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Chao TC, Chen SF, Kim HJ, Tang HC, Tseng HC, Xu A, Palao L, Khadka S, Li T, Huang MF, Lee DF, Murakami K, Boyer TG, Tsai KL. Structural basis of the human transcriptional Mediator regulated by its dissociable kinase module. Mol Cell 2024:S1097-2765(24)00734-2. [PMID: 39321804 DOI: 10.1016/j.molcel.2024.09.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Revised: 01/05/2024] [Accepted: 09/03/2024] [Indexed: 09/27/2024]
Abstract
The eukaryotic transcriptional Mediator comprises a large core (cMED) and a dissociable CDK8 kinase module (CKM). cMED recruits RNA polymerase II (RNA Pol II) and promotes pre-initiation complex formation in a manner repressed by the CKM through mechanisms presently unknown. Herein, we report cryoelectron microscopy structures of the complete human Mediator and its CKM. The CKM binds to multiple regions on cMED through both MED12 and MED13, including a large intrinsically disordered region (IDR) in the latter. MED12 and MED13 together anchor the CKM to the cMED hook, positioning CDK8 downstream and proximal to the transcription start site. Notably, the MED13 IDR obstructs the recruitment of RNA Pol II/MED26 onto cMED by direct occlusion of their respective binding sites, leading to functional repression of cMED-dependent transcription. Combined with biochemical and functional analyses, these structures provide a conserved mechanistic framework to explain the basis for CKM-mediated repression of cMED function.
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Affiliation(s)
- Ti-Chun Chao
- Department of Biochemistry and Molecular Biology, McGovern Medical School, University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Shin-Fu Chen
- Department of Biochemistry and Molecular Biology, McGovern Medical School, University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Hee Jong Kim
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Hui-Chi Tang
- Department of Biochemistry and Molecular Biology, McGovern Medical School, University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Hsiang-Ching Tseng
- Department of Biochemistry and Molecular Biology, McGovern Medical School, University of Texas Health Science Center at Houston, Houston, TX, USA
| | - An Xu
- Department of Integrative Biology and Pharmacology, McGovern Medical School, University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Leon Palao
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Subash Khadka
- Department of Molecular Medicine, University of Texas Health Science Center at San Antonio, San Antonio, TX, USA
| | - Tao Li
- Department of Biochemistry and Molecular Biology, McGovern Medical School, University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Mo-Fan Huang
- Department of Integrative Biology and Pharmacology, McGovern Medical School, University of Texas Health Science Center at Houston, Houston, TX, USA; MD Anderson Cancer Center UTHealth Houston Graduate School of Biomedical Sciences, Houston, TX, USA
| | - Dung-Fang Lee
- Department of Integrative Biology and Pharmacology, McGovern Medical School, University of Texas Health Science Center at Houston, Houston, TX, USA; MD Anderson Cancer Center UTHealth Houston Graduate School of Biomedical Sciences, Houston, TX, USA; Center for Precision Health, McWilliams School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX, USA; Center for Stem Cell and Regenerative Medicine, The Brown Foundation Institute of Molecular Medicine for the Prevention of Human Diseases, The University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Kenji Murakami
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
| | - Thomas G Boyer
- Department of Molecular Medicine, University of Texas Health Science Center at San Antonio, San Antonio, TX, USA.
| | - Kuang-Lei Tsai
- Department of Biochemistry and Molecular Biology, McGovern Medical School, University of Texas Health Science Center at Houston, Houston, TX, USA; MD Anderson Cancer Center UTHealth Houston Graduate School of Biomedical Sciences, Houston, TX, USA.
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2
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McWilliams MM, Koohestani F, Jefferson WN, Gunewardena S, Shivashankar K, Wertenberger RA, Williams CJ, Kumar TR, Chennathukuzhi VM. Estrogen receptor alpha mediated repression of PRICKLE1 destabilizes REST and promotes uterine fibroid pathogenesis. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.09.09.612036. [PMID: 39314474 PMCID: PMC11419101 DOI: 10.1101/2024.09.09.612036] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/25/2024]
Abstract
Uterine fibroids (leiomyomas), benign tumors of the myometrial smooth muscle layer, are present in over 75% of women, often causing severe pain, menorrhagia and reproductive dysfunction. The molecular pathogenesis of fibroids is poorly understood. We previously showed that the loss of REST (RE-1 Silencing Transcription factor), a tumor suppressor, in fibroids leads to activation of PI3K/AKT-mTOR pathway. We report here a critical link between estrogen receptor alpha (ERα) and the loss of REST, via PRICKLE1. PRICKLE1 expression is markedly lower in leiomyomas, and the suppression of PRICKLE1 significantly down regulates REST protein levels. Conversely, overexpression of PRICKLE1 resulted in the restoration of REST in cultured primary leiomyoma smooth muscle cells (LSMCs). Crucially, mice exposed neonatally to environmental estrogens, proven risk factors for fibroids, expressed lower levels of PRICKLE1 and REST in the myometrium. Using mice that lack either endogenous estrogen (Lhb -/- mice) or ERα (Esr1 -/- mice), we demonstrate that Prickle1 expression in the myometrium is suppressed by estrogen through ERα. Enhancer of zeste homolog 2 (EZH2) is known to participate in the repression of specific ERα target genes. Uterine leiomyomas express increased levels of EZH2 that inversely correlate with the expression of PRICKLE1. Using chromatin immunoprecipitation, we provide evidence for association of EZH2 with the PRICKLE1 promoter and for hypermethylation of H3K27 within the regulatory region of PRICKLE1 in leiomyomas. Additionally, siRNA mediated knockdown of EZH2 leads to restoration of PRICKLE1 in LSMCs. Collectively, our results identify a novel link between estrogen exposure and PRICKLE1/REST-regulated tumorigenic pathways in leiomyomas.
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Affiliation(s)
- Michelle M McWilliams
- Department of Cell Biology and Physiology, Center for Reproductive Sciences, Institute for Reproduction and Developmental Sciences, University of Kansas Medical Center, Kansas City, KS
| | - Faezeh Koohestani
- Department of Cell Biology and Physiology, Center for Reproductive Sciences, Institute for Reproduction and Developmental Sciences, University of Kansas Medical Center, Kansas City, KS
| | - Wendy N Jefferson
- Reproductive and Developmental Biology Laboratory, National Institute of Environmental Health Sciences, Research Triangle Park, NC
| | - Sumedha Gunewardena
- Department of Cell Biology and Physiology, Center for Reproductive Sciences, Institute for Reproduction and Developmental Sciences, University of Kansas Medical Center, Kansas City, KS
| | - Kavya Shivashankar
- Department of Cell Biology and Physiology, Center for Reproductive Sciences, Institute for Reproduction and Developmental Sciences, University of Kansas Medical Center, Kansas City, KS
| | - Riley A Wertenberger
- Department of Cell Biology and Physiology, Center for Reproductive Sciences, Institute for Reproduction and Developmental Sciences, University of Kansas Medical Center, Kansas City, KS
| | - Carmen J Williams
- Reproductive and Developmental Biology Laboratory, National Institute of Environmental Health Sciences, Research Triangle Park, NC
| | - T Rajendra Kumar
- Division of Reproductive Sciences, Department of Obstetrics & Gynecology, University of Colorado Denver-Anschutz Medical Campus, Aurora, CO 80045
| | - Vargheese M Chennathukuzhi
- Department of Cell Biology and Physiology, Center for Reproductive Sciences, Institute for Reproduction and Developmental Sciences, University of Kansas Medical Center, Kansas City, KS
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3
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Chen SF, Chao TC, Kim HJ, Tang HC, Khadka S, Li T, Lee DF, Murakami K, Boyer TG, Tsai KL. Structural basis of the human transcriptional Mediator complex modulated by its dissociable Kinase module. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.01.601608. [PMID: 39005267 PMCID: PMC11244988 DOI: 10.1101/2024.07.01.601608] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/16/2024]
Abstract
The eukaryotic Mediator, comprising a large Core (cMED) and a dissociable CDK8 kinase module (CKM), regulates RNA Polymerase II (Pol II)-dependent transcription. cMED recruits Pol II and promotes pre-initiation complex (PIC) formation in a manner inhibited by the CKM, which is also implicated in post-initiation control of gene expression. Herein we report cryo-electron microscopy structures of the human complete Mediator and its CKM, which explains the basis for CKM inhibition of cMED-activated transcription. The CKM binds to cMED through an intrinsically disordered region (IDR) in MED13 and HEAT repeats in MED12. The CKM inhibits transcription by allocating its MED13 IDR to occlude binding of Pol II and MED26 to cMED and further obstructing cMED-PIC assembly through steric hindrance with TFIIH and the +1 nucleosome. Notably, MED12 binds to the cMED Hook, positioning CDK8 downstream of the transcription start site, which sheds new light on its stimulatory function in post-initiation events.
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4
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Bolívar S, Sanz E, Ovelleiro D, Zochodne DW, Udina E. Neuron-specific RNA-sequencing reveals different responses in peripheral neurons after nerve injury. eLife 2024; 12:RP91316. [PMID: 38742628 PMCID: PMC11093584 DOI: 10.7554/elife.91316] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/16/2024] Open
Abstract
Peripheral neurons are heterogeneous and functionally diverse, but all share the capability to switch to a pro-regenerative state after nerve injury. Despite the assumption that the injury response is similar among neuronal subtypes, functional recovery may differ. Understanding the distinct intrinsic regenerative properties between neurons may help to improve the quality of regeneration, prioritizing the growth of axon subpopulations to their targets. Here, we present a comparative analysis of regeneration across four key peripheral neuron populations: motoneurons, proprioceptors, cutaneous mechanoreceptors, and nociceptors. Using Cre/Ai9 mice that allow fluorescent labeling of neuronal subtypes, we found that nociceptors showed the greater regeneration after a sciatic crush, followed by motoneurons, mechanoreceptors, and, finally, proprioceptors. By breeding these Cre mice with Ribotag mice, we isolated specific translatomes and defined the regenerative response of these neuronal subtypes after axotomy. Only 20% of the regulated genes were common, revealing a diverse response to injury among neurons, which was also supported by the differential influence of neurotrophins among neuron subtypes. Among differentially regulated genes, we proposed MED12 as a specific regulator of the regeneration of proprioceptors. Altogether, we demonstrate that the intrinsic regenerative capacity differs between peripheral neuron subtypes, opening the door to selectively modulate these responses.
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Affiliation(s)
- Sara Bolívar
- Institute of Neurosciences, and Department Cell Biology, Physiology and Immunology, Universitat Autònoma de BarcelonaBellaterraSpain
- Centro de Investigación Biomédica en Red sobre Enfermedades Neurodegenerativas, Instituto de Salud Carlos IIIMadridSpain
| | - Elisenda Sanz
- Institute of Neurosciences, and Department Cell Biology, Physiology and Immunology, Universitat Autònoma de BarcelonaBellaterraSpain
| | - David Ovelleiro
- Peripheral Nervous System, Vall d'Hebron Institut de Recerca (VHIR), Vall d'Hebron Hospital Universitari, Vall d'Hebron Barcelona Hospital CampusBarcelonaSpain
| | - Douglas W Zochodne
- Division of Neurology, Department of Medicine and the Neuroscience and Mental Health Institute, University of AlbertaEdmontonCanada
| | - Esther Udina
- Institute of Neurosciences, and Department Cell Biology, Physiology and Immunology, Universitat Autònoma de BarcelonaBellaterraSpain
- Centro de Investigación Biomédica en Red sobre Enfermedades Neurodegenerativas, Instituto de Salud Carlos IIIMadridSpain
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5
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Russo M, Gualdrini F, Vallelonga V, Prosperini E, Noberini R, Pedretti S, Borriero C, Di Chiaro P, Polletti S, Imperato G, Marenda M, Ghirardi C, Bedin F, Cuomo A, Rodighiero S, Bonaldi T, Mitro N, Ghisletti S, Natoli G. Acetyl-CoA production by Mediator-bound 2-ketoacid dehydrogenases boosts de novo histone acetylation and is regulated by nitric oxide. Mol Cell 2024; 84:967-980.e10. [PMID: 38242130 PMCID: PMC7615796 DOI: 10.1016/j.molcel.2023.12.033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Revised: 12/08/2023] [Accepted: 12/21/2023] [Indexed: 01/21/2024]
Abstract
Histone-modifying enzymes depend on the availability of cofactors, with acetyl-coenzyme A (CoA) being required for histone acetyltransferase (HAT) activity. The discovery that mitochondrial acyl-CoA-producing enzymes translocate to the nucleus suggests that high concentrations of locally synthesized metabolites may impact acylation of histones and other nuclear substrates, thereby controlling gene expression. Here, we show that 2-ketoacid dehydrogenases are stably associated with the Mediator complex, thus providing a local supply of acetyl-CoA and increasing the generation of hyper-acetylated histone tails. Nitric oxide (NO), which is produced in large amounts in lipopolysaccharide-stimulated macrophages, inhibited the activity of Mediator-associated 2-ketoacid dehydrogenases. Elevation of NO levels and the disruption of Mediator complex integrity both affected de novo histone acetylation within a shared set of genomic regions. Our findings indicate that the local supply of acetyl-CoA generated by 2-ketoacid dehydrogenases bound to Mediator is required to maximize acetylation of histone tails at sites of elevated HAT activity.
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Affiliation(s)
- Marta Russo
- Department of Experimental Oncology, European Institute of Oncology (IEO) IRCCS, Milan 20139, Italy.
| | - Francesco Gualdrini
- Department of Experimental Oncology, European Institute of Oncology (IEO) IRCCS, Milan 20139, Italy.
| | - Veronica Vallelonga
- Department of Experimental Oncology, European Institute of Oncology (IEO) IRCCS, Milan 20139, Italy
| | - Elena Prosperini
- Department of Experimental Oncology, European Institute of Oncology (IEO) IRCCS, Milan 20139, Italy
| | - Roberta Noberini
- Department of Experimental Oncology, European Institute of Oncology (IEO) IRCCS, Milan 20139, Italy
| | - Silvia Pedretti
- DiSFeB, Dipartimento di Scienze Farmacologiche e Biomolecolari, Università degli Studi di Milano, Milano 20133, Italy
| | - Carolina Borriero
- Department of Experimental Oncology, European Institute of Oncology (IEO) IRCCS, Milan 20139, Italy
| | - Pierluigi Di Chiaro
- Department of Experimental Oncology, European Institute of Oncology (IEO) IRCCS, Milan 20139, Italy
| | - Sara Polletti
- Department of Experimental Oncology, European Institute of Oncology (IEO) IRCCS, Milan 20139, Italy
| | - Gabriele Imperato
- DiSFeB, Dipartimento di Scienze Farmacologiche e Biomolecolari, Università degli Studi di Milano, Milano 20133, Italy
| | - Mattia Marenda
- Department of Experimental Oncology, European Institute of Oncology (IEO) IRCCS, Milan 20139, Italy
| | - Chiara Ghirardi
- Department of Experimental Oncology, European Institute of Oncology (IEO) IRCCS, Milan 20139, Italy
| | - Fabio Bedin
- Department of Experimental Oncology, European Institute of Oncology (IEO) IRCCS, Milan 20139, Italy
| | - Alessandro Cuomo
- Department of Experimental Oncology, European Institute of Oncology (IEO) IRCCS, Milan 20139, Italy
| | - Simona Rodighiero
- Department of Experimental Oncology, European Institute of Oncology (IEO) IRCCS, Milan 20139, Italy
| | - Tiziana Bonaldi
- Department of Experimental Oncology, European Institute of Oncology (IEO) IRCCS, Milan 20139, Italy; Department of Hematology and Hematology-Oncology (DIPO), Università degli Studi di Milano, Milano 20122, Italy
| | - Nico Mitro
- Department of Experimental Oncology, European Institute of Oncology (IEO) IRCCS, Milan 20139, Italy; DiSFeB, Dipartimento di Scienze Farmacologiche e Biomolecolari, Università degli Studi di Milano, Milano 20133, Italy
| | - Serena Ghisletti
- Department of Experimental Oncology, European Institute of Oncology (IEO) IRCCS, Milan 20139, Italy.
| | - Gioacchino Natoli
- Department of Experimental Oncology, European Institute of Oncology (IEO) IRCCS, Milan 20139, Italy.
