1
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Angelov D, Boopathi R, Lone IN, Menoni H, Dimitrov S, Cadet J. Capturing Protein-Nucleic Acid Interactions by High-Intensity Laser-Induced Covalent Crosslinking. Photochem Photobiol 2022; 99:296-312. [PMID: 35997098 DOI: 10.1111/php.13699] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Accepted: 07/21/2022] [Indexed: 11/30/2022]
Abstract
Interactions of DNA with structural proteins such as histones, regulatory proteins, and enzymes play a crucial role in major cellular processes such as transcription, replication and repair. The in vivo mapping and characterization of the binding sites of the involved biomolecules are of primary importance for a better understanding of genomic deployment that is implicated in tissue and developmental stage-specific gene expression regulation. The most powerful and commonly used approach to date is immunoprecipitation of chemically cross-linked chromatin (XChIP) coupled with sequencing analysis (ChIP-seq). While the resolution and the sensitivity of the high-throughput sequencing techniques have been constantly improved little progress has been achieved in the crosslinking step. Because of its low efficiency the use of the conventional UVC lamps remains very limited while the formaldehyde method was established as the "gold standard" crosslinking agent. Efficient biphotonic crosslinking of directly interacting nucleic acid-protein complexes by a single short UV laser pulse has been introduced as an innovative technique for overcoming limitations of conventionally used chemical and photochemical approaches. In this survey, the main available methods including the laser approach are critically reviewed for their ability to generate DNA-protein crosslinks in vitro model systems and cells.
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Affiliation(s)
- Dimitar Angelov
- Université de Lyon, Ecole Normale Supérieure de Lyon, CNRS, Laboratoire de Biologie et de Modélisation de la Cellule LBMC, CNRS UMR 5239, 46 Allée d'Italie, 69007, Lyon, France.,Izmir Biomedicine and Genome Center, Dokuz Eylul University Health Campus, Balçova, Izmir 35330, Turkey
| | - Ramachandran Boopathi
- Université de Lyon, Ecole Normale Supérieure de Lyon, CNRS, Laboratoire de Biologie et de Modélisation de la Cellule LBMC, CNRS UMR 5239, 46 Allée d'Italie, 69007, Lyon, France.,Université Grenoble Alpes, CNRS, CEA, Institut de Biologie Structurale (IBS), 38000, Grenoble, France
| | - Imtiaz Nisar Lone
- Izmir Biomedicine and Genome Center, Dokuz Eylul University Health Campus, Balçova, Izmir 35330, Turkey
| | - Hervé Menoni
- Université Grenoble Alpes, CNRS UMR 5309, INSERM U1209, Institute for Advanced Biosciences (IAB), Site Santé - Allée des Alpes, 38700, La Tronche, France
| | - Stefan Dimitrov
- Université Grenoble Alpes, CNRS UMR 5309, INSERM U1209, Institute for Advanced Biosciences (IAB), Site Santé - Allée des Alpes, 38700, La Tronche, France
| | - Jean Cadet
- Département de Médecine nucléaire et Radiobiologie, Faculté de Médecine, Université de Sherbrooke, Sherbrooke, J1H 5N4, Québec, Canada
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2
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Wei YB, Luo D, Xiong X, Huang YL, Xie M, Lu W, Li D. Biomimetic mimicry of formaldehyde-induced DNA-protein crosslinks in the confined space of a metal-organic framework. Chem Sci 2022; 13:4813-4820. [PMID: 35655868 PMCID: PMC9067591 DOI: 10.1039/d2sc00188h] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Accepted: 03/18/2022] [Indexed: 02/05/2023] Open
Abstract
DNA-protein crosslinks (DPCs) are highly toxic DNA lesions induced by crosslinking agents such as formaldehyde (HCHO). Building artificial models to simulate the crosslinking process would advance our understanding of the underlying mechanisms and therefore develop coping strategies accordingly. Herein we report the design and synthesis of a Zn-based metal-organic framework with mixed ligands of 2,6-diaminopurine and amine-functionalized dicarboxylate, representing DNA and protein residues, respectively. Combined characterization techniques allow us to demonstrate the unusual efficiency of HCHO-crosslinking within the confined space of the titled MOF. Particularly, in situ single-crystal X-ray diffraction studies reveal a sequential methylene-knitting process upon HCHO addition, along with strong fluorescence that was not interfered with by other metabolites, glycine, and Tris. This work has successfully constructed a purine-based metal-organic framework with unoccupied Watson-Crick sites, serving as a crystalline model for HCHO-induced DPCs by mimicking the confinement effect of protein/DNA interactions.
