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Huang Y, Li B, Wu Z, Liu K, Min J. Inhibitors targeting the PWWP domain-containing proteins. Eur J Med Chem 2024; 280:116965. [PMID: 39413441 DOI: 10.1016/j.ejmech.2024.116965] [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: 07/01/2024] [Revised: 10/10/2024] [Accepted: 10/11/2024] [Indexed: 10/18/2024]
Abstract
PWWP domain-containing proteins play a pivotal role in chromatin-mediated biological processes, and their aberrant regulation is linked to various human diseases. Recent years have witnessed remarkable strides in unraveling the structural and functional features of PWWP domain-containing proteins, propelling significant advances in targeting the PWWP domain-containing proteins for drug discovery purposes. Several drugs have already been approved, while others are currently in clinical trials. This review offers a comprehensive overview of the latest developments on PWWP domain-containing proteins, including their structural characteristics and biological significance. It also provides detailed insights into the drug discovery process targeting these proteins, including screening, design, and structural optimization.
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Affiliation(s)
- Yunyuan Huang
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan, Hubei, China
| | - Boyi Li
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan, Hubei, China
| | - Zhibin Wu
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan, Hubei, China
| | - Ke Liu
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan, Hubei, China
| | - Jinrong Min
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan, Hubei, China.
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2
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Yoon K, Williams S, Duncan EJ. DNA methylation machinery is involved in development and reproduction in the viviparous pea aphid (Acyrthosiphon pisum). INSECT MOLECULAR BIOLOGY 2024; 33:534-549. [PMID: 38923717 DOI: 10.1111/imb.12936] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/06/2024] [Accepted: 06/07/2024] [Indexed: 06/28/2024]
Abstract
Epigenetic mechanisms, such as DNA methylation, have been proposed to mediate plastic responses in insects. The pea aphid (Acyrthosiphon pisum), like the majority of extant aphids, displays cyclical parthenogenesis - the ability of mothers to switch the reproductive mode of their offspring from reproducing parthenogenetically to sexually in response to environmental cues. The pea aphid genome encodes two paralogs of the de novo DNA methyltransferase gene, dnmt3a and dnmt3x. Here we show, using phylogenetic analysis, that this gene duplication event occurred at least 150 million years ago, likely after the divergence of the lineage leading to the Aphidomorpha (phylloxerans, adelgids and true aphids) from that leading to the scale insects (Coccomorpha) and that the two paralogs are maintained in the genomes of all aphids examined. We also show that the mRNA of both dnmt3 paralogs is maternally expressed in the viviparous aphid ovary. During development both paralogs are expressed in the germ cells of embryos beginning at stage 5 and persisting throughout development. Treatment with 5-azactyidine, a chemical that generally inhibits the DNA methylation machinery, leads to defects of oocytes and early-stage embryos and causes a proportion of later stage embryos to be born dead or die soon after birth. These phenotypes suggest a role for DNA methyltransferases in reproduction, consistent with that seen in other insects. Taking the vast evolutionary history of the dnmt3 paralogs, and the localisation of their mRNAs in the ovary, we suggest there is a role for dnmt3a and/or dnmt3x in early development, and a role for DNA methylation machinery in reproduction and development of the viviparous pea aphid.
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Affiliation(s)
- Kane Yoon
- School of Biology, Faculty of Biological Sciences, University of Leeds, Leeds, UK
| | - Stephanie Williams
- School of Biology, Faculty of Biological Sciences, University of Leeds, Leeds, UK
| | - Elizabeth J Duncan
- School of Biology, Faculty of Biological Sciences, University of Leeds, Leeds, UK
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3
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German RJ, Vuocolo B, Vossaert L, Saba L, Fletcher R, Tedder ML, Sadikovic B, Kerkhof J, Wangler M, Bacino CA. Recurrent carotid paragangliomas in a syndromic patient with a heterozygous missense variant in DNA Methyltransferase 3 Alpha. Am J Med Genet A 2024:e63849. [PMID: 39166703 DOI: 10.1002/ajmg.a.63849] [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: 07/14/2023] [Revised: 07/23/2024] [Accepted: 08/05/2024] [Indexed: 08/23/2024]
Abstract
We report a 40-year-old African American female with a novel variant in exon 8 of DNA methyltransferase 3 alpha (DNMT3A), (NM_022552.4: c.905G>C, p.G302A) who presented with a history of recurrent carotid paragangliomas, mediastinal mass, intellectual disability, dysarthria, cholelithiasis, diabetes mellitus, hypertension, and dysmorphic features. We interpret this novel variant as likely pathogenic and causative for the patient's syndromic features of Heyn-Sproul-Jackson syndrome. Heyn-Sproul-Jackson syndrome is a condition caused by gain-of-function genetic changes in DNMT3A. Paragangliomas have also been observed in non-syndromic patients with genetic alterations in DNMT3A. We describe a patient with clinical features of Heyn-Sproul-Jackson syndrome such as intellectual disability, dysarthria, brachydactyly, and lack of brain MRI findings to add evidence to associate paragangliomas with DNMT3A and draw particular attention to the potential involvement of the proline-tryptophan-tryptophan-proline domain of DNMT3A.
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Affiliation(s)
- Ryan J German
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
- Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, Texas, USA
| | - Blake Vuocolo
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
- Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, Texas, USA
| | - Liesbeth Vossaert
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
- Baylor Genetics Laboratories, Houston, Texas, USA
| | - Lisa Saba
- Department of Pathology, Texas Children's Hospital, Houston, Texas, USA
| | - Robin Fletcher
- Greenwood Genetic Center, Greenwood, South Carolina, USA
| | | | - Bekim Sadikovic
- Verspeeten Clinical Genome Centre, London Health Sciences Centre, London, ON, Canada
- Department of Pathology and Laboratory Medicine, Western University, London, ON, Canada
| | - Jennifer Kerkhof
- Verspeeten Clinical Genome Centre, London Health Sciences Centre, London, ON, Canada
- Department of Pathology and Laboratory Medicine, Western University, London, ON, Canada
| | - Michael Wangler
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
- Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, Texas, USA
- Department of Genetics, Texas Children's Hospital, Houston, Texas, USA
| | - Carlos A Bacino
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
- Department of Genetics, Texas Children's Hospital, Houston, Texas, USA
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4
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Lin YY, Müller P, Karagianni E, Hepp N, Mueller-Planitz F, Vanderlinden W, Lipfert J. Epigenetic Histone Modifications H3K36me3 and H4K5/8/12/16ac Induce Open Polynucleosome Conformations via Different Mechanisms. J Mol Biol 2024; 436:168671. [PMID: 38908785 DOI: 10.1016/j.jmb.2024.168671] [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: 02/18/2024] [Revised: 05/28/2024] [Accepted: 06/16/2024] [Indexed: 06/24/2024]
Abstract
Nucleosomes are the basic compaction unit of chromatin and nucleosome structure and their higher-order assemblies regulate genome accessibility. Many post-translational modifications alter nucleosome dynamics, nucleosome-nucleosome interactions, and ultimately chromatin structure and gene expression. Here, we investigate the role of two post-translational modifications associated with actively transcribed regions, H3K36me3 and H4K5/8/12/16ac, in the contexts of tri-nucleosome arrays that provide a tractable model system for quantitative single-molecule analysis, while enabling us to probe nucleosome-nucleosome interactions. Direct visualization by AFM imaging reveals that H3K36me3 and H4K5/8/12/16ac nucleosomes adopt significantly more open and loose conformations than unmodified nucleosomes. Similarly, magnetic tweezers force spectroscopy shows a reduction in DNA outer turn wrapping and nucleosome-nucleosome interactions for the modified nucleosomes. The results suggest that for H3K36me3 the increased breathing and outer DNA turn unwrapping seen in mononucleosomes propagates to more open conformations in nucleosome arrays. In contrast, the even more open structures of H4K5/8/12/16ac nucleosome arrays do not appear to derive from the dynamics of the constituent mononucleosomes, but are driven by reduced nucleosome-nucleosome interactions, suggesting that stacking interactions can overrule DNA breathing of individual nucleosomes. We anticipate that our methodology will be broadly applicable to reveal the influence of other post-translational modifications and to observe the activity of nucleosome remodelers.
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Affiliation(s)
- Yi-Yun Lin
- Department of Physics and Center for NanoScience (CeNS), LMU Munich, Amaliensstrasse 54, 80799 Munich, Germany; Soft Condensed Matter and Biophysics, Department of Physics and Debye Institute for Nanomaterials Science, Utrecht University, Princetonplein 1, 3584 CC Utrecht, the Netherlands
| | - Peter Müller
- Department of Physics and Center for NanoScience (CeNS), LMU Munich, Amaliensstrasse 54, 80799 Munich, Germany; Soft Condensed Matter and Biophysics, Department of Physics and Debye Institute for Nanomaterials Science, Utrecht University, Princetonplein 1, 3584 CC Utrecht, the Netherlands
| | - Evdoxia Karagianni
- Soft Condensed Matter and Biophysics, Department of Physics and Debye Institute for Nanomaterials Science, Utrecht University, Princetonplein 1, 3584 CC Utrecht, the Netherlands
| | - Nicola Hepp
- Institute of Physiological Chemistry, Faculty of Medicine Carl Gustav Carus, Technische Universität Dresden, Fetscherstraße 74, 01307 Dresden, Germany; Current address: Department of Clinical Genetics, Rigshospitalet, Copenhagen University Hospital, Blegdamsvej 9, 2100 Copenhagen, Denmark
| | - Felix Mueller-Planitz
- Institute of Physiological Chemistry, Faculty of Medicine Carl Gustav Carus, Technische Universität Dresden, Fetscherstraße 74, 01307 Dresden, Germany
| | - Willem Vanderlinden
- Department of Physics and Center for NanoScience (CeNS), LMU Munich, Amaliensstrasse 54, 80799 Munich, Germany; Soft Condensed Matter and Biophysics, Department of Physics and Debye Institute for Nanomaterials Science, Utrecht University, Princetonplein 1, 3584 CC Utrecht, the Netherlands; School of Physics and Astronomy, University of Edinburg, James Clerk Maxwell Building, Peter Guthrie Tait Road, Edinburgh EH9 3FD, United Kingdom.
| | - Jan Lipfert
- Department of Physics and Center for NanoScience (CeNS), LMU Munich, Amaliensstrasse 54, 80799 Munich, Germany; Soft Condensed Matter and Biophysics, Department of Physics and Debye Institute for Nanomaterials Science, Utrecht University, Princetonplein 1, 3584 CC Utrecht, the Netherlands.