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6
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Wang B, Vartak R, Zaltsman Y, Naing ZZC, Hennick KM, Polacco BJ, Bashir A, Eckhardt M, Bouhaddou M, Xu J, Sun N, Lasser MC, Zhou Y, McKetney J, Guiley KZ, Chan U, Kaye JA, Chadha N, Cakir M, Gordon M, Khare P, Drake S, Drury V, Burke DF, Gonzalez S, Alkhairy S, Thomas R, Lam S, Morris M, Bader E, Seyler M, Baum T, Krasnoff R, Wang S, Pham P, Arbalaez J, Pratt D, Chag S, Mahmood N, Rolland T, Bourgeron T, Finkbeiner S, Swaney DL, Bandyopadhay S, Ideker T, Beltrao P, Willsey HR, Obernier K, Nowakowski TJ, Hüttenhain R, State MW, Willsey AJ, Krogan NJ. A foundational atlas of autism protein interactions reveals molecular convergence. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.12.03.569805. [PMID: 38076945 PMCID: PMC10705567 DOI: 10.1101/2023.12.03.569805] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2023]
Abstract
Translating high-confidence (hc) autism spectrum disorder (ASD) genes into viable treatment targets remains elusive. We constructed a foundational protein-protein interaction (PPI) network in HEK293T cells involving 100 hcASD risk genes, revealing over 1,800 PPIs (87% novel). Interactors, expressed in the human brain and enriched for ASD but not schizophrenia genetic risk, converged on protein complexes involved in neurogenesis, tubulin biology, transcriptional regulation, and chromatin modification. A PPI map of 54 patient-derived missense variants identified differential physical interactions, and we leveraged AlphaFold-Multimer predictions to prioritize direct PPIs and specific variants for interrogation in Xenopus tropicalis and human forebrain organoids. A mutation in the transcription factor FOXP1 led to reconfiguration of DNA binding sites and altered development of deep cortical layer neurons in forebrain organoids. This work offers new insights into molecular mechanisms underlying ASD and describes a powerful platform to develop and test therapeutic strategies for many genetically-defined conditions.
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7
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Jin L, Liu Y, Wu Y, Huang Y, Zhang D. REST Is Not Resting: REST/NRSF in Health and Disease. Biomolecules 2023; 13:1477. [PMID: 37892159 PMCID: PMC10605157 DOI: 10.3390/biom13101477] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2023] [Revised: 09/26/2023] [Accepted: 09/29/2023] [Indexed: 10/29/2023] Open
Abstract
Chromatin modifications play a crucial role in the regulation of gene expression. The repressor element-1 (RE1) silencing transcription factor (REST), also known as neuron-restrictive silencer factor (NRSF) and X2 box repressor (XBR), was found to regulate gene transcription by binding to chromatin and recruiting chromatin-modifying enzymes. Earlier studies revealed that REST plays an important role in the development and disease of the nervous system, mainly by repressing the transcription of neuron-specific genes. Subsequently, REST was found to be critical in other tissues, such as the heart, pancreas, skin, eye, and vascular. Dysregulation of REST was also found in nervous and non-nervous system cancers. In parallel, multiple strategies to target REST have been developed. In this paper, we provide a comprehensive summary of the research progress made over the past 28 years since the discovery of REST, encompassing both physiological and pathological aspects. These insights into the effects and mechanisms of REST contribute to an in-depth understanding of the transcriptional regulatory mechanisms of genes and their roles in the development and progression of disease, with a view to discovering potential therapeutic targets and intervention strategies for various related diseases.
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Affiliation(s)
- Lili Jin
- School of Life Sciences, Liaoning University, Shenyang 110036, China
| | - Ying Liu
- Department of Stem Cells and Regenerative Medicine, Key Laboratory of Cell Biology, National Health Commission of China, and Key Laboratory of Medical Cell Biology, Ministry of Education of China, China Medical University, Shenyang 110122, China
| | - Yifan Wu
- Department of Stem Cells and Regenerative Medicine, Key Laboratory of Cell Biology, National Health Commission of China, and Key Laboratory of Medical Cell Biology, Ministry of Education of China, China Medical University, Shenyang 110122, China
| | - Yi Huang
- Department of Stem Cells and Regenerative Medicine, Key Laboratory of Cell Biology, National Health Commission of China, and Key Laboratory of Medical Cell Biology, Ministry of Education of China, China Medical University, Shenyang 110122, China
| | - Dianbao Zhang
- Department of Stem Cells and Regenerative Medicine, Key Laboratory of Cell Biology, National Health Commission of China, and Key Laboratory of Medical Cell Biology, Ministry of Education of China, China Medical University, Shenyang 110122, China
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8
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Ma HY, Li Q, Wong WR, N'Diaye EN, Caplazi P, Bender H, Huang Z, Arlantico A, Jeet S, Wong A, Emson C, Brightbill H, Tam L, Newman R, Roose-Girma M, Sandoval W, Ding N. LOXL4, but not LOXL2, is the critical determinant of pathological collagen cross-linking and fibrosis in the lung. SCIENCE ADVANCES 2023; 9:eadf0133. [PMID: 37235663 DOI: 10.1126/sciadv.adf0133] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Accepted: 04/20/2023] [Indexed: 05/28/2023]
Abstract
Idiopathic pulmonary fibrosis is a progressive fibrotic disease characterized by excessive deposition of (myo)fibroblast produced collagen fibrils in alveolar areas of the lung. Lysyl oxidases (LOXs) have been proposed to be the central enzymes that catalyze the cross-linking of collagen fibers. Here, we report that, while its expression is increased in fibrotic lungs, genetic ablation of LOXL2 only leads to a modest reduction of pathological collagen cross-linking but not fibrosis in the lung. On the other hand, loss of another LOX family member, LOXL4, markedly disrupts pathological collagen cross-linking and fibrosis in the lung. Furthermore, knockout of both Loxl2 and Loxl4 does not offer any additive antifibrotic effects when compared to Loxl4 deletion only, as LOXL4 deficiency decreases the expression of other LOX family members including Loxl2. On the basis of these results, we propose that LOXL4 is the main LOX activity underlying pathological collagen cross-linking and lung fibrosis.
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Affiliation(s)
- Hsiao-Yen Ma
- Department of Discovery Immunology, Genentech, South San Francisco, CA, USA
| | - Qingling Li
- Department of Microchemistry, Proteomics, and Lipidomics, Genentech, South San Francisco, CA, USA
| | - Weng Ruh Wong
- Department of Microchemistry, Proteomics, and Lipidomics, Genentech, South San Francisco, CA, USA
| | - Elsa-Noah N'Diaye
- Department of Discovery Immunology, Genentech, South San Francisco, CA, USA
| | - Patrick Caplazi
- Department of Pathology, Genentech, South San Francisco, CA, USA
| | - Hannah Bender
- Department of Pathology, Genentech, South San Francisco, CA, USA
| | - Zhiyu Huang
- Department of Translational Immunology, Genentech, South San Francisco, CA, USA
| | - Alexander Arlantico
- Department of Translational Immunology, Genentech, South San Francisco, CA, USA
| | - Surinder Jeet
- Department of Translational Immunology, Genentech, South San Francisco, CA, USA
| | - Aaron Wong
- Department of Translational Immunology, Genentech, South San Francisco, CA, USA
| | - Claire Emson
- Department of Translational Immunology, Genentech, South San Francisco, CA, USA
| | - Hans Brightbill
- Department of Translational Immunology, Genentech, South San Francisco, CA, USA
| | - Lucinda Tam
- Department of Molecular Biology, Genentech, South San Francisco, CA, USA
| | - Robert Newman
- Department of Molecular Biology, Genentech, South San Francisco, CA, USA
| | - Merone Roose-Girma
- Department of Molecular Biology, Genentech, South San Francisco, CA, USA
| | - Wendy Sandoval
- Department of Microchemistry, Proteomics, and Lipidomics, Genentech, South San Francisco, CA, USA
| | - Ning Ding
- Department of Discovery Immunology, Genentech, South San Francisco, CA, USA
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9
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Suzuki H, Furugori K, Abe R, Ogawa S, Ito S, Akiyama T, Horiuchi K, Takahashi H. MED26-containing Mediator may orchestrate multiple transcription processes through organization of nuclear bodies. Bioessays 2023; 45:e2200178. [PMID: 36852638 DOI: 10.1002/bies.202200178] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2022] [Revised: 02/04/2023] [Accepted: 02/06/2023] [Indexed: 03/01/2023]
Abstract
Mediator is a coregulatory complex that plays essential roles in multiple processes of transcription regulation. One of the human Mediator subunits, MED26, has a role in recruitment of the super elongation complex (SEC) to polyadenylated genes and little elongation complex (LEC) to non-polyadenylated genes, including small nuclear RNAs (snRNAs) and replication-dependent histone (RDH) genes. MED26-containing Mediator plays a role in 3' Pol II pausing at the proximal region of transcript end sites in RDH genes through recruitment of Cajal bodies (CBs) to histone locus bodies (HLBs). This finding suggests that Mediator is involved in the association of CBs with HLBs to facilitate 3' Pol II pausing and subsequent 3'-end processing by supplying 3'-end processing factors from CBs. Thus, we argue the possibility that Mediator is involved in the organization of nuclear bodies to orchestrate multiple processes of gene transcription.
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Affiliation(s)
- Hidefumi Suzuki
- Department of Molecular Biology, Yokohama City University Graduate School of Medical Science, Yokohama, Kanagawa, Japan
| | - Kazuki Furugori
- Department of Molecular Biology, Yokohama City University Graduate School of Medical Science, Yokohama, Kanagawa, Japan
| | - Ryota Abe
- Department of Molecular Biology, Yokohama City University Graduate School of Medical Science, Yokohama, Kanagawa, Japan
| | - Shintaro Ogawa
- Department of Molecular Biology, Yokohama City University Graduate School of Medical Science, Yokohama, Kanagawa, Japan
| | - Sayaka Ito
- Department of Molecular Biology, Yokohama City University Graduate School of Medical Science, Yokohama, Kanagawa, Japan
| | - Tomohiko Akiyama
- Department of Molecular Biology, Yokohama City University Graduate School of Medical Science, Yokohama, Kanagawa, Japan
| | - Keiko Horiuchi
- Department of Molecular Biology, Yokohama City University Graduate School of Medical Science, Yokohama, Kanagawa, Japan
| | - Hidehisa Takahashi
- Department of Molecular Biology, Yokohama City University Graduate School of Medical Science, Yokohama, Kanagawa, Japan
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10
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Hamada N, Iwamoto I, Nagata KI. MED13L and its disease-associated variants influence the dendritic development of cerebral cortical neurons in the mammalian brain. J Neurochem 2023; 165:334-347. [PMID: 36798993 DOI: 10.1111/jnc.15783] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Revised: 11/04/2022] [Accepted: 02/13/2023] [Indexed: 02/18/2023]
Abstract
The mediator complex comprises multiple subcellular subunits that collectively function as a molecular interface between RNA polymerase II and gene-specific transcription factors. Recently, genetic variants to one subunit of the complex, known as MED13L (mediator complex subunit 13 like), have been implicated in syndromic intellectual disability and distinct facial features, frequently accompanied by congenital heart defects. We investigated the impact of five disease-associated MED13L variants on the subcellular localization and biochemical stability of MED13L protein in vitro and in vivo. In overexpression assays using cortical neurons from embryonic mouse cerebral cortices transduced by in utero electroporation-mediated gene transfer, we found that mouse orthologues of human MED13L-p.P866L and -p.T2162M missense variants accumulated in the nucleus, while the p.S2163L and p.S2177Y variants were diffusely distributed in the cytoplasm. In contrast, we found that the p.Q1922* truncation variant was barely detectable in transduced cells, a phenotype reminiscent of this variant that results in MED13L haploinsufficiency in humans. Next, we analyzed these variants for their effects on neuronal migration, dendritic growth, spine morphology, and axon elongation of cortical neurons in vivo. There, we found that overexpression of the p.P866L variant resulted in reduced number and length of dendrites of cortical layer II/III pyramidal neurons. Furthermore, we show that mMED13L-knockdown abrogated dendritic growth in vivo, and this effect was significantly rescued by co-electroporation of an RNAi-resistant mMED13L, but weakly by the p.T2162M variant, and not at all by the p.S2163L variant. However, overexpression of the p.S2163L variant inhibited mature dendritic spine formation in vivo. Expression of each of the 5 variants did not affect neuronal cell migration and callosal axon elongation in vivo. Taken together, our results demonstrate that MED13L expression is relevant to corticogenesis and influences the dendritic branching characteristics of cortical excitatory neurons. Our study also suggests that disease-associated MED13L variants may directly cause morphological and functional defects in cortical neurons in different ways.
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Affiliation(s)
- Nanako Hamada
- Department of Molecular Neurobiology, Institute for Developmental Research, Aichi Developmental Disability Center, Kasugai, Japan
| | - Ikuko Iwamoto
- Department of Molecular Neurobiology, Institute for Developmental Research, Aichi Developmental Disability Center, Kasugai, Japan
| | - Koh-Ichi Nagata
- Department of Molecular Neurobiology, Institute for Developmental Research, Aichi Developmental Disability Center, Kasugai, Japan.,Department of Neurochemistry, Nagoya University Graduate School of Medicine, Nagoya, Japan
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11
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Mouri K, Dewey HB, Castro R, Berenzy D, Kales S, Tewhey R. Whole-genome functional characterization of RE1 silencers using a modified massively parallel reporter assay. CELL GENOMICS 2023; 3:100234. [PMID: 36777181 PMCID: PMC9903721 DOI: 10.1016/j.xgen.2022.100234] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Revised: 09/12/2022] [Accepted: 11/23/2022] [Indexed: 12/23/2022]
Abstract
Both upregulation and downregulation by cis-regulatory elements help modulate precise gene expression. However, our understanding of repressive elements is far more limited than activating elements. To address this gap, we characterized RE1, a group of transcriptional silencers bound by REST, at genome-wide scale using a modified massively parallel reporter assay (MPRAduo). MPRAduo empirically defined a minimal binding strength of REST (REST motif-intrinsic value [m-value]), above which cofactors colocalize and silence transcription. We identified 1,500 human variants that alter RE1 silencing and found that their effect sizes are predictable when they overlap with REST-binding sites above the m-value. Additionally, we demonstrate that non-canonical REST-binding motifs exhibit silencer function only if they precisely align half sites with specific spacer lengths. Our results show mechanistic insights into RE1, which allow us to predict its activity and effect of variants on RE1, providing a paradigm for performing genome-wide functional characterization of transcription-factor-binding sites.
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Affiliation(s)
| | | | | | | | - Susan Kales
- The Jackson Laboratory, Bar Harbor, ME 04609, USA
| | - Ryan Tewhey
- The Jackson Laboratory, Bar Harbor, ME 04609, USA
- Graduate School of Biomedical Sciences and Engineering, University of Maine, Orono, ME, USA
- Graduate School of Biomedical Sciences, Tufts University School of Medicine, Boston, MA, USA
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12
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Richter WF, Nayak S, Iwasa J, Taatjes DJ. The Mediator complex as a master regulator of transcription by RNA polymerase II. Nat Rev Mol Cell Biol 2022; 23:732-749. [PMID: 35725906 PMCID: PMC9207880 DOI: 10.1038/s41580-022-00498-3] [Citation(s) in RCA: 95] [Impact Index Per Article: 47.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/17/2022] [Indexed: 02/08/2023]
Abstract
The Mediator complex, which in humans is 1.4 MDa in size and includes 26 subunits, controls many aspects of RNA polymerase II (Pol II) function. Apart from its size, a defining feature of Mediator is its intrinsic disorder and conformational flexibility, which contributes to its ability to undergo phase separation and to interact with a myriad of regulatory factors. In this Review, we discuss Mediator structure and function, with emphasis on recent cryogenic electron microscopy data of the 4.0-MDa transcription preinitiation complex. We further discuss how Mediator and sequence-specific DNA-binding transcription factors enable enhancer-dependent regulation of Pol II function at distal gene promoters, through the formation of molecular condensates (or transcription hubs) and chromatin loops. Mediator regulation of Pol II reinitiation is also discussed, in the context of transcription bursting. We propose a working model for Mediator function that combines experimental results and theoretical considerations related to enhancer-promoter interactions, which reconciles contradictory data regarding whether enhancer-promoter communication is direct or indirect. We conclude with a discussion of Mediator's potential as a therapeutic target and of future research directions.
