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Balakireva Y, Nikitina M, Makhnovskii P, Kukushkina I, Kuzmin I, Kim A, Nefedova L. The Lifespan of D. melanogaster Depends on the Function of the Gagr Gene, a Domesticated gag Gene of Drosophila LTR Retrotransposons. INSECTS 2024; 15:68. [PMID: 38249074 PMCID: PMC10816282 DOI: 10.3390/insects15010068] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/03/2023] [Revised: 01/10/2024] [Accepted: 01/13/2024] [Indexed: 01/23/2024]
Abstract
(1) Background: The Gagr gene in Drosophila melanogaster's genome originated from the molecular domestication of retrotransposons and retroviruses' gag gene. In all Drosophila species, the Gagr protein homologs exhibit a conserved structure, indicative of a vital role. Previous studies have suggested a potential link between the Gagr gene function and stress responses. (2) Methods: We compared flies with Gagr gene knockdown in all tissues to control flies in physiological tests and RNA-sequencing experiments. (3) Results: Flies with the Gagr gene knockdown exhibited shorter lifespans compared to control flies. Transcriptome analysis revealed that Gagr knockdown flies showed elevated transcription levels of immune response genes. We used ammonium persulfate, a potent stress inducer, to elicit a stress response. In control flies, ammonium persulfate activated the Toll, JAK/STAT, and JNK/MAPK signaling pathways. In contrast, flies with the Gagr gene knockdown displayed reduced expression of stress response genes. Gene ontology enrichment analysis identified categories of genes upregulated under ammonium persulfate stress in control flies but not in Gagr knockdown flies. These genes are involved in developmental control, morphogenesis, and central nervous system function. (4) Conclusion: Our findings indicate the significance of the Gagr gene in maintaining immune response and homeostasis.
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Affiliation(s)
- Yevgenia Balakireva
- Department of Genetics, Lomonosov Moscow State University, Leninskie Gory 1, 119991 Moscow, Russia; (Y.B.); (M.N.); (I.K.); (I.K.); (A.K.)
| | - Maria Nikitina
- Department of Genetics, Lomonosov Moscow State University, Leninskie Gory 1, 119991 Moscow, Russia; (Y.B.); (M.N.); (I.K.); (I.K.); (A.K.)
| | - Pavel Makhnovskii
- Institute of Biomedical Problems, Russian Academy of Sciences, 123007 Moscow, Russia;
| | - Inna Kukushkina
- Department of Genetics, Lomonosov Moscow State University, Leninskie Gory 1, 119991 Moscow, Russia; (Y.B.); (M.N.); (I.K.); (I.K.); (A.K.)
| | - Ilya Kuzmin
- Department of Genetics, Lomonosov Moscow State University, Leninskie Gory 1, 119991 Moscow, Russia; (Y.B.); (M.N.); (I.K.); (I.K.); (A.K.)
| | - Alexander Kim
- Department of Genetics, Lomonosov Moscow State University, Leninskie Gory 1, 119991 Moscow, Russia; (Y.B.); (M.N.); (I.K.); (I.K.); (A.K.)
- Faculty of Biology, Shenzhen MSU-BIT University, Longgang District, Shenzhen 518172, China
| | - Lidia Nefedova
- Department of Genetics, Lomonosov Moscow State University, Leninskie Gory 1, 119991 Moscow, Russia; (Y.B.); (M.N.); (I.K.); (I.K.); (A.K.)
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2
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Ding H, Ge K, Fan C, Liu D, Wu C, Li R, Yan FJ. Chlorogenic Acid Attenuates Hepatic Steatosis by Suppressing ZFP30. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2024; 72:245-258. [PMID: 38148374 DOI: 10.1021/acs.jafc.3c02988] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/28/2023]
Abstract
Nonalcoholic fatty liver disease (NAFLD) has become a major global health problem with no approved pharmacological treatment for this disease. Thus, it is urgent to develop effective therapeutic targets for clinical intervention. Here, we show for the first time that ZFP30, a member of the KRAB-ZFP family, is significantly increased in NAFLD models. ZFP30 silencing ameliorates free fatty acid (FFA)-induced lipid accumulation; in contrast, the ZFP30 overexpression exacerbates the triglyceride accumulation and steatosis in hepatocytes. Further investigation revealed that the effects of ZFP30 on hepatic lipid accumulation were mainly attributed to the PPARα downregulation in the NAFLD model. Mechanistically, ZFP30 directly binded to the promoter of PPARα and recruited KAP1 to suppress its transcription. Moreover, chlorogenic acid (CGA) reversed the upregulation of ZFP30 in NAFLD, promoting the PPARα expression, resulting in enhanced fatty acid oxidation and alleviated hepatic steatosis. Collectively, our study indicates ZFP30 as a potential target for NAFLD treatment.
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Affiliation(s)
- Han Ding
- School of Life Science, Jiangsu Normal University, Xuzhou, Jiangsu 221116, China
| | - Kunyi Ge
- School of Life Science, Jiangsu Normal University, Xuzhou, Jiangsu 221116, China
| | - Changyu Fan
- School of Life Science, Jiangsu Normal University, Xuzhou, Jiangsu 221116, China
| | - Dandan Liu
- School of Life Science, Jiangsu Normal University, Xuzhou, Jiangsu 221116, China
| | - Chenyu Wu
- School of Life Science, Jiangsu Normal University, Xuzhou, Jiangsu 221116, China
| | - Rongpeng Li
- School of Life Science, Jiangsu Normal University, Xuzhou, Jiangsu 221116, China
| | - Feng-Juan Yan
- School of Life Science, Jiangsu Normal University, Xuzhou, Jiangsu 221116, China
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3
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Hernández-Quiles M, Martinez Campesino L, Morris I, Ilyas Z, Reynolds S, Soon Tan N, Sobrevals Alcaraz P, Stigter ECA, Varga Á, Varga J, van Es R, Vos H, Wilson HL, Kiss-Toth E, Kalkhoven E. The pseudokinase TRIB3 controls adipocyte lipid homeostasis and proliferation in vitro and in vivo. Mol Metab 2023; 78:101829. [PMID: 38445671 PMCID: PMC10663684 DOI: 10.1016/j.molmet.2023.101829] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Revised: 10/11/2023] [Accepted: 10/19/2023] [Indexed: 03/07/2024] Open
Abstract
OBJECTIVE In vivo studies in humans and mice have implicated the pseudokinase Tribbles 3 (TRIB3) in various aspects of energy metabolism. Whilst cell-based studies indicate a role for TRIB3 in adipocyte differentiation and function, it is unclear if and how these cellular functions may contribute to overall metabolic health. METHODS We investigated the metabolic phenotype of whole-body Trib3 knockout (Trib3KO) mice, focusing on adipocyte and adipose tissue functions. In addition, we combined lipidomics, transcriptomics, interactomics and phosphoproteomics analyses to elucidate cell-intrinsic functions of TRIB3 in pre- and mature adipocytes. RESULTS Trib3KO mice display increased adiposity, but their insulin sensitivity remains unaltered. Trib3KO adipocytes are smaller and display higher Proliferating Cell Nuclear Antigen (PCNA) levels, indicating potential alterations in either i) proliferation-differentiation balance, ii) impaired expansion after cell division, or iii) an altered balance between lipid storage and release, or a combination thereof. Lipidome analyses suggest TRIB3 involvement in the latter two processes, as triglyceride storage is reduced and membrane composition, which can restrain cellular expansion, is altered. Integrated interactome, phosphoproteome and transcriptome analyses support a role for TRIB3 in all three cellular processes through multiple cellular pathways, including Mitogen Activated Protein Kinase- (MAPK/ERK), Protein Kinase A (PKA)-mediated signaling and Transcription Factor 7 like 2 (TCF7L2) and Beta Catenin-mediated gene expression. CONCLUSIONS Our findings support TRIB3 playing multiple distinct regulatory roles in the cytoplasm, nucleus and mitochondria, ultimately controlling adipose tissue homeostasis, rather than affecting a single cellular pathway.