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5
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Kucharski R, Ellis N, Jurkowski TP, Hurd PJ, Maleszka R. The PWWP domain and the evolution of unique DNA methylation toolkits in Hymenoptera. iScience 2023; 26:108193. [PMID: 37920666 PMCID: PMC10618690 DOI: 10.1016/j.isci.2023.108193] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2023] [Revised: 08/11/2023] [Accepted: 10/10/2023] [Indexed: 11/04/2023] Open
Abstract
DNMT3 in Hymenoptera has a unique duplication of the essential PWWP domain. Using GST-tagged PWWP fusion proteins and histone arrays we show that these domains have gained new properties and represent the first case of PWWP domains binding to H3K27 chromatin modifications, including H3K27me3, a key modification that is important during development. Phylogenetic analyses of 107 genomes indicate that the duplicated PWWP domains separated into two sister clades, and their distinct binding capacities are supported by 3D modeling. Other features of this unique DNA methylation system include variable copies, losses, and duplications of DNMT1 and DNMT3, and combinatorial generations of DNMT3 isoforms including variants missing the catalytic domain. Some of these losses and duplications of are found only in parasitic wasps. We discuss our findings in the context of the crosstalk between DNA methylation and histone methylation, and the expanded potential of epigenomic modifications in Hymenoptera to drive evolutionary novelties.
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Affiliation(s)
- Robert Kucharski
- Research School of Biology, The Australian National University, Canberra, ACT 2601, Australia
| | - Nancy Ellis
- School of Biological & Behavioural Sciences, Queen Mary University of London, London, UK
| | | | - Paul J. Hurd
- School of Biological & Behavioural Sciences, Queen Mary University of London, London, UK
| | - Ryszard Maleszka
- Research School of Biology, The Australian National University, Canberra, ACT 2601, Australia
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6
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Zheng SY, Guan BB, Yuan DY, Zhao QQ, Ge W, Tan LM, Chen SS, Li L, Chen S, Xu RM, He XJ. Dual roles of the Arabidopsis PEAT complex in histone H2A deubiquitination and H4K5 acetylation. MOLECULAR PLANT 2023; 16:1847-1865. [PMID: 37822080 DOI: 10.1016/j.molp.2023.10.006] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/18/2023] [Revised: 09/06/2023] [Accepted: 10/08/2023] [Indexed: 10/13/2023]
Abstract
Histone H2A monoubiquitination is associated with transcriptional repression and needs to be removed by deubiquitinases to facilitate gene transcription in eukaryotes. However, the deubiquitinase responsible for genome-wide H2A deubiquitination in plants has yet to be identified. In this study, we found that the previously identified PWWP-EPCR-ARID-TRB (PEAT) complex components interact with both the ubiquitin-specific protease UBP5 and the redundant histone acetyltransferases HAM1 and HAM2 (HAM1/2) to form a larger version of PEAT complex in Arabidopsis thaliana. UBP5 functions as an H2A deubiquitinase in a nucleosome substrate-dependent manner in vitro and mediates H2A deubiquitination at the whole-genome level in vivo. HAM1/2 are shared subunits of the PEAT complex and the conserved NuA4 histone acetyltransferase complex, and are responsible for histone H4K5 acetylation. Within the PEAT complex, the PWWP components (PWWP1, PWWP2, and PWWP3) directly interact with UBP5 and are necessary for UBP5-mediated H2A deubiquitination, while the EPCR components (EPCR1 and EPCR2) directly interact with HAM1/2 and are required for HAM1/2-mediated H4K5 acetylation. Collectively, our study not only identifies dual roles of the PEAT complex in H2A deubiquitination and H4K5 acetylation but also illustrates how these processes collaborate at the whole-genome level to regulate the transcription and development in plants.
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Affiliation(s)
- Si-Yao Zheng
- College of Life Sciences, Beijing Normal University, Beijing, China; National Institute of Biological Sciences, Beijing, China
| | - Bin-Bin Guan
- National Institute of Biological Sciences, Beijing, China
| | - Dan-Yang Yuan
- National Institute of Biological Sciences, Beijing, China
| | | | - Weiran Ge
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China; School of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Lian-Mei Tan
- National Institute of Biological Sciences, Beijing, China
| | - Shan-Shan Chen
- National Institute of Biological Sciences, Beijing, China
| | - Lin Li
- National Institute of Biological Sciences, Beijing, China
| | - She Chen
- National Institute of Biological Sciences, Beijing, China
| | - Rui-Ming Xu
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China; School of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Xin-Jian He
- National Institute of Biological Sciences, Beijing, China; Tsinghua Institute of Multidisciplinary Biomedical Research, Tsinghua University, Beijing, China.
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7
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Koutná E, Lux V, Kouba T, Škerlová J, Nováček J, Srb P, Hexnerová R, Šváchová H, Kukačka Z, Novák P, Fábry M, Poepsel S, Veverka V. Multivalency of nucleosome recognition by LEDGF. Nucleic Acids Res 2023; 51:10011-10025. [PMID: 37615563 PMCID: PMC10570030 DOI: 10.1093/nar/gkad674] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Revised: 07/01/2023] [Accepted: 08/09/2023] [Indexed: 08/25/2023] Open
Abstract
Eukaryotic transcription is dependent on specific histone modifications. Their recognition by chromatin readers triggers complex processes relying on the coordinated association of transcription regulatory factors. Although various modification states of a particular histone residue often lead to differential outcomes, it is not entirely clear how they are discriminated. Moreover, the contribution of intrinsically disordered regions outside of the specialized reader domains to nucleosome binding remains unexplored. Here, we report the structures of a PWWP domain from transcriptional coactivator LEDGF in complex with the H3K36 di- and trimethylated nucleosome, indicating that both methylation marks are recognized by PWWP in a highly conserved manner. We identify a unique secondary interaction site for the PWWP domain at the interface between the acidic patch and nucleosomal DNA that might contribute to an H3K36-methylation independent role of LEDGF. We reveal DNA interacting motifs in the intrinsically disordered region of LEDGF that discriminate between the intra- or extranucleosomal DNA but remain dynamic in the context of dinucleosomes. The interplay between the LEDGF H3K36-methylation reader and protein binding module mediated by multivalent interactions of the intrinsically disordered linker with chromatin might help direct the elongation machinery to the vicinity of RNA polymerase II, thereby facilitating productive elongation.
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Affiliation(s)
- Eliška Koutná
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Prague 160 00, Czech Republic
- Department of Cell Biology, Faculty of Science, Charles University, Prague 128 00, Czech Republic
| | - Vanda Lux
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Prague 160 00, Czech Republic
| | - Tomáš Kouba
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Prague 160 00, Czech Republic
| | - Jana Škerlová
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Prague 160 00, Czech Republic
| | | | - Pavel Srb
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Prague 160 00, Czech Republic
| | - Rozálie Hexnerová
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Prague 160 00, Czech Republic
| | - Hana Šváchová
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Prague 160 00, Czech Republic
| | - Zdeněk Kukačka
- Institute of Microbiology of the Czech Academy of Sciences, Prague 142 20, Czech Republic
| | - Petr Novák
- Institute of Microbiology of the Czech Academy of Sciences, Prague 142 20, Czech Republic
| | - Milan Fábry
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Prague 160 00, Czech Republic
| | - Simon Poepsel
- Center for Molecular Medicine Cologne (CMMC), Faculty of Medicine and University Hospital Cologne, Cologne 509 31, Germany
- Cologne Excellence Cluster for Cellular Stress Responses in Ageing-Associated Diseases (CECAD), University of Cologne, Cologne 509 31, Germany
| | - Václav Veverka
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Prague 160 00, Czech Republic
- Department of Cell Biology, Faculty of Science, Charles University, Prague 128 00, Czech Republic
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8
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Ortiz G, Kutateladze TG, Fujimori DG. Chemical tools targeting readers of lysine methylation. Curr Opin Chem Biol 2023; 74:102286. [PMID: 36948085 PMCID: PMC10264141 DOI: 10.1016/j.cbpa.2023.102286] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2022] [Revised: 02/01/2023] [Accepted: 02/20/2023] [Indexed: 03/22/2023]
Abstract
Reader domains that recognize methylated lysine and arginine residues on histones play a role in the recruitment, stabilization, and regulation of chromatin regulatory proteins. Targeting reader proteins with small molecule and peptidomimetic inhibitors has enabled the elucidation of the structure and function of specific domains and uncovered their role in diseases. Recent progress towards chemical probes that target readers of lysine methylation, including the Royal family and plant homeodomains (PHD), is discussed here. We highlight recently developed covalent cyclic peptide inhibitors of a plant homeodomain. Additionally, inhibitors targeting previously untargeted Tudor domains and chromodomains are discussed.
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Affiliation(s)
- Gloria Ortiz
- Department of Cellular and Molecular Pharmacology, University of California San Francisco San Francisco, CA 94158, USA
| | - Tatiana G Kutateladze
- Department of Pharmacology, University of Colorado School of Medicine, Aurora, CO 80045, USA.
| | - Danica Galonic Fujimori
- Department of Cellular and Molecular Pharmacology, University of California San Francisco San Francisco, CA 94158, USA; Department of Pharmaceutical Chemistry, University of California San Francisco San Francisco, CA 94158, USA; Quantitative Biosciences Institute (QBI), University of California San Francisco San Francisco, CA 94158, USA.
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9
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Aparicio Chacón MV, Van Dingenen J, Goormachtig S. Characterization of Arbuscular Mycorrhizal Effector Proteins. Int J Mol Sci 2023; 24:9125. [PMID: 37298075 PMCID: PMC10252856 DOI: 10.3390/ijms24119125] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Revised: 05/17/2023] [Accepted: 05/21/2023] [Indexed: 06/12/2023] Open
Abstract
Plants are colonized by various fungi with both pathogenic and beneficial lifestyles. One type of colonization strategy is through the secretion of effector proteins that alter the plant's physiology to accommodate the fungus. The oldest plant symbionts, the arbuscular mycorrhizal fungi (AMF), may exploit effectors to their benefit. Genome analysis coupled with transcriptomic studies in different AMFs has intensified research on the effector function, evolution, and diversification of AMF. However, of the current 338 predicted effector proteins from the AM fungus Rhizophagus irregularis, only five have been characterized, of which merely two have been studied in detail to understand which plant proteins they associate with to affect the host physiology. Here, we review the most recent findings in AMF effector research and discuss the techniques used for the functional characterization of effector proteins, from their in silico prediction to their mode of action, with an emphasis on high-throughput approaches for the identification of plant targets of the effectors through which they manipulate their hosts.
