). The immune system is under the circadian control, and circadian abnormalities aggravate AD progress. Here, we investigate how an AD-linked mutation deregulates expression of circadian genes and induces cognitive decline using the knock-in (KI) mice heterozygous for presenilin 2 N141I mutation. This mutation causes selective overproduction of clock gene-controlled cytokines through the DNA hypermethylation-mediated repression of REV-ERBα in innate immune cells. The KI/+ mice are vulnerable to otherwise innocuous, mild immune challenges. The antipsychotic chlorpromazine restores the REV-ERBα level by normalizing DNA methylation through the inhibition of PI3K/AKT1 pathway, and prevents the overexcitation of innate immune cells and cognitive decline in KI/+ mice. These results highlight a pathogenic link between this AD mutation and immune cell overactivation through the epigenetic suppression of REV-ERBα.


Subject(s)
Epigenetic Repression , Nuclear Receptor Subfamily 1, Group D, Member 1 , Presenilin-2/genetics , Animals , Circadian Rhythm/physiology , Immunity , Mice , Mutation , Nuclear Receptor Subfamily 1, Group D, Member 1/metabolism
7.
Mol Psychiatry ; 27(7): 3024-3033, 2022 Jul.
Article in English | MEDLINE | ID: mdl-35296808

ABSTRACT

Growing evidence supports a role for deficient Wnt signalling in Alzheimer's disease (AD). First, the Wnt antagonist DKK1 is elevated in AD brains and is required for amyloid-ß-induced synapse loss. Second, LRP6 Wnt co-receptor is required for synapse integrity and three variants of this receptor are linked to late-onset AD. However, the expression/role of other Wnt signalling components remain poorly explored in AD. Wnt receptors Frizzled1 (Fzd1), Fzd5, Fzd7 and Fzd9 are of interest due to their role in synapse formation/plasticity. Our analyses showed reduced FZD1 and FZD7 mRNA levels in the hippocampus of human early AD stages and in the hAPPNLGF/NLGF mouse model. This transcriptional downregulation was accompanied by reduced levels of the pro-transcriptional histone mark H4K16ac and a concomitant increase of its deacetylase Sirt2 at Fzd1 and Fzd7 promoters in AD. In vitro and in vivo inhibition of Sirt2 rescued Fzd1 and Fzd7 mRNA expression and H4K16ac levels at their promoters. In addition, we showed that Sirt2 recruitment to Fzd1 and Fzd7 promoters is dependent on FoxO1 activity in AD, thus acting as a co-repressor. Finally, we found reduced levels of SIRT2 inhibitory phosphorylation in nuclear samples from human early AD stages with a concomitant increase in the SIRT2 phosphatase PP2C. This results in hyperactive nuclear Sirt2 and favours Fzd1 and Fzd7 repression in AD. Collectively, our findings define a novel role for nuclear hyperactivated SIRT2 in repressing Fzd1 and Fzd7 expression via H4K16ac deacetylation in AD. We propose SIRT2 as an attractive target to ameliorate AD pathology.


Subject(s)
Alzheimer Disease , Receptors, Wnt , Alzheimer Disease/genetics , Animals , Epigenetic Repression , Frizzled Receptors , Humans , Mice , RNA, Messenger , Sirtuin 1 , Sirtuin 2 , Wnt Signaling Pathway
8.
Gene Ther ; 29(5): 294-303, 2022 05.
Article in English | MEDLINE | ID: mdl-35301447