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Affiliation(s)
- William F Richter
- Department of Biochemistry, University of Colorado, Boulder, CO, USA
| | - Shraddha Nayak
- Department of Biochemistry, University of Utah, Salt Lake City, UT, USA
| | - Janet Iwasa
- Department of Biochemistry, University of Utah, Salt Lake City, UT, USA
| | - Dylan J Taatjes
- Department of Biochemistry, University of Colorado, Boulder, CO, USA.
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13
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Xi Y, LaCanna R, Ma HY, N'Diaye EN, Gierke S, Caplazi P, Sagolla M, Huang Z, Lucio L, Arlantico A, Jeet S, Brightbill H, Emson C, Wong A, Morshead KB, DePianto DJ, Roose-Girma M, Yu C, Tam L, Jia G, Ramalingam TR, Marsters S, Ashkenazi A, Kim SH, Kelly R, Wu S, Wolters PJ, Feldstein AE, Vander Heiden JA, Ding N. A WISP1 antibody inhibits MRTF signaling to prevent the progression of established liver fibrosis. Cell Metab 2022; 34:1377-1393.e8. [PMID: 35987202 DOI: 10.1016/j.cmet.2022.07.009] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/06/2021] [Revised: 06/06/2022] [Accepted: 07/19/2022] [Indexed: 01/18/2023]
Abstract
Fibrosis is the major risk factor associated with morbidity and mortality in patients with non-alcoholic steatohepatitis (NASH)-driven chronic liver disease. Although numerous efforts have been made to identify the mediators of the initiation of liver fibrosis, the molecular underpinnings of fibrosis progression remain poorly understood, and therapies to arrest liver fibrosis progression are elusive. Here, we identify a pathway involving WNT1-inducible signaling pathway protein 1 (WISP1) and myocardin-related transcription factor (MRTF) as a central mechanism driving liver fibrosis progression through the integrin-dependent transcriptional reprogramming of myofibroblast cytoskeleton and motility. In mice, WISP1 deficiency protects against fibrosis progression, but not fibrosis onset. Moreover, the therapeutic administration of a novel antibody blocking WISP1 halted the progression of existing liver fibrosis in NASH models. These findings implicate the WISP1-MRTF axis as a crucial determinant of liver fibrosis progression and support targeting this pathway by antibody-based therapy for the treatment of NASH fibrosis.
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Affiliation(s)
- Ying Xi
- Department of Discovery Immunology, Genentech, South San Francisco, CA, USA
| | - Ryan LaCanna
- Department of Discovery Immunology, Genentech, South San Francisco, CA, USA
| | - Hsiao-Yen Ma
- Department of Discovery Immunology, Genentech, South San Francisco, CA, USA
| | - Elsa-Noah N'Diaye
- Department of Discovery Immunology, Genentech, South San Francisco, CA, USA
| | - Sarah Gierke
- Department of Pathology, Genentech, South San Francisco, CA, USA
| | - Patrick Caplazi
- Department of Pathology, Genentech, South San Francisco, CA, USA
| | - Meredith Sagolla
- Department of Pathology, Genentech, South San Francisco, CA, USA
| | - Zhiyu Huang
- Department of Translational Immunology, Genentech, South San Francisco, CA, USA
| | - Laura Lucio
- Department of Translational Immunology, Genentech, South San Francisco, CA, USA
| | - Alexander Arlantico
- Department of Translational Immunology, Genentech, South San Francisco, CA, USA
| | - Surinder Jeet
- Department of Translational Immunology, Genentech, South San Francisco, CA, USA
| | - Hans Brightbill
- Department of Translational Immunology, Genentech, South San Francisco, CA, USA
| | - Claire Emson
- Department of Translational Immunology, Genentech, South San Francisco, CA, USA
| | - Aaron Wong
- Department of Translational Immunology, Genentech, South San Francisco, CA, USA
| | - Katrina B Morshead
- Department of Discovery Immunology, Genentech, South San Francisco, CA, USA
| | - Daryle J DePianto
- Department of Discovery Immunology, Genentech, South San Francisco, CA, USA
| | - Merone Roose-Girma
- Department of Molecular Biology, Genentech, South San Francisco, CA, USA
| | - Charles Yu
- Department of Molecular Biology, Genentech, South San Francisco, CA, USA
| | - Lucinda Tam
- Department of Molecular Biology, Genentech, South San Francisco, CA, USA
| | - Guiquan Jia
- Department of Biomarker Discovery, Genentech, South San Francisco, CA, USA
| | | | - Scot Marsters
- Department of Cancer Immunology, Genentech, South San Francisco, CA, USA
| | - Avi Ashkenazi
- Department of Cancer Immunology, Genentech, South San Francisco, CA, USA
| | - Si Hyun Kim
- Department of Antibody Engineering, Genentech, South San Francisco, CA, USA
| | - Ryan Kelly
- Department of Antibody Engineering, Genentech, South San Francisco, CA, USA
| | - Shuang Wu
- Department of Antibody Engineering, Genentech, South San Francisco, CA, USA
| | - Paul J Wolters
- Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Ariel E Feldstein
- Department of Pediatrics, University of California, San Diego, San Diego, CA, USA
| | | | - Ning Ding
- Department of Discovery Immunology, Genentech, South San Francisco, CA, USA.
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14
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Yang Q, Ciebiera M, Bariani MV, Ali M, Elkafas H, Boyer TG, Al-Hendy A. Comprehensive Review of Uterine Fibroids: Developmental Origin, Pathogenesis, and Treatment. Endocr Rev 2022; 43:678-719. [PMID: 34741454 PMCID: PMC9277653 DOI: 10.1210/endrev/bnab039] [Citation(s) in RCA: 102] [Impact Index Per Article: 51.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/15/2021] [Indexed: 11/24/2022]
Abstract
Uterine fibroids are benign monoclonal neoplasms of the myometrium, representing the most common tumors in women worldwide. To date, no long-term or noninvasive treatment option exists for hormone-dependent uterine fibroids, due to the limited knowledge about the molecular mechanisms underlying the initiation and development of uterine fibroids. This paper comprehensively summarizes the recent research advances on uterine fibroids, focusing on risk factors, development origin, pathogenetic mechanisms, and treatment options. Additionally, we describe the current treatment interventions for uterine fibroids. Finally, future perspectives on uterine fibroids studies are summarized. Deeper mechanistic insights into tumor etiology and the complexity of uterine fibroids can contribute to the progress of newer targeted therapies.
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Affiliation(s)
- Qiwei Yang
- Qiwei Yang, Ph.D. Department of Obstetrics and Gynecology, University of Chicago, 5841 S. Maryland Ave, M167, Billings, Chicago, IL 60637, USA.
| | - Michal Ciebiera
- Second Department of Obstetrics and Gynecology, Center of Postgraduate Medical Education, ul. Cegłowska 80, 01-809, Warsaw, Poland
| | | | - Mohamed Ali
- Clinical Pharmacy Department, Faculty of Pharmacy, Ain Shams University, Cairo 11566, Egypt
| | - Hoda Elkafas
- Department of Anesthesiology, University of Illinois at Chicago, Chicago, IL 60612, USA
- Department of Pharmacology and Toxicology, Egyptian Drug Authority, formerly National Organization for Drug Control and Research, Cairo 35521, Egypt
| | - Thomas G Boyer
- Department of Molecular Medicine, Institute of Biotechnology, University of Texas Health Science Center at San Antonio, San Antonio, TX, 78229-3900, USA
| | - Ayman Al-Hendy
- Correspondence: Ayman Al-Hendy, MD, Ph.D. Department of Obstetrics and Gynecology, University of Chicago, 5841 S. Maryland Ave, N112, Peck Pavilion, Chicago, IL 60637. USA.
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15
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Eigenhuis KN, Somsen HB, van den Berg DLC. Transcription Pause and Escape in Neurodevelopmental Disorders. Front Neurosci 2022; 16:846272. [PMID: 35615272 PMCID: PMC9125161 DOI: 10.3389/fnins.2022.846272] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2021] [Accepted: 04/11/2022] [Indexed: 11/17/2022] Open
Abstract
Transcription pause-release is an important, highly regulated step in the control of gene expression. Modulated by various factors, it enables signal integration and fine-tuning of transcriptional responses. Mutations in regulators of pause-release have been identified in a range of neurodevelopmental disorders that have several common features affecting multiple organ systems. This review summarizes current knowledge on this novel subclass of disorders, including an overview of clinical features, mechanistic details, and insight into the relevant neurodevelopmental processes.
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16
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Yang Y, Xiao Q, Yin J, Li C, Yu D, He Y, Yang Z, Wang G. Med23 supports angiogenesis and maintains vascular integrity through negative regulation of angiopoietin2 expression. Commun Biol 2022; 5:374. [PMID: 35440711 PMCID: PMC9019027 DOI: 10.1038/s42003-022-03332-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Accepted: 03/30/2022] [Indexed: 01/17/2023] Open
Abstract
The mammalian Mediator complex consists of over 30 subunits and functions as a transcriptional hub integrating signaling for tissue-specific gene expression. Although the role of the Mediator complex in transcription has been extensively investigated, the functions of distinct Mediator subunits in development are not well understood. Here, we dissected the role of the Mediator subunit Med23 in mouse cardiovascular development. Endothelial-specific Med23 deletion caused embryonic lethality before embryonic day 13.5 (E13.5). The mutant embryos exhibited intracranial hemorrhage and diminished angiogenesis with dilated blood vessels in the head region, where the expression of Med23 was abundant at E10.5. Med23 deficiency impaired vasculogenesis in the head region and impeded retinal angiogenesis. Knocking down Med23 in human umbilical vein endothelial cells (HUVECs) resulted in angiogenic defects, recapitulating the vascular defects in Med23-mutant mice in a cell-autonomous manner. RNA sequencing in HUVECs indicated that Med23 deficiency resulted in the interruption of angiogenesis and the upregulation of angiopoietin2 (Ang2), an inducing factor for vascular network instability. Inhibition of Ang2 partially rescued angiogenic sprouting and lumen dilation defects in tube formation assays. Collectively, our findings demonstrate that Med23 promotes angiogenesis and maintains vascular integrity, in part by suppressing Ang2 signaling.
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Affiliation(s)
- Yenan Yang
- State Key Laboratory of Genetic Engineering, School of Life Sciences and Zhongshan Hospital, Fudan University, Shanghai, 200438, China
| | - Qi Xiao
- The Ministry of Education Key Laboratory of Model Animal for Disease Study, Nanjing Biomedical Research Institute, Nanjing University, Nanjing, 210061, China
| | - Jingwen Yin
- Molecular and Cell Biology Laboratory, Salk Institute for Biological Studies, La Jolla, CA, 92037, USA
| | - Chonghui Li
- State Key Laboratory of Cell Biology, Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, 200031, China
| | - Decai Yu
- Department of Hepatobiliary Surgery, the Affiliated Drum Tower Hospital, School of Medicine, Nanjing University, Nanjing, China
| | - Yulong He
- Laboratory of Vascular and Cancer Biology, Cyrus Tang Hematology Center, Jiangsu Institute of Hematology, the First Affiliated Hospital, Soochow University, Suzhou, China
| | - Zhongzhou Yang
- Department of Cardiology, State Key Laboratory of Pharmaceutical Biotechnology, Nanjing Drum Tower Hospital, The Affiliated Hospital of Medical School of Nanjing University, Nanjing, 210093, China.
| | - Gang Wang
- State Key Laboratory of Genetic Engineering, School of Life Sciences and Zhongshan Hospital, Fudan University, Shanghai, 200438, China.
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17
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Muralimanoharan S, Shamby R, Stansbury N, Schenken R, de la Pena Avalos B, Javanmardi S, Dray E, Sung P, Boyer TG. Aberrant R-loop-induced replication stress in MED12-mutant uterine fibroids. Sci Rep 2022; 12:6169. [PMID: 35418189 PMCID: PMC9008039 DOI: 10.1038/s41598-022-10188-x] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Accepted: 03/31/2022] [Indexed: 11/09/2022] Open
Abstract
Uterine fibroid (UF) driver mutations in Mediator complex subunit 12 (MED12) trigger genomic instability and tumor development through unknown mechanisms. Herein, we show that MED12 mutations trigger aberrant R-loop-induced replication stress, suggesting a possible route to genomic instability and a novel therapeutic vulnerability in this dominant UF subclass. Immunohistochemical analyses of patient-matched tissue samples revealed that MED12 mutation-positive UFs, compared to MED12 mutation-negative UFs and myometrium, exhibited significantly higher levels of R-loops and activated markers of Ataxia Telangiectasia and Rad3-related (ATR) kinase-dependent replication stress signaling in situ. Single molecule DNA fiber analysis revealed that primary cells from MED12 mutation-positive UFs, compared to those from patient-matched MED12 mutation-negative UFs and myometrium, exhibited defects in replication fork dynamics, including reduced fork speeds, increased and decreased numbers of stalled and restarted forks, respectively, and increased asymmetrical bidirectional forks. Notably, these phenotypes were recapitulated and functionally linked in cultured uterine smooth muscle cells following chemical inhibition of Mediator-associated CDK8/19 kinase activity that is known to be disrupted by UF driver mutations in MED12. Thus, Mediator kinase inhibition triggered enhanced R-loop formation and replication stress leading to an S-phase cell cycle delay, phenotypes that were rescued by overexpression of the R-loop resolving enzyme RNaseH. Altogether, these findings reveal MED12-mutant UFs to be uniquely characterized by aberrant R-loop induced replication stress, suggesting a possible basis for genomic instability and new avenues for therapeutic intervention that involve the replication stress phenotype in this dominant UF subtype.
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Affiliation(s)
- Sribalasubashini Muralimanoharan
- Department of Molecular Medicine, UT Health San Antonio, STRF, 8210 Floyd Curl Drive, Mail Code 8257, San Antonio, TX, 78229-3900, USA
| | - Ross Shamby
- Department of Molecular Medicine, UT Health San Antonio, STRF, 8210 Floyd Curl Drive, Mail Code 8257, San Antonio, TX, 78229-3900, USA
| | - Nicholas Stansbury
- Department of Obstetrics and Gynecology, UT Health San Antonio, San Antonio, TX, USA
| | - Robert Schenken
- Department of Obstetrics and Gynecology, UT Health San Antonio, San Antonio, TX, USA
| | | | - Samin Javanmardi
- Department of Molecular Medicine, UT Health San Antonio, STRF, 8210 Floyd Curl Drive, Mail Code 8257, San Antonio, TX, 78229-3900, USA
| | - Eloise Dray
- Department of Biochemistry and Structural Biology, UT Health San Antonio, San Antonio, TX, USA
| | - Patrick Sung
- Department of Biochemistry and Structural Biology, UT Health San Antonio, San Antonio, TX, USA
| | - Thomas G Boyer
- Department of Molecular Medicine, UT Health San Antonio, STRF, 8210 Floyd Curl Drive, Mail Code 8257, San Antonio, TX, 78229-3900, USA.