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Affiliation(s)
- María V. Aparicio Chacón
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium;
- Center for Plant Systems Biology, VIB, 9052 Ghent, Belgium
| | - Judith Van Dingenen
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium;
- Center for Plant Systems Biology, VIB, 9052 Ghent, Belgium
| | - Sofie Goormachtig
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium;
- Center for Plant Systems Biology, VIB, 9052 Ghent, Belgium
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10
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Discovery of cysteine-targeting covalent histone methyltransferase inhibitors. Eur J Med Chem 2023; 246:115028. [PMID: 36528996 DOI: 10.1016/j.ejmech.2022.115028] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2022] [Revised: 12/02/2022] [Accepted: 12/13/2022] [Indexed: 12/15/2022]
Abstract
Post-translational methylation of histone lysine or arginine residues by histone methyltransferases (HMTs) plays crucial roles in gene regulation and diverse physiological processes and is implicated in a plethora of human diseases, especially cancer. Therefore, histone methyltransferases have been increasingly recognized as potential therapeutic targets. Consequently, the discovery and development of histone methyltransferase inhibitors have been pursued with steadily increasing interest over the past decade. However, the disadvantages of limited clinical efficacy, moderate selectivity, and propensity for acquired resistance have hindered the development of HMTs inhibitors. Targeted covalent modification represents a proven strategy for kinase drug development and has gained increasing attention in HMTs drug discovery. In this review, we focus on the discovery, characterization, and biological applications of covalent inhibitors for HMTs with emphasis on advancements in the field. In addition, we identify the challenges and future directions in this fast-growing research area of drug discovery.
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11
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Parakkunnel R, Naik K B, Vanishree G, C S, Purru S, Bhaskar K U, Bhat KV, Kumar S. Gene fusions, micro-exons and splice variants define stress signaling by AP2/ERF and WRKY transcription factors in the sesame pan-genome. FRONTIERS IN PLANT SCIENCE 2022; 13:1076229. [PMID: 36618639 PMCID: PMC9817154 DOI: 10.3389/fpls.2022.1076229] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Accepted: 12/02/2022] [Indexed: 06/17/2023]
Abstract
Evolutionary dynamics of AP2/ERF and WRKY genes, the major components of defense response were studied extensively in the sesame pan-genome. Massive variation was observed for gene copy numbers, genome location, domain structure, exon-intron structure and protein parameters. In the pan-genome, 63% of AP2/ERF members were devoid of introns whereas >99% of WRKY genes contained multiple introns. AP2 subfamily was found to be micro-exon rich with the adjoining intronic sequences sharing sequence similarity to many stress-responsive and fatty acid metabolism genes. WRKY family included extensive multi-domain gene fusions where the additional domains significantly enhanced gene and exonic sizes as well as gene copy numbers. The fusion genes were found to have roles in acquired immunity, stress response, cell and membrane integrity as well as ROS signaling. The individual genomes shared extensive synteny and collinearity although ecological adaptation was evident among the Chinese and Indian accessions. Significant positive selection effects were noticed for both micro-exon and multi-domain genes. Splice variants with changes in acceptor, donor and branch sites were common and 6-7 splice variants were detected per gene. The study ascertained vital roles of lipid metabolism and chlorophyll biosynthesis in the defense response and stress signaling pathways. 60% of the studied genes localized in the nucleus while 20% preferred chloroplast. Unique cis-element distribution was noticed in the upstream promoter region with MYB and STRE in WRKY genes while MYC was present in the AP2/ERF genes. Intron-less genes exhibited great diversity in the promoter sequences wherein the predominance of dosage effect indicated variable gene expression levels. Mimicking the NBS-LRR genes, a chloroplast localized WRKY gene, Swetha_24868, with additional domains of chorismate mutase, cAMP and voltage-dependent potassium channel was found to act as a master regulator of defense signaling, triggering immunity and reducing ROS levels.
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Affiliation(s)
- Ramya Parakkunnel
- ICAR- Indian Institute of Seed Science, Regional Station, Gandhi Krishi Vigyana Kendra (GKVK) Campus, Bengaluru, India
| | - Bhojaraja Naik K
- ICAR- Indian Institute of Seed Science, Regional Station, Gandhi Krishi Vigyana Kendra (GKVK) Campus, Bengaluru, India
| | - Girimalla Vanishree
- ICAR- Indian Institute of Seed Science, Regional Station, Gandhi Krishi Vigyana Kendra (GKVK) Campus, Bengaluru, India
| | - Susmita C
- ICAR- Indian Institute of Seed Science, Mau, Uttar Pradesh, India
| | - Supriya Purru
- ICAR- National Academy of Agricultural Research Management, Hyderabad, Telengana, India
| | - Udaya Bhaskar K
- ICAR- Indian Institute of Seed Science, Regional Station, Gandhi Krishi Vigyana Kendra (GKVK) Campus, Bengaluru, India
| | - KV. Bhat
- Division of Genomic Resources, ICAR- National Bureau of Plant Genetic Resources, New Delhi, India
| | - Sanjay Kumar
- ICAR- Indian Institute of Seed Science, Mau, Uttar Pradesh, India
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12
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Abstract
Recent discoveries have advanced our understanding of recombination initiation beyond the placement of double-stranded DNA breaks (DSBs) from germline replication timing to the dynamic reorganization of chromatin, and defined critical players of recombination initiation. This article focuses on recombination initiation in mammals utilizing the PRDM9 protein to orchestrate crucial stages of meiotic recombination initiation by interacting with the local DNA environment and several protein complexes. The Pioneer Complex with the SNF2-type chromatin remodeling enzyme HELLS, exposes PRDM9-bound DNA. At the same time, a Compass-Complex containing EWSR1, CXXC1, CDYL, EHMT2 and PRDM9 facilitates the association of putative hotspot sites in DNA loops with the chromosomal axis where DSB-promoting complexes are located, and DSBs are catalyzed by the SPO11/TOPOVIBL complex. Finally, homology search is facilitated at PRDM9-directed sites by ANKRD31. The Reader-Writer system consists of PRDM9 writing characteristic histone methylation signatures, which are read by ZCWPW1, promoting efficient homology engagement.
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Affiliation(s)
- Elena Damm
- Department Evolutionary Genetics, Research Group Meiotic Recombination and Genome Instability, Max Planck Institute for Evolutionary Biology, Plön, Germany
| | - Linda Odenthal-Hesse
- Department Evolutionary Genetics, Research Group Meiotic Recombination and Genome Instability, Max Planck Institute for Evolutionary Biology, Plön, Germany.
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13
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Li J, Bergmann L, Rafael de Almeida A, Webb KM, Gogol M, Voigt P, Liu Y, Liang H, Smolle M. H3K36 methylation and DNA-binding both promote Ioc4 recruitment and Isw1b remodeler function. Nucleic Acids Res 2022; 50:2549-2565. [PMID: 35188579 PMCID: PMC8934638 DOI: 10.1093/nar/gkac077] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2021] [Revised: 01/20/2022] [Accepted: 02/15/2022] [Indexed: 11/23/2022] Open
Abstract
The Isw1b chromatin-remodeling complex is specifically recruited to gene bodies to help retain pre-existing histones during transcription by RNA polymerase II. Recruitment is dependent on H3K36 methylation and the Isw1b subunit Ioc4, which contains an N-terminal PWWP domain. Here, we present the crystal structure of the Ioc4-PWWP domain, including a detailed functional characterization of the domain on its own as well as in the context of full-length Ioc4 and the Isw1b remodeler. The Ioc4-PWWP domain preferentially binds H3K36me3-containing nucleosomes. Its ability to bind DNA is required for nucleosome binding. It is also furthered by the unique insertion motif present in Ioc4-PWWP. The ability to bind H3K36me3 and DNA promotes the interaction of full-length Ioc4 with nucleosomes in vitro and they are necessary for its recruitment to gene bodies in vivo. Furthermore, a fully functional Ioc4-PWWP domain promotes efficient remodeling by Isw1b and the maintenance of ordered chromatin in vivo, thereby preventing the production of non-coding RNAs.
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Affiliation(s)
- Jian Li
- State Key Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Road, Chaoyang District, Beijing 100101, China
| | - Lena Bergmann
- Physiological Chemistry, Biomedical Center, Medical Faculty, Ludwig-Maximilian-University Munich, Grosshaderner Str. 9, 82152 Martinsried-Planegg, Germany
| | - Andreia Rafael de Almeida
- Physiological Chemistry, Biomedical Center, Medical Faculty, Ludwig-Maximilian-University Munich, Grosshaderner Str. 9, 82152 Martinsried-Planegg, Germany
| | - Kimberly M Webb
- Wellcome Centre for Cell Biology, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3BF, UK
| | - Madelaine M Gogol
- Stowers Institute for Medical Research, 1000 E 50th Street, Kansas City, MO 64110, USA
| | - Philipp Voigt
- Wellcome Centre for Cell Biology, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3BF, UK
- Epigenetics Programme, Babraham Institute, Cambridge CB22 3AT, UK
| | - Yingfang Liu
- State Key Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Road, Chaoyang District, Beijing 100101, China
- School of Medicine, Sun Yat-Sen University, Guangzhou 510275, China
| | - Huanhuan Liang
- State Key Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Road, Chaoyang District, Beijing 100101, China
- Pharmaceutical Sciences (Shenzhen), Sun Yat-sen University, Guangzhou 510275, China
| | - Michaela M Smolle
- Physiological Chemistry, Biomedical Center, Medical Faculty, Ludwig-Maximilian-University Munich, Grosshaderner Str. 9, 82152 Martinsried-Planegg, Germany
- BioPhysics Core Facility, Biomedical Center, Medical Faculty, Ludwig-Maximilian-University Munich, Grosshaderner Str. 9, 82152 Martinsried-Planegg, Germany
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14
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Guo C, Chen L, Cui Y, Tang M, Guo Y, Yi Y, Li Y, Liu L, Chen L. RNA Binding Protein OsTZF7 Traffics Between the Nucleus and Processing Bodies/Stress Granules and Positively Regulates Drought Stress in Rice. FRONTIERS IN PLANT SCIENCE 2022; 13:802337. [PMID: 35265093 PMCID: PMC8899535 DOI: 10.3389/fpls.2022.802337] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Accepted: 01/05/2022] [Indexed: 05/16/2023]
Abstract
Tandem CCCH zinc finger (TZF) proteins are the essential components of processing bodies (PBs) and stress granules (SGs), which play critical roles in growth development and stress response in both animals and plants through posttranscriptional regulation of target mRNA. In this study, we characterized the biological and molecular functions of a novel tandem zinc finger protein, OsTZF7. The expression of OsTZF7 was upregulated by abiotic stresses, including polyethylene glycol (PEG) 4000, NaCl, and abscisic acid (ABA) in rice. Accordingly, the overexpression of OsTZF7 increased drought tolerance and enhanced sensitivity to exogenous ABA in rice, whereas the knockdown of OsTZF7 resulted in the opposite phenotype. RNA-seq analysis revealed that genes related to "response to stress," "abscisic acid signaling," "methylated histone binding," and "cytoplasmic mRNA processing body" are regulated by OsTZF7. We demonstrated that OsTZF7 can traffic between the nucleus and PBs/SGs, and the leucine-rich nuclear export signal (NES) mediates the nuclear export of OsTZF7. Additionally, we revealed that OsTZF7 can bind adenine- and uridine-rich (AU-rich) element (ARE) or ARE-like motifs within the 3' untranslated region of downregulated mRNAs, and interact with PWWP family proteins in vitro. Together, these results indicate that OsTZF7 positively regulates drought response in rice via ABA signaling and may be involved in mRNA turnover.
