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Liu Y, Kong J, Liu G, Li Z, Xiao Y. Precise Gene Knock-In Tools with Minimized Risk of DSBs: A Trend for Gene Manipulation. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2401797. [PMID: 38728624 PMCID: PMC11267366 DOI: 10.1002/advs.202401797] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/20/2024] [Revised: 04/29/2024] [Indexed: 05/12/2024]
Abstract
Gene knock-in refers to the insertion of exogenous functional genes into a target genome to achieve continuous expression. Currently, most knock-in tools are based on site-directed nucleases, which can induce double-strand breaks (DSBs) at the target, following which the designed donors carrying functional genes can be inserted via the endogenous gene repair pathway. The size of donor genes is limited by the characteristics of gene repair, and the DSBs induce risks like genotoxicity. New generation tools, such as prime editing, transposase, and integrase, can insert larger gene fragments while minimizing or eliminating the risk of DSBs, opening new avenues in the development of animal models and gene therapy. However, the elimination of off-target events and the production of delivery carriers with precise requirements remain challenging, restricting the application of the current knock-in treatments to mainly in vitro settings. Here, a comprehensive review of the knock-in tools that do not/minimally rely on DSBs and use other mechanisms is provided. Moreover, the challenges and recent advances of in vivo knock-in treatments in terms of the therapeutic process is discussed. Collectively, the new generation of DSBs-minimizing and large-fragment knock-in tools has revolutionized the field of gene editing, from basic research to clinical treatment.
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Affiliation(s)
- Yongfeng Liu
- Department of PharmacologySchool of PharmacyChina Pharmaceutical UniversityNanjing210009China
- State Key Laboratory of Natural MedicinesChina Pharmaceutical UniversityNanjing210009China
- Mudi Meng Honors CollegeChina Pharmaceutical UniversityNanjing210009China
| | - Jianping Kong
- Department of PharmacologySchool of PharmacyChina Pharmaceutical UniversityNanjing210009China
- State Key Laboratory of Natural MedicinesChina Pharmaceutical UniversityNanjing210009China
| | - Gongyu Liu
- Department of PharmacologySchool of PharmacyChina Pharmaceutical UniversityNanjing210009China
- State Key Laboratory of Natural MedicinesChina Pharmaceutical UniversityNanjing210009China
| | - Zhaoxing Li
- Department of PharmacologySchool of PharmacyChina Pharmaceutical UniversityNanjing210009China
- State Key Laboratory of Natural MedicinesChina Pharmaceutical UniversityNanjing210009China
- Chongqing Innovation Institute of China Pharmaceutical UniversityChongqing401135China
| | - Yibei Xiao
- Department of PharmacologySchool of PharmacyChina Pharmaceutical UniversityNanjing210009China
- State Key Laboratory of Natural MedicinesChina Pharmaceutical UniversityNanjing210009China
- Chongqing Innovation Institute of China Pharmaceutical UniversityChongqing401135China
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2
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Yarnall MTN, Ioannidi EI, Schmitt-Ulms C, Krajeski RN, Lim J, Villiger L, Zhou W, Jiang K, Garushyants SK, Roberts N, Zhang L, Vakulskas CA, Walker JA, Kadina AP, Zepeda AE, Holden K, Ma H, Xie J, Gao G, Foquet L, Bial G, Donnelly SK, Miyata Y, Radiloff DR, Henderson JM, Ujita A, Abudayyeh OO, Gootenberg JS. Drag-and-drop genome insertion of large sequences without double-strand DNA cleavage using CRISPR-directed integrases. Nat Biotechnol 2023; 41:500-512. [PMID: 36424489 PMCID: PMC10257351 DOI: 10.1038/s41587-022-01527-4] [Citation(s) in RCA: 122] [Impact Index Per Article: 122.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2022] [Accepted: 09/23/2022] [Indexed: 11/26/2022]
Abstract
Programmable genome integration of large, diverse DNA cargo without DNA repair of exposed DNA double-strand breaks remains an unsolved challenge in genome editing. We present programmable addition via site-specific targeting elements (PASTE), which uses a CRISPR-Cas9 nickase fused to both a reverse transcriptase and serine integrase for targeted genomic recruitment and integration of desired payloads. We demonstrate integration of sequences as large as ~36 kilobases at multiple genomic loci across three human cell lines, primary T cells and non-dividing primary human hepatocytes. To augment PASTE, we discovered 25,614 serine integrases and cognate attachment sites from metagenomes and engineered orthologs with higher activity and shorter recognition sequences for efficient programmable integration. PASTE has editing efficiencies similar to or exceeding those of homology-directed repair and non-homologous end joining-based methods, with activity in non-dividing cells and in vivo with fewer detectable off-target events. PASTE expands the capabilities of genome editing by allowing large, multiplexed gene insertion without reliance on DNA repair pathways.
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Affiliation(s)
- Matthew T N Yarnall
- McGovern Institute for Brain Research at MIT, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Eleonora I Ioannidi
- McGovern Institute for Brain Research at MIT, Massachusetts Institute of Technology, Cambridge, MA, USA
- ETH Zürich, Zürich, Switzerland
| | - Cian Schmitt-Ulms
- McGovern Institute for Brain Research at MIT, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Rohan N Krajeski
- McGovern Institute for Brain Research at MIT, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Justin Lim
- McGovern Institute for Brain Research at MIT, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Lukas Villiger
- McGovern Institute for Brain Research at MIT, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Wenyuan Zhou
- McGovern Institute for Brain Research at MIT, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Kaiyi Jiang
- McGovern Institute for Brain Research at MIT, Massachusetts Institute of Technology, Cambridge, MA, USA
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Sofya K Garushyants
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
| | | | - Liyang Zhang
- Integrated DNA Technologies, Coralville, IA, USA
| | | | | | | | | | | | - Hong Ma
- University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Jun Xie
- University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Guangping Gao
- University of Massachusetts Chan Medical School, Worcester, MA, USA
| | | | - Greg Bial
- Yecuris Corporation, Tualatin, OR, USA
| | | | | | | | | | | | - Omar O Abudayyeh
- McGovern Institute for Brain Research at MIT, Massachusetts Institute of Technology, Cambridge, MA, USA.
| | - Jonathan S Gootenberg
- McGovern Institute for Brain Research at MIT, Massachusetts Institute of Technology, Cambridge, MA, USA.
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3
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Miyashita R, Nishiyama A, Qin W, Chiba Y, Kori S, Kato N, Konishi C, Kumamoto S, Kozuka-Hata H, Oyama M, Kawasoe Y, Tsurimoto T, Takahashi TS, Leonhardt H, Arita K, Nakanishi M. The termination of UHRF1-dependent PAF15 ubiquitin signaling is regulated by USP7 and ATAD5. eLife 2023; 12:79013. [PMID: 36734974 PMCID: PMC9943068 DOI: 10.7554/elife.79013] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Accepted: 02/02/2023] [Indexed: 02/04/2023] Open
Abstract
UHRF1-dependent ubiquitin signaling plays an integral role in the regulation of maintenance DNA methylation. UHRF1 catalyzes transient dual mono-ubiquitylation of PAF15 (PAF15Ub2), which regulates the localization and activation of DNMT1 at DNA methylation sites during DNA replication. Although the initiation of UHRF1-mediated PAF15 ubiquitin signaling has been relatively well characterized, the mechanisms underlying its termination and how they are coordinated with the completion of maintenance DNA methylation have not yet been clarified. This study shows that deubiquitylation by USP7 and unloading by ATAD5 (ELG1 in yeast) are pivotal processes for the removal of PAF15 from chromatin. On replicating chromatin, USP7 specifically interacts with PAF15Ub2 in a complex with DNMT1. USP7 depletion or inhibition of the interaction between USP7 and PAF15 results in abnormal accumulation of PAF15Ub2 on chromatin. Furthermore, we also find that the non-ubiquitylated form of PAF15 (PAF15Ub0) is removed from chromatin in an ATAD5-dependent manner. PAF15Ub2 was retained at high levels on chromatin when the catalytic activity of DNMT1 was inhibited, suggesting that the completion of maintenance DNA methylation is essential for the termination of UHRF1-mediated ubiquitin signaling. This finding provides a molecular understanding of how the maintenance DNA methylation machinery is disassembled at the end of the S phase.
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Affiliation(s)
- Ryota Miyashita
- Division of Cancer Cell Biology, The Institute of Medical Science, The University of TokyoTokyoJapan
| | - Atsuya Nishiyama
- Division of Cancer Cell Biology, The Institute of Medical Science, The University of TokyoTokyoJapan
| | - Weihua Qin
- Faculty of Biology, Ludwig-Maximilians-Universität MünchenMunichGermany
| | - Yoshie Chiba
- Division of Cancer Cell Biology, The Institute of Medical Science, The University of TokyoTokyoJapan
| | - Satomi Kori
- Structural Biology Laboratory, Graduate School of Medical Life Science, Yokohama City UniversityYokohamaJapan
| | - Norie Kato
- Structural Biology Laboratory, Graduate School of Medical Life Science, Yokohama City UniversityYokohamaJapan
| | - Chieko Konishi
- Division of Cancer Cell Biology, The Institute of Medical Science, The University of TokyoTokyoJapan
| | - Soichiro Kumamoto
- Division of Cancer Cell Biology, The Institute of Medical Science, The University of TokyoTokyoJapan
| | - Hiroko Kozuka-Hata
- Medical Proteomics Laboratory, The Institute of Medical Science, The University of TokyoTokyoJapan
| | - Masaaki Oyama
- Medical Proteomics Laboratory, The Institute of Medical Science, The University of TokyoTokyoJapan
| | - Yoshitaka Kawasoe
- Laboratory of Chromosome Biology, Department of Biology, Faculty of Science, Kyushu UniversityFukuokaJapan
| | - Toshiki Tsurimoto
- Laboratory of Chromosome Biology, Department of Biology, Faculty of Science, Kyushu UniversityFukuokaJapan
| | - Tatsuro S Takahashi
- Laboratory of Chromosome Biology, Department of Biology, Faculty of Science, Kyushu UniversityFukuokaJapan
| | | | - Kyohei Arita
- Structural Biology Laboratory, Graduate School of Medical Life Science, Yokohama City UniversityYokohamaJapan
| | - Makoto Nakanishi
- Division of Cancer Cell Biology, The Institute of Medical Science, The University of TokyoTokyoJapan
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4
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Hata K, Kobayashi N, Sugimura K, Qin W, Haxholli D, Chiba Y, Yoshimi S, Hayashi G, Onoda H, Ikegami T, Mulholland C, Nishiyama A, Nakanishi M, Leonhardt H, Konuma T, Arita K. Structural basis for the unique multifaceted interaction of DPPA3 with the UHRF1 PHD finger. Nucleic Acids Res 2022; 50:12527-12542. [PMID: 36420895 PMCID: PMC9757060 DOI: 10.1093/nar/gkac1082] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2022] [Revised: 09/20/2022] [Accepted: 10/27/2022] [Indexed: 11/27/2022] Open
Abstract
Ubiquitin-like with PHD and RING finger domain-containing protein 1 (UHRF1)-dependent DNA methylation is essential for maintaining cell fate during cell proliferation. Developmental pluripotency-associated 3 (DPPA3) is an intrinsically disordered protein that specifically interacts with UHRF1 and promotes passive DNA demethylation by inhibiting UHRF1 chromatin localization. However, the molecular basis of how DPPA3 interacts with and inhibits UHRF1 remains unclear. We aimed to determine the structure of the mouse UHRF1 plant homeodomain (PHD) complexed with DPPA3 using nuclear magnetic resonance. Induced α-helices in DPPA3 upon binding of UHRF1 PHD contribute to stable complex formation with multifaceted interactions, unlike canonical ligand proteins of the PHD domain. Mutations in the binding interface and unfolding of the DPPA3 helical structure inhibited binding to UHRF1 and its chromatin localization. Our results provide structural insights into the mechanism and specificity underlying the inhibition of UHRF1 by DPPA3.