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Affiliation(s)
- Yu-Bai Wei
- College of Chemistry and Materials Science, Guangdong Provincial Key Laboratory of Functional Supramolecular Coordination Materials and Applications, Jinan University Guangzhou 510632 P. R. China
| | - Dong Luo
- College of Chemistry and Materials Science, Guangdong Provincial Key Laboratory of Functional Supramolecular Coordination Materials and Applications, Jinan University Guangzhou 510632 P. R. China
| | - Xiao Xiong
- College of Chemistry and Materials Science, Guangdong Provincial Key Laboratory of Functional Supramolecular Coordination Materials and Applications, Jinan University Guangzhou 510632 P. R. China
| | - Yong-Liang Huang
- Department of Chemistry, Shantou University Medical College Shantou Guangdong 515041 P. R. China
| | - Mo Xie
- College of Chemistry and Materials Science, Guangdong Provincial Key Laboratory of Functional Supramolecular Coordination Materials and Applications, Jinan University Guangzhou 510632 P. R. China
| | - Weigang Lu
- College of Chemistry and Materials Science, Guangdong Provincial Key Laboratory of Functional Supramolecular Coordination Materials and Applications, Jinan University Guangzhou 510632 P. R. China
| | - Dan Li
- College of Chemistry and Materials Science, Guangdong Provincial Key Laboratory of Functional Supramolecular Coordination Materials and Applications, Jinan University Guangzhou 510632 P. R. China
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3
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Dirks RAM, Thomas PC, Wu H, Jones RC, Stunnenberg HG, Marks H. A plug and play microfluidic platform for standardized sensitive low-input chromatin immunoprecipitation. Genome Res 2021; 31:919-933. [PMID: 33707229 PMCID: PMC8092002 DOI: 10.1101/gr.260745.120] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2020] [Accepted: 02/22/2021] [Indexed: 11/24/2022]
Abstract
Epigenetic profiling by chromatin immunoprecipitation followed by sequencing (ChIP-seq) has become a powerful tool for genome-wide identification of regulatory elements, for defining transcriptional regulatory networks, and for screening for biomarkers. However, the ChIP-seq protocol for low-input samples is laborious and time-consuming and suffers from experimental variation, resulting in poor reproducibility and low throughput. Although prototypic microfluidic ChIP-seq platforms have been developed, these are poorly transferable as they require sophisticated custom-made equipment and in-depth microfluidic and ChIP expertise, while lacking parallelization. To enable standardized, automated ChIP-seq profiling of low-input samples, we constructed microfluidic PDMS-based plates capable of performing 24 sensitive ChIP reactions within 30 min of hands-on time and 4.5 h of machine-running time. These disposable plates can be conveniently loaded into a widely available controller for pneumatics and thermocycling. In light of the plug and play (PnP) ChIP plates and workflow, we named our procedure PnP-ChIP-seq. We show high-quality ChIP-seq on hundreds to a few thousand of cells for all six post-translational histone modifications that are included in the International Human Epigenome Consortium set of reference epigenomes. PnP-ChIP-seq robustly detects epigenetic differences on promoters and enhancers between naive and more primed mouse embryonic stem cells (mESCs). Furthermore, we used our platform to generate epigenetic profiles of rare subpopulations of mESCs that resemble the two-cell stage of embryonic development. PnP-ChIP-seq allows nonexpert laboratories worldwide to conveniently run robust, standardized ChIP-seq, whereas its high throughput, consistency, and sensitivity pave the way toward large-scale profiling of precious sample types such as rare subpopulations of cells or biopsies.
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Affiliation(s)
- René A M Dirks
- Department of Molecular Biology, Faculty of Science, Radboud University, Radboud Institute for Molecular Life Sciences (RIMLS), 6525GA Nijmegen, the Netherlands
| | - Peter C Thomas
- Fluidigm Corporation, South San Francisco, California 94080, USA
| | - Haoyu Wu
- Department of Molecular Biology, Faculty of Science, Radboud University, Radboud Institute for Molecular Life Sciences (RIMLS), 6525GA Nijmegen, the Netherlands
| | - Robert C Jones
- Fluidigm Corporation, South San Francisco, California 94080, USA
| | - Hendrik G Stunnenberg
- Department of Molecular Biology, Faculty of Science, Radboud University, Radboud Institute for Molecular Life Sciences (RIMLS), 6525GA Nijmegen, the Netherlands
| | - Hendrik Marks
- Department of Molecular Biology, Faculty of Science, Radboud University, Radboud Institute for Molecular Life Sciences (RIMLS), 6525GA Nijmegen, the Netherlands
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4
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Arrigoni L, Ferrari F, Weller J, Bella C, Bönisch U, Manke T. AutoRELACS: automated generation and analysis of ultra-parallel ChIP-seq. Sci Rep 2020; 10:12400. [PMID: 32709929 PMCID: PMC7381599 DOI: 10.1038/s41598-020-69443-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Accepted: 07/07/2020] [Indexed: 11/09/2022] Open
Abstract
Chromatin immunoprecipitation followed by sequencing (ChIP-seq) is a method used to profile protein-DNA interactions genome-wide. Restriction Enzyme-based Labeling of Chromatin in Situ (RELACS) is a recently developed ChIP-seq protocol that deploys a chromatin barcoding strategy to enable standardized and high-throughput generation of ChIP-seq data. The manual implementation of RELACS is constrained by human processivity in both data generation and data analysis. To overcome these limitations, we have developed AutoRELACS, an automated implementation of the RELACS protocol using the liquid handler Biomek i7 workstation. We match the unprecedented processivity in data generation allowed by AutoRELACS with the automated computation pipelines offered by snakePipes. In doing so, we build a continuous workflow that streamlines epigenetic profiling, from sample collection to biological interpretation. Here, we show that AutoRELACS successfully automates chromatin barcode integration, and is able to generate high-quality ChIP-seq data comparable with the standards of the manual protocol, also for limited amounts of biological samples.