ABSTRACT

The reproductive axis is activated by gonadotropin-releasing hormone (GnRH), which stimulates the pituitary gonadotropes to secrete hormones that drive gonadal function and steroidogenesis. Thus repression of this axis, which is conserved across mammals and sexes, can reduce steroid levels and/or prevent reproduction. Steroid-dependent pathologies, including various cancers, are commonly treated with GnRH super-analogs which have long-term side-effects, while humane solutions for controlling reproduction in domestic and wild animal populations are lacking. GnRH-conjugated toxins are undergoing clinical trials for GnRHR-expressing cancer cells, and have been examined for gonadotrope ablation in animals, but showed low and/or transient effects and administration of toxins has many potential complications. Here we exploit GnRH targeting to gonadotropes to deliver DNA encoding an effector that induces gonadotropin gene repressive epigenetic modifications which are perpetuated over time. Several layers of specificity are endowed through targeting to GnRHR-expressing cells and due to local cleavage of the peptide packaging the DNA; the DNA-encoded effector is expressed and directed to the target genes by the DNA binding domain of a highly specific transcription factor. This design has multiple advantages over existing methods of shutting down the reproductive axis, and its modular design should allow adaptation for broad applications.


Subject(s)
Epigenetic Repression , Gonadotropin-Releasing Hormone , Animals , DNA/genetics , Gene Expression , Gonadotropin-Releasing Hormone/genetics , Gonadotropin-Releasing Hormone/metabolism , Gonadotropins/genetics , Gonadotropins/metabolism , Mammals/genetics , Mammals/metabolism
9.
Development ; 149(5)2022 03 01.
Article in English | MEDLINE | ID: mdl-35245348

ABSTRACT

The hypothalamus displays staggering cellular diversity, chiefly established during embryogenesis by the interplay of several signalling pathways and a battery of transcription factors. However, the contribution of epigenetic cues to hypothalamus development remains unclear. We mutated the polycomb repressor complex 2 gene Eed in the developing mouse hypothalamus, which resulted in the loss of H3K27me3, a fundamental epigenetic repressor mark. This triggered ectopic expression of posteriorly expressed regulators (e.g. Hox homeotic genes), upregulation of cell cycle inhibitors and reduced proliferation. Surprisingly, despite these effects, single cell transcriptomic analysis revealed that most neuronal subtypes were still generated in Eed mutants. However, we observed an increase in glutamatergic/GABAergic double-positive cells, as well as loss/reduction of dopamine, hypocretin and Tac2-Pax6 neurons. These findings indicate that many aspects of the hypothalamic gene regulatory flow can proceed without the key H3K27me3 epigenetic repressor mark, but points to a unique sensitivity of particular neuronal subtypes to a disrupted epigenomic landscape.


Subject(s)
Embryonic Development/physiology , Hypothalamus/physiology , Neurons/physiology , Polycomb Repressive Complex 2/genetics , Polycomb-Group Proteins/genetics , Animals , Cell Proliferation/genetics , Epigenetic Repression/genetics , Female , Male , Mice , Mutation/genetics , Transcriptome/genetics
10.
Sci Total Environ ; 826: 154095, 2022 Jun 20.
Article in English | MEDLINE | ID: mdl-35219660

ABSTRACT

The prevalence of diabetes in children and adolescents has been rising gradually, which is relevant to adverse environment during development, especially prepartum. We aimed to explore the effects of prenatal dexamethasone exposure (PDE) on ß-cell function and glucose homeostasis in juvenile offspring rats. Pregnant Wistar rats were subcutaneously administered with dexamethasone [0.1, 0.2, 0.4mg/(kg.d)] from gestational day 9 to 20. PDE impaired glucose tolerance in the male offspring rather than the females. In male offspring, PDE impaired the development and function of ß-cells, accompanied with lower H3K9ac, H3K14ac and H3K27ac levels in the promoter region of angiotensin-converting enzyme 2 (ACE2) as well as suppressed ACE2 expression. Meanwhile, PDE increased expression of glucocorticoid receptor (GR) and histone deacetylase 3 (HDAC3) in fetal pancreas. Dexamethasone also inhibited ACE2 expression and insulin production in vitro. Recombinant expression of ACE2 restored insulin production inhibited by dexamethasone. In addition, dexamethasone activated GR and HDAC3, increased protein interaction of GR with HDAC3, and promoted the binding of GR-HDAC3 complex to ACE2 promoter region. Both RU486 and TSA abolished dexamethasone-induced decline of histone acetylation and ACE2 expression. In summary, suppression of ACE2 is involved in PDE induced ß-cell dysfunction and glucose intolerance in juvenile male offspring rats.