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Affiliation(s)
- Chiming Guo
- Fujian Key Laboratory of Subtropical Plant Physiology and Biochemistry, Fujian Institute of Subtropical Botany, Xiamen, China
| | - Lingli Chen
- Xiamen Key Laboratory for Plant Genetics, School of Life Sciences, Xiamen University, Xiamen, China
| | - Yuchao Cui
- Xiamen Key Laboratory for Plant Genetics, School of Life Sciences, Xiamen University, Xiamen, China
| | - Ming Tang
- Key Laboratory of State Forestry Administration on Biodiversity Conservation in Karst Area of Southwestern, School of Life Sciences, Guizhou Normal University, Guiyang, China
- Key Laboratory of Plant Physiology and Developmental Regulation, School of Life Sciences, Guizhou Normal University, Guiyang, China
| | - Ying Guo
- Fujian Key Laboratory of Subtropical Plant Physiology and Biochemistry, Fujian Institute of Subtropical Botany, Xiamen, China
| | - Yin Yi
- Key Laboratory of State Forestry Administration on Biodiversity Conservation in Karst Area of Southwestern, School of Life Sciences, Guizhou Normal University, Guiyang, China
- Key Laboratory of Plant Physiology and Developmental Regulation, School of Life Sciences, Guizhou Normal University, Guiyang, China
| | - Yan Li
- Xiamen Key Laboratory for Plant Genetics, School of Life Sciences, Xiamen University, Xiamen, China
| | - Liqing Liu
- Fujian Key Laboratory of Subtropical Plant Physiology and Biochemistry, Fujian Institute of Subtropical Botany, Xiamen, China
| | - Liang Chen
- Xiamen Key Laboratory for Plant Genetics, School of Life Sciences, Xiamen University, Xiamen, China
- *Correspondence: Liang Chen,
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15
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Wedd L, Kucharski R, Maleszka R. DNA Methylation in Honey Bees and the Unresolved Questions in Insect Methylomics. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2022; 1389:159-176. [DOI: 10.1007/978-3-031-11454-0_7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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16
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Vaidergorn MM, da Silva Emery F, Ganesan A. From Hit Seeking to Magic Bullets: The Successful Union of Epigenetic and Fragment Based Drug Discovery (EPIDD + FBDD). J Med Chem 2021; 64:13980-14010. [PMID: 34591474 DOI: 10.1021/acs.jmedchem.1c00787] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
We review progress in the application of fragment-based drug discovery (FBDD) to epigenetic drug discovery (EPIDD) targeted at epigenetic writer and eraser enzymes as well as reader domains over the last 15 years. The greatest successes to date are in prospecting for bromodomain binding ligands. From a diverse array of fragment hits, multiple potent and selective compounds ensued, including the oncology clinical candidates mivebresib, ABBV-744, pelabresib, and PLX51107.
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Affiliation(s)
- Miguel M Vaidergorn
- School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo, Ribeirão Preto, São Paulo 14040-903, Brazil
| | - Flavio da Silva Emery
- School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo, Ribeirão Preto, São Paulo 14040-903, Brazil
| | - A Ganesan
- School of Pharmacy, University of East Anglia, Norwich NR4 7TJ, United Kingdom
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17
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Yang C, Wang K, Liang Q, Tian TT, Zhong Z. Role of NSD1 as potential therapeutic target in tumor. Pharmacol Res 2021; 173:105888. [PMID: 34536546 DOI: 10.1016/j.phrs.2021.105888] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/03/2021] [Revised: 09/10/2021] [Accepted: 09/12/2021] [Indexed: 12/29/2022]
Abstract
Nuclear receptor binding SET Domain Protein 1 (NSD1) is a bifunctional transcriptional regulatory protein that encodes histone methyltransferase. Mono- and di-methylation of H3K36 by NSD1 is mainly primarily involved in the regulation of gene expression, DNA repair, alternative splicing, and other important biological processes. Many types of cancers, including acute myelogenous leukemia (AML), liver cancer, lung cancer, endometrial carcinoma, colorectal cancer, and pancreatic cancer, are associated with NSD1 fusion, missense mutation, nonsense mutation, silent mutation, deletion, and insertion of frameshift, and deletion in a frame. Therefore, targeting NSD1 may be a potential strategy for tumor therapy. An in-depth study of the structure and biological activities of NSD1 sets the groundwork for improving tumor therapy and creating NSD1 inhibitors. This article emphasizes the role of NSD1 in tumorigenesis and the development of NSD1 targeted small-molecule inhibitors.
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Affiliation(s)
- Chao Yang
- National Engineering Research Center for Marine Aquaculture, Institute of Innovation & Application, Zhejiang Ocean University, Zhoushan, Zhejiang Province 316022, China
| | - Kai Wang
- Key Laboratory of Epigenetics and Oncology, The Research Center for Preclinical Medicine, Southwest Medical University, Luzhou, Sichuan Province 646000, China
| | - Qilian Liang
- Oncology Center, Affiliated Hospital of Guangdong Medical University, Zhanjiang, Guangdong Province 524001, China
| | - Tian-Tian Tian
- Center for Biological Science and Technology, Beijing Normal University, Zhuhai, Guangdong Province 519087, China.
| | - Zhangfeng Zhong
- Macau Centre for Research and Development in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Macao SAR 999078, China.
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18
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Yan L, Jin W, Zhao Q, Cui X, Shi T, Xu Y, Li F, Jin W, Zhang Z, Zhang Z, Tang Q, Pan D. PWWP2B Fine-Tunes Adipose Thermogenesis by Stabilizing HDACs in a NuRD Subcomplex. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2021; 8:e2102060. [PMID: 34180153 PMCID: PMC8373154 DOI: 10.1002/advs.202102060] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/18/2021] [Indexed: 05/05/2023]
Abstract
Histone deacetylases (HDACs) are widely involved in many biological processes, as well as in control of brown and beige adipose physiology, but the precise molecular mechanisms by which HDACs are assembled into transcriptional machinery to fine-tune thermogenic program remain ill-defined. PWWP domain containing 2b (PWWP2B), which is identified as a component of the nucleosome remodeling and deacetylation complex (NuRD), interacts and stabilizes HDAC1/2 at the thermogenic gene promoters to suppress their expression. Ablation of Pwwp2b promotes adipocyte thermogenesis and ameliorates diet-induced obesity in vivo. Intriguingly, Pwwp2b is not only a brown fat-enriched gene but also dramatically induced by cold and sympathetic stimulation, which may serve as a physiological brake to avoid over-activation of thermogenesis in brown and beige fat cells.
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Affiliation(s)
- Linyu Yan
- Key Laboratory of Metabolism and Molecular Medicine of the Ministry of Education Department of Biochemistry and Molecular Biology of School of Basic Medical SciencesFudan UniversityShanghai200 032China
| | - Weiwei Jin
- Key Laboratory of Metabolism and Molecular Medicine of the Ministry of Education Department of Biochemistry and Molecular Biology of School of Basic Medical SciencesFudan UniversityShanghai200 032China
| | - Qingwen Zhao
- Key Laboratory of Metabolism and Molecular Medicine of the Ministry of Education Department of Biochemistry and Molecular Biology of School of Basic Medical SciencesFudan UniversityShanghai200 032China
| | - Xuan Cui
- Key Laboratory of Metabolism and Molecular Medicine of the Ministry of Education Department of Biochemistry and Molecular Biology of School of Basic Medical SciencesFudan UniversityShanghai200 032China
| | - Ting Shi
- Key Laboratory of Metabolism and Molecular Medicine of the Ministry of Education Department of Biochemistry and Molecular Biology of School of Basic Medical SciencesFudan UniversityShanghai200 032China
| | - Yingjiang Xu
- Key Laboratory of Metabolism and Molecular Medicine of the Ministry of Education Department of Biochemistry and Molecular Biology of School of Basic Medical SciencesFudan UniversityShanghai200 032China
| | - Feiyan Li
- Key Laboratory of Metabolism and Molecular Medicine of the Ministry of Education Department of Biochemistry and Molecular Biology of School of Basic Medical SciencesFudan UniversityShanghai200 032China
| | - Wenfang Jin
- Key Laboratory of Metabolism and Molecular Medicine of the Ministry of Education Department of Biochemistry and Molecular Biology of School of Basic Medical SciencesFudan UniversityShanghai200 032China
| | - Zhe Zhang
- Key Laboratory of Metabolism and Molecular Medicine of the Ministry of Education Department of Biochemistry and Molecular Biology of School of Basic Medical SciencesFudan UniversityShanghai200 032China
| | - Zhao Zhang
- Key Laboratory of Metabolism and Molecular Medicine of the Ministry of Education Department of Biochemistry and Molecular Biology of School of Basic Medical SciencesFudan UniversityShanghai200 032China
| | - Qi‐Qun Tang
- Key Laboratory of Metabolism and Molecular Medicine of the Ministry of Education Department of Biochemistry and Molecular Biology of School of Basic Medical SciencesFudan UniversityShanghai200 032China
| | - Dongning Pan
- Key Laboratory of Metabolism and Molecular Medicine of the Ministry of Education Department of Biochemistry and Molecular Biology of School of Basic Medical SciencesFudan UniversityShanghai200 032China
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19
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Structures of chromatin modulators in complex with nucleosome. Curr Opin Chem Biol 2021; 63:105-114. [PMID: 33823458 DOI: 10.1016/j.cbpa.2021.02.018] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2020] [Revised: 02/11/2021] [Accepted: 02/25/2021] [Indexed: 12/17/2022]
Abstract
The chromatin structure is dynamically regulated by many different modulators that post-translationally modify histones, replace canonical histones with histone variants, and unwind nucleosomal DNA, thereby modulating the accessibility of nucleosomal DNA and facilitating downstream DNA-templated nuclear processes. To understand how these modulators change the chromatin structure, it is essential to determine the 3D structures of chromatin modulators in complex with nucleosome. Here, we review the very recent progress in structural studies of some selected chromatin modulators in complex with nucleosome, including those of histone demethylases LSD1/2, some pioneer transcription factors, and the PWWP domain-containing protein LEDGF.