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Affiliation(s)
- Miguel Hernández-Quiles
- Center for Molecular Medicine, University Medical Center Utrecht, Utrecht University, 3C584 CG Utrecht, The Netherlands
| | - Laura Martinez Campesino
- Division of Clinical Medicine, School of Medicine and Population Health, University of Sheffield, Sheffield S10 2TN, UK
| | - Imogen Morris
- Center for Molecular Medicine, University Medical Center Utrecht, Utrecht University, 3C584 CG Utrecht, The Netherlands
| | - Zabran Ilyas
- Division of Clinical Medicine, School of Medicine and Population Health, University of Sheffield, Sheffield S10 2TN, UK
| | - Steve Reynolds
- Division of Clinical Medicine, School of Medicine and Population Health, University of Sheffield, Sheffield S10 2TN, UK
| | - Nguan Soon Tan
- Lee Kong Chian School of Medicine, Nanyang Technological University Singapore, Clinical Sciences Building, 11 Mandalay Road, 308232 Singapore, Singapore; School of Biological Sciences, Nanyang Technological University Singapore, 60 Nanyang Drive, 637551 Singapore, Singapore
| | - Paula Sobrevals Alcaraz
- Oncode Institute and Molecular Cancer Research, Center for Molecular Medicine, University Medical Center Utrecht, Utrecht University, 3C584 CG Utrecht, The Netherlands
| | - Edwin C A Stigter
- Center for Molecular Medicine, University Medical Center Utrecht, Utrecht University, 3C584 CG Utrecht, The Netherlands
| | - Ákos Varga
- Department of Dermatology and Allergology, University of Szeged, H-6720 Szeged, Hungary
| | - János Varga
- Department of Dermatology and Allergology, University of Szeged, H-6720 Szeged, Hungary
| | - Robert van Es
- Oncode Institute and Molecular Cancer Research, Center for Molecular Medicine, University Medical Center Utrecht, Utrecht University, 3C584 CG Utrecht, The Netherlands
| | - Harmjan Vos
- Oncode Institute and Molecular Cancer Research, Center for Molecular Medicine, University Medical Center Utrecht, Utrecht University, 3C584 CG Utrecht, The Netherlands
| | - Heather L Wilson
- Division of Clinical Medicine, School of Medicine and Population Health, University of Sheffield, Sheffield S10 2TN, UK
| | - Endre Kiss-Toth
- Division of Clinical Medicine, School of Medicine and Population Health, University of Sheffield, Sheffield S10 2TN, UK
| | - Eric Kalkhoven
- Center for Molecular Medicine, University Medical Center Utrecht, Utrecht University, 3C584 CG Utrecht, The Netherlands.
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4
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Rosspopoff O, Trono D. Take a walk on the KRAB side. Trends Genet 2023; 39:844-857. [PMID: 37716846 DOI: 10.1016/j.tig.2023.08.003] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Revised: 08/18/2023] [Accepted: 08/18/2023] [Indexed: 09/18/2023]
Abstract
Canonical Krüppel-associated box (KRAB)-containing zinc finger proteins (KZFPs) act as major repressors of transposable elements (TEs) via the KRAB-mediated recruitment of the heterochromatin scaffold KRAB-associated protein (KAP)1. KZFP genes emerged some 420 million years ago in the last common ancestor of coelacanth, lungfish, and tetrapods, and dramatically expanded to give rise to lineage-specific repertoires in contemporary species paralleling their TE load and turnover. However, the KRAB domain displays sequence and function variations that reveal repeated diversions from a linear TE-KZFP trajectory. This Review summarizes current knowledge on the evolution of KZFPs and discusses how ancestral noncanonical KZFPs endowed with variant KRAB, SCAN or DUF3669 domains have been utilized to achieve KAP1-independent functions.
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Affiliation(s)
- Olga Rosspopoff
- School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Didier Trono
- School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland.
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5
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de Tribolet-Hardy J, Thorball CW, Forey R, Planet E, Duc J, Coudray A, Khubieh B, Offner S, Pulver C, Fellay J, Imbeault M, Turelli P, Trono D. Genetic features and genomic targets of human KRAB-zinc finger proteins. Genome Res 2023; 33:1409-1423. [PMID: 37730438 PMCID: PMC10547255 DOI: 10.1101/gr.277722.123] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2023] [Accepted: 07/18/2023] [Indexed: 09/22/2023]
Abstract
Krüppel-associated box (KRAB) domain-containing zinc finger proteins (KZFPs) are one of the largest groups of transcription factors encoded by tetrapods, with 378 members in human alone. KZFP genes are often grouped in clusters reflecting amplification by gene and segment duplication since the gene family first emerged more than 400 million years ago. Previous work has revealed that many KZFPs recognize transposable element (TE)-embedded sequences as genomic targets, and that KZFPs facilitate the co-option of the regulatory potential of TEs for the benefit of the host. Here, we present a comprehensive survey of the genetic features and genomic targets of human KZFPs, notably completing past analyses by adding data on close to a hundred family members. General principles emerge from our study of the TE-KZFP regulatory system, which point to multipronged evolutionary mechanisms underlaid by highly complex and combinatorial modes of action with strong influences on human speciation.