Subject(s)
Glucose Intolerance , Insulins , Prenatal Exposure Delayed Effects , Adolescent , Angiotensin-Converting Enzyme 2 , Animals , Dexamethasone/toxicity , Epigenetic Repression , Female , Glucose Intolerance/chemically induced , Humans , Insulins/metabolism , Insulins/toxicity , Male , Pancreas/metabolism , Pregnancy , Prenatal Exposure Delayed Effects/chemically induced , Rats , Rats, Wistar , Receptors, Glucocorticoid
11.
Acta Crystallogr D Struct Biol ; 78(Pt 1): 59-68, 2022 Jan 01.
Article in English | MEDLINE | ID: mdl-34981762

ABSTRACT

CRISPR-Cas systems are well known host defense mechanisms that are conserved in bacteria and archaea. To counteract CRISPR-Cas systems, phages and viruses have evolved to possess multiple anti-CRISPR (Acr) proteins that can inhibit the host CRISPR-Cas system via different strategies. The expression of acr genes is controlled by anti-CRISPR-associated (Aca) proteins that bind to an upstream promoter and regulate the expression of acr genes during transcription. Although the role of Aca as a transcriptional repressor has been demonstrated, the mechanism of action of Aca has not been determined. Here, the molecular mechanism underlying the Aca2-mediated transcriptional control of acr genes was elucidated by determining the crystal structure of Aca2 from Oceanimonas smirnovii at a high resolution of 1.92 Å. Aca2 forms a dimer in solution, and dimerization of Aca2 is critical for specific promoter binding. The promoter-binding strategy of dimeric Aca2 was also revealed by performing mutagenesis studies. The atomic structure of the Aca family shown in this study provides insights into the fine regulation of host defense and immune-escape mechanisms and also demonstrates the conserved working mechanism of the Aca family.


Subject(s)
CRISPR-Associated Proteins/genetics , CRISPR-Cas Systems , AIDS-Related Complex , Aeromonadaceae , CRISPR-Associated Proteins/chemistry , Crystallography, X-Ray , Epigenetic Repression , Molecular Structure , Mutagenesis , Promoter Regions, Genetic , Transcription, Genetic
12.
Nat Commun ; 13(1): 66, 2022 01 10.
Article in English | MEDLINE | ID: mdl-35013187

ABSTRACT

The Human Silencing Hub (HUSH) complex constituted of TASOR, MPP8 and Periphilin recruits the histone methyl-transferase SETDB1 to spread H3K9me3 repressive marks across genes and transgenes in an integration site-dependent manner. The deposition of these repressive marks leads to heterochromatin formation and inhibits gene expression, but the underlying mechanism is not fully understood. Here, we show that TASOR silencing or HIV-2 Vpx expression, which induces TASOR degradation, increases the accumulation of transcripts derived from the HIV-1 LTR promoter at a post-transcriptional level. Furthermore, using a yeast 2-hybrid screen, we identify new TASOR partners involved in RNA metabolism including the RNA deadenylase CCR4-NOT complex scaffold CNOT1. TASOR and CNOT1 synergistically repress HIV expression from its LTR. Similar to the RNA-induced transcriptional silencing complex found in fission yeast, we show that TASOR interacts with the RNA exosome and RNA Polymerase II, predominantly under its elongating state. Finally, we show that TASOR facilitates the association of RNA degradation proteins with RNA polymerase II and is detected at transcriptional centers. Altogether, we propose that HUSH operates at the transcriptional and post-transcriptional levels to repress HIV proviral expression.