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20
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Farhangdoost N, Horth C, Hu B, Bareke E, Chen X, Li Y, Coradin M, Garcia BA, Lu C, Majewski J. Chromatin dysregulation associated with NSD1 mutation in head and neck squamous cell carcinoma. Cell Rep 2021; 34:108769. [PMID: 33626351 PMCID: PMC8006058 DOI: 10.1016/j.celrep.2021.108769] [Citation(s) in RCA: 41] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2020] [Revised: 11/12/2020] [Accepted: 01/28/2021] [Indexed: 12/17/2022] Open
Abstract
Chromatin dysregulation has emerged as an important mechanism of oncogenesis. To develop targeted treatments, it is important to understand the transcriptomic consequences of mutations in chromatin modifier genes. Recently, mutations in the histone methyltransferase gene nuclear receptor binding SET domain protein 1 (NSD1) have been identified in a subset of common and deadly head and neck squamous cell carcinomas (HNSCCs). Here, we use genome-wide approaches and genome editing to dissect the downstream effects of loss of NSD1 in HNSCC. We demonstrate that NSD1 mutations are responsible for loss of intergenic H3K36me2 domains, followed by loss of DNA methylation and gain of H3K27me3 in the affected genomic regions. In addition, those regions are enriched in cis-regulatory elements, and subsequent loss of H3K27ac correlates with reduced expression of their target genes. Our analysis identifies genes and pathways affected by the loss of NSD1 and paves the way to further understanding the interplay among chromatin modifications in cancer. Farhangdoost et al. use genome editing and TCGA primary tumor data to provide a link between NSD1 loss, chromatin and regulatory landscape, gene expression, and molecular characteristics of this tumor subtype. Their study extends the understanding of tumorigenic mechanisms underlying head and neck cancers with mutations in NSD1.
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Affiliation(s)
- Nargess Farhangdoost
- Department of Human Genetics, McGill University, Montreal, QC H3A 1B1, Canada; McGill University Genome Centre, Montreal, QC H3A 0G1, Canada
| | - Cynthia Horth
- Department of Human Genetics, McGill University, Montreal, QC H3A 1B1, Canada; McGill University Genome Centre, Montreal, QC H3A 0G1, Canada
| | - Bo Hu
- Department of Human Genetics, McGill University, Montreal, QC H3A 1B1, Canada; McGill University Genome Centre, Montreal, QC H3A 0G1, Canada
| | - Eric Bareke
- Department of Human Genetics, McGill University, Montreal, QC H3A 1B1, Canada; McGill University Genome Centre, Montreal, QC H3A 0G1, Canada
| | - Xiao Chen
- Department of Genetics and Development, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Yinglu Li
- Department of Genetics and Development, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Mariel Coradin
- Biochemistry and Molecular Biophysics Graduate Group, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Benjamin A Garcia
- Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Chao Lu
- Department of Genetics and Development, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Jacek Majewski
- Department of Human Genetics, McGill University, Montreal, QC H3A 1B1, Canada; McGill University Genome Centre, Montreal, QC H3A 0G1, Canada.
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21
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Maas MN, Hintzen JCJ, Porzberg MRB, Mecinović J. Trimethyllysine: From Carnitine Biosynthesis to Epigenetics. Int J Mol Sci 2020; 21:E9451. [PMID: 33322546 PMCID: PMC7764450 DOI: 10.3390/ijms21249451] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2020] [Revised: 12/09/2020] [Accepted: 12/09/2020] [Indexed: 12/14/2022] Open
Abstract
Trimethyllysine is an important post-translationally modified amino acid with functions in the carnitine biosynthesis and regulation of key epigenetic processes. Protein lysine methyltransferases and demethylases dynamically control protein lysine methylation, with each state of methylation changing the biophysical properties of lysine and the subsequent effect on protein function, in particular histone proteins and their central role in epigenetics. Epigenetic reader domain proteins can distinguish between different lysine methylation states and initiate downstream cellular processes upon recognition. Dysregulation of protein methylation is linked to various diseases, including cancer, inflammation, and genetic disorders. In this review, we cover biomolecular studies on the role of trimethyllysine in carnitine biosynthesis, different enzymatic reactions involved in the synthesis and removal of trimethyllysine, trimethyllysine recognition by reader proteins, and the role of trimethyllysine on the nucleosome assembly.
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Affiliation(s)
| | | | | | - Jasmin Mecinović
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, 5230 Odense, Denmark; (M.N.M.); (J.C.J.H.); (M.R.B.P.)
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22
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Abstract
The characteristics of fetal membrane cells and their phenotypic adaptations to support pregnancy or promote parturition are defined by global patterns of gene expression controlled by chromatin structure. Heritable epigenetic chromatin modifications that include DNA methylation and covalent histone modifications establish chromatin regions permissive or exclusive of regulatory interactions defining the cell-specific scope and potential of gene activity. Non-coding RNAs acting at the transcriptional and post-transcriptional levels complement the system by robustly stabilizing gene expression patterns and contributing to ordered phenotype transitions. Here we review currently available information about epigenetic gene regulation in the amnion and the chorion laeve. In addition, we provide an overview of epigenetic phenomena in the decidua, which is the maternal tissue fused to the chorion membrane forming the anatomical and functional unit called choriodecidua. The relationship of gene expression with DNA (CpG) methylation, histone acetylation and methylation, micro RNAs, long non-coding RNAs and chromatin accessibility is discussed in the context of normal pregnancy, parturition and pregnancy complications. Data generated using clinical samples and cell culture models strongly suggests that epigenetic events are associated with the phenotypic transitions of fetal membrane cells during the establishment, maintenance and termination of pregnancy potentially driving and consolidating the changes as pregnancy progresses. Disease conditions and environmental factors may produce epigenetic footprints that indicate exposures and mediate adverse pregnancy outcomes. Although knowledge is expanding rapidly, fetal membrane epigenetics is still in an early stage of development necessitating further research to realize its remarkable basic and translational potential.
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Affiliation(s)
- Tamas Zakar
- Department of Maternity & Gynaecology, John Hunter Hospital, New Lambton Heights, NSW, Australia
- School of Medicine and Public Health, Faculty of Health and Medicine, The University of Newcastle, Callaghan, NSW, Australia
- Priority Research Centre for Reproductive Science, The University of Newcastle, Callaghan, NSW, Australia
- Hunter Medical Research Institute, New Lambton Heights, NSW, Australia
| | - Jonathan W. Paul
- School of Medicine and Public Health, Faculty of Health and Medicine, The University of Newcastle, Callaghan, NSW, Australia
- Priority Research Centre for Reproductive Science, The University of Newcastle, Callaghan, NSW, Australia
- Hunter Medical Research Institute, New Lambton Heights, NSW, Australia
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23
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Vincenzi M, Mercurio FA, Leone M. Protein Interaction Domains and Post-Translational Modifications: Structural Features and Drug Discovery Applications. Curr Med Chem 2020; 27:6306-6355. [DOI: 10.2174/0929867326666190620101637] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2019] [Revised: 05/16/2019] [Accepted: 05/22/2019] [Indexed: 12/15/2022]
Abstract
Background:
Many pathways regarding healthy cells and/or linked to diseases onset and progression depend on large assemblies including multi-protein complexes. Protein-protein interactions may occur through a vast array of modules known as protein interaction domains (PIDs).
Objective:
This review concerns with PIDs recognizing post-translationally modified peptide sequences and intends to provide the scientific community with state of art knowledge on their 3D structures, binding topologies and potential applications in the drug discovery field.
Method:
Several databases, such as the Pfam (Protein family), the SMART (Simple Modular Architecture Research Tool) and the PDB (Protein Data Bank), were searched to look for different domain families and gain structural information on protein complexes in which particular PIDs are involved. Recent literature on PIDs and related drug discovery campaigns was retrieved through Pubmed and analyzed.
Results and Conclusion:
PIDs are rather versatile as concerning their binding preferences. Many of them recognize specifically only determined amino acid stretches with post-translational modifications, a few others are able to interact with several post-translationally modified sequences or with unmodified ones. Many PIDs can be linked to different diseases including cancer. The tremendous amount of available structural data led to the structure-based design of several molecules targeting protein-protein interactions mediated by PIDs, including peptides, peptidomimetics and small compounds. More studies are needed to fully role out, among different families, PIDs that can be considered reliable therapeutic targets, however, attacking PIDs rather than catalytic domains of a particular protein may represent a route to obtain selective inhibitors.
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Affiliation(s)
- Marian Vincenzi
- Institute of Biostructures and Bioimaging, National Research Council (CNR), Via Mezzocannone 16, 80134 Naples, Italy
| | - Flavia Anna Mercurio
- Institute of Biostructures and Bioimaging, National Research Council (CNR), Via Mezzocannone 16, 80134 Naples, Italy
| | - Marilisa Leone
- Institute of Biostructures and Bioimaging, National Research Council (CNR), Via Mezzocannone 16, 80134 Naples, Italy
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24
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Bohnsack JP, Pandey SC. Histone modifications, DNA methylation, and the epigenetic code of alcohol use disorder. INTERNATIONAL REVIEW OF NEUROBIOLOGY 2020; 156:1-62. [PMID: 33461661 DOI: 10.1016/bs.irn.2020.08.005] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Alcohol use disorder (AUD) is a leading cause of morbidity and mortality. Despite AUD's substantial contributions to lost economic productivity and quality of life, there are only a limited number of approved drugs for treatment of AUD in the United States. This chapter will update progress made on the epigenetic basis of AUD, with particular focus on histone post-translational modifications and DNA methylation and how these two epigenetic mechanisms interact to contribute to neuroadaptive processes leading to initiation, maintenance and progression of AUD pathophysiology. We will also evaluate epigenetic therapeutic strategies that have arisen from preclinical models of AUD and epigenetic biomarkers that have been discovered in human populations with AUD.