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Affiliation(s)
- Jonas de Tribolet-Hardy
- School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland
| | - Christian W Thorball
- School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland
| | - Romain Forey
- School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland
| | - Evarist Planet
- School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland
| | - Julien Duc
- School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland
| | - Alexandre Coudray
- School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland
| | - Bara Khubieh
- School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland
| | - Sandra Offner
- School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland
| | - Cyril Pulver
- School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland
| | - Jacques Fellay
- School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland
- Precision Medicine Unit, Lausanne University Hospital (CHUV) and University of Lausanne, 1010 Lausanne, Switzerland
| | - Michael Imbeault
- School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland
| | - Priscilla Turelli
- School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland
| | - Didier Trono
- School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland;
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6
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Carotti E, Carducci F, Barucca M, Canapa A, Biscotti MA. Transposable Elements: Epigenetic Silencing Mechanisms or Modulating Tools for Vertebrate Adaptations? Two Sides of the Same Coin. Int J Mol Sci 2023; 24:11591. [PMID: 37511347 PMCID: PMC10380595 DOI: 10.3390/ijms241411591] [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: 07/04/2023] [Revised: 07/13/2023] [Accepted: 07/14/2023] [Indexed: 07/30/2023] Open
Abstract
Transposable elements constitute one of the main components of eukaryotic genomes. In vertebrates, they differ in content, typology, and family diversity and played a crucial role in the evolution of this taxon. However, due to their transposition ability, TEs can be responsible for genome instability, and thus silencing mechanisms were evolved to allow the coexistence between TEs and eukaryotic host-coding genes. Several papers are highlighting in TEs the presence of regulatory elements involved in regulating nearby genes in a tissue-specific fashion. This suggests that TEs are not sequences merely to silence; rather, they can be domesticated for the regulation of host-coding gene expression, permitting species adaptation and resilience as well as ensuring human health. This review presents the main silencing mechanisms acting in vertebrates and the importance of exploiting these mechanisms for TE control to rewire gene expression networks, challenging the general view of TEs as threatening elements.
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Affiliation(s)
| | - Federica Carducci
- Dipartimento di Scienze della Vita e dell’Ambiente, Università Politecnica delle Marche, 60131 Ancona, Italy; (E.C.); (M.B.); (A.C.); (M.A.B.)
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7
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Osipovich AB, Dudek KD, Trinh LT, Kim LH, Shrestha S, Cartailler JP, Magnuson MA. ZFP92, a KRAB domain zinc finger protein enriched in pancreatic islets, binds to B1/Alu SINE transposable elements and regulates retroelements and genes. PLoS Genet 2023; 19:e1010729. [PMID: 37155670 PMCID: PMC10166502 DOI: 10.1371/journal.pgen.1010729] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2023] [Accepted: 04/02/2023] [Indexed: 05/10/2023] Open
Abstract
Repressive KRAB domain-containing zinc-finger proteins (KRAB-ZFPs) are abundant in mammalian genomes and contribute both to the silencing of transposable elements (TEs) and to the regulation of developmental stage- and cell type-specific gene expression. Here we describe studies of zinc finger protein 92 (Zfp92), an X-linked KRAB-ZFP that is highly expressed in pancreatic islets of adult mice, by analyzing global Zfp92 knockout (KO) mice. Physiological, transcriptomic and genome-wide chromatin binding studies indicate that the principal function of ZFP92 in mice is to bind to and suppress the activity of B1/Alu type of SINE elements and modulate the activity of surrounding genomic entities. Deletion of Zfp92 leads to changes in expression of select LINE and LTR retroelements and genes located in the vicinity of ZFP92-bound chromatin. The absence of Zfp92 leads to altered expression of specific genes in islets, adipose and muscle that result in modest sex-specific alterations in blood glucose homeostasis, body mass and fat accumulation. In islets, Zfp92 influences blood glucose concentration in postnatal mice via transcriptional effects on Mafb, whereas in adipose and muscle, it regulates Acacb, a rate-limiting enzyme in fatty acid metabolism. In the absence of Zfp92, a novel TE-Capn11 fusion transcript is overexpressed in islets and several other tissues due to de-repression of an IAPez TE adjacent to ZFP92-bound SINE elements in intron 3 of the Capn11 gene. Together, these studies show that ZFP92 functions both to repress specific TEs and to regulate the transcription of specific genes in discrete tissues.
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Affiliation(s)
- Anna B. Osipovich
- Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, Tennessee, United States of America
- Center for Stem Cell Biology, Vanderbilt University, Nashville, Tennessee, United States of America
| | - Karrie D. Dudek
- Center for Stem Cell Biology, Vanderbilt University, Nashville, Tennessee, United States of America
- Department of Cell and Developmental Biology, Vanderbilt University, Nashville, Tennessee, United States of America
| | - Linh T. Trinh
- Center for Stem Cell Biology, Vanderbilt University, Nashville, Tennessee, United States of America
- Department of Cell and Developmental Biology, Vanderbilt University, Nashville, Tennessee, United States of America
| | - Lily H. Kim
- College of Arts and Sciences, Vanderbilt University, Nashville, Tennessee, United States of America
| | - Shristi Shrestha
- Center for Stem Cell Biology, Vanderbilt University, Nashville, Tennessee, United States of America
| | - Jean-Philippe Cartailler
- Center for Stem Cell Biology, Vanderbilt University, Nashville, Tennessee, United States of America
| | - Mark A. Magnuson
- Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, Tennessee, United States of America
- Center for Stem Cell Biology, Vanderbilt University, Nashville, Tennessee, United States of America
- Department of Cell and Developmental Biology, Vanderbilt University, Nashville, Tennessee, United States of America
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8
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An S, Ko H, Jang H, Park IG, Ahn S, Hwang SY, Gong J, Oh S, Kwak SY, Lee Y, Kim H, Noh M. Prenylated Chrysin Derivatives as Partial PPARγ Agonists with Adiponectin Secretion-Inducing Activity. ACS Med Chem Lett 2023; 14:425-431. [PMID: 37077388 PMCID: PMC10107909 DOI: 10.1021/acsmedchemlett.2c00511] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2022] [Accepted: 03/02/2023] [Indexed: 03/08/2023] Open
Abstract
Decreased circulating adiponectin levels are associated with an increased risk of human metabolic diseases. The chemical-mediated upregulation of adiponectin biosynthesis has been proposed as a novel therapeutic approach to managing hypoadiponectinemia-associated diseases. In preliminary screening, the natural flavonoid chrysin (1) exhibited adiponectin secretion-inducing activity during adipogenesis in human bone marrow mesenchymal stem cells (hBM-MSCs). Here, we provide the 7-prenylated chrysin derivatives, chrysin 5-benzyl-7-prenylether compound 10 and chrysin 5,7-diprenylether compound 11, with the improved pharmacological profile compared with chrysin (1). Nuclear receptor binding and ligand-induced coactivator recruitment assays revealed that compounds 10 and 11 functioned as peroxisome proliferator-activated receptor (PPAR)γ partial agonists. These findings were supported by molecular docking simulation, followed by experimental validation. Notably, compound 11 showed PPARγ binding affinity as potent as that of the PPARγ agonists pioglitazone and telmisartan. This study presents a novel PPARγ partial agonist pharmacophore and suggests that prenylated chrysin derivatives have therapeutic potential in various human diseases associated with hypoadiponectinemia.