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18
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Munabi NCO, Mikhail S, Toubat O, Webb M, Auslander A, Sanchez-Lara PA, Manojlovic Z, Schmidt RJ, Craig D, Magee WP, Kumar SR. High prevalence of deleterious mutations in concomitant nonsyndromic cleft and outflow tract heart defects. Am J Med Genet A 2022; 188:2082-2095. [PMID: 35385219 PMCID: PMC9197864 DOI: 10.1002/ajmg.a.62748] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2021] [Revised: 02/26/2022] [Accepted: 03/18/2022] [Indexed: 11/18/2022]
Abstract
Our previous work demonstrating enrichment of outflow tract (OFT) congenital heart disease (CHD) in children with cleft lip and/or palate (CL/P) suggests derangements in common underlying developmental pathways. The current pilot study examines the underlying genetics of concomitant nonsyndromic CL/P and OFT CHD phenotype. Of 575 patients who underwent CL/P surgery at Children's Hospital Los Angeles, seven with OFT CHD, negative chromosomal microarray analysis, and no recognizable syndromic association were recruited with their parents (as available). Whole genome sequencing of blood samples paired with whole‐blood‐based RNA sequencing for probands was performed. A pathogenic or potentially pathogenic variant was identified in 6/7 (85.7%) probands. A total of seven candidate genes were mutated (CHD7, SMARCA4, MED12, APOB, RNF213, SETX, and JAG1). Gene ontology analysis of variants predicted involvement in binding (100%), regulation of transcription (42.9%), and helicase activity (42.9%). Four patients (57.1%) expressed gene variants (CHD7, SMARCA4, MED12, and RNF213) previously involved in the Wnt signaling pathway. Our pilot analysis of a small cohort of patients with combined CL/P and OFT CHD phenotype suggests a potentially significant prevalence of deleterious mutations. In our cohort, an overrepresentation of mutations in molecules associated with Wnt‐signaling was found. These variants may represent an expanded phenotypic heterogeneity within known monogenic disease genes or provide novel evidence of shared developmental pathways. The mechanistic implications of these mutations and subsequent developmental derangements resulting in the CL/P and OFT CHD phenotype require further analysis in a larger cohort of patients.
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Affiliation(s)
- Naikhoba C O Munabi
- Division of Plastic and Reconstructive Surgery, Keck School of Medicine of USC, Los Angeles, California, USA
| | | | - Omar Toubat
- Division of Cardiac Surgery, Department of Surgery, Keck School of Medicine of USC, Los Angeles, California, USA
| | - Michelle Webb
- Department of Translational Genomics, Keck School of Medicine of USC, Los Angeles, California, USA
| | | | - Pedro A Sanchez-Lara
- Department of Pediatrics, Cedars-Sinai Medical Center, Los Angeles, California, USA
| | - Zarko Manojlovic
- Department of Translational Genomics, Keck School of Medicine of USC, Los Angeles, California, USA
| | - Ryan J Schmidt
- Department of Pathology and Laboratory Medicine, Children's Hospital Los Angeles, Los Angeles, California, USA.,Department of Pathology, Keck School of Medicine of USC, Los Angeles, California, USA
| | - David Craig
- Department of Translational Genomics, Keck School of Medicine of USC, Los Angeles, California, USA
| | - William P Magee
- Division of Plastic and Reconstructive Surgery, Keck School of Medicine of USC, Los Angeles, California, USA.,Division of Plastic and Maxillofacial Surgery, Children's Hospital Los Angeles, Los Angeles, California, USA.,Department of Plastic Surgery, Shriners Hospital for Children, Los Angeles, California, USA
| | - Subramanyan Ram Kumar
- Division of Cardiac Surgery, Department of Surgery, Keck School of Medicine of USC, Los Angeles, California, USA.,Heart Institute, Children's Hospital Los Angeles, Los Angeles, California, USA
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19
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Ma HY, N'Diaye EN, Caplazi P, Huang Z, Arlantico A, Jeet S, Wong A, Brightbill HD, Li Q, Wong WR, Sandoval W, Tam L, Newman R, Roose-Girma M, Ding N. BMP1 is not required for lung fibrosis in mice. Sci Rep 2022; 12:5466. [PMID: 35361882 PMCID: PMC8971496 DOI: 10.1038/s41598-022-09557-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2021] [Accepted: 03/24/2022] [Indexed: 01/01/2023] Open
Abstract
Bone morphogenetic protein 1 (BMP1) belongs to the astacin/BMP1/tolloid-like family of zinc metalloproteinases, which play a fundamental role in the development and formation of extracellular matrix (ECM). BMP1 mediates the cleavage of carboxyl terminal (C-term) propeptides from procollagens, a crucial step in fibrillar collagen fiber formation. Blocking BMP1 by small molecule or antibody inhibitors has been linked to anti-fibrotic activity in the preclinical models of skin, kidney and liver fibrosis. Therefore, we reason that BMP1 may be important for the pathogenesis of lung fibrosis and BMP1 could be a potential therapeutic target for progressive fibrotic disease such as idiopathic pulmonary fibrosis (IPF). Here, we observed the increased expression of BMP1 in both human IPF lungs and mouse fibrotic lungs induced by bleomycin. Furthermore, we developed an inducible Bmp1 conditional knockout (cKO) mouse strain. We found that Bmp1 deletion does not protect mice from lung fibrosis triggered by bleomycin. Moreover, we found no significant impact of BMP1 deficiency upon C-term propeptide of type I procollagen (CICP) production in the fibrotic mouse lungs. Based on these results, we propose that BMP1 is not required for lung fibrosis in mice and BMP1 may not be considered a candidate therapeutic target for IPF.
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Affiliation(s)
- Hsiao-Yen Ma
- Department of Discovery Immunology, Genentech, South San Francisco, CA, USA
| | - Elsa-Noah N'Diaye
- Department of Discovery Immunology, Genentech, South San Francisco, CA, USA
| | - Patrick Caplazi
- Department of Pathology, Genentech, South San Francisco, CA, USA
| | - Zhiyu Huang
- Department of Translational Immunology, Genentech, South San Francisco, CA, USA
| | - Alexander Arlantico
- Department of Translational Immunology, Genentech, South San Francisco, CA, USA
| | - Surinder Jeet
- Department of Translational Immunology, Genentech, South San Francisco, CA, USA
| | - Aaron Wong
- Department of Translational Immunology, Genentech, South San Francisco, CA, USA
| | - Hans D Brightbill
- Department of Translational Immunology, Genentech, South San Francisco, CA, USA
| | - Qingling Li
- Department of Microchemistry, Proteomics and Lipidomics, Genentech, South San Francisco, CA, USA
| | - Weng Ruth Wong
- Department of Microchemistry, Proteomics and Lipidomics, Genentech, South San Francisco, CA, USA
| | - Wendy Sandoval
- Department of Microchemistry, Proteomics and Lipidomics, Genentech, South San Francisco, CA, USA
| | - Lucinda Tam
- Department of Molecular Biology, Genentech, South San Francisco, CA, USA
| | - Robert Newman
- Department of Molecular Biology, Genentech, South San Francisco, CA, USA
| | - Merone Roose-Girma
- Department of Molecular Biology, Genentech, South San Francisco, CA, USA
| | - Ning Ding
- Department of Discovery Immunology, Genentech, South San Francisco, CA, USA.
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20
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Ciptasari U, van Bokhoven H. The phenomenal epigenome in neurodevelopmental disorders. Hum Mol Genet 2021; 29:R42-R50. [PMID: 32766754 PMCID: PMC7530535 DOI: 10.1093/hmg/ddaa175] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2020] [Revised: 07/16/2020] [Accepted: 07/30/2020] [Indexed: 12/12/2022] Open
Abstract
Disruption of chromatin structure due to epimutations is a leading genetic etiology of neurodevelopmental disorders, collectively known as chromatinopathies. We show that there is an increasing level of convergence from the high diversity of genes that are affected by mutations to the molecular networks and pathways involving the respective proteins, the disrupted cellular and subcellular processes, and their consequence for higher order cellular network function. This convergence is ultimately reflected by specific phenotypic features shared across the various chromatinopathies. Based on these observations, we propose that the commonly disrupted molecular and cellular anomalies might provide a rational target for the development of symptomatic interventions for defined groups of genetically distinct neurodevelopmental disorders.
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Affiliation(s)
- Ummi Ciptasari
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behavior, Radboud university medical center, 6500 HB Nijmegen, The Netherlands
| | - Hans van Bokhoven
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behavior, Radboud university medical center, 6500 HB Nijmegen, The Netherlands.,Department of Cognitive Neuroscience, Donders Institute for Brain, Cognition and Behavior, Radboud university medical center, 6500 HB Nijmegen, The Netherlands
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21
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Bhatti GK, Khullar N, Sidhu IS, Navik US, Reddy AP, Reddy PH, Bhatti JS. Emerging role of non-coding RNA in health and disease. Metab Brain Dis 2021; 36:1119-1134. [PMID: 33881724 PMCID: PMC8058498 DOI: 10.1007/s11011-021-00739-y] [Citation(s) in RCA: 100] [Impact Index Per Article: 33.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/07/2021] [Accepted: 04/14/2021] [Indexed: 12/12/2022]
Abstract
Human diseases have always been a significant turf of concern since the origin of mankind. It is cardinal to know the cause, treatment, and cure for every disease condition. With the advent and advancement in technology, the molecular arena at the microscopic level to study the mechanism, progression, and therapy is more rational and authentic pave than a macroscopic approach. Non-coding RNAs (ncRNAs) have now emerged as indispensable players in the diagnosis, development, and therapeutics of every abnormality concerning physiology, pathology, genetics, epigenetics, oncology, and developmental diseases. This is a comprehensive attempt to collate all the existing and proven strategies, techniques, mechanisms of genetic disorders including Silver Russell Syndrome, Fascio- scapula humeral muscular dystrophy, cardiovascular diseases (atherosclerosis, cardiac fibrosis, hypertension, etc.), neurodegenerative diseases (Spino-cerebral ataxia type 7, Spino-cerebral ataxia type 8, Spinal muscular atrophy, Opitz-Kaveggia syndrome, etc.) cancers (cervix, breast, lung cancer, etc.), and infectious diseases (viral) studied so far. This article encompasses discovery, biogenesis, classification, and evolutionary prospects of the existence of this junk RNA along with the integrated networks involving chromatin remodelling, dosage compensation, genome imprinting, splicing regulation, post-translational regulation and proteomics. In conclusion, all the major human diseases are discussed with a facilitated technology transfer, advancements, loopholes, and tentative future research prospects have also been proposed.
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Affiliation(s)
- Gurjit Kaur Bhatti
- Department of Medical Lab Technology, University Institute of Applied Health Sciences, Chandigarh University, Mohali, Punjab India
| | - Naina Khullar
- Department of Zoology, Mata Gujri College, Fatehgarh Sahib, Punjab India
| | | | - Uma Shanker Navik
- Department of Pharmacology, Central University of Punjab, Bathinda, India
| | | | - P. Hemachandra Reddy
- Neuroscience & Pharmacology, Texas Tech University Health Sciences Center, Lubbock, TX USA
- Department of Internal Medicine, Texas Tech University Health Sciences Center, Lubbock, TX USA
- Departments of Neurology, School of Medicine, Texas Tech University Health Sciences Center, Lubbock, TX USA
- Public Health Department of Graduate School of Biomedical Sciences, Texas Tech University Health Sciences Center, Lubbock, TX USA
- Department of Speech, Language and Hearing Sciences, School Health Professions, Texas Tech University Health Sciences Center, Lubbock, TX USA
- Cell Biology & Biochemistry, Neuroscience & Pharmacology, Neurology, Public Health, School of Health Professions, Texas Tech University Health Sciences Center, 3601 4th Street, Lubbock, TX 79430 USA
| | - Jasvinder Singh Bhatti
- Department of Human Genetics and Molecular Medicine, School of Health Sciences, Central University of Punjab, Bathinda, India
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22
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Kerchner KM, Mou TC, Sun Y, Rusnac DV, Sprang SR, Briknarová K. The structure of the cysteine-rich region from human histone-lysine N-methyltransferase EHMT2 (G9a). JOURNAL OF STRUCTURAL BIOLOGY-X 2021; 5:100050. [PMID: 34278292 PMCID: PMC8261083 DOI: 10.1016/j.yjsbx.2021.100050] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/04/2021] [Revised: 06/21/2021] [Accepted: 06/22/2021] [Indexed: 11/28/2022]
Abstract
Euchromatic histone-lysine N-methyltransferase 1 (EHMT1; G9a-like protein; GLP) and euchromatic histone-lysine N-methyltransferase 2 (EHMT2; G9a) are protein lysine methyltransferases that regulate gene expression and are essential for development and the ability of organisms to change and adapt. In addition to ankyrin repeats and the catalytic SET domain, the EHMT proteins contain a unique cysteine-rich region (CRR) that mediates protein-protein interactions and recruitment of the methyltransferases to specific sites in chromatin. We have determined the structure of the CRR from human EHMT2 by X-ray crystallography and show that the CRR adopts an unusual compact fold with four bound zinc atoms. The structure consists of a RING domain preceded by a smaller zinc-binding motif and an N-terminal segment. The smaller zinc-binding motif straddles the N-terminal end of the RING domain, and the N-terminal segment runs in an extended conformation along one side of the structure and interacts with both the smaller zinc-binding motif and the RING domain. The interface between the N-terminal segment and the RING domain includes one of the zinc atoms. The RING domain is partially sequestered within the CRR and unlikely to function as a ubiquitin ligase.
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Affiliation(s)
- Keshia M Kerchner
- Department of Chemistry and Biochemistry, University of Montana, Missoula, MT 59812, USA
| | - Tung-Chung Mou
- Division of Biological Sciences, University of Montana, Missoula, MT 59812, USA.,Center for Biomolecular Structure and Dynamics, University of Montana, Missoula, MT 59812, USA
| | - Yizhi Sun
- Department of Chemistry and Biochemistry, University of Montana, Missoula, MT 59812, USA
| | - Domniţa-Valeria Rusnac
- Department of Chemistry and Biochemistry, University of Montana, Missoula, MT 59812, USA
| | - Stephen R Sprang
- Division of Biological Sciences, University of Montana, Missoula, MT 59812, USA.,Center for Biomolecular Structure and Dynamics, University of Montana, Missoula, MT 59812, USA
| | - Klára Briknarová
- Department of Chemistry and Biochemistry, University of Montana, Missoula, MT 59812, USA.,Center for Biomolecular Structure and Dynamics, University of Montana, Missoula, MT 59812, USA
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23
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Compe E, Egly JM. The Long Road to Understanding RNAPII Transcription Initiation and Related Syndromes. Annu Rev Biochem 2021; 90:193-219. [PMID: 34153211 DOI: 10.1146/annurev-biochem-090220-112253] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
In eukaryotes, transcription of protein-coding genes requires the assembly at core promoters of a large preinitiation machinery containing RNA polymerase II (RNAPII) and general transcription factors (GTFs). Transcription is potentiated by regulatory elements called enhancers, which are recognized by specific DNA-binding transcription factors that recruit cofactors and convey, following chromatin remodeling, the activating cues to the preinitiation complex. This review summarizes nearly five decades of work on transcription initiation by describing the sequential recruitment of diverse molecular players including the GTFs, the Mediator complex, and DNA repair factors that support RNAPII to enable RNA synthesis. The elucidation of the transcription initiation mechanism has greatly benefited from the study of altered transcription components associated with human diseases that could be considered transcription syndromes.
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Affiliation(s)
- Emmanuel Compe
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, CNRS, INSERM, Université de Strasbourg, 67404 Illkirch CEDEX, Commune Urbaine de Strasbourg, France; ,
| | - Jean-Marc Egly
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, CNRS, INSERM, Université de Strasbourg, 67404 Illkirch CEDEX, Commune Urbaine de Strasbourg, France; , .,College of Medicine, National Taiwan University, Taipei 10051, Taiwan
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24
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REST Inhibits Direct Reprogramming of Pancreatic Exocrine to Endocrine Cells by Preventing PDX1-Mediated Activation of Endocrine Genes. Cell Rep 2021; 31:107591. [PMID: 32375045 DOI: 10.1016/j.celrep.2020.107591] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2019] [Revised: 01/29/2020] [Accepted: 04/09/2020] [Indexed: 12/13/2022] Open
Abstract
The emerging appreciation of plasticity among pancreatic lineages has created interest in harnessing cellular reprogramming for β cell replacement therapy of diabetes. Current reprogramming methodologies are inefficient, largely because of a limited understanding of the underlying mechanisms. Using an in vitro reprogramming system, we reveal the transcriptional repressor RE-1 silencing transcription factor (REST) as a barrier for β cell gene expression in the reprogramming of pancreatic exocrine cells. We observe that REST-bound loci lie adjacent to the binding sites of multiple key β cell transcription factors, including PDX1. Accordingly, a loss of REST function combined with PDX1 expression results in the synergistic activation of endocrine genes. This is accompanied by increased histone acetylation and PDX1 binding at endocrine gene loci. Collectively, our data identify a mechanism for REST activity involving the prevention of PDX1-mediated activation of endocrine genes and uncover REST downregulation and the resulting chromatin alterations as key events in β cell reprogramming.