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Affiliation(s)
| | | | - Keita Sugimura
- Division of Cancer Cell Biology, The Institute of Medical Science, The University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo 108-8639, Japan
| | - Weihua Qin
- Faculty of Biology, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Deis Haxholli
- Faculty of Biology, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Yoshie Chiba
- Division of Cancer Cell Biology, The Institute of Medical Science, The University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo 108-8639, Japan
| | - Sae Yoshimi
- Structural Biology Laboratory, Graduate School of Medical Life Science, Yokohama City University, 1-7-29, Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
| | - Gosuke Hayashi
- Department of Biomolecular Engineering, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8603, Japan
| | - Hiroki Onoda
- Structural Biology Laboratory, Graduate School of Medical Life Science, Yokohama City University, 1-7-29, Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
| | - Takahisa Ikegami
- Structural Epigenetics Laboratory, Graduate School of Medical Life Science, Yokohama City University, 1-7-29, Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
| | | | - Atsuya Nishiyama
- Division of Cancer Cell Biology, The Institute of Medical Science, The University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo 108-8639, Japan
| | - Makoto Nakanishi
- Division of Cancer Cell Biology, The Institute of Medical Science, The University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo 108-8639, Japan
| | - Heinrich Leonhardt
- Faculty of Biology, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Tsuyoshi Konuma
- Correspondence may also be addressed to Tsuyoshi Konuma. Tel: +81 45 508 7218; Fax: +81 45 508 7362;
| | - Kyohei Arita
- To whom correspondence should be addressed. Tel: +81 45 508 7225; Fax: +81 45 508 7365;
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5
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Qin W, Steinek C, Kolobynina K, Forné I, Imhof A, Cardoso M, Leonhardt H. Probing protein ubiquitination in live cells. Nucleic Acids Res 2022; 50:e125. [PMID: 36189882 PMCID: PMC9757074 DOI: 10.1093/nar/gkac805] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Revised: 08/26/2022] [Accepted: 09/08/2022] [Indexed: 12/24/2022] Open
Abstract
The reversible attachment of ubiquitin governs the interaction, activity and degradation of proteins whereby the type and target of this conjugation determine the biological response. The investigation of this complex and multi-faceted protein ubiquitination mostly relies on painstaking biochemical analyses. Here, we employ recombinant binding domains to probe the ubiquitination of proteins in living cells. We immobilize GFP-fused proteins of interest at a distinct cellular structure and detect their ubiquitination state with red fluorescent ubiquitin binders. With this ubiquitin fluorescent three-hybrid (ubiF3H) assay we identified HP1β as a novel ubiquitination target of UHRF1. The use of linkage specific ubiquitin binding domains enabled the discrimination of K48 and K63 linked protein ubiquitination. To enhance signal-to-noise ratio, we implemented fluorescence complementation (ubiF3Hc) with split YFP. Using in addition a cell cycle marker we could show that HP1β is mostly ubiquitinated by UHRF1 during S phase and deubiquitinated by the protease USP7. With this complementation assay we could also directly detect the ubiquitination of the tumor suppressor p53 and monitor its inhibition by the anti-cancer drug Nutlin-3. Altogether, we demonstrate the utility of the ubiF3H assay to probe the ubiquitination of specific proteins and to screen for ligases, proteases and small molecules controlling this posttranslational modification.
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Affiliation(s)
- Weihua Qin
- Correspondence may also be addressed to Weihua Qin. Tel: +49 89 2180 71132; Fax: +49 89 2180 74236;
| | - Clemens Steinek
- Faculty of Biology, Ludwig-Maximilians-Universität München, Großhaderner Str. 2, 82152 Planegg-Martinsried, Germany
| | - Ksenia Kolobynina
- Cell Biology and Epigenetics, Department of Biology, Technical University of Darmstadt, Schnittspahnstr. 10, 64287 Darmstadt, Germany
| | - Ignasi Forné
- Biomedical Center Munich, Faculty of Medicine, Ludwig-Maximilians-Universität München, Großhaderner Str. 9, 82152 Planegg-Martinsried, Germany
| | - Axel Imhof
- Biomedical Center Munich, Faculty of Medicine, Ludwig-Maximilians-Universität München, Großhaderner Str. 9, 82152 Planegg-Martinsried, Germany
| | - M Cristina Cardoso
- Cell Biology and Epigenetics, Department of Biology, Technical University of Darmstadt, Schnittspahnstr. 10, 64287 Darmstadt, Germany
| | - Heinrich Leonhardt
- To whom correspondence should be addressed. Tel: +49 89 2180 74232; Fax: +49 89 2180 74236;
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6
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Arroyo M, Hastert FD, Zhadan A, Schelter F, Zimbelmann S, Rausch C, Ludwig AK, Carell T, Cardoso MC. Isoform-specific and ubiquitination dependent recruitment of Tet1 to replicating heterochromatin modulates methylcytosine oxidation. Nat Commun 2022; 13:5173. [PMID: 36056023 PMCID: PMC9440122 DOI: 10.1038/s41467-022-32799-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Accepted: 08/15/2022] [Indexed: 01/26/2023] Open
Abstract
Oxidation of the epigenetic DNA mark 5-methylcytosine by Tet dioxygenases is an established route to diversify the epigenetic information, modulate gene expression and overall cellular (patho-)physiology. Here, we demonstrate that Tet1 and its short isoform Tet1s exhibit distinct nuclear localization during DNA replication resulting in aberrant cytosine modification levels in human and mouse cells. We show that Tet1 is tethered away from heterochromatin via its zinc finger domain, which is missing in Tet1s allowing its targeting to these regions. We find that Tet1s interacts with and is ubiquitinated by CRL4(VprBP). The ubiquitinated Tet1s is then recognized by Uhrf1 and recruited to late replicating heterochromatin. This leads to spreading of 5-methylcytosine oxidation to heterochromatin regions, LINE 1 activation and chromatin decondensation. In summary, we elucidate a dual regulation mechanism of Tet1, contributing to the understanding of how epigenetic information can be diversified by spatio-temporal directed Tet1 catalytic activity.
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Affiliation(s)
- María Arroyo
- grid.6546.10000 0001 0940 1669Cell Biology and Epigenetics, Department of Biology, Technical University of Darmstadt, Schnittspahnstr. 10, 64287 Darmstadt, Germany
| | - Florian D. Hastert
- grid.6546.10000 0001 0940 1669Cell Biology and Epigenetics, Department of Biology, Technical University of Darmstadt, Schnittspahnstr. 10, 64287 Darmstadt, Germany ,grid.425396.f0000 0001 1019 0926Section AIDS and newly emerging pathogens, Paul Ehrlich Institute, Paul-Ehrlich-Str. 51-59, 63225 Langen, Germany
| | - Andreas Zhadan
- grid.6546.10000 0001 0940 1669Cell Biology and Epigenetics, Department of Biology, Technical University of Darmstadt, Schnittspahnstr. 10, 64287 Darmstadt, Germany
| | - Florian Schelter
- grid.5252.00000 0004 1936 973XDepartment of Chemistry, Ludwig Maximilians University, Butenandstr. 5-13, 81377 Munich, Germany
| | - Susanne Zimbelmann
- grid.6546.10000 0001 0940 1669Cell Biology and Epigenetics, Department of Biology, Technical University of Darmstadt, Schnittspahnstr. 10, 64287 Darmstadt, Germany
| | - Cathia Rausch
- grid.6546.10000 0001 0940 1669Cell Biology and Epigenetics, Department of Biology, Technical University of Darmstadt, Schnittspahnstr. 10, 64287 Darmstadt, Germany ,grid.16008.3f0000 0001 2295 9843Present Address: Luxembourg Centre for Systems Biomedicine, University of Luxembourg, 6, avenue du Swing, L-4367 Belvaux, Luxembourg
| | - Anne K. Ludwig
- grid.6546.10000 0001 0940 1669Cell Biology and Epigenetics, Department of Biology, Technical University of Darmstadt, Schnittspahnstr. 10, 64287 Darmstadt, Germany ,grid.5253.10000 0001 0328 4908Present Address: Department of Medicine, Hematology, Oncology and Rheumatology, University Hospital Heidelberg, Im Neuenheimer Feld 410, 69120 Heidelberg, Germany
| | - Thomas Carell
- grid.5252.00000 0004 1936 973XDepartment of Chemistry, Ludwig Maximilians University, Butenandstr. 5-13, 81377 Munich, Germany
| | - M. Cristina Cardoso
- grid.6546.10000 0001 0940 1669Cell Biology and Epigenetics, Department of Biology, Technical University of Darmstadt, Schnittspahnstr. 10, 64287 Darmstadt, Germany
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7
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Stolz P, Mantero AS, Tvardovskiy A, Ugur E, Wange LE, Mulholland CB, Cheng Y, Wierer M, Enard W, Schneider R, Bartke T, Leonhardt H, Elsässer SJ, Bultmann S. TET1 regulates gene expression and repression of endogenous retroviruses independent of DNA demethylation. Nucleic Acids Res 2022; 50:8491-8511. [PMID: 35904814 PMCID: PMC9410877 DOI: 10.1093/nar/gkac642] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2021] [Revised: 04/25/2022] [Accepted: 07/20/2022] [Indexed: 11/13/2022] Open
Abstract
DNA methylation (5-methylcytosine (5mC)) is critical for genome stability and transcriptional regulation in mammals. The discovery that ten-eleven translocation (TET) proteins catalyze the oxidation of 5mC to 5-hydroxymethylcytosine (5hmC), 5-formylcytosine (5fC), and 5-carboxylcytosine (5caC) revolutionized our perspective on the complexity and regulation of DNA modifications. However, to what extent the regulatory functions of TET1 can be attributed to its catalytic activity remains unclear. Here, we use genome engineering and quantitative multi-omics approaches to dissect the precise catalytic vs. non-catalytic functions of TET1 in murine embryonic stem cells (mESCs). Our study identifies TET1 as an essential interaction hub for multiple chromatin modifying complexes and a global regulator of histone modifications. Strikingly, we find that the majority of transcriptional regulation depends on non-catalytic functions of TET1. In particular, we show that TET1 is critical for the establishment of H3K9me3 and H4K20me3 at endogenous retroviral elements (ERVs) and their silencing that is independent of its canonical role in DNA demethylation. Furthermore, we provide evidence that this repression of ERVs depends on the interaction between TET1 and SIN3A. In summary, we demonstrate that the non-catalytic functions of TET1 are critical for regulation of gene expression and the silencing of endogenous retroviruses in mESCs.