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Affiliation(s)
- Seungchan An
- Natural
Products Research Institute, College of Pharmacy, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul 08826, Republic of Korea
| | - Hyejin Ko
- Natural
Products Research Institute, College of Pharmacy, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul 08826, Republic of Korea
| | - Hongjun Jang
- Research
Institute of Pharmaceutical Science and Technology, College of Pharmacy, Ajou University, 206 World cup-ro, Yeongtong-gu, Suwon, Gyeonggi-do 16499, Republic of Korea
| | - In Guk Park
- Natural
Products Research Institute, College of Pharmacy, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul 08826, Republic of Korea
| | - Sungjin Ahn
- Natural
Products Research Institute, College of Pharmacy, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul 08826, Republic of Korea
| | - Seok Young Hwang
- Natural
Products Research Institute, College of Pharmacy, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul 08826, Republic of Korea
| | - Junpyo Gong
- Natural
Products Research Institute, College of Pharmacy, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul 08826, Republic of Korea
| | - Soyeon Oh
- Natural
Products Research Institute, College of Pharmacy, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul 08826, Republic of Korea
| | - Soo Yeon Kwak
- Research
Institute of Pharmaceutical Science and Technology, College of Pharmacy, Ajou University, 206 World cup-ro, Yeongtong-gu, Suwon, Gyeonggi-do 16499, Republic of Korea
| | - Yeonjin Lee
- Natural
Products Research Institute, College of Pharmacy, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul 08826, Republic of Korea
| | - Hyoungsu Kim
- Research
Institute of Pharmaceutical Science and Technology, College of Pharmacy, Ajou University, 206 World cup-ro, Yeongtong-gu, Suwon, Gyeonggi-do 16499, Republic of Korea
| | - Minsoo Noh
- Natural
Products Research Institute, College of Pharmacy, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul 08826, Republic of Korea
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9
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Hurst CD, Cheng G, Platt FM, Alder O, Black EV, Burns JE, Brown J, Jain S, Roulson JA, Knowles MA. Molecular profile of pure squamous cell carcinoma of the bladder identifies major roles for OSMR and YAP signalling. JOURNAL OF PATHOLOGY CLINICAL RESEARCH 2022; 8:279-293. [PMID: 35289095 PMCID: PMC8977277 DOI: 10.1002/cjp2.261] [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: 12/10/2021] [Revised: 01/13/2022] [Accepted: 01/18/2022] [Indexed: 11/20/2022]
Abstract
Pure squamous cell carcinoma (SCC) is the most common pure variant form of bladder cancer, found in 2–5% of cases. It often presents late and is unresponsive to cisplatin‐based chemotherapy. The molecular features of these tumours have not been elucidated in detail. We carried out whole‐exome sequencing (WES), copy number, and transcriptome analysis of bladder SCC. Muscle‐invasive bladder cancer (MIBC) samples with no evidence of squamous differentiation (non‐SD) were used for comparison. To assess commonality of features with urothelial carcinoma with SD, we examined data from SD samples in The Cancer Genome Atlas (TCGA) study of MIBC. TP53 was the most commonly mutated gene in SCC (64%) followed by FAT1 (45%). Copy number analysis revealed complex changes in SCC, many differing from those in samples with SD. Gain of 5p and 7p was the most common feature, and focal regions on 5p included OSMR and RICTOR. In addition to 9p deletions, we found some samples with focal gain of 9p24 containing CD274 (PD‐L1). Loss of 4q35 containing FAT1 was found in many samples such that all but one sample analysed by WES had FAT1 mutation or deletion. Expression features included upregulation of oncostatin M receptor (OSMR), metalloproteinases, metallothioneins, keratinisation genes, extracellular matrix components, inflammatory response genes, stem cell markers, and immune response modulators. Exploration of differentially expressed transcription factors identified BNC1 and TFAP2A, a gene repressed by PPARG, as the most upregulated factors. Known urothelial differentiation factors were downregulated along with 72 Kruppel‐associated (KRAB) domain‐containing zinc finger family protein (KZFP) genes. Novel therapies are urgently needed for these tumours. In addition to upregulated expression of EGFR, which has been suggested as a therapeutic target in basal/squamous bladder cancer, we identified expression signatures that indicate upregulated OSMR and YAP/TAZ signalling. Preclinical evaluation of the effects of inhibition of these pathways alone or in combination is merited.