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Affiliation(s)
- John Peyton Bohnsack
- Center for Alcohol Research in Epigenetics, Department of Psychiatry, College of Medicine, University of Illinois at Chicago, Chicago, IL, United States
| | - Subhash C Pandey
- Center for Alcohol Research in Epigenetics, Department of Psychiatry, College of Medicine, University of Illinois at Chicago, Chicago, IL, United States; Jesse Brown VA Medical Center, Chicago, IL, United States; Department of Anatomy and Cell Biology, University of Illinois at Chicago, Chicago, IL, United States.
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25
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PCAF-Mediated Histone Acetylation Promotes Replication Fork Degradation by MRE11 and EXO1 in BRCA-Deficient Cells. Mol Cell 2020; 80:327-344.e8. [PMID: 32966758 DOI: 10.1016/j.molcel.2020.08.018] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2020] [Revised: 07/22/2020] [Accepted: 08/26/2020] [Indexed: 12/12/2022]
Abstract
Stabilization of stalled replication forks is a prominent mechanism of PARP (Poly(ADP-ribose) Polymerase) inhibitor (PARPi) resistance in BRCA-deficient tumors. Epigenetic mechanisms of replication fork stability are emerging but remain poorly understood. Here, we report the histone acetyltransferase PCAF (p300/CBP-associated) as a fork-associated protein that promotes fork degradation in BRCA-deficient cells by acetylating H4K8 at stalled replication forks, which recruits MRE11 and EXO1. A H4K8ac binding domain within MRE11/EXO1 is required for their recruitment to stalled forks. Low PCAF levels, which we identify in a subset of BRCA2-deficient tumors, stabilize stalled forks, resulting in PARPi resistance in BRCA-deficient cells. Furthermore, PCAF activity is tightly regulated by ATR (ataxia telangiectasia and Rad3-related), which phosphorylates PCAF on serine 264 (S264) to limit its association and activity at stalled forks. Our results reveal PCAF and histone acetylation as critical regulators of fork stability and PARPi responses in BRCA-deficient cells, which provides key insights into targeting BRCA-deficient tumors and identifying epigenetic modulators of chemotherapeutic responses.
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Wells D, Bitoun E, Moralli D, Zhang G, Hinch A, Jankowska J, Donnelly P, Green C, Myers SR. ZCWPW1 is recruited to recombination hotspots by PRDM9 and is essential for meiotic double strand break repair. eLife 2020; 9:53392. [PMID: 32744506 PMCID: PMC7494361 DOI: 10.7554/elife.53392] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2019] [Accepted: 07/31/2020] [Indexed: 12/13/2022] Open
Abstract
During meiosis, homologous chromosomes pair and recombine, enabling balanced segregation and generating genetic diversity. In many vertebrates, double-strand breaks (DSBs) initiate recombination within hotspots where PRDM9 binds, and deposits H3K4me3 and H3K36me3. However, no protein(s) recognising this unique combination of histone marks have been identified. We identified Zcwpw1, containing H3K4me3 and H3K36me3 recognition domains, as having highly correlated expression with Prdm9. Here, we show that ZCWPW1 has co-evolved with PRDM9 and, in human cells, is strongly and specifically recruited to PRDM9 binding sites, with higher affinity than sites possessing H3K4me3 alone. Surprisingly, ZCWPW1 also recognises CpG dinucleotides. Male Zcwpw1 knockout mice show completely normal DSB positioning, but persistent DMC1 foci, severe DSB repair and synapsis defects, and downstream sterility. Our findings suggest ZCWPW1 recognition of PRDM9-bound sites at DSB hotspots is critical for synapsis, and hence fertility. Sexual reproduction – that is, the combination of sex cells from two different individuals to produce an embryo – is one of the many mechanisms that have evolved to maintain genetic diversity. Most human cells contain 23 pairs of chromosomes, with each chromosome in a pair carrying either a paternal or maternal copy of the same gene. To form an embryo with the right number of chromosomes, each sex cell (the egg or sperm cell) must only contain one chromosome from each pair. Sex cells are produced from parent cells containing two sets of paternal and maternal chromosomes: these cells then divide twice to form four sex cells which contain only one chromosome from each pair. Before the parent cell divides, a process known as ‘recombination’ takes place, which allows chromosomes in a pair to exchange bits of genetic information. This reshuffling ensures that each chromosome in a sex cell is unique. A protein called PRDM9 helps control which sections of genetic information are recombined by modifying proteins attached to the chromosomes, marking them as locations for exchange. The DNA at each of these sites is then broken and repaired using the genetic sequence of the chromosome it is paired with as a template, thus causing the two chromosomes to swap genes. In 2019, a group of researchers found a set of genes in the testis of mice that are expressed at the same time as the gene for PRDM9. This suggested that another protein called ZCWPW1 is likely involved in recombination, but the precise role of this protein was unclear. To answer this question, Wells, Bitoun et al. – including many of the researchers involved in the 2019 study – examined human cells grown in the laboratory to determine where ZCWPW1 binds to in the chromosome. This revealed that ZCWPW1 can be found at the same sites as PRDM9, which is responsible for bringing it there. Furthermore, cells from male mice lacking the gene for ZCWPW1 cannot complete the exchange of genetic information between chromosomes, meaning that the mice are infertile. As such, ZCWPW1 seems to connect location selection by PRDM9 to the DNA repair mechanisms needed for gene exchange between chromosomes. Infertility is a significant issue for humans affecting as many as one in every six couples. Fertility is complex and many of the biological mechanisms involved are not fully understood. This work suggests that both PRDM9 and ZCWPW1 are key to the production of sex cells and may be worth investigating as factors that affect fertility in humans.
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Affiliation(s)
- Daniel Wells
- The Wellcome Centre for Human Genetics, Roosevelt Drive, University of Oxford, Oxford, United Kingdom.,Department of Statistics, University of Oxford, Oxford, United Kingdom
| | - Emmanuelle Bitoun
- The Wellcome Centre for Human Genetics, Roosevelt Drive, University of Oxford, Oxford, United Kingdom.,Department of Statistics, University of Oxford, Oxford, United Kingdom
| | - Daniela Moralli
- The Wellcome Centre for Human Genetics, Roosevelt Drive, University of Oxford, Oxford, United Kingdom
| | - Gang Zhang
- The Wellcome Centre for Human Genetics, Roosevelt Drive, University of Oxford, Oxford, United Kingdom
| | - Anjali Hinch
- The Wellcome Centre for Human Genetics, Roosevelt Drive, University of Oxford, Oxford, United Kingdom
| | - Julia Jankowska
- The Wellcome Centre for Human Genetics, Roosevelt Drive, University of Oxford, Oxford, United Kingdom
| | - Peter Donnelly
- The Wellcome Centre for Human Genetics, Roosevelt Drive, University of Oxford, Oxford, United Kingdom.,Department of Statistics, University of Oxford, Oxford, United Kingdom
| | - Catherine Green
- The Wellcome Centre for Human Genetics, Roosevelt Drive, University of Oxford, Oxford, United Kingdom
| | - Simon R Myers
- The Wellcome Centre for Human Genetics, Roosevelt Drive, University of Oxford, Oxford, United Kingdom.,Department of Statistics, University of Oxford, Oxford, United Kingdom
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Linhares BM, Grembecka J, Cierpicki T. Targeting epigenetic protein-protein interactions with small-molecule inhibitors. Future Med Chem 2020; 12:1305-1326. [PMID: 32551894 PMCID: PMC7421387 DOI: 10.4155/fmc-2020-0082] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2020] [Accepted: 05/01/2020] [Indexed: 02/07/2023] Open
Abstract
Epigenetic protein-protein interactions (PPIs) play essential roles in regulating gene expression, and their dysregulations have been implicated in many diseases. These PPIs are comprised of reader domains recognizing post-translational modifications on histone proteins, and of scaffolding proteins that maintain integrities of epigenetic complexes. Targeting PPIs have become focuses for development of small-molecule inhibitors and anticancer therapeutics. Here we summarize efforts to develop small-molecule inhibitors targeting common epigenetic PPI domains. Potent small molecules have been reported for many domains, yet small domains that recognize methylated lysine side chains on histones are challenging in inhibitor development. We posit that the development of potent inhibitors for difficult-to-prosecute epigenetic PPIs may be achieved by interdisciplinary approaches and extensive explorations of chemical space.
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Affiliation(s)
- Brian M Linhares
- Biophysics Program, University of Michigan, Ann Arbor, MI 48109, USA
- Department of Molecular, Cellular & Developmental Biology, Yale University, New Haven, CT 06511, USA
| | - Jolanta Grembecka
- Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Tomasz Cierpicki
- Biophysics Program, University of Michigan, Ann Arbor, MI 48109, USA
- Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA
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28
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Structure of H3K36-methylated nucleosome-PWWP complex reveals multivalent cross-gyre binding. Nat Struct Mol Biol 2019; 27:8-13. [PMID: 31819277 PMCID: PMC6955156 DOI: 10.1038/s41594-019-0345-4] [Citation(s) in RCA: 50] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2019] [Accepted: 10/30/2019] [Indexed: 01/05/2023]
Abstract
Recognition of histone-modified nucleosomes by specific reader domains underlies the regulation of chromatin-associated processes. Whereas structural studies revealed how reader domains bind modified histone peptides, it is unclear how reader domains interact with modified nucleosomes. Here we report the cryo-electron microscopy (cryo-EM) structure of the PWWP reader domain of human transcriptional coactivator LEDGF in complex with a H3K36-methylated nucleosome at 3.2 Å resolution. The structure reveals multivalent binding of the reader domain to the methylated histone tail and to both gyres of nucleosomal DNA, explaining the known cooperative interactions. The observed cross-gyre binding may contribute to nucleosome integrity during transcription. The structure also explains how human PWWP domain-containing proteins are recruited to H3K36-methylated regions of the genome for transcription, histone acetylation and methylation, and for DNA methylation and repair.