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Affiliation(s)
- Paul Stolz
- Faculty of Biology and Center for Molecular Biosystems (BioSysM), Human Biology and BioImaging, Ludwig-Maximilians-Universität München, Munich 81377, Germany
| | - Angelo Salazar Mantero
- Science for Life Laboratory, Department of Medical Biochemistry and Biophysics, Karolinska Institutet 17165 Stockholm, Sweden, Ming Wai Lau Centre for Reparative Medicine, Stockholm Node, Karolinska Institutet 17177 Stockholm, Sweden
| | - Andrey Tvardovskiy
- Institute of Functional Epigenetics (IFE), Helmholtz Zentrum München, 85764 Neuherberg, Germany
| | - Enes Ugur
- Faculty of Biology and Center for Molecular Biosystems (BioSysM), Human Biology and BioImaging, Ludwig-Maximilians-Universität München, Munich 81377, Germany.,Department of Proteomics and Signal Transduction, Max-Planck Institute of Biochemistry, Martinsried 82152, Germany
| | - Lucas E Wange
- Faculty of Biology, Anthropology and Human Genomics, Ludwig-Maximilians-Universität München 82152, Planegg-Martinsried, Germany
| | - Christopher B Mulholland
- Faculty of Biology and Center for Molecular Biosystems (BioSysM), Human Biology and BioImaging, Ludwig-Maximilians-Universität München, Munich 81377, Germany
| | - Yuying Cheng
- Science for Life Laboratory, Department of Medical Biochemistry and Biophysics, Karolinska Institutet 17165 Stockholm, Sweden, Ming Wai Lau Centre for Reparative Medicine, Stockholm Node, Karolinska Institutet 17177 Stockholm, Sweden
| | - Michael Wierer
- Department of Proteomics and Signal Transduction, Max-Planck Institute of Biochemistry, Martinsried 82152, Germany
| | - Wolfgang Enard
- Faculty of Biology, Anthropology and Human Genomics, Ludwig-Maximilians-Universität München 82152, Planegg-Martinsried, Germany
| | - Robert Schneider
- Institute of Functional Epigenetics (IFE), Helmholtz Zentrum München, 85764 Neuherberg, Germany
| | - Till Bartke
- Institute of Functional Epigenetics (IFE), Helmholtz Zentrum München, 85764 Neuherberg, Germany
| | - Heinrich Leonhardt
- Faculty of Biology and Center for Molecular Biosystems (BioSysM), Human Biology and BioImaging, Ludwig-Maximilians-Universität München, Munich 81377, Germany
| | - Simon J Elsässer
- Science for Life Laboratory, Department of Medical Biochemistry and Biophysics, Karolinska Institutet 17165 Stockholm, Sweden, Ming Wai Lau Centre for Reparative Medicine, Stockholm Node, Karolinska Institutet 17177 Stockholm, Sweden
| | - Sebastian Bultmann
- Faculty of Biology and Center for Molecular Biosystems (BioSysM), Human Biology and BioImaging, Ludwig-Maximilians-Universität München, Munich 81377, Germany
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8
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Qin W, Ugur E, Mulholland CB, Bultmann S, Solovei I, Modic M, Smets M, Wierer M, Forné I, Imhof A, Cardoso MC, Leonhardt H. Phosphorylation of the HP1β hinge region sequesters KAP1 in heterochromatin and promotes the exit from naïve pluripotency. Nucleic Acids Res 2021; 49:7406-7423. [PMID: 34214177 PMCID: PMC8287961 DOI: 10.1093/nar/gkab548] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Revised: 05/31/2021] [Accepted: 06/11/2021] [Indexed: 12/26/2022] Open
Abstract
Heterochromatin binding protein HP1β plays an important role in chromatin organization and cell differentiation, however the underlying mechanisms remain unclear. Here, we generated HP1β−/− embryonic stem cells and observed reduced heterochromatin clustering and impaired differentiation. We found that during stem cell differentiation, HP1β is phosphorylated at serine 89 by CK2, which creates a binding site for the pluripotency regulator KAP1. This phosphorylation dependent sequestration of KAP1 in heterochromatin compartments causes a downregulation of pluripotency factors and triggers pluripotency exit. Accordingly, HP1β−/− and phospho-mutant cells exhibited impaired differentiation, while ubiquitination-deficient KAP1−/− cells had the opposite phenotype with enhanced differentiation. These results suggest that KAP1 regulates pluripotency via its ubiquitination activity. We propose that the formation of subnuclear membraneless heterochromatin compartments may serve as a dynamic reservoir to trap or release cellular factors. The sequestration of essential regulators defines a novel and active role of heterochromatin in gene regulation and represents a dynamic mode of remote control to regulate cellular processes like cell fate decisions.
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Affiliation(s)
- Weihua Qin
- Faculty of Biology, Ludwig-Maximilians-Universität München, Butenandtstraße 1, D-81377 Munich, Germany
| | - Enes Ugur
- Faculty of Biology, Ludwig-Maximilians-Universität München, Butenandtstraße 1, D-81377 Munich, Germany.,Department of Proteomics and Signal Transduction, Max Planck Institute for Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany
| | - Christopher B Mulholland
- Faculty of Biology, Ludwig-Maximilians-Universität München, Butenandtstraße 1, D-81377 Munich, Germany
| | - Sebastian Bultmann
- Faculty of Biology, Ludwig-Maximilians-Universität München, Butenandtstraße 1, D-81377 Munich, Germany
| | - Irina Solovei
- Faculty of Biology, Ludwig-Maximilians-Universität München, Butenandtstraße 1, D-81377 Munich, Germany
| | - Miha Modic
- The Francis Crick Institute and UCL Queen Square Institute of Neurology, London NW1 1AT, United Kingdom
| | - Martha Smets
- Faculty of Biology, Ludwig-Maximilians-Universität München, Butenandtstraße 1, D-81377 Munich, Germany
| | - Michael Wierer
- Department of Proteomics and Signal Transduction, Max Planck Institute for Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany
| | - Ignasi Forné
- Biomedical Center Munich, Faculty of Medicine, Ludwig-Maximilians-Universität München, Großhaderner Str. 9, 82152 Planegg-Martinsried, Germany
| | - Axel Imhof
- Biomedical Center Munich, Faculty of Medicine, Ludwig-Maximilians-Universität München, Großhaderner Str. 9, 82152 Planegg-Martinsried, Germany
| | - M Cristina Cardoso
- Cell Biology and Epigenetics, Department of Biology, Technical University of Darmstadt, 64287 Darmstadt, Germany
| | - Heinrich Leonhardt
- Faculty of Biology, Ludwig-Maximilians-Universität München, Butenandtstraße 1, D-81377 Munich, Germany
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9
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Bartoschek MD, Ugur E, Nguyen TA, Rodschinka G, Wierer M, Lang K, Bultmann S. Identification of permissive amber suppression sites for efficient non-canonical amino acid incorporation in mammalian cells. Nucleic Acids Res 2021; 49:e62. [PMID: 33684219 PMCID: PMC8216290 DOI: 10.1093/nar/gkab132] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2020] [Revised: 02/16/2021] [Accepted: 02/17/2021] [Indexed: 12/20/2022] Open
Abstract
The genetic code of mammalian cells can be expanded to allow the incorporation of non-canonical amino acids (ncAAs) by suppressing in-frame amber stop codons (UAG) with an orthogonal pyrrolysyl-tRNA synthetase (PylRS)/tRNAPylCUA (PylT) pair. However, the feasibility of this approach is substantially hampered by unpredictable variations in incorporation efficiencies at different stop codon positions within target proteins. Here, we apply a proteomics-based approach to quantify ncAA incorporation rates at hundreds of endogenous amber stop codons in mammalian cells. With these data, we compute iPASS (Identification of Permissive Amber Sites for Suppression; available at www.bultmannlab.eu/tools/iPASS), a linear regression model to predict relative ncAA incorporation efficiencies depending on the surrounding sequence context. To verify iPASS, we develop a dual-fluorescence reporter for high-throughput flow-cytometry analysis that reproducibly yields context-specific ncAA incorporation efficiencies. We show that nucleotides up- and downstream of UAG synergistically influence ncAA incorporation efficiency independent of cell line and ncAA identity. Additionally, we demonstrate iPASS-guided optimization of ncAA incorporation rates by synonymous exchange of codons flanking the amber stop codon. This combination of in silico analysis followed by validation in living mammalian cells substantially simplifies identification as well as adaptation of sites within a target protein to confer high ncAA incorporation rates.
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Affiliation(s)
- Michael D Bartoschek
- Department of Biology II and Center for Molecular Biosystems (BioSysM), Human Biology and BioImaging, Ludwig-Maximilians-Universität München, Munich 81377, Germany
| | - Enes Ugur
- Department of Biology II and Center for Molecular Biosystems (BioSysM), Human Biology and BioImaging, Ludwig-Maximilians-Universität München, Munich 81377, Germany.,Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried 82152, Germany
| | - Tuan-Anh Nguyen
- Department of Chemistry, Synthetic Biochemistry, Technical University of Munich, Garching 85748, Germany
| | - Geraldine Rodschinka
- Department of Biology II and Center for Molecular Biosystems (BioSysM), Human Biology and BioImaging, Ludwig-Maximilians-Universität München, Munich 81377, Germany
| | - Michael Wierer
- Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried 82152, Germany
| | - Kathrin Lang
- Department of Chemistry, Synthetic Biochemistry, Technical University of Munich, Garching 85748, Germany
| | - Sebastian Bultmann
- Department of Biology II and Center for Molecular Biosystems (BioSysM), Human Biology and BioImaging, Ludwig-Maximilians-Universität München, Munich 81377, Germany
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10
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Qin W, Stengl A, Ugur E, Leidescher S, Ryan J, Cardoso MC, Leonhardt H. HP1β carries an acidic linker domain and requires H3K9me3 for phase separation. Nucleus 2021; 12:44-57. [PMID: 33660589 PMCID: PMC7939559 DOI: 10.1080/19491034.2021.1889858] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Liquid-liquid phase separation (LLPS) mediated formation of membraneless organelles has been proposed to coordinate biological processes in space and time. Previously, the formation of phase-separated droplets was described as a unique property of HP1α. Here, we demonstrate that the positive net charge of the intrinsically disordered hinge region (IDR-H) of HP1 proteins is critical for phase separation and that the exchange of four acidic amino acids is sufficient to confer LLPS properties to HP1β. Surprisingly, the addition of mono-nucleosomes promoted H3K9me3-dependent LLPS of HP1β which could be specifically disrupted with methylated but not acetylated H3K9 peptides. HP1β mutants defective in H3K9me3 binding were less efficient in phase separationin vitro and failed to accumulate at heterochromatin in vivo. We propose that multivalent interactions of HP1β with H3K9me3-modified nucleosomes via its chromodomain and dimerization via its chromoshadow domain enable phase separation and contribute to the formation of heterochromatin compartments in vivo.