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Affiliation(s)
- Carolyn D Hurst
- Division of Molecular Medicine, Leeds Institute of Medical Research at St James's, St James's University Hospital, Leeds, UK
| | - Guo Cheng
- Division of Molecular Medicine, Leeds Institute of Medical Research at St James's, St James's University Hospital, Leeds, UK
| | - Fiona M Platt
- Division of Molecular Medicine, Leeds Institute of Medical Research at St James's, St James's University Hospital, Leeds, UK
| | - Olivia Alder
- Division of Molecular Medicine, Leeds Institute of Medical Research at St James's, St James's University Hospital, Leeds, UK
| | - Emma Vi Black
- Division of Molecular Medicine, Leeds Institute of Medical Research at St James's, St James's University Hospital, Leeds, UK
| | - Julie E Burns
- Division of Molecular Medicine, Leeds Institute of Medical Research at St James's, St James's University Hospital, Leeds, UK
| | - Joanne Brown
- Division of Molecular Medicine, Leeds Institute of Medical Research at St James's, St James's University Hospital, Leeds, UK
| | - Sunjay Jain
- Pyrah Department of Urology, St James's University Hospital, Leeds, UK
| | - Jo-An Roulson
- Department of Histopathology, St James's University Hospital, Leeds, UK
| | - Margaret A Knowles
- Division of Molecular Medicine, Leeds Institute of Medical Research at St James's, St James's University Hospital, Leeds, UK
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10
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Almeida MV, Vernaz G, Putman AL, Miska EA. Taming transposable elements in vertebrates: from epigenetic silencing to domestication. Trends Genet 2022; 38:529-553. [DOI: 10.1016/j.tig.2022.02.009] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2021] [Revised: 02/14/2022] [Accepted: 02/15/2022] [Indexed: 12/20/2022]
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11
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Playfoot CJ, Duc J, Sheppard S, Dind S, Coudray A, Planet E, Trono D. Transposable elements and their KZFP controllers are drivers of transcriptional innovation in the developing human brain. Genome Res 2021; 31:1531-1545. [PMID: 34400477 PMCID: PMC8415367 DOI: 10.1101/gr.275133.120] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2020] [Accepted: 07/15/2021] [Indexed: 11/25/2022]
Abstract
Transposable elements (TEs) account for more than 50% of the human genome and many have been co-opted throughout evolution to provide regulatory functions for gene expression networks. Several lines of evidence suggest that these networks are fine-tuned by the largest family of TE controllers, the KRAB-containing zinc finger proteins (KZFPs). One tissue permissive for TE transcriptional activation (termed "transposcription") is the adult human brain, however comprehensive studies on the extent of this process and its potential contribution to human brain development are lacking. To elucidate the spatiotemporal transposcriptome of the developing human brain, we have analyzed two independent RNA-seq data sets encompassing 16 brain regions from eight weeks postconception into adulthood. We reveal a distinct KZFP:TE transcriptional profile defining the late prenatal to early postnatal transition, and the spatiotemporal and cell type-specific activation of TE-derived alternative promoters driving the expression of neurogenesis-associated genes. Long-read sequencing confirmed these TE-driven isoforms as significant contributors to neurogenic transcripts. We also show experimentally that a co-opted antisense L2 element drives temporal protein relocalization away from the endoplasmic reticulum, suggestive of novel TE dependent protein function in primate evolution. This work highlights the widespread dynamic nature of the spatiotemporal KZFP:TE transcriptome and its importance throughout TE mediated genome innovation and neurotypical human brain development. To facilitate interactive exploration of these spatiotemporal gene and TE expression dynamics, we provide the "Brain TExplorer" web application freely accessible for the community.
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Affiliation(s)
- Christopher J Playfoot
- School of Life Sciences, École Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland
| | - Julien Duc
- School of Life Sciences, École Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland
| | - Shaoline Sheppard
- School of Life Sciences, École Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland
| | - Sagane Dind
- School of Life Sciences, École Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland
| | - Alexandre Coudray
- School of Life Sciences, École Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland
| | - Evarist Planet
- School of Life Sciences, École Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland
| | - Didier Trono
- School of Life Sciences, École Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland
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12
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Abstract
Since the discovery of manifest Zn deficiency in 1961, the increasing number of studies demonstrated the association between altered Zn status and multiple diseases. In this chapter, we provide a review of the most recent advances on the role of Zn in health and disease (2010-20), with a special focus on the role of Zn in neurodegenerative and neurodevelopmental disorders, diabetes and obesity, male and female reproduction, as well as COVID-19. In parallel with the revealed tight association between ASD risk and severity and Zn status, the particular mechanisms linking Zn2+ and ASD pathogenesis like modulation of synaptic plasticity through ProSAP/Shank scaffold, neurotransmitter metabolism, and gut microbiota, have been elucidated. The increasing body of data indicate the potential involvement of Zn2+ metabolism in neurodegeneration. Systemic Zn levels in Alzheimer's and Parkinson's disease were found to be reduced, whereas its sequestration in brain may result in modulation of amyloid β and α-synuclein processing with subsequent toxic effects. Zn2+ was shown to possess adipotropic effects through the role of zinc transporters, zinc finger proteins, and Zn-α2-glycoprotein in adipose tissue physiology, underlying its particular role in pathogenesis of obesity and diabetes mellitus type 2. Recent findings also contribute to further understanding of the role of Zn2+ in spermatogenesis and sperm functioning, as well as oocyte development and fertilization. Finally, Zn2+ was shown to be the potential adjuvant therapy in management of novel coronavirus infection (COVID-19), underlining the perspectives of zinc in management of old and new threats.
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Affiliation(s)
- Anatoly V Skalny
- IM Sechenov First Moscow State Medical University (Sechenov University), Moscow, Russia; Yaroslavl State University, Yaroslavl, Russia
| | - Michael Aschner
- IM Sechenov First Moscow State Medical University (Sechenov University), Moscow, Russia; Department of Molecular Pharmacology, Albert Einstein College of Medicine, Bronx, NY, United States
| | - Alexey A Tinkov
- IM Sechenov First Moscow State Medical University (Sechenov University), Moscow, Russia; Yaroslavl State University, Yaroslavl, Russia.
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13
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ZNF91 deletion in human embryonic stem cells leads to ectopic activation of SVA retrotransposons and up-regulation of KRAB zinc finger gene clusters. Genome Res 2021; 31:551-563. [PMID: 33722937 PMCID: PMC8015857 DOI: 10.1101/gr.265348.120] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Accepted: 02/02/2021] [Indexed: 01/27/2023]
Abstract
Transposable element (TE) invasions have shaped vertebrate genomes over the course of evolution. They have contributed an extra layer of species-specific gene regulation by providing novel transcription factor binding sites. In humans, SINE-VNTR-Alu (SVA) elements are one of three still active TE families; approximately 2800 SVA insertions exist in the human genome, half of which are human-specific. TEs are often silenced by KRAB zinc finger (KZNF) proteins recruiting corepressor proteins that establish a repressive chromatin state. A number of KZNFs have been reported to bind SVAs, but their individual contribution to repressing SVAs and their roles in suppressing SVA-mediated gene-regulatory effects remains elusive. We analyzed the genome-wide binding profile for ZNF91 in human cells and found that ZNF91 interacts with the VNTR region of SVAs. Through CRISPR-Cas9-mediated deletion of ZNF91 in human embryonic stem cells, we established that loss of ZNF91 results in increased transcriptional activity of SVAs. In contrast, SVA activation was not observed upon genetic deletion of the ZNF611 gene encoding another strong SVA interactor. Epigenetic profiling confirmed the loss of SVA repression in the absence of ZNF91 and revealed that mainly evolutionary young SVAs gain gene activation-associated epigenetic modifications. Genes close to activated SVAs showed a mild up-regulation, indicating SVAs adopt properties of cis-regulatory elements in the absence of repression. Notably, genome-wide derepression of SVAs elicited the communal up-regulation of KZNFs that reside in KZNF clusters. This phenomenon may provide new insights into the potential mechanisms used by the host genome to sense and counteract TE invasions.