Subject(s)
Epigenetic Repression , HIV-2/metabolism , Nuclear Proteins/genetics , Nuclear Proteins/metabolism , RNA Stability , Transcription Factors/genetics , Transcription Factors/metabolism , Chromatin Assembly and Disassembly , Gene Expression , Gene Silencing , HIV Infections/virology , HIV Long Terminal Repeat , HeLa Cells , Histone-Lysine N-Methyltransferase/genetics , Histone-Lysine N-Methyltransferase/metabolism , Histones/metabolism , Humans , Phosphoproteins , Proviruses/genetics , RNA Polymerase II/metabolism , Schizosaccharomyces
14.
J Neurogenet ; 36(1): 11-20, 2022 Mar.
Article in English | MEDLINE | ID: mdl-35098860

ABSTRACT

Alzheimer's disease (AD) is the leading cause of dementia globally, but effective treatment is lacking. We aimed to explore lncRNA XIST role in AD and the mechanisms involved in the effect of changes in lncRNA XIST on the expression of Aß-degrading enzymes. The mouse model of AD and the cell model induced by Aß were established. LncRNA XIST, IDE, NEP, Plasmin, ACE, EZH2 expressions and distribution of XIST in the nucleus and cytoplasm were detected by qRT-PCR. Inflammatory cytokines IL-6, IL-1ß, TNFα, IL-8, and Aß42 levels were detected by ELISA. TUNEL was used to measure brain tissue damage. Cell proliferation was detected by CCK-8 assay. Flow cytometry detected cell apoptosis. RIP validated the combination of XIST and EZH2. ChIP verified that XIST recruits EZH2 to mediate enrichment of HEK27me3 in the NEP promoter region. The protein expression in brain tissues and cells was detected by Western blot. The expression of lncRNA XIST was increased in AD mice and cell models. Inflammation and injury of nerve cells occurred in AD mice and cell models. The knockdown of lncRNA XIST alleviated Aß-induced neuronal inflammation and damage. LncRNA XIST affected the expression of Aß-degrading enzyme NEP, and lncRNA XIST was negatively correlated with NEP expression in AD mice. LncRNA XIST regulated NEP expression partly through epigenetic regulation by binding with EZH2. LncRNA XIST mediated neuronal inflammation and injury through epigenetic regulation of NEP. Overall, our study found that lncRNA XIST induced Aß accumulation and neuroinflammation by the epigenetic repression of NEP in AD.


Subject(s)
Alzheimer Disease , MicroRNAs , RNA, Long Noncoding , Alzheimer Disease/genetics , Alzheimer Disease/metabolism , Animals , Epigenesis, Genetic , Epigenetic Repression , Mice , Neprilysin/genetics , Neprilysin/metabolism , RNA, Long Noncoding/genetics
15.
J Mol Cell Cardiol ; 162: 119-129, 2022 01.
Article in English | MEDLINE | ID: mdl-34492228

ABSTRACT

Histone deacetylase 4 (HDAC4) is a member of class IIa histone deacetylases (class IIa HDACs) and is believed to possess a low intrinsic deacetylase activity. However, HDAC4 sufficiently represses distinct transcription factors (TFs) such as the myocyte enhancer factor 2 (MEF2). Transcriptional repression by HDAC4 has been suggested to be mediated by the recruitment of other chromatin-modifying enzymes, such as methyltransferases or class I histone deacetylases. However, this concept has not been investigated by an unbiased approach. Therefore, we studied the histone modifications H3K4me3, H3K9ac, H3K27ac, H3K9me2 and H3K27me3 in a genome-wide approach using HDAC4-deficient cardiomyocytes. We identified a general epigenetic shift from a 'repressive' to an 'active' status, characterized by an increase of H3K4me3, H3K9ac and H3K27ac and a decrease of H3K9me2 and H3K27me3. In HDAC4-deficient cardiomyocytes, MEF2 binding sites were considerably overrepresented in upregulated promoter regions of H3K9ac and H3K4me3. For example, we identified the promoter of Adprhl1 as a new genomic target of HDAC4 and MEF2. Overexpression of HDAC4 in cardiomyocytes was able to repress the transcription of the Adprhl1 promoter in the presence of the methyltransferase SUV39H1. On a genome-wide level, the decrease of H3K9 methylation did not change baseline expression but was associated with exercise-induced gene expression. We conclude that HDAC4, on the one hand, associates with activating histone modifications, such as H3K4me3 and H3K9ac. A functional consequence, on the other hand, requires an indirect regulation of H3K9me2. H3K9 hypomethylation in HDAC4 target genes ('first hit') plus a 'second hit' (e.g., exercise) determines the transcriptional response.