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Affiliation(s)
- Weihua Qin
- Center for Molecular Biosystems (BioSysM), Faculty of Biology, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Andreas Stengl
- Center for Molecular Biosystems (BioSysM), Faculty of Biology, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Enes Ugur
- Center for Molecular Biosystems (BioSysM), Faculty of Biology, Ludwig-Maximilians-Universität München, Munich, Germany.,Department of Proteomics and Signal Transduction, Max Planck Institute for Biochemistry, Martinsried, Germany
| | - Susanne Leidescher
- Center for Molecular Biosystems (BioSysM), Faculty of Biology, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Joel Ryan
- Center for Molecular Biosystems (BioSysM), Faculty of Biology, Ludwig-Maximilians-Universität München, Munich, Germany
| | - M Cristina Cardoso
- Cell Biology and Epigenetics, Department of Biology, Technical University of Darmstadt, Darmstadt, Germany
| | - Heinrich Leonhardt
- Center for Molecular Biosystems (BioSysM), Faculty of Biology, Ludwig-Maximilians-Universität München, Munich, Germany
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11
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Mulholland CB, Nishiyama A, Ryan J, Nakamura R, Yiğit M, Glück IM, Trummer C, Qin W, Bartoschek MD, Traube FR, Parsa E, Ugur E, Modic M, Acharya A, Stolz P, Ziegenhain C, Wierer M, Enard W, Carell T, Lamb DC, Takeda H, Nakanishi M, Bultmann S, Leonhardt H. Recent evolution of a TET-controlled and DPPA3/STELLA-driven pathway of passive DNA demethylation in mammals. Nat Commun 2020; 11:5972. [PMID: 33235224 PMCID: PMC7686362 DOI: 10.1038/s41467-020-19603-1] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2020] [Accepted: 10/22/2020] [Indexed: 12/12/2022] Open
Abstract
Genome-wide DNA demethylation is a unique feature of mammalian development and naïve pluripotent stem cells. Here, we describe a recently evolved pathway in which global hypomethylation is achieved by the coupling of active and passive demethylation. TET activity is required, albeit indirectly, for global demethylation, which mostly occurs at sites devoid of TET binding. Instead, TET-mediated active demethylation is locus-specific and necessary for activating a subset of genes, including the naïve pluripotency and germline marker Dppa3 (Stella, Pgc7). DPPA3 in turn drives large-scale passive demethylation by directly binding and displacing UHRF1 from chromatin, thereby inhibiting maintenance DNA methylation. Although unique to mammals, we show that DPPA3 alone is capable of inducing global DNA demethylation in non-mammalian species (Xenopus and medaka) despite their evolutionary divergence from mammals more than 300 million years ago. Our findings suggest that the evolution of Dppa3 facilitated the emergence of global DNA demethylation in mammals.
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Affiliation(s)
- Christopher B Mulholland
- Department of Biology II and Center for Integrated Protein Science Munich (CIPSM), Human Biology and BioImaging, Ludwig-Maximilians-Universität München, Planegg-Martinsried, Germany
| | - Atsuya Nishiyama
- Division of Cancer Cell Biology, The Institute of Medical Science, The University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo, 108-8639, Japan
| | - Joel Ryan
- Department of Biology II and Center for Integrated Protein Science Munich (CIPSM), Human Biology and BioImaging, Ludwig-Maximilians-Universität München, Planegg-Martinsried, Germany
| | - Ryohei Nakamura
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan
| | - Merve Yiğit
- Department of Biology II and Center for Integrated Protein Science Munich (CIPSM), Human Biology and BioImaging, Ludwig-Maximilians-Universität München, Planegg-Martinsried, Germany
| | - Ivo M Glück
- Physical Chemistry, Department of Chemistry, Center for Nanoscience, Nanosystems Initiative Munich and Center for Integrated Protein Science Munich, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Carina Trummer
- Department of Biology II and Center for Integrated Protein Science Munich (CIPSM), Human Biology and BioImaging, Ludwig-Maximilians-Universität München, Planegg-Martinsried, Germany
| | - Weihua Qin
- Department of Biology II and Center for Integrated Protein Science Munich (CIPSM), Human Biology and BioImaging, Ludwig-Maximilians-Universität München, Planegg-Martinsried, Germany
| | - Michael D Bartoschek
- Department of Biology II and Center for Integrated Protein Science Munich (CIPSM), Human Biology and BioImaging, Ludwig-Maximilians-Universität München, Planegg-Martinsried, Germany
| | - Franziska R Traube
- Center for Integrated Protein Science (CIPSM) at the Department of Chemistry, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Edris Parsa
- Center for Integrated Protein Science (CIPSM) at the Department of Chemistry, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Enes Ugur
- Department of Biology II and Center for Integrated Protein Science Munich (CIPSM), Human Biology and BioImaging, Ludwig-Maximilians-Universität München, Planegg-Martinsried, Germany
- Department of Proteomics and Signal Transduction, Max Planck Institute for Biochemistry, Am Klopferspitz 18, 82152, Martinsried, Germany
| | - Miha Modic
- The Francis Crick Institute and UCL Queen Square Institute of Neurology, London, UK
| | - Aishwarya Acharya
- Department of Biology II and Center for Integrated Protein Science Munich (CIPSM), Human Biology and BioImaging, Ludwig-Maximilians-Universität München, Planegg-Martinsried, Germany
| | - Paul Stolz
- Department of Biology II and Center for Integrated Protein Science Munich (CIPSM), Human Biology and BioImaging, Ludwig-Maximilians-Universität München, Planegg-Martinsried, Germany
| | - Christoph Ziegenhain
- Department of Biology II, Anthropology and Human Genomics, Ludwig-Maximilians-Universität München, Planegg-Martinsried, Germany
| | - Michael Wierer
- Department of Proteomics and Signal Transduction, Max Planck Institute for Biochemistry, Am Klopferspitz 18, 82152, Martinsried, Germany
| | - Wolfgang Enard
- Department of Biology II, Anthropology and Human Genomics, Ludwig-Maximilians-Universität München, Planegg-Martinsried, Germany
| | - Thomas Carell
- Center for Integrated Protein Science (CIPSM) at the Department of Chemistry, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Don C Lamb
- Physical Chemistry, Department of Chemistry, Center for Nanoscience, Nanosystems Initiative Munich and Center for Integrated Protein Science Munich, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Hiroyuki Takeda
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan
| | - Makoto Nakanishi
- Division of Cancer Cell Biology, The Institute of Medical Science, The University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo, 108-8639, Japan
| | - Sebastian Bultmann
- Department of Biology II and Center for Integrated Protein Science Munich (CIPSM), Human Biology and BioImaging, Ludwig-Maximilians-Universität München, Planegg-Martinsried, Germany.
| | - Heinrich Leonhardt
- Department of Biology II and Center for Integrated Protein Science Munich (CIPSM), Human Biology and BioImaging, Ludwig-Maximilians-Universität München, Planegg-Martinsried, Germany.
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12
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Ignatova VV, Kaiser S, Ho JSY, Bing X, Stolz P, Tan YX, Lee CL, Gay FPH, Lastres PR, Gerlini R, Rathkolb B, Aguilar-Pimentel A, Sanz-Moreno A, Klein-Rodewald T, Calzada-Wack J, Ibragimov E, Valenta M, Lukauskas S, Pavesi A, Marschall S, Leuchtenberger S, Fuchs H, Gailus-Durner V, de Angelis MH, Bultmann S, Rando OJ, Guccione E, Kellner SM, Schneider R. METTL6 is a tRNA m 3C methyltransferase that regulates pluripotency and tumor cell growth. SCIENCE ADVANCES 2020; 6:eaaz4551. [PMID: 32923617 PMCID: PMC7449687 DOI: 10.1126/sciadv.aaz4551] [Citation(s) in RCA: 46] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/19/2019] [Accepted: 07/14/2020] [Indexed: 06/11/2023]
Abstract
Recently, covalent modifications of RNA, such as methylation, have emerged as key regulators of all aspects of RNA biology and have been implicated in numerous diseases, for instance, cancer. Here, we undertook a combination of in vitro and in vivo screens to test 78 potential methyltransferases for their roles in hepatocellular carcinoma (HCC) cell proliferation. We identified methyltransferase-like protein 6 (METTL6) as a crucial regulator of tumor cell growth. We show that METTL6 is a bona fide transfer RNA (tRNA) methyltransferase, catalyzing the formation of 3-methylcytidine at C32 of specific serine tRNA isoacceptors. Deletion of Mettl6 in mouse stem cells results in changes in ribosome occupancy and RNA levels, as well as impaired pluripotency. In mice, Mettl6 knockout results in reduced energy expenditure. We reveal a previously unknown pathway in the maintenance of translation efficiency with a role in maintaining stem cell self-renewal, as well as impacting tumor cell growth profoundly.