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14
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Shen P, Xu A, Hou Y, Wang H, Gao C, He F, Yang D. Conserved paradoxical relationships among the evolutionary, structural and expressional features of KRAB zinc-finger proteins reveal their special functional characteristics. BMC Mol Cell Biol 2021; 22:7. [PMID: 33482715 PMCID: PMC7821633 DOI: 10.1186/s12860-021-00346-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2020] [Accepted: 01/13/2021] [Indexed: 12/03/2022] Open
Abstract
Background One striking feature of the large KRAB domain-containing zinc finger protein (KZFP) family is its rapid evolution, leading to hundreds of member genes with various origination time in a certain mammalian genome. However, a comprehensive genome-wide and across-taxa analysis of the structural and expressional features of KZFPs with different origination time is lacking. This type of analysis will provide valuable clues about the functional characteristics of this special family. Results In this study, we found several conserved paradoxical phenomena about this issue. 1) Ordinary young domains/proteins tend to be disordered, but most of KRAB domains are completely structured in 64 representative species across the superclass of Sarcopterygii and most of KZFPs are also highly structured, indicating their rigid and unique structural and functional characteristics; as exceptions, old-zinc-finger-containing KZFPs have relatively disordered KRAB domains and linker regions, contributing to diverse interacting partners and functions. 2) In general, young or highly structured proteins tend to be spatiotemporal specific and have low abundance. However, by integrated analysis of 29 RNA-seq datasets, including 725 samples across early embryonic development, embryonic stem cell differentiation, embryonic and adult organs, tissues in 7 mammals, we found that KZFPs tend to express ubiquitously with medium abundance regardless of evolutionary age and structural disorder degree, indicating the wide functional requirements of KZFPs in various states. 3) Clustering and correlation analysis reveal that there are differential expression patterns across different spatiotemporal states, suggesting the specific-high-expression KZFPs may play important roles in the corresponding states. In particular, part of young-zinc-finger-containing KZFPs are highly expressed in early embryonic development and ESCs differentiation into endoderm or mesoderm. Co-expression analysis revealed that young-zinc-finger-containing KZFPs are significantly enriched in five co-expression modules. Among them, one module, including 13 young-zinc-finger-containing KZFPs, showed an ‘early-high and late-low’ expression pattern. Further functional analysis revealed that they may function in early embryonic development and ESC differentiation via participating in cell cycle related processes. Conclusions This study shows the conserved and special structural, expressional features of KZFPs, providing new clues about their functional characteristics and potential causes of their rapid evolution. Supplementary Information The online version contains supplementary material available at 10.1186/s12860-021-00346-w.
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Affiliation(s)
- Pan Shen
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing, 102206, China
| | - Aishi Xu
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing, 102206, China.,Animal Sciences College of Jilin University, Changchun, 130062, China
| | - Yushan Hou
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing, 102206, China
| | - Huqiang Wang
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing, 102206, China
| | - Chao Gao
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing, 102206, China
| | - Fuchu He
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing, 102206, China.
| | - Dong Yang
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing, 102206, China.
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15
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Pant R, Firmal P, Shah VK, Alam A, Chattopadhyay S. Epigenetic Regulation of Adipogenesis in Development of Metabolic Syndrome. Front Cell Dev Biol 2021; 8:619888. [PMID: 33511131 PMCID: PMC7835429 DOI: 10.3389/fcell.2020.619888] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2020] [Accepted: 12/14/2020] [Indexed: 12/12/2022] Open
Abstract
Obesity is one of the biggest public health concerns identified by an increase in adipose tissue mass as a result of adipocyte hypertrophy and hyperplasia. Pertaining to the importance of adipose tissue in various biological processes, any alteration in its function results in impaired metabolic health. In this review, we discuss how adipose tissue maintains the metabolic health through secretion of various adipokines and inflammatory mediators and how its dysfunction leads to the development of severe metabolic disorders and influences cancer progression. Impairment in the adipocyte function occurs due to individuals' genetics and/or environmental factor(s) that largely affect the epigenetic profile leading to altered gene expression and onset of obesity in adults. Moreover, several crucial aspects of adipose biology, including the regulation of different transcription factors, are controlled by epigenetic events. Therefore, understanding the intricacies of adipogenesis is crucial for recognizing its relevance in underlying disease conditions and identifying the therapeutic interventions for obesity and metabolic syndrome.
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Affiliation(s)
- Richa Pant
- National Centre for Cell Science, SP Pune University Campus, Pune, India
| | - Priyanka Firmal
- National Centre for Cell Science, SP Pune University Campus, Pune, India
| | - Vibhuti Kumar Shah
- National Centre for Cell Science, SP Pune University Campus, Pune, India
| | - Aftab Alam
- Roswell Park Comprehensive Cancer Center, Buffalo, NY, United States
| | - Samit Chattopadhyay
- National Centre for Cell Science, SP Pune University Campus, Pune, India.,Department of Biological Sciences, BITS Pilani, Goa, India
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16
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Laudermilk LT, Tovar A, Homstad AK, Thomas JM, McFadden KM, Tune MK, Cowley DO, Mock JR, Ideraabdullah F, Kelada SNP. Baseline and innate immune response characterization of a Zfp30 knockout mouse strain. Mamm Genome 2020; 31:205-214. [PMID: 32860515 DOI: 10.1007/s00335-020-09847-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2020] [Accepted: 08/17/2020] [Indexed: 12/01/2022]
Abstract
Airway neutrophilia is correlated with disease severity in a number of chronic and acute pulmonary diseases, and dysregulation of neutrophil chemotaxis can lead to host tissue damage. The gene Zfp30 was previously identified as a candidate regulator of neutrophil recruitment to the lungs and secretion of CXCL1, a potent neutrophil chemokine, in a genome-wide mapping study using the Collaborative Cross. ZFP30 is a putative transcriptional repressor with a KRAB domain capable of inducing heterochromatin formation. Using a CRISPR-mediated knockout mouse model, we investigated the role that Zfp30 plays in recruitment of neutrophils to the lung using models of allergic airway disease and acute lung injury. We found that the Zfp30 null allele did not affect CXCL1 secretion or neutrophil recruitment to the lungs in response to various innate immune stimuli. Intriguingly, despite the lack of neutrophil phenotype, we found there was a significant reduction in the proportion of live Zfp30 homozygous female mutant mice produced from heterozygous matings. This deviation from the expected Mendelian ratios implicates Zfp30 in fertility or embryonic development. Overall, our results indicate that Zfp30 is an essential gene but does not influence neutrophilic inflammation in this particular knockout model.