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29
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Albig C, Wang C, Dann GP, Wojcik F, Schauer T, Krause S, Maenner S, Cai W, Li Y, Girton J, Muir TW, Johansen J, Johansen KM, Becker PB, Regnard C. JASPer controls interphase histone H3S10 phosphorylation by chromosomal kinase JIL-1 in Drosophila. Nat Commun 2019; 10:5343. [PMID: 31767855 PMCID: PMC6877644 DOI: 10.1038/s41467-019-13174-6] [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: 04/30/2019] [Accepted: 10/22/2019] [Indexed: 01/02/2023] Open
Abstract
In flies, the chromosomal kinase JIL-1 is responsible for most interphase histone H3S10 phosphorylation and has been proposed to protect active chromatin from acquiring heterochromatic marks, such as dimethylated histone H3K9 (H3K9me2) and HP1. Here, we show that JIL-1's targeting to chromatin depends on a PWWP domain-containing protein JASPer (JIL-1 Anchoring and Stabilizing Protein). JASPer-JIL-1 (JJ)-complex is the major form of kinase in vivo and is targeted to active genes and telomeric transposons via binding of the PWWP domain of JASPer to H3K36me3 nucleosomes, to modulate transcriptional output. JIL-1 and JJ-complex depletion in cycling cells lead to small changes in H3K9me2 distribution at active genes and telomeric transposons. Finally, we identify interactors of the endogenous JJ-complex and propose that JIL-1 not only prevents heterochromatin formation but also coordinates chromatin-based regulation in the transcribed part of the genome.
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Affiliation(s)
- Christian Albig
- Molecular Biology Division, Biomedical Center, Faculty of Medicine and Center for Integrated Protein Science Munich (CIPSM), LMU Munich, 82152, Martinsried, Germany
- Graduate School for Quantitative Biosciences (QBM), LMU Munich, 81377, Munich, Germany
| | - Chao Wang
- Roy J. Carver Department of Biochemistry, Biophysics, and Molecular Biology, Iowa State University, Ames, IA, 50011, USA
| | - Geoffrey P Dann
- Department of Chemistry, Frick Laboratory, Princeton University, Princeton, NJ, 08544, USA
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Felix Wojcik
- Department of Chemistry, Frick Laboratory, Princeton University, Princeton, NJ, 08544, USA
| | - Tamás Schauer
- Bioinformatics Unit, Biomedical Center, Faculty of Medicine, LMU Munich, 82152, Martinsried, Germany
| | - Silke Krause
- Molecular Biology Division, Biomedical Center, Faculty of Medicine and Center for Integrated Protein Science Munich (CIPSM), LMU Munich, 82152, Martinsried, Germany
| | - Sylvain Maenner
- Molecular Biology Division, Biomedical Center, Faculty of Medicine and Center for Integrated Protein Science Munich (CIPSM), LMU Munich, 82152, Martinsried, Germany
- UMR7365 CNRS-UL, IMoPA, University of Lorraine, 54505, Vandoeuvre-lès-Nancy, France
| | - Weili Cai
- Roy J. Carver Department of Biochemistry, Biophysics, and Molecular Biology, Iowa State University, Ames, IA, 50011, USA
| | - Yeran Li
- Roy J. Carver Department of Biochemistry, Biophysics, and Molecular Biology, Iowa State University, Ames, IA, 50011, USA
| | - Jack Girton
- Roy J. Carver Department of Biochemistry, Biophysics, and Molecular Biology, Iowa State University, Ames, IA, 50011, USA
| | - Tom W Muir
- Department of Chemistry, Frick Laboratory, Princeton University, Princeton, NJ, 08544, USA
| | - Jørgen Johansen
- Roy J. Carver Department of Biochemistry, Biophysics, and Molecular Biology, Iowa State University, Ames, IA, 50011, USA
| | - Kristen M Johansen
- Roy J. Carver Department of Biochemistry, Biophysics, and Molecular Biology, Iowa State University, Ames, IA, 50011, USA
| | - Peter B Becker
- Molecular Biology Division, Biomedical Center, Faculty of Medicine and Center for Integrated Protein Science Munich (CIPSM), LMU Munich, 82152, Martinsried, Germany.
| | - Catherine Regnard
- Molecular Biology Division, Biomedical Center, Faculty of Medicine and Center for Integrated Protein Science Munich (CIPSM), LMU Munich, 82152, Martinsried, Germany.
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30
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Jung M, Wells D, Rusch J, Ahmad S, Marchini J, Myers SR, Conrad DF. Unified single-cell analysis of testis gene regulation and pathology in five mouse strains. eLife 2019; 8:e43966. [PMID: 31237565 PMCID: PMC6615865 DOI: 10.7554/elife.43966] [Citation(s) in RCA: 82] [Impact Index Per Article: 16.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2018] [Accepted: 06/17/2019] [Indexed: 12/13/2022] Open
Abstract
To fully exploit the potential of single-cell functional genomics in the study of development and disease, robust methods are needed to simplify the analysis of data across samples, time-points and individuals. Here we introduce a model-based factor analysis method, SDA, to analyze a novel 57,600 cell dataset from the testes of wild-type mice and mice with gonadal defects due to disruption of the genes Mlh3, Hormad1, Cul4a or Cnp. By jointly analyzing mutant and wild-type cells we decomposed our data into 46 components that identify novel meiotic gene-regulatory programs, mutant-specific pathological processes, and technical effects, and provide a framework for imputation. We identify, de novo, DNA sequence motifs associated with individual components that define temporally varying modes of gene expression control. Analysis of SDA components also led us to identify a rare population of macrophages within the seminiferous tubules of Mlh3-/- and Hormad1-/- mice, an area typically associated with immune privilege.
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Affiliation(s)
- Min Jung
- Department of GeneticsWashington University School of MedicineSt. LouisUnited States
| | - Daniel Wells
- The Wellcome Centre for Human GeneticsUniversity of OxfordOxfordUnited Kingdom
- Department of StatisticsUniversity of OxfordOxfordUnited Kingdom
| | - Jannette Rusch
- Department of GeneticsWashington University School of MedicineSt. LouisUnited States
| | - Suhaira Ahmad
- Department of GeneticsWashington University School of MedicineSt. LouisUnited States
| | - Jonathan Marchini
- The Wellcome Centre for Human GeneticsUniversity of OxfordOxfordUnited Kingdom
- Department of StatisticsUniversity of OxfordOxfordUnited Kingdom
| | - Simon R Myers
- The Wellcome Centre for Human GeneticsUniversity of OxfordOxfordUnited Kingdom
- Department of StatisticsUniversity of OxfordOxfordUnited Kingdom
| | - Donald F Conrad
- Department of GeneticsWashington University School of MedicineSt. LouisUnited States
- Division of Genetics, Oregon National Primate Research CenterOregon Health & Science UniversityPortlandUnited States
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31
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Tian W, Yan P, Xu N, Chakravorty A, Liefke R, Xi Q, Wang Z. The HRP3 PWWP domain recognizes the minor groove of double-stranded DNA and recruits HRP3 to chromatin. Nucleic Acids Res 2019; 47:5436-5448. [PMID: 31162607 PMCID: PMC6547440 DOI: 10.1093/nar/gkz294] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2018] [Revised: 04/09/2019] [Accepted: 04/11/2019] [Indexed: 12/12/2022] Open
Abstract
HDGF-related protein 3 (HRP3, also known as HDGFL3) belongs to the family of HDGF-related proteins (HRPs) and plays an essential role in hepatocellular carcinoma pathogenesis. All HRPs have a PWWP domain at the N-terminus that binds both histone and DNA substrates. Despite previous advances in PWWP domains, the molecular basis by which HRP3 interacts with chromatin is unclear. In this study, we solved the crystal structures of the HRP3 PWWP domain in complex with various double-stranded DNAs with/without bound histone peptides. We found that HRP3 PWWP bound to the phosphate backbone of the DNA minor groove and showed a preference for DNA molecules bearing a narrow minor groove width. In addition, HRP3 PWWP preferentially bound to histone peptides bearing the H3K36me3/2 modification. HRP3 PWWP uses two adjacent surfaces to bind both DNA and histone substrates simultaneously, enabling us to generate a model illustrating the recruitment of PWWP to H3K36me3-containing nucleosomes. Cell-based analysis indicated that both DNA and histone binding by the HRP3 PWWP domain is important for HRP3 recruitment to chromatin in vivo. Our work establishes that HRP3 PWWP is a new family of minor groove-specific DNA-binding proteins, which improves our understanding of HRP3 and other PWWP domain-containing proteins.
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Affiliation(s)
- Wei Tian
- Key Laboratory of Cell Proliferation and Regulation Biology of Ministry of Education, College of Life Sciences, Beijing Normal University, 19 Xinjiekouwai Avenue, Beijing 100875, China
| | - Peiqiang Yan
- MOE Key Laboratory of Protein Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Ning Xu
- Beijing Advanced Innovation Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Arghya Chakravorty
- Department of Physics and Astronomy, Clemson University, Clemson, SC 29634, USA
| | - Robert Liefke
- Institute of Molecular Biology and Tumor Research (IMT), Philipps University of Marburg, Marburg 35043, Germany
- Department of Hematology, Oncology and Immunology, University Hospital Giessen and Marburg, 35043 Marburg, Germany
| | - Qiaoran Xi
- MOE Key Laboratory of Protein Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Zhanxin Wang
- Key Laboratory of Cell Proliferation and Regulation Biology of Ministry of Education, College of Life Sciences, Beijing Normal University, 19 Xinjiekouwai Avenue, Beijing 100875, China
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32
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Link S, Spitzer RMM, Sana M, Torrado M, Völker-Albert MC, Keilhauer EC, Burgold T, Pünzeler S, Low JKK, Lindström I, Nist A, Regnard C, Stiewe T, Hendrich B, Imhof A, Mann M, Mackay JP, Bartkuhn M, Hake SB. PWWP2A binds distinct chromatin moieties and interacts with an MTA1-specific core NuRD complex. Nat Commun 2018; 9:4300. [PMID: 30327463 PMCID: PMC6191444 DOI: 10.1038/s41467-018-06665-5] [Citation(s) in RCA: 34] [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: 02/09/2018] [Accepted: 09/17/2018] [Indexed: 12/31/2022] Open
Abstract
Chromatin structure and function is regulated by reader proteins recognizing histone modifications and/or histone variants. We recently identified that PWWP2A tightly binds to H2A.Z-containing nucleosomes and is involved in mitotic progression and cranial-facial development. Here, using in vitro assays, we show that distinct domains of PWWP2A mediate binding to free linker DNA as well as H3K36me3 nucleosomes. In vivo, PWWP2A strongly recognizes H2A.Z-containing regulatory regions and weakly binds H3K36me3-containing gene bodies. Further, PWWP2A binds to an MTA1-specific subcomplex of the NuRD complex (M1HR), which consists solely of MTA1, HDAC1, and RBBP4/7, and excludes CHD, GATAD2 and MBD proteins. Depletion of PWWP2A leads to an increase of acetylation levels on H3K27 as well as H2A.Z, presumably by impaired chromatin recruitment of M1HR. Thus, this study identifies PWWP2A as a complex chromatin-binding protein that serves to direct the deacetylase complex M1HR to H2A.Z-containing chromatin, thereby promoting changes in histone acetylation levels.