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Affiliation(s)
- Valentina V. Ignatova
- Institute of Functional Epigenetics, Helmholtz Zentrum München, 85764 Neuherberg, Germany
| | - Steffen Kaiser
- Chemical Faculty, Ludwig-Maximilians Universität München, Munich, Germany
| | - Jessica Sook Yuin Ho
- Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Xinyang Bing
- University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Paul Stolz
- Department of Biology II, Human Biology and BioImaging, Ludwig-Maximilians Universität München, Munich, Germany
| | - Ying Xim Tan
- Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Chee Leng Lee
- Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Florence Pik Hoon Gay
- Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Palma Rico Lastres
- Institute of Functional Epigenetics, Helmholtz Zentrum München, 85764 Neuherberg, Germany
| | - Raffaele Gerlini
- German Mouse Clinic, Institute of Experimental Genetics, Helmholtz Zentrum München, 85764 Neuherberg, Germany
- German Center for Diabetes Research (DZD), 85764 Neuherberg, Germany
| | - Birgit Rathkolb
- German Mouse Clinic, Institute of Experimental Genetics, Helmholtz Zentrum München, 85764 Neuherberg, Germany
- German Center for Diabetes Research (DZD), 85764 Neuherberg, Germany
- Institute of Molecular Animal Breeding and Biotechnology, Gene Center, Ludwig-Maximilians-University München, Munich, Germany
| | - Antonio Aguilar-Pimentel
- German Mouse Clinic, Institute of Experimental Genetics, Helmholtz Zentrum München, 85764 Neuherberg, Germany
| | - Adrián Sanz-Moreno
- German Mouse Clinic, Institute of Experimental Genetics, Helmholtz Zentrum München, 85764 Neuherberg, Germany
| | - Tanja Klein-Rodewald
- German Mouse Clinic, Institute of Experimental Genetics, Helmholtz Zentrum München, 85764 Neuherberg, Germany
| | - Julia Calzada-Wack
- German Mouse Clinic, Institute of Experimental Genetics, Helmholtz Zentrum München, 85764 Neuherberg, Germany
| | - Emil Ibragimov
- Institute of Functional Epigenetics, Helmholtz Zentrum München, 85764 Neuherberg, Germany
| | - Magdalena Valenta
- Institute of Functional Epigenetics, Helmholtz Zentrum München, 85764 Neuherberg, Germany
| | - Saulius Lukauskas
- Institute of Functional Epigenetics, Helmholtz Zentrum München, 85764 Neuherberg, Germany
| | - Andrea Pavesi
- Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Susan Marschall
- German Mouse Clinic, Institute of Experimental Genetics, Helmholtz Zentrum München, 85764 Neuherberg, Germany
| | - Stefanie Leuchtenberger
- German Mouse Clinic, Institute of Experimental Genetics, Helmholtz Zentrum München, 85764 Neuherberg, Germany
| | - Helmut Fuchs
- German Mouse Clinic, Institute of Experimental Genetics, Helmholtz Zentrum München, 85764 Neuherberg, Germany
| | - Valerie Gailus-Durner
- German Mouse Clinic, Institute of Experimental Genetics, Helmholtz Zentrum München, 85764 Neuherberg, Germany
| | - Martin Hrabe de Angelis
- German Mouse Clinic, Institute of Experimental Genetics, Helmholtz Zentrum München, 85764 Neuherberg, Germany
- German Center for Diabetes Research (DZD), 85764 Neuherberg, Germany
- Chair of Experimental Genetics, School of Life Science Weihenstephan, Technische Universität München, 85354 Freising, Germany
| | - Sebastian Bultmann
- Department of Biology II, Human Biology and BioImaging, Ludwig-Maximilians Universität München, Munich, Germany
| | - Oliver J. Rando
- University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Ernesto Guccione
- Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
- Mount Sinai Center for Therapeutics Discovery, Departments of Pharmacological Sciences and Oncological Sciences, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | | | - Robert Schneider
- Institute of Functional Epigenetics, Helmholtz Zentrum München, 85764 Neuherberg, Germany
- German Center for Diabetes Research (DZD), 85764 Neuherberg, Germany
- Faculty of Biology, Ludwig-Maximilians Universität München, Munich, Germany
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13
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Distinct and stage-specific contributions of TET1 and TET2 to stepwise cytosine oxidation in the transition from naive to primed pluripotency. Sci Rep 2020; 10:12066. [PMID: 32694513 PMCID: PMC7374584 DOI: 10.1038/s41598-020-68600-3] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2020] [Accepted: 06/29/2020] [Indexed: 12/17/2022] Open
Abstract
Cytosine DNA bases can be methylated by DNA methyltransferases and subsequently oxidized by TET proteins. The resulting 5-hydroxymethylcytosine (5hmC), 5-formylcytosine (5fC), and 5-carboxylcytosine (5caC) are considered demethylation intermediates as well as stable epigenetic marks. To dissect the contributions of these cytosine modifying enzymes, we generated combinations of Tet knockout (KO) embryonic stem cells (ESCs) and systematically measured protein and DNA modification levels at the transition from naive to primed pluripotency. Whereas the increase of genomic 5-methylcytosine (5mC) levels during exit from pluripotency correlated with an upregulation of the de novo DNA methyltransferases DNMT3A and DNMT3B, the subsequent oxidation steps turned out to be far more complex. The strong increase of oxidized cytosine bases (5hmC, 5fC, and 5caC) was accompanied by a drop in TET2 levels, yet the analysis of KO cells suggested that TET2 is responsible for most 5fC formation. The comparison of modified cytosine and enzyme levels in Tet KO cells revealed distinct and differentiation-dependent contributions of TET1 and TET2 to 5hmC and 5fC formation arguing against a processive mechanism of 5mC oxidation. The apparent independent steps of 5hmC and 5fC formation suggest yet to be identified mechanisms regulating TET activity that may constitute another layer of epigenetic regulation.
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14
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Cathepsin S Alterations Induce a Tumor-Promoting Immune Microenvironment in Follicular Lymphoma. Cell Rep 2020; 31:107522. [PMID: 32330423 DOI: 10.1016/j.celrep.2020.107522] [Citation(s) in RCA: 46] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2019] [Revised: 02/10/2020] [Accepted: 03/26/2020] [Indexed: 12/17/2022] Open
Abstract
Tumor cells orchestrate their microenvironment. Here, we provide biochemical, structural, functional, and clinical evidence that Cathepsin S (CTSS) alterations induce a tumor-promoting immune microenvironment in follicular lymphoma (FL). We found CTSS mutations at Y132 in 6% of FL (19/305). Another 13% (37/286) had CTSS amplification, which was associated with higher CTSS expression. CTSS Y132 mutations lead to accelerated autocatalytic conversion from an enzymatically inactive profrom to active CTSS and increased substrate cleavage, including CD74, which regulates major histocompatibility complex class II (MHC class II)-restricted antigen presentation. Lymphoma cells with hyperactive CTSS more efficiently activated antigen-specific CD4+ T cells in vitro. Tumors with hyperactive CTSS showed increased CD4+ T cell infiltration and proinflammatory cytokine perturbation in a mouse model and in human FLs. In mice, this CTSS-induced immune microenvironment promoted tumor growth. Clinically, patients with CTSS-hyperactive FL had better treatment outcomes with standard immunochemotherapies, indicating that these immunosuppressive regimens target both the lymphoma cells and the tumor-promoting immune microenvironment.
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15
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The rRNA m 6A methyltransferase METTL5 is involved in pluripotency and developmental programs. Genes Dev 2020; 34:715-729. [PMID: 32217665 PMCID: PMC7197354 DOI: 10.1101/gad.333369.119] [Citation(s) in RCA: 80] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2019] [Accepted: 03/05/2020] [Indexed: 01/12/2023]
Abstract
Covalent chemical modifications of cellular RNAs directly impact all biological processes. However, our mechanistic understanding of the enzymes catalyzing these modifications, their substrates and biological functions, remains vague. Amongst RNA modifications N6-methyladenosine (m6A) is widespread and found in messenger (mRNA), ribosomal (rRNA), and noncoding RNAs. Here, we undertook a systematic screen to uncover new RNA methyltransferases. We demonstrate that the methyltransferase-like 5 (METTL5) protein catalyzes m6A in 18S rRNA at position A1832 We report that absence of Mettl5 in mouse embryonic stem cells (mESCs) results in a decrease in global translation rate, spontaneous loss of pluripotency, and compromised differentiation potential. METTL5-deficient mice are born at non-Mendelian rates and develop morphological and behavioral abnormalities. Importantly, mice lacking METTL5 recapitulate symptoms of patients with DNA variants in METTL5, thereby providing a new mouse disease model. Overall, our biochemical, molecular, and in vivo characterization highlights the importance of m6A in rRNA in stemness, differentiation, development, and diseases.
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16
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Nishiyama A, Mulholland CB, Bultmann S, Kori S, Endo A, Saeki Y, Qin W, Trummer C, Chiba Y, Yokoyama H, Kumamoto S, Kawakami T, Hojo H, Nagae G, Aburatani H, Tanaka K, Arita K, Leonhardt H, Nakanishi M. Two distinct modes of DNMT1 recruitment ensure stable maintenance DNA methylation. Nat Commun 2020; 11:1222. [PMID: 32144273 PMCID: PMC7060239 DOI: 10.1038/s41467-020-15006-4] [Citation(s) in RCA: 74] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2019] [Accepted: 02/10/2020] [Indexed: 12/31/2022] Open
Abstract
Stable inheritance of DNA methylation is critical for maintaining differentiated phenotypes in multicellular organisms. We have recently identified dual mono-ubiquitylation of histone H3 (H3Ub2) by UHRF1 as an essential mechanism to recruit DNMT1 to chromatin. Here, we show that PCNA-associated factor 15 (PAF15) undergoes UHRF1-dependent dual mono-ubiquitylation (PAF15Ub2) on chromatin in a DNA replication-coupled manner. This event will, in turn, recruit DNMT1. During early S-phase, UHRF1 preferentially ubiquitylates PAF15, whereas H3Ub2 predominates during late S-phase. H3Ub2 is enhanced under PAF15 compromised conditions, suggesting that H3Ub2 serves as a backup for PAF15Ub2. In mouse ES cells, loss of PAF15Ub2 results in DNA hypomethylation at early replicating domains. Together, our results suggest that there are two distinct mechanisms underlying replication timing-dependent recruitment of DNMT1 through PAF15Ub2 and H3Ub2, both of which are prerequisite for high fidelity DNA methylation inheritance. Ubiquitylation of histone H3 (H3Ub2) by UHRF1 recruits DNMT1 to chromatin, which is essential for DNA methylation inheritance. Here, the authors provide evidence that there are two distinct mechanisms underlying replication timing-dependent recruitment of DNMT1 through PAF15Ub2 and H3Ub2, both of which are required for high fidelity DNA methylation inheritance.
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Affiliation(s)
- Atsuya Nishiyama
- Division of Cancer Cell Biology, The Institute of Medical Science, The University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo, Japan.
| | - Christopher B Mulholland
- Department of Biology II and Center for Integrated Protein Science Munich (CIPSM), Human Biology and BioImaging, Ludwig-Maximilians-Universität München, 82152, Planegg-Martinsried, Germany
| | - Sebastian Bultmann
- Department of Biology II and Center for Integrated Protein Science Munich (CIPSM), Human Biology and BioImaging, Ludwig-Maximilians-Universität München, 82152, Planegg-Martinsried, Germany
| | - Satomi Kori
- Structure Biology Laboratory, Graduate School of Medical Life Science, Yokohama City University, 1-7-29, Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, Japan
| | - Akinori Endo
- Laboratory of Protein Metabolism, Tokyo Metropolitan Institute of Medical Science, 2-1-6 Kamikitazawa, Setagaya-ku, Tokyo, Japan
| | - Yasushi Saeki
- Laboratory of Protein Metabolism, Tokyo Metropolitan Institute of Medical Science, 2-1-6 Kamikitazawa, Setagaya-ku, Tokyo, Japan
| | - Weihua Qin
- Department of Biology II and Center for Integrated Protein Science Munich (CIPSM), Human Biology and BioImaging, Ludwig-Maximilians-Universität München, 82152, Planegg-Martinsried, Germany
| | - Carina Trummer
- Department of Biology II and Center for Integrated Protein Science Munich (CIPSM), Human Biology and BioImaging, Ludwig-Maximilians-Universität München, 82152, Planegg-Martinsried, Germany
| | - Yoshie Chiba
- Division of Cancer Cell Biology, The Institute of Medical Science, The University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo, Japan
| | - Haruka Yokoyama
- Structure Biology Laboratory, Graduate School of Medical Life Science, Yokohama City University, 1-7-29, Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, Japan
| | - Soichiro Kumamoto
- Division of Cancer Cell Biology, The Institute of Medical Science, The University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo, Japan
| | - Toru Kawakami
- Laboratory of Protein Organic Chemistry, Institute for Protein Research, Osaka University, Suita, Osaka, Japan
| | - Hironobu Hojo
- Laboratory of Protein Organic Chemistry, Institute for Protein Research, Osaka University, Suita, Osaka, Japan
| | - Genta Nagae
- The Research Center for Advanced Science and Technology, University of Tokyo, 4-6-1 Komaba, Meguro-ku, Tokyo, Japan
| | - Hiroyuki Aburatani
- The Research Center for Advanced Science and Technology, University of Tokyo, 4-6-1 Komaba, Meguro-ku, Tokyo, Japan
| | - Keiji Tanaka
- Laboratory of Protein Metabolism, Tokyo Metropolitan Institute of Medical Science, 2-1-6 Kamikitazawa, Setagaya-ku, Tokyo, Japan
| | - Kyohei Arita
- Structure Biology Laboratory, Graduate School of Medical Life Science, Yokohama City University, 1-7-29, Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, Japan.
| | - Heinrich Leonhardt
- Department of Biology II and Center for Integrated Protein Science Munich (CIPSM), Human Biology and BioImaging, Ludwig-Maximilians-Universität München, 82152, Planegg-Martinsried, Germany.
| | - Makoto Nakanishi
- Division of Cancer Cell Biology, The Institute of Medical Science, The University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo, Japan.