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Affiliation(s)
- Lucas T Laudermilk
- Department of Genetics, University of North Carolina, 120 Mason Farm Road, Chapel Hill, NC, 27599, USA.,Curriculum in Genetics and Molecular Biology, University of North Carolina, Chapel Hill, NC, USA
| | - Adelaide Tovar
- Department of Genetics, University of North Carolina, 120 Mason Farm Road, Chapel Hill, NC, 27599, USA.,Curriculum in Genetics and Molecular Biology, University of North Carolina, Chapel Hill, NC, USA
| | - Alison K Homstad
- Department of Genetics, University of North Carolina, 120 Mason Farm Road, Chapel Hill, NC, 27599, USA.,Curriculum in Genetics and Molecular Biology, University of North Carolina, Chapel Hill, NC, USA
| | - Joseph M Thomas
- Department of Genetics, University of North Carolina, 120 Mason Farm Road, Chapel Hill, NC, 27599, USA
| | - Kathryn M McFadden
- Department of Genetics, University of North Carolina, 120 Mason Farm Road, Chapel Hill, NC, 27599, USA
| | - Miriya K Tune
- Marsico Lung Institute, University of North Carolina, Chapel Hill, NC, USA
| | - Dale O Cowley
- Department of Genetics, University of North Carolina, 120 Mason Farm Road, Chapel Hill, NC, 27599, USA.,Animal Models Core Facility, University of North Carolina, Chapel Hill, NC, USA
| | - Jason R Mock
- Marsico Lung Institute, University of North Carolina, Chapel Hill, NC, USA
| | - Folami Ideraabdullah
- Department of Genetics, University of North Carolina, 120 Mason Farm Road, Chapel Hill, NC, 27599, USA.,Curriculum in Genetics and Molecular Biology, University of North Carolina, Chapel Hill, NC, USA.,Department of Nutrition, University of North Carolina, Chapel Hill, NC, USA
| | - Samir N P Kelada
- Department of Genetics, University of North Carolina, 120 Mason Farm Road, Chapel Hill, NC, 27599, USA. .,Curriculum in Genetics and Molecular Biology, University of North Carolina, Chapel Hill, NC, USA. .,Marsico Lung Institute, University of North Carolina, Chapel Hill, NC, USA.
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17
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Gibbs ZA, Reza LC, Cheng CC, Westcott JM, McGlynn K, Whitehurst AW. The testis protein ZNF165 is a SMAD3 cofactor that coordinates oncogenic TGFβ signaling in triple-negative breast cancer. eLife 2020; 9:57679. [PMID: 32515734 PMCID: PMC7302877 DOI: 10.7554/elife.57679] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2020] [Accepted: 06/09/2020] [Indexed: 12/19/2022] Open
Abstract
Cancer/testis (CT) antigens are proteins whose expression is normally restricted to germ cells yet aberrantly activated in tumors, where their functions remain relatively cryptic. Here we report that ZNF165, a CT antigen frequently expressed in triple-negative breast cancer (TNBC), associates with SMAD3 to modulate transcription of transforming growth factor β (TGFβ)-dependent genes and thereby promote growth and survival of human TNBC cells. In addition, we identify the KRAB zinc finger protein, ZNF446, and its associated tripartite motif protein, TRIM27, as obligate components of the ZNF165-SMAD3 complex that also support tumor cell viability. Importantly, we find that TRIM27 alone is necessary for ZNF165 transcriptional activity and is required for TNBC tumor growth in vivo using an orthotopic xenograft model in immunocompromised mice. Our findings indicate that aberrant expression of a testis-specific transcription factor is sufficient to co-opt somatic transcriptional machinery to drive a pro-tumorigenic gene expression program in TNBC.
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Affiliation(s)
- Zane A Gibbs
- Department of Pharmacology, University of Texas Southwestern Medical Center, Dallas, United States.,Harold C. Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, United States
| | - Luis C Reza
- Department of Pharmacology, University of Texas Southwestern Medical Center, Dallas, United States.,Harold C. Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, United States
| | - Chun-Chun Cheng
- Department of Pharmacology, University of Texas Southwestern Medical Center, Dallas, United States.,Harold C. Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, United States
| | - Jill M Westcott
- Hamon Center for Therapeutic Oncology Research, University of Texas Southwestern Medical Center, Dallas, United States
| | - Kathleen McGlynn
- Department of Pharmacology, University of Texas Southwestern Medical Center, Dallas, United States.,Harold C. Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, United States
| | - Angelique W Whitehurst
- Department of Pharmacology, University of Texas Southwestern Medical Center, Dallas, United States.,Harold C. Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, United States
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18
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Kauzlaric A, Jang SM, Morchikh M, Cassano M, Planet E, Benkirane M, Trono D. KAP1 targets actively transcribed genomic loci to exert pleomorphic effects on RNA polymerase II activity. Philos Trans R Soc Lond B Biol Sci 2020; 375:20190334. [PMID: 32068487 PMCID: PMC7061982 DOI: 10.1098/rstb.2019.0334] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
KAP1 (KRAB-associated protein 1) is best known as a co-repressor responsible for inducing heterochromatin formation, notably at transposable elements. However, it has also been observed to bind the transcription start site of actively expressed genes. To address this paradox, we characterized the protein interactome of KAP1 in the human K562 erythro-leukaemia cell line. We found that the regulator can associate with a wide range of nucleic acid binding proteins, nucleosome remodellers, chromatin modifiers and other transcription modulators. We further determined that KAP1 is recruited at actively transcribed polymerase II promoters, where its depletion resulted in pleomorphic effects, whether expression of these genes was normally constitutive or inducible, consistent with the breadth of possible KAP1 interactors. This article is part of a discussion meeting issue ‘Crossroads between transposons and gene regulation’.