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25
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Gonzalez A, Kapur S, Walsh M, Vengoechea J. Two females with distinct de novo missense pathogenic variants in MED12 and vastly differing phenotypes. Am J Med Genet A 2021; 185:2582-2585. [PMID: 33913598 DOI: 10.1002/ajmg.a.62233] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2021] [Revised: 03/08/2021] [Accepted: 04/07/2021] [Indexed: 11/07/2022]
Affiliation(s)
- Aixa Gonzalez
- Department of Human Genetics, Emory University, Atlanta, Georgia, USA
| | - Sunaina Kapur
- Department of Human Genetics, Emory University, Atlanta, Georgia, USA
| | - Matthew Walsh
- Department of Human Genetics, Emory University, Atlanta, Georgia, USA
| | - Jaime Vengoechea
- Department of Human Genetics, Emory University, Atlanta, Georgia, USA.,Department of Medicine, Emory University, Atlanta, Georgia, USA
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26
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van de Plassche SR, de Brouwer APM. MED12-Related (Neuro)Developmental Disorders: A Question of Causality. Genes (Basel) 2021; 12:663. [PMID: 33925166 PMCID: PMC8146938 DOI: 10.3390/genes12050663] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2021] [Revised: 04/22/2021] [Accepted: 04/23/2021] [Indexed: 12/24/2022] Open
Abstract
MED12 is a member of the Mediator complex that is involved in the regulation of transcription. Missense variants in MED12 cause FG syndrome, Lujan-Fryns syndrome, and Ohdo syndrome, as well as non-syndromic intellectual disability (ID) in hemizygous males. Recently, female patients with de novo missense variants and de novo protein truncating variants in MED12 were described, resulting in a clinical spectrum centered around ID and Hardikar syndrome without ID. The missense variants are found throughout MED12, whether they are inherited in hemizygous males or de novo in females. They can result in syndromic or nonsyndromic ID. The de novo nonsense variants resulting in Hardikar syndrome that is characterized by facial clefting, pigmentary retinopathy, biliary anomalies, and intestinal malrotation, are found more N-terminally, whereas the more C-terminally positioned variants are de novo protein truncating variants that cause a severe, syndromic phenotype consisting of ID, facial dysmorphism, short stature, skeletal abnormalities, feeding difficulties, and variable other abnormalities. This broad range of distinct phenotypes calls for a method to distinguish between pathogenic and non-pathogenic variants in MED12. We propose an isogenic iNeuron model to establish the unique gene expression patterns that are associated with the specific MED12 variants. The discovery of these patterns would help in future diagnostics and determine the causality of the MED12 variants.
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Affiliation(s)
| | - Arjan P. M. de Brouwer
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behavior, Radboud University Medical Center, 6500 HB Nijmegen, The Netherlands;
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27
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Tian T, Cao X, Chen Y, Jin L, Li Z, Han X, Lin Y, Wlodarczyk BJ, Finnell RH, Yuan Z, Wang L, Ren A, Lei Y. Somatic and de novo Germline Variants of MEDs in Human Neural Tube Defects. Front Cell Dev Biol 2021; 9:641831. [PMID: 33748132 PMCID: PMC7969791 DOI: 10.3389/fcell.2021.641831] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Accepted: 02/15/2021] [Indexed: 02/05/2023] Open
Abstract
BACKGROUND Neural tube defects (NTDs) are among the most common and severe congenital defects in humans. Their genetic etiology is complex and remains poorly understood. The Mediator complex (MED) plays a vital role in neural tube development in animal models. However, no studies have yet examined the role of its human homolog in the etiology of NTDs. METHODS In this study, 48 pairs of neural lesion site and umbilical cord tissues from NTD and 21 case-parent trios were involved in screening for NTD-related somatic and germline de novo variants. A series of functional cell assays were performed. We generated a Med12 p.Arg1784Cys knock-in mouse using CRISPR/Cas9 technology to validate the human findings. RESULTS One somatic variant, MED12 p.Arg1782Cys, was identified in the lesion site tissue from an NTD fetus. This variant was absent in any other normal tissue from different germ layers of the same case. In 21 case-parent trios, one de novo stop-gain variant, MED13L p.Arg1760∗, was identified. Cellular functional studies showed that MED12 p.Arg1782Cys decreased MED12 protein level and affected the regulation of MED12 on the canonical-WNT signaling pathway. The Med12 p.Arg1784Cys knock-in mouse exhibited exencephaly and spina bifida. CONCLUSION These findings provide strong evidence that functional variants of MED genes are associated with the etiology of some NTDs. We demonstrated a potentially important role for somatic variants in the occurrence of NTDs. Our study is the first study in which an NTD-related variant identified in humans was validated in mice using CRISPR/Cas9 technology.
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Affiliation(s)
- Tian Tian
- National Health Commission Key Laboratory of Reproductive Health, Institute of Reproductive and Child Health, Peking University, Beijing, China
- Department of Epidemiology and Biostatistics, School of Public Health, Peking University, Beijing, China
| | - Xuanye Cao
- Department of Molecular and Cellular Biology, Center for Precision Environmental Health, Baylor College of Medicine, Houston, TX, United States
| | - Yongyan Chen
- National Health Commission Key Laboratory of Reproductive Health, Institute of Reproductive and Child Health, Peking University, Beijing, China
- Department of Epidemiology and Biostatistics, School of Public Health, Peking University, Beijing, China
| | - Lei Jin
- National Health Commission Key Laboratory of Reproductive Health, Institute of Reproductive and Child Health, Peking University, Beijing, China
- Department of Epidemiology and Biostatistics, School of Public Health, Peking University, Beijing, China
| | - Zhiwen Li
- National Health Commission Key Laboratory of Reproductive Health, Institute of Reproductive and Child Health, Peking University, Beijing, China
- Department of Epidemiology and Biostatistics, School of Public Health, Peking University, Beijing, China
| | - Xiao Han
- Department of Molecular and Cellular Biology, Center for Precision Environmental Health, Baylor College of Medicine, Houston, TX, United States
| | - Ying Lin
- Department of Molecular and Cellular Biology, Center for Precision Environmental Health, Baylor College of Medicine, Houston, TX, United States
| | - Bogdan J. Wlodarczyk
- Department of Molecular and Cellular Biology, Center for Precision Environmental Health, Baylor College of Medicine, Houston, TX, United States
| | - Richard H. Finnell
- Department of Molecular and Cellular Biology, Center for Precision Environmental Health, Baylor College of Medicine, Houston, TX, United States
- Departments of Molecular and Human Genetics and Medicine, Baylor College of Medicine, Houston, TX, United States
| | - Zhengwei Yuan
- Key Laboratory of Health Ministry for Congenital Malformation, Shengjing Hospital, China Medical University, Shenyang, China
| | - Linlin Wang
- National Health Commission Key Laboratory of Reproductive Health, Institute of Reproductive and Child Health, Peking University, Beijing, China
- Department of Epidemiology and Biostatistics, School of Public Health, Peking University, Beijing, China
| | - Aiguo Ren
- National Health Commission Key Laboratory of Reproductive Health, Institute of Reproductive and Child Health, Peking University, Beijing, China
- Department of Epidemiology and Biostatistics, School of Public Health, Peking University, Beijing, China
| | - Yunping Lei
- Department of Molecular and Cellular Biology, Center for Precision Environmental Health, Baylor College of Medicine, Houston, TX, United States
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28
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Kim HT, Ohn T, Jeong SG, Song A, Jang CH, Cho GW. Oxidative stress-induced aberrant G9a activation disturbs RE-1-containing neuron-specific genes expression, leading to degeneration in human SH-SY5Y neuroblastoma cells. THE KOREAN JOURNAL OF PHYSIOLOGY & PHARMACOLOGY : OFFICIAL JOURNAL OF THE KOREAN PHYSIOLOGICAL SOCIETY AND THE KOREAN SOCIETY OF PHARMACOLOGY 2021; 25:51-58. [PMID: 33361537 PMCID: PMC7756531 DOI: 10.4196/kjpp.2021.25.1.51] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/18/2020] [Revised: 10/12/2020] [Accepted: 10/12/2020] [Indexed: 11/15/2022]
Abstract
Oxidative stress-induced neurodegeneration is one of several etiologies underlying neurodegenerative disease. In the present study, we investigated the functional role of histone methyltransferase G9a in oxidative stress-induced degeneration in human SH-SY5Y neuroblastoma cells. Cell viability significantly decreased on H2O2 treatment; however, treatment with the G9a inhibitor BIX01294 partially attenuated this effect. The expression of neuron-specific genes also decreased in H2O2- treated cells; however, it recovered on G9a inhibition. H2O2-treated cells showed high levels of H3K9me2 (histone H3 demethylated at the lysine 9 residue), which is produced by G9a activation; BIX01294 treatment reduced aberrant activation of G9a. H3K9me2 occupancy of the RE-1 site in neuron-specific genes was significantly increased in H2O2-treated cells, whereas it was decreased in BIX01294-treated cells. The differentiation of H2O2-treated cells also recovered on G9a inhibition by BIX01294. Consistent results were observed when used another G9a inhibitor UCN0321. These results demonstrate that oxidative stress induces aberrant activation of G9a, which disturbs the expression of neuron-specific genes and progressively mediates neuronal cell death. Moreover, a G9a inhibitor can lessen aberrant G9a activity and prevent neuronal damage. G9a inhibition may therefore contribute to the prevention of oxidative stress-induced neurodegeneration.
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Affiliation(s)
- Ho-Tae Kim
- Department of Biology, College of Natural Science, Chosun University, Gwangju 61452, Korea.,Department of Integrative Biological Science, BK21 FOUR Education Research Group for Age-Associated Disorder Control Technology, Chosun University, Gwangju 61452, Korea
| | - Takbum Ohn
- Department of Cellular and Molecular Medicine, College of Medicine, Chosun University, Gwangju 61452, Korea
| | - Sin-Gu Jeong
- Department of Biology, College of Natural Science, Chosun University, Gwangju 61452, Korea.,Department of Integrative Biological Science, BK21 FOUR Education Research Group for Age-Associated Disorder Control Technology, Chosun University, Gwangju 61452, Korea.,Department of Bio Research and Business Development, Biot Korea Inc., Gwangju 61001, Korea
| | - Anji Song
- Department of Biology, College of Natural Science, Chosun University, Gwangju 61452, Korea.,Department of Integrative Biological Science, BK21 FOUR Education Research Group for Age-Associated Disorder Control Technology, Chosun University, Gwangju 61452, Korea
| | - Chul Ho Jang
- Department of Otolaryngology, Chonnam National University Medical School, Gwangju 61469, Korea
| | - Gwang-Won Cho
- Department of Biology, College of Natural Science, Chosun University, Gwangju 61452, Korea.,Department of Integrative Biological Science, BK21 FOUR Education Research Group for Age-Associated Disorder Control Technology, Chosun University, Gwangju 61452, Korea
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29
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Li YC, Chao TC, Kim HJ, Cholko T, Chen SF, Li G, Snyder L, Nakanishi K, Chang CE, Murakami K, Garcia BA, Boyer TG, Tsai KL. Structure and noncanonical Cdk8 activation mechanism within an Argonaute-containing Mediator kinase module. SCIENCE ADVANCES 2021; 7:7/3/eabd4484. [PMID: 33523904 PMCID: PMC7810384 DOI: 10.1126/sciadv.abd4484] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/22/2020] [Accepted: 11/25/2020] [Indexed: 05/02/2023]
Abstract
The Cdk8 kinase module (CKM) in Mediator, comprising Med13, Med12, CycC, and Cdk8, regulates RNA polymerase II transcription through kinase-dependent and -independent functions. Numerous pathogenic mutations causative for neurodevelopmental disorders and cancer congregate in CKM subunits. However, the structure of the intact CKM and the mechanism by which Cdk8 is non-canonically activated and functionally affected by oncogenic CKM alterations are poorly understood. Here, we report a cryo-electron microscopy structure of Saccharomyces cerevisiae CKM that redefines prior CKM structural models and explains the mechanism of Med12-dependent Cdk8 activation. Med12 interacts extensively with CycC and activates Cdk8 by stabilizing its activation (T-)loop through conserved Med12 residues recurrently mutated in human tumors. Unexpectedly, Med13 has a characteristic Argonaute-like bi-lobal architecture. These findings not only provide a structural basis for understanding CKM function and pathological dysfunction, but also further impute a previously unknown regulatory mechanism of Mediator in transcriptional modulation through its Med13 Argonaute-like features.
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Affiliation(s)
- Yi-Chuan Li
- Department of Biochemistry and Molecular Biology, McGovern Medical School, University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Ti-Chun Chao
- Department of Biochemistry and Molecular Biology, McGovern Medical School, University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Hee Jong Kim
- Biochemistry and Molecular Biophysics Graduate Group, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Timothy Cholko
- Department of Chemistry, University of California, Riverside, CA, USA
| | - Shin-Fu Chen
- Department of Biochemistry and Molecular Biology, McGovern Medical School, University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Guojie Li
- Department of Biochemistry and Molecular Biology, McGovern Medical School, University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Laura Snyder
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Kotaro Nakanishi
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH, USA
| | - Chia-En Chang
- Department of Chemistry, University of California, Riverside, CA, USA
| | - Kenji Murakami
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Benjamin A Garcia
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Thomas G Boyer
- Department of Molecular Medicine, University of Texas Health Science Center at San Antonio, San Antonio, TX, USA.
| | - Kuang-Lei Tsai
- Department of Biochemistry and Molecular Biology, McGovern Medical School, University of Texas Health Science Center at Houston, Houston, TX, USA.
- MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences, Houston, TX, USA
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30
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Srivastava S, Kulshreshtha R. Insights into the regulatory role and clinical relevance of mediator subunit, MED12, in human diseases. J Cell Physiol 2020; 236:3163-3177. [PMID: 33174211 DOI: 10.1002/jcp.30099] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2020] [Revised: 09/15/2020] [Accepted: 09/28/2020] [Indexed: 12/13/2022]
Abstract
Transcriptional dysregulation is central to many diseases including cancer. Mutation or deregulated expression of proteins involved in transcriptional machinery leads to aberrant gene expression that disturbs intricate cellular processes of division and differentiation. The subunits of the mediator complex are master regulators of stimuli-derived transcription and are essential for transcription by RNA polymerase II. MED12 is a part of the CDK8 kinase module of the mediator complex and is essential for kinase assembly and function. Other than its function in activation of the kinase activity of CDK8 mediator, it also brings about transcription repression or activation, in response to several signalling pathways, a function that is independent of its role as a part of kinase assembly. Accumulating evidence suggests that MED12 controls complex transcription programs that are defining in cell fate determination, differentiation, and carcinogenesis. Mutations or differential expression of MED12 manifest in several human disorders and diseases. For instance, MED12 mutations are the gold standard for the diagnosis of several X-linked intellectual disability syndromes. Further, certain MED12 mutations are categorised as driver mutations in carcinogenesis as well. This is a timely review that provides for the first time a wholesome view on the critical roles and pathways regulated by MED12, its interactions along with the implications of MED12 alterations/mutations in various cancers and nonneoplastic disorders. Based on the preclinical studies, MED12 indeed emerges as an attractive novel therapeutic target for various diseases and intellectual disorders.