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17
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Deng W, Bates JA, Wei H, Bartoschek MD, Conradt B, Leonhardt H. Tunable light and drug induced depletion of target proteins. Nat Commun 2020; 11:304. [PMID: 31949141 PMCID: PMC6965615 DOI: 10.1038/s41467-019-14160-8] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2019] [Accepted: 12/12/2019] [Indexed: 12/28/2022] Open
Abstract
Biological processes in development and disease are controlled by the abundance, localization and modification of cellular proteins. We have developed versatile tools based on recombinant E3 ubiquitin ligases that are controlled by light or drug induced heterodimerization for nanobody or DARPin targeted depletion of endogenous proteins in cells and organisms. We use this rapid, tunable and reversible protein depletion for functional studies of essential proteins like PCNA in DNA repair and to investigate the role of CED-3 in apoptosis during Caenorhabditis elegans development. These independent tools can be combined for spatial and temporal depletion of different sets of proteins, can help to distinguish immediate cellular responses from long-term adaptation effects and can facilitate the exploration of complex networks.
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Affiliation(s)
- Wen Deng
- Department of Biology II, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Jack A Bates
- Department of Biology II, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Hai Wei
- Department of Biology II, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Michael D Bartoschek
- Department of Biology II, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Barbara Conradt
- Department of Biology II, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Heinrich Leonhardt
- Department of Biology II, Ludwig-Maximilians-Universität München, Munich, Germany.
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18
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Vandemoortele G, De Sutter D, Moliere A, Pauwels J, Gevaert K, Eyckerman S. A Well-Controlled BioID Design for Endogenous Bait Proteins. J Proteome Res 2018; 18:95-106. [PMID: 30525648 DOI: 10.1021/acs.jproteome.8b00367] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
The CRISPR/Cas9 revolution is profoundly changing the way life sciences technologies are used. Many assays now rely on engineered clonal cell lines to eliminate the overexpression of bait proteins. Control cell lines are typically nonengineered cells or engineered clones, implying a considerable risk for artifacts because of clonal variation. Genome engineering can also transform BioID, a proximity labeling method that relies on fusing a bait protein to a promiscuous biotin ligase, BirA*, resulting in the tagging of vicinal proteins. We here propose an innovative design to enable BioID for endogenous proteins wherein we introduce a T2A-BirA* module at the C-terminus of endogenous p53 by genome engineering, leading to bicistronic expression of both p53 and BirA* under control of the endogenous promoter. By targeting a Cas9-cytidine deaminase base editor to the T2A autocleavage site, we can efficiently derive an isogenic population expressing a functional p53-BirA* fusion protein. Using quantitative proteomics we show significant benefits over the classical ectopic expression of p53-BirA*, and we provide a first well-controlled view of the proximal proteins of endogenous p53 in colon carcinoma cells. This novel application for base editors expands the CRISPR/Cas9 toolbox and can be a valuable addition for synthetic biology.
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Affiliation(s)
- Giel Vandemoortele
- VIB Center for Medical Biotechnology, VIB , B-9000 Ghent , Belgium.,Department of Biomolecular Medicine , Ghent University , B-9000 Ghent , Belgium
| | - Delphine De Sutter
- VIB Center for Medical Biotechnology, VIB , B-9000 Ghent , Belgium.,Department of Biomolecular Medicine , Ghent University , B-9000 Ghent , Belgium
| | - Aline Moliere
- VIB Center for Medical Biotechnology, VIB , B-9000 Ghent , Belgium.,Department of Biomolecular Medicine , Ghent University , B-9000 Ghent , Belgium
| | - Jarne Pauwels
- VIB Center for Medical Biotechnology, VIB , B-9000 Ghent , Belgium.,Department of Biomolecular Medicine , Ghent University , B-9000 Ghent , Belgium
| | - Kris Gevaert
- VIB Center for Medical Biotechnology, VIB , B-9000 Ghent , Belgium.,Department of Biomolecular Medicine , Ghent University , B-9000 Ghent , Belgium
| | - Sven Eyckerman
- VIB Center for Medical Biotechnology, VIB , B-9000 Ghent , Belgium.,Department of Biomolecular Medicine , Ghent University , B-9000 Ghent , Belgium
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19
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Foster BM, Stolz P, Mulholland CB, Montoya A, Kramer H, Bultmann S, Bartke T. Critical Role of the UBL Domain in Stimulating the E3 Ubiquitin Ligase Activity of UHRF1 toward Chromatin. Mol Cell 2018; 72:739-752.e9. [PMID: 30392929 PMCID: PMC6242706 DOI: 10.1016/j.molcel.2018.09.028] [Citation(s) in RCA: 50] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2018] [Revised: 08/09/2018] [Accepted: 09/20/2018] [Indexed: 12/31/2022]
Abstract
The RING E3 ubiquitin ligase UHRF1 controls DNA methylation through its ability to target the maintenance DNA methyltransferase DNMT1 to newly replicated chromatin. DNMT1 recruitment relies on ubiquitylation of histone H3 by UHRF1; however, how UHRF1 deposits ubiquitin onto the histone is unknown. Here, we demonstrate that the ubiquitin-like domain (UBL) of UHRF1 is essential for RING-mediated H3 ubiquitylation. Using chemical crosslinking and mass spectrometry, biochemical assays, and recombinant chromatin substrates, we show that the UBL participates in structural rearrangements of UHRF1 upon binding to chromatin and the E2 ubiquitin conjugating enzyme UbcH5a/UBE2D1. Similar to ubiquitin, the UBL exerts its effects through a hydrophobic patch that contacts a regulatory surface on the “backside” of the E2 to stabilize the E2-E3-chromatin complex. Our analysis of the enzymatic mechanism of UHRF1 uncovers an unexpected function of the UBL domain and defines a new role for this domain in DNMT1-dependent inheritance of DNA methylation. The UBL domain of UHRF1 is required for its E3 ubiquitin ligase activity A hydrophobic patch on the UBL is required to form a stable E2/E3/chromatin complex The UHRF1 N terminus and UBL hydrophobic patch control targeted H3 ubiquitylation DNMT1-mediated maintenance DNA methylation requires the UBL hydrophobic patch
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Affiliation(s)
- Benjamin M Foster
- Institute of Functional Epigenetics, Helmholtz Zentrum München, 85764 Neuherberg, Germany; MRC London Institute of Medical Sciences (LMS), Du Cane Road, London W12 0NN, UK; Institute of Clinical Sciences (ICS), Faculty of Medicine, Imperial College London, Du Cane Road, London W12 0NN, UK
| | - Paul Stolz
- Department of Biology II, Center for Integrated Protein Science Munich, Ludwig Maximilians University (LMU Munich), 82152 Planegg-Martinsried, Germany
| | - Christopher B Mulholland
- Department of Biology II, Center for Integrated Protein Science Munich, Ludwig Maximilians University (LMU Munich), 82152 Planegg-Martinsried, Germany
| | - Alex Montoya
- MRC London Institute of Medical Sciences (LMS), Du Cane Road, London W12 0NN, UK
| | - Holger Kramer
- MRC London Institute of Medical Sciences (LMS), Du Cane Road, London W12 0NN, UK
| | - Sebastian Bultmann
- Department of Biology II, Center for Integrated Protein Science Munich, Ludwig Maximilians University (LMU Munich), 82152 Planegg-Martinsried, Germany
| | - Till Bartke
- Institute of Functional Epigenetics, Helmholtz Zentrum München, 85764 Neuherberg, Germany; MRC London Institute of Medical Sciences (LMS), Du Cane Road, London W12 0NN, UK; Institute of Clinical Sciences (ICS), Faculty of Medicine, Imperial College London, Du Cane Road, London W12 0NN, UK.
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20
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Fischer K, Kind A, Schnieke A. Assembling multiple xenoprotective transgenes in pigs. Xenotransplantation 2018; 25:e12431. [PMID: 30055014 DOI: 10.1111/xen.12431] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2018] [Revised: 04/24/2018] [Accepted: 05/24/2018] [Indexed: 12/20/2022]
Abstract
This review gives a brief overview of the genetic modifications necessary for grafted porcine tissues and organs to overcome rejection in human recipients. It then focuses on the problem of generating and breeding herds of donor pigs carrying modified endogenous genes and multiple xenoprotective transgenes. A xenodonor pig optimised for human clinical use could well require the addition of ten or more xenoprotective transgenes. It is impractical to produce the required combination of transgene by cross-breeding animals bearing individual transgenes at unlinked genetic loci, because independent segregation means that huge numbers of pigs would be required to produce relatively few donor animals. A better approach is to colocate groups of transgenes at a single genomic locus. We outline current methods to assemble transgene arrays and consider their pros and cons. These include polycistronic expression systems, in vitro recombination of large DNA fragments in PAC and BAC vectors, transposon vectors, classical gene targeting by homologous recombination at permissive loci such as ROSA26, targeted transgene placement aided by gene editing systems such as CRISPR/Cas9, and transgene placement by site-specific recombination such as Min-tagging using the Bxb1recombinase.
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Affiliation(s)
- Konrad Fischer
- Chair of Livestock Biotechnology, School of Life Sciences Weihenstephan, Technische Universität München, Freising, Germany
| | - Alexander Kind
- Chair of Livestock Biotechnology, School of Life Sciences Weihenstephan, Technische Universität München, Freising, Germany
| | - Angelika Schnieke
- Chair of Livestock Biotechnology, School of Life Sciences Weihenstephan, Technische Universität München, Freising, Germany
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21
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Ubiquitome Analysis Reveals PCNA-Associated Factor 15 (PAF15) as a Specific Ubiquitination Target of UHRF1 in Embryonic Stem Cells. J Mol Biol 2017; 429:3814-3824. [DOI: 10.1016/j.jmb.2017.10.014] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2017] [Revised: 09/26/2017] [Accepted: 10/12/2017] [Indexed: 12/30/2022]
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22
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Matreyek KA, Stephany JJ, Fowler DM. A platform for functional assessment of large variant libraries in mammalian cells. Nucleic Acids Res 2017; 45:e102. [PMID: 28335006 PMCID: PMC5499817 DOI: 10.1093/nar/gkx183] [Citation(s) in RCA: 77] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2016] [Accepted: 03/08/2017] [Indexed: 01/01/2023] Open
Abstract
Sequencing-based, massively parallel genetic assays have revolutionized our ability to quantify the relationship between many genotypes and a phenotype of interest. Unfortunately, variant library expression platforms in mammalian cells are far from ideal, hindering the study of human gene variants in their physiologically relevant cellular contexts. Here, we describe a platform for phenotyping variant libraries in transfectable mammalian cell lines in two steps. First, a landing pad cell line with a genomically integrated, Tet-inducible cassette containing a Bxb1 recombination site is created. Second, a single variant from a library of transfected, promoter-less plasmids is recombined into the landing pad in each cell. Thus, every cell in the recombined pool expresses a single variant, allowing for parallel, sequencing-based assessment of variant effect. We describe a method for incorporating a single landing pad into a defined site of a cell line of interest, and show that our approach can be used generate more than 20 000 recombinant cells in a single experiment. Finally, we use our platform in combination with a sequencing-based assay to explore the N-end rule by simultaneously measuring the effects of all possible N-terminal amino acids on protein expression.