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Affiliation(s)
- Annamaria Kauzlaric
- School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland
| | - Suk Min Jang
- School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland
| | - Mehdi Morchikh
- Laboratory of Molecular Virology, Institute of Human Genetics, CNRS UPR1142, MGX-Montpellier GenomiX, 141 rue de la Cardonille, 34396 Montpellier, France.,Institute of Molecular Genetics of Montpellier, CNRS, Université de Montpellier, 34090 Montpellier, France
| | - Marco Cassano
- School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland
| | - Evarist Planet
- School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland
| | - Monsef Benkirane
- Laboratory of Molecular Virology, Institute of Human Genetics, CNRS UPR1142, MGX-Montpellier GenomiX, 141 rue de la Cardonille, 34396 Montpellier, France
| | - Didier Trono
- School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland
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19
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Farmiloe G, Lodewijk GA, Robben SF, van Bree EJ, Jacobs FMJ. Widespread correlation of KRAB zinc finger protein binding with brain-developmental gene expression patterns. Philos Trans R Soc Lond B Biol Sci 2020; 375:20190333. [PMID: 32075554 DOI: 10.1098/rstb.2019.0333] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The large family of KRAB zinc finger (KZNF) genes are transcription factors implicated in recognizing and repressing repetitive sequences such as transposable elements (TEs) in our genome. Through successive waves of retrotransposition-mediated insertions, various classes of TEs have invaded mammalian genomes at multiple timepoints throughout evolution. Even though most of the TE classes in our genome lost the capability to retrotranspose millions of years ago, it remains elusive why the KZNFs that evolved to repress them are still retained in our genome. One hypothesis is that KZNFs become repurposed for other regulatory roles. Here, we find evidence that evolutionary changes in KZNFs provide them not only with the ability to repress TEs, but also to bind to gene promoters independent of TEs. Using KZNF binding site data in conjunction with gene expression values from the Allen Brain Atlas, we show that KZNFs have the ability to regulate gene expression in the human brain in a region-specific manner. Our analysis shows that the expression of KZNFs shows correlation with the expression of their target genes, suggesting that KZNFs have a direct influence on gene expression in the developing human brain. The extent of this regulation and the impact it has on primate brain evolution are still to be determined, but our results imply that KZNFs have become widely integrated into neuronal gene regulatory networks. Our analysis predicts that gene expression networks have been repeatedly innovated throughout primate evolution, continuously gaining new layers of gene regulation mediated by both TEs and KZNFs in our genome. This article is part of a discussion meeting issue 'Crossroads between transposons and gene regulation'.
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Affiliation(s)
- Grace Farmiloe
- Swammerdam Institute for Life Sciences, Amsterdam Neuroscience, University of Amsterdam, 1098XH Amsterdam, The Netherlands
| | - Gerrald A Lodewijk
- Swammerdam Institute for Life Sciences, Amsterdam Neuroscience, University of Amsterdam, 1098XH Amsterdam, The Netherlands
| | - Stijn F Robben
- Swammerdam Institute for Life Sciences, Amsterdam Neuroscience, University of Amsterdam, 1098XH Amsterdam, The Netherlands
| | - Elisabeth J van Bree
- Swammerdam Institute for Life Sciences, Amsterdam Neuroscience, University of Amsterdam, 1098XH Amsterdam, The Netherlands
| | - Frank M J Jacobs
- Swammerdam Institute for Life Sciences, Amsterdam Neuroscience, University of Amsterdam, 1098XH Amsterdam, The Netherlands
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20
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Al Chiblak M, Steinbeck F, Thiesen HJ, Lorenz P. DUF3669, a "domain of unknown function" within ZNF746 and ZNF777, oligomerizes and contributes to transcriptional repression. BMC Mol Cell Biol 2019; 20:60. [PMID: 31856708 PMCID: PMC6923878 DOI: 10.1186/s12860-019-0243-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2019] [Accepted: 12/12/2019] [Indexed: 11/10/2022] Open
Abstract
Background ZNF746 and ZNF777 belong to a subset of the large Krüppel-associated box (KRAB) zinc finger (ZNF) transcription factor family. They contain, like four other members in human, an additional conserved domain, the “domain of unknown function 3669” (DUF3669). Previous work on members of this subfamily suggested involvement in transcriptional regulation and aberrant ZNF746 overexpression leads to neuronal cell death in Parkinson’s disease. Results Here we demonstrate that N-terminal protein segments of the ZNF746a major isoform and ZNF777 act in concert to exert moderate transcriptional repression activities. Full potency depended on the intact configuration consisting of DUF3669, a variant KRAB domain and adjacent sequences. While DUF3669 contributes an intrinsic weak inhibitory activity, the isolated KRAB-AB domains did not repress. Importantly, DUF3669 provides a novel protein-protein interaction interface and mediates direct physical interaction between the members of the subfamily in oligomers. The ZNF746 protein segment encoded by exons 5 and 6 boosted repressor potency, potentially due to the presence of an acceptor lysine for sumoylation at K189. Repressor activity of the potent canonical ZNF10 KRAB domain was not augmented by heterologous transfer of DUF3669, pointing to the importance of context for DUF3669’s impact on transcription. Neither ZNF746a nor ZNF777 protein segments stably associated with TRIM28 within cells. Isoform ZNF746b that contains, unlike the major isoform, a full-length KRAB-A subdomain, displayed substantially increased repressor potency. This increase is due to canonical mechanisms known for KRAB domains since it did not take place in HAP1 knockout models of TRIM28 and SETDB1. A glycine to glutamic acid replacement that complies with a bona fide conserved “MLE” sequence within KRAB-A led to a further strong gain in repressor potency to levels comparable to those of the canonical ZNF10 KRAB domain. Each gain of repressive activity was accompanied by an enhanced interaction with TRIM28 protein. Conclusion DUF3669 adds a protein-protein interaction surface to a subgroup of KRAB-ZNF proteins within an N-terminal configuration with variant KRAB and adjacent sequences likely regulated by sumoylation. DUF3669 contributes to transcriptional repression strength and its homo- and hetero-oligomerization characteristics probably extended the regulatory repertoire of KRAB-ZNF transcription factors during amniote evolution.
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Affiliation(s)
- Mohannad Al Chiblak
- Institute of Immunology, Rostock University Medical Center, Schillingallee 70, 18057, Rostock, Germany
| | - Felix Steinbeck
- Institute of Immunology, Rostock University Medical Center, Schillingallee 70, 18057, Rostock, Germany
| | - Hans-Jürgen Thiesen
- Institute of Immunology, Rostock University Medical Center, Schillingallee 70, 18057, Rostock, Germany
| | - Peter Lorenz
- Institute of Immunology, Rostock University Medical Center, Schillingallee 70, 18057, Rostock, Germany.
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