Subject(s)
Epigenetic Repression , Histone Deacetylases , Histone Deacetylases/genetics , Histone Deacetylases/metabolism , MEF2 Transcription Factors/genetics , MEF2 Transcription Factors/metabolism , Methylation , Protein Processing, Post-Translational
16.
Nat Commun ; 12(1): 5541, 2021 09 20.
Article in English | MEDLINE | ID: mdl-34545097

ABSTRACT

Human Immunodeficiency Virus (HIV-1) produces a persistent latent infection. Control of HIV-1 using combination antiretroviral therapy (cART) comes at the cost of life-shortening side effects and development of drug-resistant HIV-1. An ideal and safer therapy should be deliverable in vivo and target the stable epigenetic repression of the virus, inducing a stable "block and lock" of virus expression. Towards this goal, we developed an HIV-1 promoter-targeting Zinc Finger Protein (ZFP-362) fused to active domains of DNA methyltransferase 3 A to induce long-term stable epigenetic repression of HIV-1. Cells were engineered to produce exosomes packaged with RNAs encoding this HIV-1 repressor protein. We find here that the repressor loaded anti-HIV-1 exosomes suppress virus expression and that this suppression is mechanistically driven by DNA methylation of HIV-1 in humanized NSG mouse models. The observations presented here pave the way for an exosome-mediated systemic delivery platform of therapeutic cargo to epigenetically repress HIV-1 infection.


Subject(s)
Epigenetic Repression/genetics , Exosomes/metabolism , HIV-1/genetics , Animals , Brain/pathology , Brain/virology , Cell Line , DNA (Cytosine-5-)-Methyltransferases/metabolism , DNA Methylation/genetics , Exosomes/ultrastructure , Gene Expression Regulation, Viral , Genetic Vectors/metabolism , HEK293 Cells , HIV Infections/virology , Humans , Lentivirus/metabolism , Leukocytes, Mononuclear/metabolism , Mice , RNA, Messenger/genetics , RNA, Messenger/metabolism , Terminal Repeat Sequences/genetics , Viral Load , Zinc Fingers
18.
Elife ; 102021 07 08.
Article in English | MEDLINE | ID: mdl-34236315

ABSTRACT

MGA, a transcription factor and member of the MYC network, is mutated or deleted in a broad spectrum of malignancies. As a critical test of a tumor suppressive role, we inactivated Mga in two mouse models of non-small cell lung cancer using a CRISPR-based approach. MGA loss significantly accelerated tumor growth in both models and led to de-repression of non-canonical Polycomb ncPRC1.6 targets, including genes involved in metastasis and meiosis. Moreover, MGA deletion in human lung adenocarcinoma lines augmented invasive capabilities. We further show that MGA-MAX, E2F6, and L3MBTL2 co-occupy thousands of promoters and that MGA stabilizes these ncPRC1.6 subunits. Lastly, we report that MGA loss also induces a pro-growth effect in human colon organoids. Our studies establish MGA as a bona fide tumor suppressor in vivo and suggest a tumor suppressive mechanism in adenocarcinomas resulting from widespread transcriptional attenuation of MYC and E2F target genes mediated by MGA-MAX associated with a non-canonical Polycomb complex.