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Affiliation(s)
- Srishti Srivastava
- Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology Delhi, New Delhi, India
| | - Ritu Kulshreshtha
- Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology Delhi, New Delhi, India
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31
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Uehara T, Abe K, Oginuma M, Ishitani S, Yoshihashi H, Okamoto N, Takenouchi T, Kosaki K, Ishitani T. Pathogenesis of CDK8-associated disorder: two patients with novel CDK8 variants and in vitro and in vivo functional analyses of the variants. Sci Rep 2020; 10:17575. [PMID: 33067521 PMCID: PMC7567849 DOI: 10.1038/s41598-020-74642-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2019] [Accepted: 09/03/2020] [Indexed: 11/09/2022] Open
Abstract
Cyclin-dependent kinase 8 (CDK8) is a member of the CDK/Cyclin module of the mediator complex. A recent study reported that heterozygous missense CDK8 mutations cause a neurodevelopmental disorder in humans. The mechanistic basis of CDK8-related disorder has yet to be delineated. Here, we report 2 patients with de novo missense mutations within the kinase domain of CDK8 along with the results of in vitro and in vivo functional analyses using a zebrafish model. Patient 1 and Patient 2 had intellectual disabilities and congenital anomalies. Exome analyses showed that patient 1 had a heterozygous de novo missense p.G28A variant in the CDK8 (NM_001260.3) gene and patient 2 had a heterozygous de novo missense p.N156S variant in the CDK8 gene. We assessed the pathogenicity of these two variants using cultured-cells and zebrafish model. An in vitro kinase assay of human CDK8 showed that enzymes with a p.G28A or p.N156S substitution showed decreased kinase activity. An in vivo assays of zebrafish overexpression analyses also showed that the p.G28A and p.N156S alleles were hypomorphic alleles. Importantly, the inhibition of CDK8 kinase activity in zebrafish embryos using a specific chemical inhibitor induced craniofacial and heart defects similar to the patients' phenotype. Taken together, zebrafish studies showed that non-synonymous variants in the kinase domain of CDK8 act as hypomorphic alleles causing human congenital disorder.
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Affiliation(s)
- Tomoko Uehara
- Center for Medical Genetics, Keio University Hospital, Tokyo, Japan
| | - Kota Abe
- Institute for Molecular and Cellular Regulation, Gunma University, Maebashi, Japan.,Department of Homeostatic Regulation, Research Institute for Microbial Diseases, Osaka University, 3-1 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Masayuki Oginuma
- Institute for Molecular and Cellular Regulation, Gunma University, Maebashi, Japan.,Department of Homeostatic Regulation, Research Institute for Microbial Diseases, Osaka University, 3-1 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Shizuka Ishitani
- Institute for Molecular and Cellular Regulation, Gunma University, Maebashi, Japan.,Department of Homeostatic Regulation, Research Institute for Microbial Diseases, Osaka University, 3-1 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Hiroshi Yoshihashi
- Department of Genetics, Tokyo Metropolitan Children's Medical Center, Tokyo, Japan
| | - Nobuhiko Okamoto
- Department of Medical Genetics, Osaka Women's and Children's Hospital, Osaka, Japan
| | - Toshiki Takenouchi
- Department of Pediatrics, Keio University School of Medicine, Tokyo, Japan
| | - Kenjiro Kosaki
- Center for Medical Genetics, Keio University Hospital, Tokyo, Japan
| | - Tohru Ishitani
- Institute for Molecular and Cellular Regulation, Gunma University, Maebashi, Japan. .,Department of Homeostatic Regulation, Research Institute for Microbial Diseases, Osaka University, 3-1 Yamadaoka, Suita, Osaka, 565-0871, Japan.
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32
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Cui W, Marcho C, Wang Y, Degani R, Golan M, Tremblay KD, Rivera-Pérez JA, Mager J. MED20 is essential for early embryogenesis and regulates NANOG expression. Reproduction 2020; 157:215-222. [PMID: 30571656 DOI: 10.1530/rep-18-0508] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2018] [Accepted: 12/17/2018] [Indexed: 12/15/2022]
Abstract
Mediator is an evolutionarily conserved multi-subunit complex, bridging transcriptional activators and repressors to the general RNA polymerase II (Pol II) initiation machinery. Though the Mediator complex is crucial for the transcription of almost all Pol II promoters in eukaryotic organisms, the phenotypes of individual Mediator subunit mutants are each distinct. Here, we report for the first time, the essential role of subunit MED20 in early mammalian embryo development. Although Med20 mutant mouse embryos exhibit normal morphology at E3.5 blastocyst stage, they cannot be recovered at early post-gastrulation stages. Outgrowth assays show that mutant blastocysts cannot hatch from the zona pellucida, indicating impaired blastocyst function. Assessments of cell death and cell lineage specification reveal that apoptosis, inner cell mass, trophectoderm and primitive endoderm markers are normal in mutant blastocysts. However, the epiblast marker NANOG is ectopically expressed in the trophectoderm of Med20 mutants, indicative of defects in trophoblast specification. These results suggest that MED20 specifically, and the Mediator complex in general, are essential for the earliest steps of mammalian development and cell lineage specification.
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Affiliation(s)
- Wei Cui
- Department of Veterinary and Animal Sciences, University of Massachusetts, Amherst, Massachusetts, USA.,Animal Models Core Facility, Institute for Applied Life Sciences (IALS), University of Massachusetts, Amherst, Massachusetts, USA
| | - Chelsea Marcho
- Department of Veterinary and Animal Sciences, University of Massachusetts, Amherst, Massachusetts, USA
| | - Yongsheng Wang
- Key Laboratory of Animal Biotechnology of the Ministry of Agriculture, College of Veterinary Medicine, Northwest A&F University, Yangling, Shaanxi, PR China
| | - Rinat Degani
- Department of Veterinary and Animal Sciences, University of Massachusetts, Amherst, Massachusetts, USA
| | - Morgane Golan
- Department of Veterinary and Animal Sciences, University of Massachusetts, Amherst, Massachusetts, USA
| | - Kimberly D Tremblay
- Department of Veterinary and Animal Sciences, University of Massachusetts, Amherst, Massachusetts, USA
| | - Jaime A Rivera-Pérez
- Division of Genes and Development, Department of Pediatrics, University of Massachusetts Medical School, Worcester, Massachusetts, USA
| | - Jesse Mager
- Department of Veterinary and Animal Sciences, University of Massachusetts, Amherst, Massachusetts, USA
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Li Q, Xiang YH, Liang XJ, Zhang Y, Zhao PP, Wang M, Bao XM, Zhu XB, Deng AC. Expression of G9a in Auditory Cortex Is Downregulated in a Rat Model of Age-Related Hearing Loss. J Mol Neurosci 2020; 71:409-418. [PMID: 32671696 DOI: 10.1007/s12031-020-01663-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2020] [Accepted: 07/08/2020] [Indexed: 01/11/2023]
Abstract
G9a is essential for dendritic plasticity and is associated with neurological disorders. The possible relationship between age-related hearing loss and G9a expression in the auditory cortex has not been fully explored. This study aimed to understand the expression patterns of G9a-mediated histone methylations in the auditory cortex during aging. Using immunofluorescence and western blotting, we demonstrated that a significant reduction in G9a expression observed in the auditory cortex of 24-month-old rats compared to 3-month-old rats, was associated with remarkable hearing threshold elevation and hair cell loss. Correspondingly, histone H3 lysine 9 (H3K9) mono- and dimethylation (marked by H3K9me1 and H3K9me2, respectively), which were regulated by G9a activity, also evidently decreased during aging. These findings, which merit further investigation, suggest a possible association between G9a-mediated histone methylations and central age-related hearing disorders.
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Affiliation(s)
- Qian Li
- Department of Otolaryngology Head and Neck Surgery, Xinqiao Hospital, Army Medical University, Chongqing, 400037, China
| | - Yang-Hong Xiang
- Department of Otolaryngology Head and Neck Surgery, Xinqiao Hospital, Army Medical University, Chongqing, 400037, China
| | - Xiao-Jun Liang
- Department of Otolaryngology Head and Neck Surgery, Xinqiao Hospital, Army Medical University, Chongqing, 400037, China
| | - Yun Zhang
- Department of Otolaryngology Head and Neck Surgery, Xinqiao Hospital, Army Medical University, Chongqing, 400037, China
| | - Peng-Peng Zhao
- Department of Otolaryngology Head and Neck Surgery, Xinqiao Hospital, Army Medical University, Chongqing, 400037, China
| | - Min Wang
- Department of Otolaryngology Head and Neck Surgery, Xinqiao Hospital, Army Medical University, Chongqing, 400037, China
| | - Xiao-Min Bao
- Department of Otolaryngology Head and Neck Surgery, Xinqiao Hospital, Army Medical University, Chongqing, 400037, China
| | - Xian-Bai Zhu
- Department of Otolaryngology Head and Neck Surgery, Xinqiao Hospital, Army Medical University, Chongqing, 400037, China
| | - An-Chun Deng
- Department of Otolaryngology Head and Neck Surgery, Xinqiao Hospital, Army Medical University, Chongqing, 400037, China.
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34
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Liu Q, Bischof S, Harris CJ, Zhong Z, Zhan L, Nguyen C, Rashoff A, Barshop WD, Sun F, Feng S, Potok M, Gallego-Bartolome J, Zhai J, Wohlschlegel JA, Carey MF, Long JA, Jacobsen SE. The characterization of Mediator 12 and 13 as conditional positive gene regulators in Arabidopsis. Nat Commun 2020; 11:2798. [PMID: 32493925 PMCID: PMC7271234 DOI: 10.1038/s41467-020-16651-5] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2020] [Accepted: 05/14/2020] [Indexed: 12/18/2022] Open
Abstract
Mediator 12 (MED12) and MED13 are components of the Mediator multi-protein complex, that facilitates the initial steps of gene transcription. Here, in an Arabidopsis mutant screen, we identify MED12 and MED13 as positive gene regulators, both of which contribute broadly to morc1 de-repressed gene expression. Both MED12 and MED13 are preferentially required for the expression of genes depleted in active chromatin marks, a chromatin signature shared with morc1 re-activated loci. We further discover that MED12 tends to interact with genes that are responsive to environmental stimuli, including light and radiation. We demonstrate that light-induced transient gene expression depends on MED12, and is accompanied by a concomitant increase in MED12 enrichment during induction. In contrast, the steady-state expression level of these genes show little dependence on MED12, suggesting that MED12 is primarily required to aid the expression of genes in transition from less-active to more active states. Mediator is a multiprotein complex required to activate gene transcription by RNAPII. Here, the authors report that MED12 and MED13 are conditional positive regulators that facilitate the expression of genes depleted in active chromatin marks and the induction of gene expression in response to environmental stimuli in Arabidopsis.
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Affiliation(s)
- Qikun Liu
- School of Advanced Agricultural Sciences, Peking University, 100871, Beijing, China. .,Department of Molecular, Cell and Developmental Biology, University of California at Los Angeles, Los Angeles, CA, 90095, USA.
| | - Sylvain Bischof
- Department of Molecular, Cell and Developmental Biology, University of California at Los Angeles, Los Angeles, CA, 90095, USA.,Department of Plant and Microbial Biology and Zurich-Basel Plant Science Center, University of Zurich, Zollikerstrasse 107, 8008, Zurich, Switzerland
| | - C Jake Harris
- Department of Molecular, Cell and Developmental Biology, University of California at Los Angeles, Los Angeles, CA, 90095, USA
| | - Zhenhui Zhong
- Department of Molecular, Cell and Developmental Biology, University of California at Los Angeles, Los Angeles, CA, 90095, USA.,Basic Forestry and Proteomics Center, Fujian Agriculture and Forestry University, 350002, Fuzhou, China
| | - Lingyu Zhan
- Department of Molecular, Cell and Developmental Biology, University of California at Los Angeles, Los Angeles, CA, 90095, USA
| | - Calvin Nguyen
- Department of Molecular, Cell and Developmental Biology, University of California at Los Angeles, Los Angeles, CA, 90095, USA
| | - Andrew Rashoff
- Department of Molecular, Cell and Developmental Biology, University of California at Los Angeles, Los Angeles, CA, 90095, USA
| | - William D Barshop
- Department of Biological Chemistry, David Geffen School of Medicine, University of California at Los Angeles, Los Angeles, CA, 90095, USA
| | - Fei Sun
- Department of Biological Chemistry, David Geffen School of Medicine, University of California at Los Angeles, Los Angeles, CA, 90095, USA
| | - Suhua Feng
- Department of Molecular, Cell and Developmental Biology, University of California at Los Angeles, Los Angeles, CA, 90095, USA
| | - Magdalena Potok
- Department of Molecular, Cell and Developmental Biology, University of California at Los Angeles, Los Angeles, CA, 90095, USA
| | - Javier Gallego-Bartolome
- Department of Molecular, Cell and Developmental Biology, University of California at Los Angeles, Los Angeles, CA, 90095, USA
| | - Jixian Zhai
- Institute of Plant and Food Science, Department of Biology, Southern University of Science and Technology, Shenzhen, China
| | - James A Wohlschlegel
- Department of Biological Chemistry, David Geffen School of Medicine, University of California at Los Angeles, Los Angeles, CA, 90095, USA
| | - Michael F Carey
- Department of Biological Chemistry, David Geffen School of Medicine, University of California at Los Angeles, Los Angeles, CA, 90095, USA
| | - Jeffrey A Long
- Department of Molecular, Cell and Developmental Biology, University of California at Los Angeles, Los Angeles, CA, 90095, USA
| | - Steven E Jacobsen
- Department of Molecular, Cell and Developmental Biology, University of California at Los Angeles, Los Angeles, CA, 90095, USA. .,Howard Hughes Medical Institute, University of California at Los Angeles, Los Angeles, CA, 90095, USA.
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35
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Suppression of a Subset of Interferon-Induced Genes by Human Papillomavirus Type 16 E7 via a Cyclin Dependent Kinase 8-Dependent Mechanism. Viruses 2020; 12:v12030311. [PMID: 32183180 PMCID: PMC7150855 DOI: 10.3390/v12030311] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Revised: 03/09/2020] [Accepted: 03/10/2020] [Indexed: 12/16/2022] Open
Abstract
Persistent infection by human papillomaviruses (HPVs), small, double-stranded DNA viruses that infect keratinocytes of the squamous epithelia, can lead to the development of cervical and other cancers. The viral oncoprotein E7 contributes to viral persistence in part by regulating host gene expression through binding host transcriptional regulators, although mechanisms responsible for E7-mediated transcriptional regulation are incompletely understood. Type I IFN signaling promotes the expression of anti-viral genes, called interferon-stimulated genes (ISGs), through the phosphorylation and activation of STAT1. In this study, we have observed that the CR3 domain of E7 contributes to the episomal maintenance of viral genomes. Transcriptome analysis revealed that E7 transcriptionally suppresses a subset of ISGs but not through regulation of STAT1 activation. Instead, we discovered that E7 associates with Mediator kinase CDK8 and this is correlated with the recruitment of CDK8 to ISG promoters and reduced ISG expression. E7 fails to suppress ISGs in the absence of CDK8, indicating that CDK8 function contributes to the suppression of ISGs by E7. Altogether, E7/CDK8 association may be a novel mechanism by which E7 inhibits innate immune signaling.
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36
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Wang Z, Cao D, Li C, Min L, Wang G. Mediator MED23 regulates inflammatory responses and liver fibrosis. PLoS Biol 2019; 17:e3000563. [PMID: 31805036 PMCID: PMC6917294 DOI: 10.1371/journal.pbio.3000563] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2019] [Revised: 12/17/2019] [Accepted: 11/15/2019] [Indexed: 12/13/2022] Open
Abstract
Liver fibrosis, often associated with cirrhosis and hepatocellular carcinomas, is characterized by hepatic damage, an inflammatory response, and hepatic stellate cell (HSC) activation, although the underlying mechanisms are largely unknown. Here, we show that the transcriptional Mediator complex subunit 23 (MED23) participates in the development of experimental liver fibrosis. Compared with their control littermates, mice with hepatic Med23 deletion exhibited aggravated carbon tetrachloride (CCl4)-induced liver fibrosis, with enhanced chemokine production and inflammatory infiltration as well as increased hepatocyte regeneration. Mechanistically, the orphan nuclear receptor RAR-related orphan receptor alpha (RORα) activates the expression of the liver fibrosis-related chemokines C-C motif chemokine ligand 5 (CCL5) and C-X-C motif chemokine ligand 10 (CXCL10), which is suppressed by the Mediator subunit MED23. We further found that the inhibition of Ccl5 and Cxcl10 expression by MED23 likely occurs because of G9a (also known as euchromatic histone-lysine N-methyltransferase 2 [EHMT2])-mediated H3K9 dimethylation of the target promoters. Collectively, these findings reveal hepatic MED23 as a key modulator of chemokine production and inflammatory responses and define the MED23-CCL5/CXCL10 axis as a potential target for clinical intervention in liver fibrosis.