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Affiliation(s)
- Kenneth A Matreyek
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
| | - Jason J Stephany
- Department of Bioengineering, University of Washington, Seattle, WA 98195, USA
| | - Douglas M Fowler
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA.,Department of Bioengineering, University of Washington, Seattle, WA 98195, USA
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23
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Gressel S, Schwalb B, Decker TM, Qin W, Leonhardt H, Eick D, Cramer P. CDK9-dependent RNA polymerase II pausing controls transcription initiation. eLife 2017; 6:29736. [PMID: 28994650 PMCID: PMC5669633 DOI: 10.7554/elife.29736] [Citation(s) in RCA: 150] [Impact Index Per Article: 21.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2017] [Accepted: 10/06/2017] [Indexed: 12/11/2022] Open
Abstract
Gene transcription can be activated by decreasing the duration of RNA polymerase II pausing in the promoter-proximal region, but how this is achieved remains unclear. Here we use a 'multi-omics' approach to demonstrate that the duration of polymerase pausing generally limits the productive frequency of transcription initiation in human cells ('pause-initiation limit'). We further engineer a human cell line to allow for specific and rapid inhibition of the P-TEFb kinase CDK9, which is implicated in polymerase pause release. CDK9 activity decreases the pause duration but also increases the productive initiation frequency. This shows that CDK9 stimulates release of paused polymerase and activates transcription by increasing the number of transcribing polymerases and thus the amount of mRNA synthesized per time. CDK9 activity is also associated with long-range chromatin interactions, suggesting that enhancers can influence the pause-initiation limit to regulate transcription.
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Affiliation(s)
- Saskia Gressel
- Department of Molecular Biology, Max-Planck-Institute for Biophysical Chemistry, Göttingen, Germany
| | - Björn Schwalb
- Department of Molecular Biology, Max-Planck-Institute for Biophysical Chemistry, Göttingen, Germany
| | - Tim Michael Decker
- Department of Molecular Epigenetics, Helmholtz Center Munich, Center of Integrated Protein Science, Munich, Germany
| | - Weihua Qin
- Department of Biology II, Ludwig-Maximilians-Universität München, Center of Integrated Protein Science, Martinsried, Germany
| | - Heinrich Leonhardt
- Department of Biology II, Ludwig-Maximilians-Universität München, Center of Integrated Protein Science, Martinsried, Germany
| | - Dirk Eick
- Department of Molecular Epigenetics, Helmholtz Center Munich, Center of Integrated Protein Science, Munich, Germany
| | - Patrick Cramer
- Department of Molecular Biology, Max-Planck-Institute for Biophysical Chemistry, Göttingen, Germany
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24
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Dahlhoff M, Gaborit N, Bultmann S, Leonhardt H, Yarden Y, Schneider MR. CRISPR-assisted receptor deletion reveals distinct roles for ERBB2 and ERBB3 in skin keratinocytes. FEBS J 2017; 284:3339-3349. [DOI: 10.1111/febs.14196] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2017] [Revised: 07/25/2017] [Accepted: 08/10/2017] [Indexed: 01/06/2023]
Affiliation(s)
- Maik Dahlhoff
- Institute of Molecular Animal Breeding and Biotechnology; LMU Munich; Germany
| | - Nadège Gaborit
- Department of Biological Regulation; Weizmann Institute of Science; Rehovot Israel
| | - Sebastian Bultmann
- Human Biology and BioImaging; Department of Biology II; LMU Munich; Germany
| | - Heinrich Leonhardt
- Human Biology and BioImaging; Department of Biology II; LMU Munich; Germany
| | - Yosef Yarden
- Department of Biological Regulation; Weizmann Institute of Science; Rehovot Israel
| | - Marlon R. Schneider
- German Centre for the Protection of Laboratory Animals (Bf3R); German Federal Institute for Risk Assessment (BfR); Berlin Germany
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25
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Pünzeler S, Link S, Wagner G, Keilhauer EC, Kronbeck N, Spitzer RM, Leidescher S, Markaki Y, Mentele E, Regnard C, Schneider K, Takahashi D, Kusakabe M, Vardabasso C, Zink LM, Straub T, Bernstein E, Harata M, Leonhardt H, Mann M, Rupp RA, Hake SB. Multivalent binding of PWWP2A to H2A.Z regulates mitosis and neural crest differentiation. EMBO J 2017. [PMID: 28645917 DOI: 10.15252/embj.201695757] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
Replacement of canonical histones with specialized histone variants promotes altering of chromatin structure and function. The essential histone variant H2A.Z affects various DNA-based processes via poorly understood mechanisms. Here, we determine the comprehensive interactome of H2A.Z and identify PWWP2A as a novel H2A.Z-nucleosome binder. PWWP2A is a functionally uncharacterized, vertebrate-specific protein that binds very tightly to chromatin through a concerted multivalent binding mode. Two internal protein regions mediate H2A.Z-specificity and nucleosome interaction, whereas the PWWP domain exhibits direct DNA binding. Genome-wide mapping reveals that PWWP2A binds selectively to H2A.Z-containing nucleosomes with strong preference for promoters of highly transcribed genes. In human cells, its depletion affects gene expression and impairs proliferation via a mitotic delay. While PWWP2A does not influence H2A.Z occupancy, the C-terminal tail of H2A.Z is one important mediator to recruit PWWP2A to chromatin. Knockdown of PWWP2A in Xenopus results in severe cranial facial defects, arising from neural crest cell differentiation and migration problems. Thus, PWWP2A is a novel H2A.Z-specific multivalent chromatin binder providing a surprising link between H2A.Z, chromosome segregation, and organ development.
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Affiliation(s)
- Sebastian Pünzeler
- Department of Molecular Biology, BioMedical Center (BMC), Ludwig-Maximilians-Universität München, Planegg-Martinsried, Germany
| | - Stephanie Link
- Department of Molecular Biology, BioMedical Center (BMC), Ludwig-Maximilians-Universität München, Planegg-Martinsried, Germany
| | - Gabriele Wagner
- Department of Molecular Biology, BioMedical Center (BMC), Ludwig-Maximilians-Universität München, Planegg-Martinsried, Germany
| | - Eva C Keilhauer
- Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Nina Kronbeck
- Department of Molecular Biology, BioMedical Center (BMC), Ludwig-Maximilians-Universität München, Planegg-Martinsried, Germany
| | - Ramona Mm Spitzer
- Department of Molecular Biology, BioMedical Center (BMC), Ludwig-Maximilians-Universität München, Planegg-Martinsried, Germany
| | - Susanne Leidescher
- Department of Biology, Biozentrum, Ludwig-Maximilians-Universität München, Planegg-Martinsried, Germany
| | - Yolanda Markaki
- Department of Biology, Biozentrum, Ludwig-Maximilians-Universität München, Planegg-Martinsried, Germany
| | - Edith Mentele
- Department of Molecular Biology, BioMedical Center (BMC), Ludwig-Maximilians-Universität München, Planegg-Martinsried, Germany
| | - Catherine Regnard
- Department of Molecular Biology, BioMedical Center (BMC), Ludwig-Maximilians-Universität München, Planegg-Martinsried, Germany
| | - Katrin Schneider
- Department of Biology, Biozentrum, Ludwig-Maximilians-Universität München, Planegg-Martinsried, Germany
| | - Daisuke Takahashi
- Laboratory of Molecular Biology, Graduate School of Agricultural Science, Tohoku University, Aoba-ku Sendai, Japan
| | - Masayuki Kusakabe
- Laboratory of Molecular Biology, Graduate School of Agricultural Science, Tohoku University, Aoba-ku Sendai, Japan
| | - Chiara Vardabasso
- Department of Oncological Sciences and Dermatology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Lisa M Zink
- Department of Molecular Biology, BioMedical Center (BMC), Ludwig-Maximilians-Universität München, Planegg-Martinsried, Germany
| | - Tobias Straub
- Department of Molecular Biology, BioMedical Center (BMC), Ludwig-Maximilians-Universität München, Planegg-Martinsried, Germany
| | - Emily Bernstein
- Department of Oncological Sciences and Dermatology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Masahiko Harata
- Laboratory of Molecular Biology, Graduate School of Agricultural Science, Tohoku University, Aoba-ku Sendai, Japan
| | - Heinrich Leonhardt
- Department of Biology, Biozentrum, Ludwig-Maximilians-Universität München, Planegg-Martinsried, Germany.,Center for Integrated Protein Science Munich (CIPSM), Munich, Germany
| | - Matthias Mann
- Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, Germany.,Center for Integrated Protein Science Munich (CIPSM), Munich, Germany
| | - Ralph Aw Rupp
- Department of Molecular Biology, BioMedical Center (BMC), Ludwig-Maximilians-Universität München, Planegg-Martinsried, Germany
| | - Sandra B Hake
- Department of Molecular Biology, BioMedical Center (BMC), Ludwig-Maximilians-Universität München, Planegg-Martinsried, Germany .,Center for Integrated Protein Science Munich (CIPSM), Munich, Germany
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26
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Abstract
When constructing transgenic cell lines via plasmid DNA integration, precise targeting to a desired genomic location is advantageous. It is also often advantageous to remove the bacterial backbone, since bacterial elements can lead to the epigenetic silencing of neighboring DNA. The least cumbersome method to remove the plasmid backbone is recombinase-mediated cassette exchange (RMCE). RMCE is accomplished by arranging recombinase sites in the genome and in a donor plasmid such that a recombinase can both integrate the donor plasmid and excise its bacterial backbone. When a single recombinase is used for RMCE, recombination between undesired pairings of the sites can lead to a significant number of unwanted cell lines. To reduce the frequency with which these side products occur, several variants of RMCE that increase desired outcomes have been developed. Nevertheless, an important feature lacking from these improved RMCE methods is that none have fully utilized the recombinases that have been demonstrated to be the most robust and stringent at performing genomic integration in plants and animals, i.e., the phiC31 and Bxb1 phage integrases. To address this need, we have developed an RMCE protocol using these two serine integrases that we call dual integrase cassette exchange (DICE). Our DICE system provides a means to achieve high-precision DNA integration at a desired location and is especially well suited for repeated recombination into the same locus. In this chapter, we provide our most current protocols for using DICE in feeder-free human-induced pluripotent stem cells .