Subject(s)
Basic Helix-Loop-Helix Transcription Factors/genetics , Carcinoma, Non-Small-Cell Lung/genetics , Epigenetic Repression , Polycomb-Group Proteins/genetics , Adenocarcinoma of Lung/genetics , Animals , Basic Helix-Loop-Helix Transcription Factors/metabolism , Cell Line, Tumor , Disease Progression , Female , Humans , Male , Mice , Neoplasm Invasiveness/genetics , Polycomb-Group Proteins/metabolism
19.
EMBO Rep ; 22(9): e53496, 2021 09 06.
Article in English | MEDLINE | ID: mdl-34313382

ABSTRACT

The dynamic nature of interactions between invading viral pathogens and their hosts has fascinated scientists for several decades. The well-known capacity of herpes simplex virus (HSV) to establish life-long infections in humans reflects a dynamic balance between maintaining a latent state in which viral genomes are silenced and re-entry into the lytic phase during reactivation. Silencing of the viral genome has been shown to be a function of innate immune signalling, intrinsic cellular antiviral mechanisms and epigenetic repression. Thus, although many important observations have been made identifying cellular processes that contribute to the repression of the viral genome and latency, the field has lacked an understanding of how these factors work together. In this issue of EMBO Reports, Suzich et al (2021) present convincing evidence that brings together individual observations into a cohesive model that explains many of these outstanding mysteries. Here, we will review the background data that lead to this outstanding piece of work.


Subject(s)
Herpesvirus 1, Human , Epigenetic Repression , Genome, Viral , Herpesvirus 1, Human/genetics , Humans , Virus Latency/genetics
20.
Nat Struct Mol Biol ; 28(6): 501-511, 2021 06.
Article in English | MEDLINE | ID: mdl-34117481

ABSTRACT

The mammalian SWI/SNF complex, or BAF complex, has a conserved and direct role in antagonizing Polycomb-mediated repression. Yet, BAF also promotes repression by Polycomb in stem cells and cancer. How BAF both antagonizes and promotes Polycomb-mediated repression remains unknown. Here, we utilize targeted protein degradation to dissect the BAF-Polycomb axis in mouse embryonic stem cells on short timescales. We report that rapid BAF depletion redistributes Polycomb repressive complexes PRC1 and PRC2 from highly occupied domains, like Hox clusters, to weakly occupied sites normally opposed by BAF. Polycomb redistribution from highly repressed domains results in their decompaction, gain of active epigenomic features and transcriptional derepression. Surprisingly, through dose-dependent degradation of PRC1 and PRC2, we identify a conventional role for BAF in Polycomb-mediated repression, in addition to global Polycomb redistribution. These findings provide new mechanistic insight into the highly dynamic state of the Polycomb-Trithorax axis.


Subject(s)
Chromatin Assembly and Disassembly/physiology , Epigenetic Repression/physiology , Gene Expression Regulation/physiology , Multiprotein Complexes/physiology , Polycomb-Group Proteins/physiology , Animals , CRISPR-Cas Systems , Cells, Cultured , Chromatin Assembly and Disassembly/genetics , DNA Helicases/genetics , DNA Helicases/metabolism , DNA-Binding Proteins/physiology , Embryonic Stem Cells/metabolism , Epigenesis, Genetic , Epigenetic Repression/genetics , Gene Editing , Gene Expression Regulation/genetics , Genes, Homeobox , Genome , HEK293 Cells , Homeodomain Proteins/genetics , Homeodomain Proteins/metabolism , Humans , Loss of Function Mutation , Mice , Nuclear Proteins/genetics , Nuclear Proteins/metabolism , Proteolysis , Recombinant Fusion Proteins/metabolism , Transcription Factors/genetics , Transcription Factors/metabolism , Transcription Factors/physiology
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