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Affiliation(s)
- Zhichao Wang
- State Key Laboratory of Genetic Engineering, School of Life Sciences and Zhongshan Hospital, Fudan University, Shanghai, China
| | - Dan Cao
- State Key Laboratory of Cell Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, China
| | - Chonghui Li
- State Key Laboratory of Cell Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, China
| | - Lihua Min
- State Key Laboratory of Cell Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, China
| | - Gang Wang
- State Key Laboratory of Genetic Engineering, School of Life Sciences and Zhongshan Hospital, Fudan University, Shanghai, China
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37
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Dufour C, Perbet R, Leblond P, Vasseur R, Stechly L, Pierache A, Reyns N, Touzet G, Le Rhun E, Vinchon M, Maurage CA, Escande F, Renaud F. Identification of prognostic markers in diffuse midline gliomas H3K27M-mutant. Brain Pathol 2019; 30:179-190. [PMID: 31348837 DOI: 10.1111/bpa.12768] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2019] [Accepted: 07/18/2019] [Indexed: 12/19/2022] Open
Abstract
Pediatric diffuse midline gliomas are devastating diseases. Among them, diffuse midline gliomas H3K27M-mutant are associated with worse prognosis. However, recent studies have highlighted significant differences in clinical behavior and biological alterations within this specific subgroup. In this context, simple markers are needed to refine the prognosis of diffuse midline gliomas H3K27M-mutant and guide the clinical management of patients. The aims of this study were (i) to describe the molecular, immunohistochemical and, especially, chromosomal features of a cohort of diffuse midline gliomas and (ii) to focus on H3K27M-mutant tumors to identify new prognostic markers. Patients were retrospectively selected from 2001 to 2017. Tumor samples were analyzed by immunohistochemistry (including H3K27me3, EGFR, c-MET and p53), next-generation sequencing and comparative genomic hybridization array. Forty-nine patients were included in the study. The median age at diagnosis was 9 years, and the median overall survival (OS) was 9.4 months. H3F3A or HIST1H3B mutations were identified in 80% of the samples. Within the H3K27M-mutant tumors, PDGFRA amplification, loss of 17p and a complex chromosomal profile were significantly associated with worse survival. Three prognostic markers were identified in diffuse midline gliomas H3K27M-mutant: PDGFRA amplification, loss of 17p and a complex chromosomal profile. These markers are easy to detect in daily practice and should be considered to refine the prognosis of this entity.
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Affiliation(s)
- Charlotte Dufour
- Institute of Pathology, Centre de Biologie Pathologie, Lille University Hospital, Lille, F-59000, France
| | - Romain Perbet
- Institute of Pathology, Centre de Biologie Pathologie, Lille University Hospital, Lille, F-59000, France.,Univ Lille, Inserm, UMR 1172 - JPARC - Centre de Recherche Jean-Pierre AUBERT Neurosciences et Cancer, Lille, F-59000, France
| | - Pierre Leblond
- Department of Paediatric Oncology, Centre Oscar Lambret, Lille, F-59000, France
| | - Romain Vasseur
- Univ Lille, Inserm, UMR 1172 - JPARC - Centre de Recherche Jean-Pierre AUBERT Neurosciences et Cancer, Lille, F-59000, France
| | - Laurence Stechly
- Department of Biochemistry and Molecular Biology, Centre de Biologie Pathologie, Lille University Hospital, Lille, F-59000, France
| | - Adeline Pierache
- Department of Biostatistics and Data Management, Lille University Hospital, Lille, F-59000, France
| | - Nicolas Reyns
- Department of Stereotactic Neurosurgery, Lille University Hospital, Lille, F-59000, France
| | - Gustavo Touzet
- Department of Stereotactic Neurosurgery, Lille University Hospital, Lille, F-59000, France
| | - Emilie Le Rhun
- Univ Lille, Inserm, U-1192, Lille, F-59000, France.,Department of Neuro-Oncology and Neurosurgery, Lille University Hospital, Lille, F-59000, France.,Department of Neurology, Breast Cancer, Centre Oscar Lambret, Lille, F-59000, France
| | - Matthieu Vinchon
- Department of Paediatric Neurosurgery, Lille University Hospital, Lille, F-59000, France
| | - Claude-Alain Maurage
- Institute of Pathology, Centre de Biologie Pathologie, Lille University Hospital, Lille, F-59000, France.,Univ Lille, Inserm, UMR 1172 - JPARC - Centre de Recherche Jean-Pierre AUBERT Neurosciences et Cancer, Lille, F-59000, France
| | - Fabienne Escande
- Department of Biochemistry and Molecular Biology, Centre de Biologie Pathologie, Lille University Hospital, Lille, F-59000, France
| | - Florence Renaud
- Institute of Pathology, Centre de Biologie Pathologie, Lille University Hospital, Lille, F-59000, France.,Univ Lille, Inserm, UMR 1172 - JPARC - Centre de Recherche Jean-Pierre AUBERT Neurosciences et Cancer, Lille, F-59000, France
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38
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Srivastava S, Niranjan T, May MM, Tarpey P, Allen W, Hackett A, Jouk P, Raymond L, Briault S, Skinner C, Toutain A, Gecz J, Heath W, Stevenson RE, Schwartz CE, Wang T. Dysregulations of sonic hedgehog signaling in MED12-related X-linked intellectual disability disorders. Mol Genet Genomic Med 2019; 7:e00569. [PMID: 30729724 PMCID: PMC6465656 DOI: 10.1002/mgg3.569] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2018] [Revised: 12/05/2018] [Accepted: 12/11/2018] [Indexed: 11/11/2022] Open
Abstract
BACKGROUND Mutations in mediator of RNA polymerase II transcription subunit 12 homolog (MED12, OMIM 300188) cause X-linked intellectual disability (XLID) disorders including FG, Lujan, and Ohdo syndromes. The Gli3-dependent Sonic Hedgehog (SHH) signaling pathway has been implicated in the original FG syndrome and Lujan syndrome. How are SHH-signaling defects related to the complex clinical phenotype of MED12-associated XLID syndromes are not fully understood. METHODS Quantitative RT-PCR was used to study expression levels of three SHH-signaling genes in lymophoblast cell lines carrying four MED12 mutations from four unrelated XLID families. Genotype and phenotype correlation studies were performed on these mutations. RESULTS Three newly identified and one novel MED12 mutations in six affected males from four unrelated XLID families were studied. Three mutations (c.2692A>G; p.N898D, c.3640C>T; p.R1214C, and c.3884G>A; p.R1295H) are located in the LS domain and one (c.617G>A; p.R206Q) is in the L domain of MED12. These mutations involve highly conserved amino acid residues and segregate with ID and related congenital malformations in respective probands families. Patients with the LS-domain mutations share many features of FG syndrome and some features of Lujan syndrome. The patient with the L-domain mutation presented with ID and predominant neuropsychiatric features but little dysmorphic features of either FG or Lujan syndrome. Transcript levels of three Gli3-dependent SHH-signaling genes, CREB5, BMP4, and NEUROG2, were determined by quantitative RT-PCR and found to be significantly elevated in lymphoblasts from patients with three mutations in the MED12-LS domain. CONCLUSIONS These results support a critical role of MED12 in regulating Gli3-dependent SHH signaling and in developing ID and related congenital malformations in XLID syndromes. Differences in the expression profile of SHH-signaling genes potentially contribute to variability in clinical phenotypes in patients with MED12-related XLID disorders.
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Affiliation(s)
- Siddharth Srivastava
- Institute of Genetic Medicine and Department of PediatricsJohns Hopkins UniversityBaltimoreMaryland
| | - Tejasvi Niranjan
- Institute of Genetic Medicine and Department of PediatricsJohns Hopkins UniversityBaltimoreMaryland
| | | | | | | | - Anna Hackett
- Genetics of Learning Disability ServiceHunter GeneticsWaratahNSWAustralia
| | | | - Lucy Raymond
- Cambridge Institute of Medical ResearchCambridgeUK
| | | | | | - Annick Toutain
- Service de Génétique Clinique, Hôpital BretonneauToursFrance
| | - Jozef Gecz
- Adelaide Medical School and Robinson Research InstituteThe University of AdelaideAdelaideAustralia
| | - William Heath
- J.I. Riddle Developmental CenterMorgantonNorth Carolina
| | | | | | - Tao Wang
- Institute of Genetic Medicine and Department of PediatricsJohns Hopkins UniversityBaltimoreMaryland
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39
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Sparber P, Filatova A, Khantemirova M, Skoblov M. The role of long non-coding RNAs in the pathogenesis of hereditary diseases. BMC Med Genomics 2019; 12:42. [PMID: 30871545 PMCID: PMC6416829 DOI: 10.1186/s12920-019-0487-6] [Citation(s) in RCA: 52] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Background Thousands of long non-coding RNA (lncRNA) genes are annotated in the human genome. Recent studies showed the key role of lncRNAs in a variety of fundamental cellular processes. Dysregulation of lncRNAs can drive tumorigenesis and they are now considered to be a promising therapeutic target in cancer. However, how lncRNAs contribute to the development of hereditary diseases in human is still mostly unknown. Results This review is focused on hereditary diseases in the pathogenesis of which long non-coding RNAs play an important role. Conclusions Fundamental research in the field of molecular genetics of lncRNA is necessary for a more complete understanding of their significance. Future research will help translate this knowledge into clinical practice which will not only lead to an increase in the diagnostic rate but also in the future can help with the development of etiotropic treatments for hereditary diseases.
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Affiliation(s)
- Peter Sparber
- Research Center for Medical Genetics, Moscow, Russia.
| | | | - Mira Khantemirova
- Novosibirsk State University, Novosibirsk, Russia.,Institute of Cytology and Genetics SB RAS, Novosibirsk, Russia
| | - Mikhail Skoblov
- Research Center for Medical Genetics, Moscow, Russia.,School of Biomedicine, Far Eastern Federal University, Vladivostok, Russia
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40
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St. John ME, McGirr JA, Martin CH. The behavioral origins of novelty: did increased aggression lead to scale-eating in pupfishes? Behav Ecol 2019; 30:557-569. [PMID: 30971862 PMCID: PMC6450202 DOI: 10.1093/beheco/ary196] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2018] [Revised: 11/08/2018] [Accepted: 12/14/2018] [Indexed: 11/13/2022] Open
Abstract
Behavioral changes in a new environment are often assumed to precede the origins of evolutionary novelties. Here, we examined whether an increase in aggression is associated with a novel scale-eating trophic niche within a recent radiation of Cyprinodon pupfishes endemic to San Salvador Island, Bahamas. We measured aggression using multiple behavioral assays and used transcriptomic analyses to identify differentially expressed genes in aggression and other behavioral pathways across 3 sympatric species in the San Salvador radiation (generalist, snail-eating specialist, and scale-eating specialist) and 2 generalist outgroups. Surprisingly, we found increased behavioral aggression and differential expression of aggression-related pathways in both the scale-eating and snail-eating specialists, despite their independent evolutionary origins. Increased behavioral aggression varied across both sex and stimulus context in both species. Our results indicate that aggression is not unique to scale-eating specialists. Instead, selection may increase aggression in other contexts such as niche specialization in general or mate competition. Alternatively, increased aggression may result from indirect selection on craniofacial traits, pigmentation, or metabolism-all traits which are highly divergent, exhibit signs of selective sweeps, and are affected by aggression-related genetic pathways which are differentially expressed in this system. In conclusion, the evolution of a novel predatory trophic niche within a recent adaptive radiation does not have clear-cut behavioral origins as previously assumed, highlighting the multivariate nature of adaptation and the complex integration of behavior with other phenotypic traits.
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Affiliation(s)
| | - Joseph A McGirr
- Department of Biology, University of North Carolina at Chapel Hill, NC, USA
| | - Christopher H Martin
- Department of Biology, University of North Carolina at Chapel Hill, NC, USA
- Department of Integrative Biology and Museum of Vertebrate Zoology, University of California, Berkeley, CA, USA
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41
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Carullo NVN, Day JJ. Genomic Enhancers in Brain Health and Disease. Genes (Basel) 2019; 10:E43. [PMID: 30646598 PMCID: PMC6357130 DOI: 10.3390/genes10010043] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2018] [Revised: 01/08/2019] [Accepted: 01/08/2019] [Indexed: 01/18/2023] Open
Abstract
Enhancers are non-coding DNA elements that function in cis to regulate transcription from nearby genes. Through direct interactions with gene promoters, enhancers give rise to spatially and temporally precise gene expression profiles in distinct cell or tissue types. In the brain, the accurate regulation of these intricate expression programs across different neuronal classes gives rise to an incredible cellular and functional diversity. Newly developed technologies have recently allowed more accurate enhancer mapping and more sophisticated enhancer manipulation, producing rapid progress in our understanding of enhancer biology. Furthermore, identification of disease-linked genetic variation in enhancer regions has highlighted the potential influence of enhancers in brain health and disease. This review outlines the key role of enhancers as transcriptional regulators, reviews the current understanding of enhancer regulation in neuronal development, function and dysfunction and provides our thoughts on how enhancers can be targeted for technological and therapeutic goals.
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Affiliation(s)
- Nancy V N Carullo
- Department of Neurobiology, University of Alabama at Birmingham, Birmingham, AL 35294, USA.
| | - Jeremy J Day
- Department of Neurobiology, University of Alabama at Birmingham, Birmingham, AL 35294, USA.
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Hall DD, Spitler KM, Grueter CE. Disruption of cardiac Med1 inhibits RNA polymerase II promoter occupancy and promotes chromatin remodeling. Am J Physiol Heart Circ Physiol 2018; 316:H314-H325. [PMID: 30461303 DOI: 10.1152/ajpheart.00580.2018] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
The Mediator coactivator complex directs gene-specific expression by binding distal enhancer-bound transcription factors through its Med1 subunit while bridging to RNA polymerase II (Pol II) at gene promoters. In addition, Mediator scaffolds epigenetic modifying enzymes that determine local DNA accessibility. Previously, we found that deletion of Med1 in cardiomyocytes deregulates more than 5,000 genes and promotes acute heart failure. Therefore, we hypothesized that Med1 deficiency disrupts enhancer-promoter coupling. Using chromatin immunoprecipitation-coupled deep sequencing (ChIP-seq; n = 3/ChIP assay), we found that the Pol II pausing index is increased in Med1 knockout versus floxed control mouse hearts primarily due to a decrease in Pol II occupancy at the majority of transcriptional start sites without a corresponding increase in elongating species. Parallel ChIP-seq assays reveal that Med1-dependent gene expression correlates strongly with histone H3 K27 acetylation, which is indicative of open and active chromatin at transcriptional start sites, whereas H3 K27 trimethylated levels, representing condensed and repressed DNA, are broadly increased and inversely correlate with absolute expression levels. Furthermore, Med1 deletion leads to dynamic changes in acetyl-K27 associated superenhancer regions and their enriched transcription factor-binding motifs that are consistent with altered gene expression. Our findings suggest that Med1 is important in establishing enhancer-promoter coupling in the heart and supports the proposed role of Mediator in establishing preinitiation complex formation. We also found that Med1 determines chromatin accessibility within genes and enhancer regions and propose that the composition of transcription factors associated with superenhancer changes to direct gene-specific expression. NEW & NOTEWORTHY Based on our previous findings that transcriptional homeostasis and cardiac function are disturbed by cardiomyocyte deletion of the Mediator coactivator Med1 subunit, we investigated potential underlying changes in RNA polymerase II localization and global chromatin accessibility. Using chromatin immunoprecipitation sequencing, we found that disrupted transcription arises from a deficit in RNA polymerase II recruitment to gene promoters. Furthermore, active versus repressive chromatin marks are redistributed within gene loci and at enhancer regions correlated with gene expression changes.