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Affiliation(s)
- Alfonso P Farruggio
- Department of Genetics, Stanford University School of Medicine, 300 Pasteur Drive, Alway Building, M316, Stanford, CA, 94305-5120, USA
| | - Mital S Bhakta
- Department of Genetics, Stanford University School of Medicine, 300 Pasteur Drive, Alway Building, M316, Stanford, CA, 94305-5120, USA
| | - Michele P Calos
- Department of Genetics, Stanford University School of Medicine, 300 Pasteur Drive, Alway Building, M316, Stanford, CA, 94305-5120, USA.
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27
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Abstract
Chromatin structure and function are determined by a plethora of proteins whose genome-wide distribution is typically assessed by immunoprecipitation (ChIP). Here, we developed a novel tool to investigate the local chromatin environment at specific DNA sequences. We combined the programmable DNA binding of dCas9 with the promiscuous biotin ligase BirA* (CasID) to biotinylate proteins in the direct vicinity of specific loci. Subsequent streptavidin-mediated precipitation and mass spectrometry identified both known and previously unknown chromatin factors associated with repetitive telomeric, major satellite and minor satellite DNA. With super-resolution microscopy, we confirmed the localization of the putative transcription factor ZNF512 at chromocenters. The versatility of CasID facilitates the systematic elucidation of functional protein complexes and locus-specific chromatin composition.
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Affiliation(s)
- Elisabeth Schmidtmann
- a Department of Biology II and Center for Integrated Protein Science Munich (CIPSM) , LMU Munich , Martinsried , Germany
| | - Tobias Anton
- a Department of Biology II and Center for Integrated Protein Science Munich (CIPSM) , LMU Munich , Martinsried , Germany
| | - Pascaline Rombaut
- b Gene Center and Department of Biochemistry , LMU Munich , Munich , Germany
| | - Franz Herzog
- b Gene Center and Department of Biochemistry , LMU Munich , Munich , Germany
| | - Heinrich Leonhardt
- a Department of Biology II and Center for Integrated Protein Science Munich (CIPSM) , LMU Munich , Martinsried , Germany
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28
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Filling the Void: Proximity-Based Labeling of Proteins in Living Cells. Trends Cell Biol 2016; 26:804-817. [PMID: 27667171 DOI: 10.1016/j.tcb.2016.09.004] [Citation(s) in RCA: 186] [Impact Index Per Article: 23.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2016] [Revised: 08/30/2016] [Accepted: 09/02/2016] [Indexed: 12/17/2022]
Abstract
There are inherent limitations with traditional methods to study protein behavior or to determine the constituency of proteins in discrete subcellular compartments. In response to these limitations, several methods have recently been developed that use proximity-dependent labeling. By fusing proteins to enzymes that generate reactive molecules, most commonly biotin, proximate proteins are covalently labeled to enable their isolation and identification. In this review we describe current methods for proximity-dependent labeling in living cells and discuss their applications and future use in the study of protein behavior.
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29
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Callesen MM, Berthelsen MF, Lund S, Füchtbauer AC, Füchtbauer EM, Jakobsen JE. Recombinase-Mediated Cassette Exchange (RMCE)-in Reporter Cell Lines as an Alternative to the Flp-in System. PLoS One 2016; 11:e0161471. [PMID: 27541869 PMCID: PMC4991790 DOI: 10.1371/journal.pone.0161471] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2016] [Accepted: 08/06/2016] [Indexed: 11/18/2022] Open
Abstract
Recombinase mediated cassette exchange (RMCE) is a powerful tool for targeted insertion of transgenes. Here we describe non-proprietary 'RMCE-in' cell lines as an alternative to the 'Flp-in' system and cell lines. RMCE-in cell lines offer a number of advantages including increased efficiency of integration of the genetic element of interest (GEI) at a single docking site, lack of bacterial backbone at the docking site both before and after GEI integration, removal of selection and visual markers initially present at the docking site upon GEI integration and the possibility to validate GEI integration by loss of a red fluorescence reporter. Moreover, the RMCE-in cell lines are compatible with GEI donors used for the Flp-in system. We demonstrate a three-step procedure for generating RMCE-in cell lines, (I) RMCE-in transposon and SB10 transposase transfection, (II) clone isolation, and (III) selecting single integrated clones with highest RFP level, which could in principle be used to turn any cell line into an RMCE-in cell line. The RMCE-in system was used as a proof of concept to produce three new RMCE-in cell lines using HEK293, HeLa, and murine embryonic stem (mES) cells. The established RMCE-in cell lines and vector are freely available from the ATCC cell bank and Addgene respectively.
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Affiliation(s)
- Morten M. Callesen
- Department of Biomedicine, Faculty of Health, Aarhus University, Aarhus C, Denmark
- Department of Clinical Medicine, Faculty of Health, Aarhus University, Aarhus N, Denmark
| | - Martin F. Berthelsen
- Department of Biomedicine, Faculty of Health, Aarhus University, Aarhus C, Denmark
- Department of Clinical Medicine, Faculty of Health, Aarhus University, Aarhus N, Denmark
| | - Sira Lund
- Department of Biomedicine, Faculty of Health, Aarhus University, Aarhus C, Denmark
| | | | | | - Jannik E. Jakobsen
- Department of Biomedicine, Faculty of Health, Aarhus University, Aarhus C, Denmark
- Department of Clinical Medicine, Faculty of Health, Aarhus University, Aarhus N, Denmark
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Varnaitė R, MacNeill SA. Meet the neighbors: Mapping local protein interactomes by proximity-dependent labeling with BioID. Proteomics 2016; 16:2503-2518. [PMID: 27329485 PMCID: PMC5053326 DOI: 10.1002/pmic.201600123] [Citation(s) in RCA: 109] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2016] [Revised: 05/23/2016] [Accepted: 06/16/2016] [Indexed: 12/13/2022]
Abstract
Proximity-dependent biotin identification (BioID) is a recently developed method that allows the identification of proteins in the close vicinity of a protein of interest in living cells. BioID relies on fusion of the protein of interest with a mutant form of the biotin ligase enzyme BirA (BirA*) that is capable of promiscuously biotinylating proximal proteins irrespective of whether these interact directly or indirectly with the fusion protein or are merely located in the same subcellular neighborhood. The covalent addition of biotin allows the labeled proteins to be purified from cell extracts on the basis of their affinity for streptavidin and identified by mass spectrometry. To date, BioID has been successfully applied to study a variety of proteins and processes in mammalian cells and unicellular eukaryotes and has been shown to be particularly suited to the study of insoluble or inaccessible cellular structures and for detecting weak or transient protein associations. Here, we provide an introduction to BioID, together with a detailed summary of where and how the method has been applied to date, and briefly discuss technical aspects involved in the planning and execution of a BioID study.
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Affiliation(s)
- Renata Varnaitė
- School of Biology, University of St Andrews, North Haugh, St Andrews, Scotland, UK
| | - Stuart A MacNeill
- School of Biology, University of St Andrews, North Haugh, St Andrews, Scotland, UK.
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Kim DI, Jensen SC, Noble KA, Kc B, Roux KH, Motamedchaboki K, Roux KJ. An improved smaller biotin ligase for BioID proximity labeling. Mol Biol Cell 2016; 27:1188-96. [PMID: 26912792 PMCID: PMC4831873 DOI: 10.1091/mbc.e15-12-0844] [Citation(s) in RCA: 517] [Impact Index Per Article: 64.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2015] [Accepted: 02/16/2016] [Indexed: 12/20/2022] Open
Abstract
A smaller promiscuous biotin ligase for proximity biotinylation called BioID2 enables more-selective targeting of fusion proteins, requires less biotin supplementation, exhibits enhanced labeling of proximate proteins, and demonstrates the use of a flexible linker to modulate the biotin-labeling radius. The BioID method uses a promiscuous biotin ligase to detect protein–protein associations as well as proximate proteins in living cells. Here we report improvements to the BioID method centered on BioID2, a substantially smaller promiscuous biotin ligase. BioID2 enables more-selective targeting of fusion proteins, requires less biotin supplementation, and exhibits enhanced labeling of proximate proteins. Thus BioID2 improves the efficiency of screening for protein–protein associations. We also demonstrate that the biotinylation range of BioID2 can be considerably modulated using flexible linkers, thus enabling application-specific adjustment of the biotin-labeling radius.
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Affiliation(s)
- Dae In Kim
- Sanford Children's Health Research Center, Sanford Research, Sioux Falls, SD 57104
| | - Samuel C Jensen
- Sanford Children's Health Research Center, Sanford Research, Sioux Falls, SD 57104
| | - Kyle A Noble
- Department of Biological Science, Florida State University, Tallahassee, FL 32306
| | - Birendra Kc
- Sanford Children's Health Research Center, Sanford Research, Sioux Falls, SD 57104
| | - Kenneth H Roux
- Department of Biological Science, Florida State University, Tallahassee, FL 32306
| | - Khatereh Motamedchaboki
- Sanford-Burnham Proteomics Facility, Sanford-Burnham Medical Research Institute, La Jolla, CA 92037
| | - Kyle J Roux
- Sanford Children's Health Research Center, Sanford Research, Sioux Falls, SD 57104 Department of Pediatrics, Sanford School of Medicine, University of South Dakota, Sioux Falls, SD 57105
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Engqvist MKM. Highlighting the Need for Systems-Level Experimental Characterization of Plant Metabolic Enzymes. FRONTIERS IN PLANT SCIENCE 2016; 7:1127. [PMID: 27516767 PMCID: PMC4963410 DOI: 10.3389/fpls.2016.01127] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/17/2016] [Accepted: 07/14/2016] [Indexed: 05/15/2023]
Abstract
The biology of living organisms is determined by the action and interaction of a large number of individual gene products, each with specific functions. Discovering and annotating the function of gene products is key to our understanding of these organisms. Controlled experiments and bioinformatic predictions both contribute to functional gene annotation. For most species it is difficult to gain an overview of what portion of gene annotations are based on experiments and what portion represent predictions. Here, I survey the current state of experimental knowledge of enzymes and metabolism in Arabidopsis thaliana as well as eleven economically important crops and forestry trees - with a particular focus on reactions involving organic acids in central metabolism. I illustrate the limited availability of experimental data for functional annotation of enzymes in most of these species. Many enzymes involved in metabolism of citrate, malate, fumarate, lactate, and glycolate in crops and forestry trees have not been characterized. Furthermore, enzymes involved in key biosynthetic pathways which shape important traits in crops and forestry trees have not been characterized. I argue for the development of novel high-throughput platforms with which limited functional characterization of gene products can be performed quickly and relatively cheaply. I refer to this approach as systems-level experimental characterization. The data collected from such platforms would form a layer intermediate between bioinformatic gene function predictions and in-depth experimental studies of these functions. Such a data layer would greatly aid in the pursuit of understanding a multiplicity of biological processes in living organisms.
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