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Affiliation(s)
- Stephanie Link
- Department of Molecular Biology, BioMedical Center (BMC), Ludwig-Maximilians-University Munich, 82152, Planegg-Martinsried, Germany
- Institute for Genetics, Justus-Liebig University Giessen, 35392, Giessen, Germany
| | - Ramona M M Spitzer
- Department of Molecular Biology, BioMedical Center (BMC), Ludwig-Maximilians-University Munich, 82152, Planegg-Martinsried, Germany
- Institute for Genetics, Justus-Liebig University Giessen, 35392, Giessen, Germany
| | - Maryam Sana
- School of Life and Environmental Sciences, University of Sydney, New South Wales, 2006, Australia
| | - Mario Torrado
- School of Life and Environmental Sciences, University of Sydney, New South Wales, 2006, Australia
| | - Moritz C Völker-Albert
- Department of Molecular Biology, BioMedical Center (BMC), Ludwig-Maximilians-University Munich, 82152, Planegg-Martinsried, Germany
| | - Eva C Keilhauer
- Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, 82152, Martinsried, Germany
- Coriolis Pharma, Fraunhoferstr. 18B, 82152, Planegg, Germany
| | - Thomas Burgold
- Wellcome Trust - MRC Stem Cell Institute and Department of Biochemistry, University of Cambridge, Cambridge, CB2 1QR, UK
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - Sebastian Pünzeler
- Department of Molecular Biology, BioMedical Center (BMC), Ludwig-Maximilians-University Munich, 82152, Planegg-Martinsried, Germany
- Coparion GmbH & Co. KG, Charles-de-Gaulle-Platz 1d, 50679, Cologne, Germany
| | - Jason K K Low
- School of Life and Environmental Sciences, University of Sydney, New South Wales, 2006, Australia
| | - Ida Lindström
- School of Life and Environmental Sciences, University of Sydney, New South Wales, 2006, Australia
| | - Andrea Nist
- Genomics Core Facility, Philipps-University Marburg, 35043, Marburg, Germany
| | - Catherine Regnard
- Department of Molecular Biology, BioMedical Center (BMC), Ludwig-Maximilians-University Munich, 82152, Planegg-Martinsried, Germany
| | - Thorsten Stiewe
- Genomics Core Facility, Philipps-University Marburg, 35043, Marburg, Germany
- Institute for Molecular Oncology, Philipps-University Marburg, 35043, Marburg, Germany
| | - Brian Hendrich
- Wellcome Trust - MRC Stem Cell Institute and Department of Biochemistry, University of Cambridge, Cambridge, CB2 1QR, UK
| | - Axel Imhof
- Department of Molecular Biology, BioMedical Center (BMC), Ludwig-Maximilians-University Munich, 82152, Planegg-Martinsried, Germany
- Center for Integrated Protein Science Munich (CIPSM), 81377, Munich, Germany
| | - Matthias Mann
- Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, 82152, Martinsried, Germany
- Center for Integrated Protein Science Munich (CIPSM), 81377, Munich, Germany
| | - Joel P Mackay
- School of Life and Environmental Sciences, University of Sydney, New South Wales, 2006, Australia
| | - Marek Bartkuhn
- Institute for Genetics, Justus-Liebig University Giessen, 35392, Giessen, Germany.
| | - Sandra B Hake
- Institute for Genetics, Justus-Liebig University Giessen, 35392, Giessen, Germany.
- Center for Integrated Protein Science Munich (CIPSM), 81377, Munich, Germany.
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Rona GB, Almeida NP, Santos GC, Fidalgo TKS, Almeida FCL, Eleutherio ECA, Pinheiro AS. 1
H NMR metabolomics reveals increased glutaminolysis upon overexpression of NSD3s or Pdp3 in
Saccharomyces cerevisiae. J Cell Biochem 2018; 120:5377-5385. [DOI: 10.1002/jcb.27816] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2018] [Accepted: 09/12/2018] [Indexed: 12/16/2022]
Affiliation(s)
- Germana B Rona
- Department of Biochemistry Institute of Chemistry, Federal University of Rio de Janeiro Rio de Janeiro Brazil
| | - Natalia P Almeida
- Department of Biochemistry Institute of Chemistry, Federal University of Rio de Janeiro Rio de Janeiro Brazil
| | - Gilson C Santos
- National Center for Nuclear Magnetic Resonance Jiri Jonas (CNRMN), Structural Biology Program, Medical Biochemistry Institute and Center for Structural Biology and Bioimaging I (CENABIO I), Federal University of Rio de Janeiro Rio de Janeiro Brazil
| | - Tatiana KS Fidalgo
- Department of Preventive and Community Dentistry, School of Dentistry, State University of Rio de Janeiro Rio de Janeiro Brazil
| | - Fabio CL Almeida
- National Center for Nuclear Magnetic Resonance Jiri Jonas (CNRMN), Structural Biology Program, Medical Biochemistry Institute and Center for Structural Biology and Bioimaging I (CENABIO I), Federal University of Rio de Janeiro Rio de Janeiro Brazil
| | - Elis CA Eleutherio
- Department of Biochemistry Institute of Chemistry, Federal University of Rio de Janeiro Rio de Janeiro Brazil
| | - Anderson S Pinheiro
- Department of Biochemistry Institute of Chemistry, Federal University of Rio de Janeiro Rio de Janeiro Brazil
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34
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Min X, Wen J, Zhao L, Wang K, Li Q, Huang G, Liu J, Zhao X. Role of hepatoma-derived growth factor in promoting de novo lipogenesis and tumorigenesis in hepatocellular carcinoma. Mol Oncol 2018; 12:1480-1497. [PMID: 30004626 PMCID: PMC6120245 DOI: 10.1002/1878-0261.12357] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2018] [Revised: 06/11/2018] [Accepted: 06/26/2018] [Indexed: 01/05/2023] Open
Abstract
Although identified as a growth factor, the mechanism by which hepatoma‐derived growth factor (HDGF) promotes cancer development remains unclear. We found that nuclear but not cytoplasmic HDGF is closely associated with prognosis of hepatocellular carcinoma (HCC). RNA‐sequencing analysis further demonstrated that the nuclear role of HDGF involved regulation of transcription of lipid metabolism genes. HDGF‐induced expression of lipogenic genes was mainly associated with activation of sterol regulatory element binding protein (SREBP) transcription factor. Coexpression of SREBP‐1 and nuclear HDGF predicts poor prognosis for HCC. In addition, by changing the first amino acid of the PWWP domain from proline to alanine, the type of PWWP domain changed from P‐ to A‐type, resulting in inability to induce SREBP‐1‐mediated gene transcription. The type of PWWP domain affects the recruitment of the C‐terminal binding protein‐1 transcriptional repressor on the promoter of the lipogenic gene. Our data indicate that HDGF acts as a coactivator of SREBP1‐mediated transcription of lipogenic genes. The PWWP domain is crucial for HDGF to promote lipogenesis. Moreover, transcriptional regulation of nuclear HDGF plays important roles in the development of HCC.
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Affiliation(s)
- Xuejie Min
- Department of Nuclear Medicine, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, China
| | - Jun Wen
- Department of Nuclear Medicine, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, China
| | - Li Zhao
- Department of Nuclear Medicine, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, China
| | - Kaiying Wang
- Department of Nuclear Medicine, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, China
| | - Qingli Li
- Department of Nuclear Medicine, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, China
| | - Gang Huang
- Shanghai University of Medicine & Health Sciences, China
| | - Jianjun Liu
- Department of Nuclear Medicine, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, China
| | - Xiaoping Zhao
- Department of Nuclear Medicine, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, China
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35
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Lu W, Zhang R, Jiang H, Zhang H, Luo C. Computer-Aided Drug Design in Epigenetics. Front Chem 2018; 6:57. [PMID: 29594101 PMCID: PMC5857607 DOI: 10.3389/fchem.2018.00057] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2018] [Accepted: 02/23/2018] [Indexed: 12/31/2022] Open
Abstract
Epigenetic dysfunction has been widely implicated in several diseases especially cancers thus highlights the therapeutic potential for chemical interventions in this field. With rapid development of computational methodologies and high-performance computational resources, computer-aided drug design has emerged as a promising strategy to speed up epigenetic drug discovery. Herein, we make a brief overview of major computational methods reported in the literature including druggability prediction, virtual screening, homology modeling, scaffold hopping, pharmacophore modeling, molecular dynamics simulations, quantum chemistry calculation, and 3D quantitative structure activity relationship that have been successfully applied in the design and discovery of epi-drugs and epi-probes. Finally, we discuss about major limitations of current virtual drug design strategies in epigenetics drug discovery and future directions in this field.
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Affiliation(s)
- Wenchao Lu
- Drug Discovery and Design Center, CAS Key Laboratory of Receptor Research, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
- Department of Pharmacy, University of Chinese Academy of Sciences, Beijing, China
| | - Rukang Zhang
- Drug Discovery and Design Center, CAS Key Laboratory of Receptor Research, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
- Department of Pharmacy, University of Chinese Academy of Sciences, Beijing, China
| | - Hao Jiang
- Drug Discovery and Design Center, CAS Key Laboratory of Receptor Research, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
- Department of Pharmacy, University of Chinese Academy of Sciences, Beijing, China
| | - Huimin Zhang
- Drug Discovery and Design Center, CAS Key Laboratory of Receptor Research, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China
| | - Cheng Luo
- Drug Discovery and Design Center, CAS Key Laboratory of Receptor Research, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
- Department of Pharmacy, University of Chinese Academy of Sciences, Beijing, China
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36
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Dos Remedios C. A review and summary of the contents of biophysical reviews volume 8, 2016. Biophys Rev 2017; 9:1-4. [PMID: 28510044 DOI: 10.1007/s12551-017-0249-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2017] [Accepted: 01/16/2017] [Indexed: 12/12/2022] Open
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