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Affiliation(s)
- Duane D Hall
- Division of Cardiovascular Medicine, Department of Internal Medicine, Francois M. Abboud Cardiovascular Research Center, Fraternal Order of Eagles Diabetes Research Center, University of Iowa Carver College of Medicine , Iowa City, Iowa
| | - Kathryn M Spitler
- Division of Cardiovascular Medicine, Department of Internal Medicine, Francois M. Abboud Cardiovascular Research Center, Fraternal Order of Eagles Diabetes Research Center, University of Iowa Carver College of Medicine , Iowa City, Iowa
| | - Chad E Grueter
- Division of Cardiovascular Medicine, Department of Internal Medicine, Francois M. Abboud Cardiovascular Research Center, Fraternal Order of Eagles Diabetes Research Center, University of Iowa Carver College of Medicine , Iowa City, Iowa
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43
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Wu J, Yu P, Jin X, Xu X, Li J, Li Z, Wang M, Wang T, Wu X, Jiang Y, Cai W, Mei J, Min Q, Xu Q, Zhou B, Guo H, Wang P, Zhou W, Hu Z, Li Y, Cai T, Wang Y, Xia K, Jiang YH, Sun ZS. Genomic landscapes of Chinese sporadic autism spectrum disorders revealed by whole-genome sequencing. J Genet Genomics 2018; 45:527-538. [PMID: 30392784 DOI: 10.1016/j.jgg.2018.09.002] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2018] [Revised: 08/25/2018] [Accepted: 09/09/2018] [Indexed: 12/12/2022]
Abstract
Autism spectrum disorder (ASD) is a neurodevelopmental disorder with considerable clinical and genetic heterogeneity. In this study, we identified all classes of genomic variants from whole-genome sequencing (WGS) dataset of 32 Chinese trios with ASD, including de novo mutations, inherited variants, copy number variants (CNVs) and genomic structural variants. A higher mutation rate (Poisson test, P < 2.2 × 10-16) in exonic (1.37 × 10-8) and 3'-UTR regions (1.42 × 10-8) was revealed in comparison with that of whole genome (1.05 × 10-8). Using an integrated model, we identified 87 potentially risk genes (P < 0.01) from 4832 genes harboring various rare deleterious variants, including CHD8 and NRXN2, implying that the disorders may be in favor to multiple-hit. In particular, frequent rare inherited mutations of several microcephaly-associated genes (ASPM, WDR62, and ZNF335) were found in ASD. In chromosomal structure analyses, we found four de novo CNVs and one de novo chromosomal rearrangement event, including a de novo duplication of UBE3A-containing region at 15q11.2-q13.1, which causes Angelman syndrome and microcephaly, and a disrupted TNR due to de novo chromosomal translocation t(1; 5)(q25.1; q33.2). Taken together, our results suggest that abnormalities of centrosomal function and chromatin remodeling of the microcephaly-associated genes may be implicated in pathogenesis of ASD. Adoption of WGS as a new yet efficient technique to illustrate the full genetic spectrum in complex disorders, such as ASD, could provide novel insights into pathogenesis, diagnosis and treatment.
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Affiliation(s)
- Jinyu Wu
- Institute of Genomic Medicine, Wenzhou Medical University, Wenzhou 325000, China
| | - Ping Yu
- Institute of Genomic Medicine, Wenzhou Medical University, Wenzhou 325000, China
| | - Xin Jin
- BGI-Shenzhen, Shenzhen 518083, China
| | - Xiu Xu
- Department of Child Healthcare, Children's Hospital of Fudan University, Shanghai 200032, China
| | - Jinchen Li
- State Key Laboratory of Medical Genetics, Central South University, Changsha 410078, China
| | - Zhongshan Li
- Institute of Genomic Medicine, Wenzhou Medical University, Wenzhou 325000, China
| | | | - Tao Wang
- Institute of Genomic Medicine, Wenzhou Medical University, Wenzhou 325000, China
| | - Xueli Wu
- BGI-Shenzhen, Shenzhen 518083, China
| | - Yi Jiang
- Institute of Genomic Medicine, Wenzhou Medical University, Wenzhou 325000, China
| | - Wanshi Cai
- Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing 100101, China
| | - Junpu Mei
- BGI-Shenzhen, Shenzhen 518083, China
| | - Qingjie Min
- Institute of Genomic Medicine, Wenzhou Medical University, Wenzhou 325000, China
| | - Qiong Xu
- Department of Child Healthcare, Children's Hospital of Fudan University, Shanghai 200032, China
| | - Bingrui Zhou
- Department of Child Healthcare, Children's Hospital of Fudan University, Shanghai 200032, China
| | - Hui Guo
- State Key Laboratory of Medical Genetics, Central South University, Changsha 410078, China
| | - Ping Wang
- Department of Pediatrics and Neurobiology, Duke University School of Medicine, Durham, NC 27710, USA
| | - Wenhao Zhou
- Department of Child Healthcare, Children's Hospital of Fudan University, Shanghai 200032, China
| | - Zhengmao Hu
- State Key Laboratory of Medical Genetics, Central South University, Changsha 410078, China
| | | | - Tao Cai
- Institute of Genomic Medicine, Wenzhou Medical University, Wenzhou 325000, China
| | - Yi Wang
- Department of Child Healthcare, Children's Hospital of Fudan University, Shanghai 200032, China
| | - Kun Xia
- State Key Laboratory of Medical Genetics, Central South University, Changsha 410078, China.
| | - Yong-Hui Jiang
- Department of Pediatrics and Neurobiology, Duke University School of Medicine, Durham, NC 27710, USA.
| | - Zhong Sheng Sun
- Institute of Genomic Medicine, Wenzhou Medical University, Wenzhou 325000, China; Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing 100101, China.
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44
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Diament A, Tuller T. Modeling three-dimensional genomic organization in evolution and pathogenesis. Semin Cell Dev Biol 2018; 90:78-93. [PMID: 30030143 DOI: 10.1016/j.semcdb.2018.07.008] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2018] [Accepted: 07/08/2018] [Indexed: 12/17/2022]
Abstract
The regulation of gene expression is mediated via the complex three-dimensional (3D) conformation of the genetic material and its interactions with various intracellular factors. Various experimental and computational approaches have been developed in recent years for understating the relation between the 3D conformation of the genome and the phenotypes of cells in normal condition and diseases. In this review, we will discuss novel approaches for analyzing and modeling the 3D genomic conformation, focusing on deciphering disease-causing mutations that affect gene expression. We conclude that as this is a very challenging mission, an important direction should involve the comparative analysis of various 3D models from various organisms or cells.
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Affiliation(s)
- Alon Diament
- Dept. of Biomedical Engineering, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Tamir Tuller
- Dept. of Biomedical Engineering, Tel Aviv University, Tel Aviv 6997801, Israel; The Sagol School of Neuroscience, Tel-Aviv University, Tel Aviv 6997801, Israel.
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45
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Beadle EP, Straub JA, Bunnell BA, Newman JJ. MED31 involved in regulating self-renewal and adipogenesis of human mesenchymal stem cells. Mol Biol Rep 2018; 45:1545-1550. [PMID: 30006772 DOI: 10.1007/s11033-018-4241-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2018] [Accepted: 07/06/2018] [Indexed: 01/14/2023]
Abstract
Regulation of gene expression is critical for the maintenance of cell state and homeostasis. Aberrant regulation of genes can lead to unwanted cell proliferation or misdirected differentiation. Here we investigate the role of MED31, a highly conserved subunit of the Mediator complex, to determine the role this subunit plays in the maintenance of human mesenchymal stem cell (hMSC) state. Using siRNA-mediated knockdown of MED31 we demonstrate a decrease in self-renewal based on cell assays and monitoring of gene expression. In addition, in the absence of MED31, hMSCs also displayed a reduction in adipogenesis as evidenced by diminished lipid vesicle formation and expression of specific adipogenic markers. These data present evidence for a significant role for MED31 in maintaining adult stem cell homeostasis, thereby introducing potential novel targets for future investigation and use in better understanding stem cell behavior and adipogenesis.
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Affiliation(s)
- Erik P Beadle
- School of Biological Sciences, Louisiana Tech University, Ruston, LA, USA
| | - Joseph A Straub
- School of Biological Sciences, Louisiana Tech University, Ruston, LA, USA
| | - Bruce A Bunnell
- Center for Stem Cell Research and Regenerative Medicine, Tulane University School of Medicine, New Orleans, LA, USA
- Departments of Pharmacology, Tulane University School of Medicine, New Orleans, LA, USA
- Division of Regenerative Medicine, Tulane National Primate Research Center, Tulane University School of Medicine, New Orleans, LA, USA
| | - Jamie J Newman
- School of Biological Sciences, Louisiana Tech University, Ruston, LA, USA.
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Jamaluddin MFB, Nahar P, Tanwar PS. Proteomic Characterization of the Extracellular Matrix of Human Uterine Fibroids. Endocrinology 2018; 159:2656-2669. [PMID: 29788081 DOI: 10.1210/en.2018-00151] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/08/2018] [Accepted: 05/08/2018] [Indexed: 01/04/2023]
Abstract
Uterine leiomyomas (fibroids) are the most common benign tumors that are associated with increased production of extracellular matrix (ECM). Excessive ECM deposition plays a major role in the enlargement and stiffness of these tumors and contributes to clinical symptoms, such as abnormal bleeding and abdominal pain. However, no study so far has explored the global composition of the ECM of fibroids and normal myometrium. In this study, we performed a systematic ECM enrichment procedure and comparative proteomic analyses to profile the ECM composition of genetically annotated different-sized fibroids (small, medium, and large) and adjacent normal myometrium (ANM). Our matrisome analysis identified a combined total of 108, 126, 126, and 130 unique ECM and ECM-associated proteins with a confidence corresponding to a false discovery rate <1% in ANM and in small, medium, and large fibroids, respectively. The majority of fibroid ECM proteins belong to the core matrisome that includes glycoproteins, collagens, and proteoglycans. Considering that the small-sized fibroids represent the initial stages of leiomyogenesis, we highlighted some of the most abundant and important upregulated ECM proteins in small fibroids (i.e., POSTN, TNC, COL3A1, COL24A1, and ASPN). Furthermore, we revealed 30 unique ECM proteins that exist only in fibroids but that are not present in ANM regardless of MED12 mutation. We propose that some of the proteins identified represent potential novel ECM drug targets that may change the paradigm of fibroid treatment.
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Affiliation(s)
- M Fairuz B Jamaluddin
- School of Biomedical Sciences and Pharmacy, University of Newcastle, Callaghan, New South Wales, Australia
| | - Pravin Nahar
- School of Medicine and Public Health, University of Newcastle, Callaghan, New South Wales, Australia
- Department of Maternity and Gynecology, John Hunter Hospital, New Lambton Heights, New South Wales, Australia
| | - Pradeep S Tanwar
- School of Biomedical Sciences and Pharmacy, University of Newcastle, Callaghan, New South Wales, Australia
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47
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Putlyaev EV, Ibragimov AN, Lebedeva LA, Georgiev PG, Shidlovskii YV. Structure and Functions of the Mediator Complex. BIOCHEMISTRY (MOSCOW) 2018; 83:423-436. [PMID: 29626929 DOI: 10.1134/s0006297918040132] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Mediator is a key factor in the regulation of expression of RNA polymerase II-transcribed genes. Recent studies have shown that Mediator acts as a coordinator of transcription activation and participates in maintaining chromatin architecture in the cell nucleus. In this review, we present current concepts on the structure and functions of Mediator.
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Affiliation(s)
- E V Putlyaev
- Institute of Gene Biology, Russian Academy of Sciences, Moscow, 119334, Russia.
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48
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Larizza L, Finelli P. Developmental disorders with intellectual disability driven by chromatin dysregulation: Clinical overlaps and molecular mechanisms. Clin Genet 2018; 95:231-240. [DOI: 10.1111/cge.13365] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2018] [Revised: 03/28/2018] [Accepted: 04/14/2018] [Indexed: 12/30/2022]
Affiliation(s)
- L. Larizza
- Laboratory of Cytogenetics and Molecular Genetics; Istituto Auxologico Italiano; Milan Italy
| | - P. Finelli
- Laboratory of Cytogenetics and Molecular Genetics; Istituto Auxologico Italiano; Milan Italy
- Department of Medical Biotechnology and Translational Medicine; Università degli Studi di Milano; Milan Italy
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49
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Chen J, Qi Y, Liu CF, Lu JM, Shi J, Shi Y. MicroRNA expression data analysis to identify key miRNAs associated with Alzheimer's disease. J Gene Med 2018. [PMID: 29543360 DOI: 10.1002/jgm.3014] [Citation(s) in RCA: 52] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
BACKGROUND MicroRNAs (miRNAs) have become increasingly prevalent as a result of the association of their deregulation with neurodegenerative disorders, especially Alzheimer's disease (AD). However, the association between miRNAs and AD remains unclear. METHODS In the present study, Nine representative miRNA datasets were selected for the identification of the critical miRNAs by analyzing the overlapping relationships among them. TargetScan software (http://www.targetscan.org) was used to predict the target genes of these miRNAs. In addition, the Database for Annotation Visualization and Integrated Discovery (DAVID; http://david.abcc.ncifcrf.gov) and TfactS (http://www.tfacts.org) datasets were used for combined analysis of functional enrichment and transcription factor (TF) analysis. RESULTS Thirteen key miRNAs were identified, of which four were significantly up-regulated (hsa-miR-101,hsa-miR-155, has-miR-34a, has-miR-9) and eight were found to be significantly down-regulated (hsa-let-7d-5p, hsa-let-7 g-5p, hsa-miR-15b, has-miR-191-5p, hsa-miR-125b, has-miR-26b-5p, hsa-miR-29b, hsa-miR-342-3p). The functional enrichment analysis indicated that up-regulated signature miRNA targets were associated with transcription from the RNA polymerase II promoter process and the chemical synaptic transmission process. Down-regulated signature miRNA targets were mostly enriched with respect to positive regulation of transcription from the RNA polymerase II promoter process, p53 signaling, and microRNAs in cancer pathways. TF analysis showed that 87 TFs were influenced by the up-regulated miRNAs, and 134 TFs were influenced by the down-regulated miRNAs. In total, 70 (45.5%) TFs were affected by both up-regulated and down-regulated miRNAs. CONCLUSIONS In summary, 13 key miRNAs were found to have a vital function in the pathological progress of AD, as well as the target genes and TFs of these miRNAs. The potential functions of these miRNAs as diagnostic and therapeutic targets of the AD are revealed by the present study.
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Affiliation(s)
- Jing Chen
- Shanghai Tenth People's Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Yan Qi
- Shanghai Tenth People's Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Cui-Fang Liu
- Department of Rehabilitation, The Central Hospital of Xianning, The First Affiliated Hospital of Hubei University of Science and Technology, Xianning, Hubei, China
| | - Jing-Min Lu
- Department of Neurology, Huai'an Second People's Hospital and The Affiliated Huai'an Hospital of Xuzhou Medical University, Huai'an, China
| | - Jing Shi
- Geriatric Department, The Central Hospital of Wuhan, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Yan Shi
- Shanghai Tenth People's Hospital, School of Medicine, Tongji University, Shanghai, China
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50
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Abstract
Upon stimulation, small numbers of naive CD8+ T cells proliferate and differentiate into a variety of memory and effector cell types. CD8+ T cells can persist for years and kill tumour cells and virally infected cells. The functional and phenotypic changes that occur during CD8+ T cell differentiation are well characterized, but the epigenetic states that underlie these changes are incompletely understood. Here, we review the epigenetic processes that direct CD8+ T cell differentiation and function. We focus on epigenetic modification of DNA and associated histones at genes and their regulatory elements. We also describe structural changes in chromatin organization that affect gene expression. Finally, we examine the translational potential of epigenetic interventions to improve CD8+ T cell function in individuals with chronic infections and cancer.
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Affiliation(s)
- Amanda N Henning
- Center for Cell-Based Therapy, National Cancer Institute (NCI)
- Surgery Branch, National Cancer Institute (NCI), National Institutes of Health (NIH), Bethesda, Maryland 20892, USA
| | - Rahul Roychoudhuri
- Laboratory of Lymphocyte Signalling and Development, The Babraham Institute, Cambridge CB22 3AT, UK
| | - Nicholas P Restifo
- Center for Cell-Based Therapy, National Cancer Institute (NCI)
- Surgery Branch, National Cancer Institute (NCI), National Institutes of Health (NIH), Bethesda, Maryland 20892, USA
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