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Affiliation(s)
- L Arrigoni
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
| | - F Ferrari
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany.,Faculty of Biology, University of Freiburg, Freiburg, Germany
| | - J Weller
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
| | - C Bella
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
| | - U Bönisch
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
| | - T Manke
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany.
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5
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A parallelized, automated platform enabling individual or sequential ChIP of histone marks and transcription factors. Proc Natl Acad Sci U S A 2020; 117:13828-13838. [PMID: 32461370 DOI: 10.1073/pnas.1913261117] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
Despite its popularity, chromatin immunoprecipitation followed by sequencing (ChIP-seq) remains a tedious (>2 d), manually intensive, low-sensitivity and low-throughput approach. Here, we combine principles of microengineering, surface chemistry, and molecular biology to address the major limitations of standard ChIP-seq. The resulting technology, FloChIP, automates and miniaturizes ChIP in a beadless fashion while facilitating the downstream library preparation process through on-chip chromatin tagmentation. FloChIP is fast (<2 h), has a wide dynamic range (from 106 to 500 cells), is scalable and parallelized, and supports antibody- or sample-multiplexed ChIP on both histone marks and transcription factors. In addition, FloChIP's interconnected design allows for straightforward chromatin reimmunoprecipitation, which allows this technology to also act as a microfluidic sequential ChIP-seq system. Finally, we ran FloChIP for the transcription factor MEF2A in 32 distinct human lymphoblastoid cell lines, providing insights into the main factors driving collaborative DNA binding of MEF2A and into its role in B cell-specific gene regulation. Together, our results validate FloChIP as a flexible and reproducible automated solution for individual or sequential ChIP-seq.
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6
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Lipinski M, Muñoz-Viana R, Del Blanco B, Marquez-Galera A, Medrano-Relinque J, Caramés JM, Szczepankiewicz AA, Fernandez-Albert J, Navarrón CM, Olivares R, Wilczyński GM, Canals S, Lopez-Atalaya JP, Barco A. KAT3-dependent acetylation of cell type-specific genes maintains neuronal identity in the adult mouse brain. Nat Commun 2020; 11:2588. [PMID: 32444594 PMCID: PMC7244750 DOI: 10.1038/s41467-020-16246-0] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2019] [Accepted: 04/22/2020] [Indexed: 02/06/2023] Open
Abstract
The lysine acetyltransferases type 3 (KAT3) family members CBP and p300 are important transcriptional co-activators, but their specific functions in adult post-mitotic neurons remain unclear. Here, we show that the combined elimination of both proteins in forebrain excitatory neurons of adult mice resulted in a rapidly progressing neurological phenotype associated with severe ataxia, dendritic retraction and reduced electrical activity. At the molecular level, we observed the downregulation of neuronal genes, as well as decreased H3K27 acetylation and pro-neural transcription factor binding at the promoters and enhancers of canonical neuronal genes. The combined deletion of CBP and p300 in hippocampal neurons resulted in the rapid loss of neuronal molecular identity without de- or transdifferentiation. Restoring CBP expression or lysine acetylation rescued neuronal-specific transcription in cultured neurons. Together, these experiments show that KAT3 proteins maintain the excitatory neuron identity through the regulation of histone acetylation at cell type-specific promoter and enhancer regions. Neuronal identity maintenance is highly regulated. Here, the authors showed that CBP and p300 safeguard neuronal identity through histone acetylation at promoters and enhancers of neuronal specific genes. The loss of both CBP and p300 impairs gene expression, circuit activity, and behavior in mice.
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Affiliation(s)
- Michal Lipinski
- Instituto de Neurociencias, Universidad Miguel Hernández-Consejo Superior de Investigaciones Científicas, Avenida Santiago Ramón y Cajal, s/n, Sant Joan d'Alacant, 03550, Alicante, Spain
| | - Rafael Muñoz-Viana
- Instituto de Neurociencias, Universidad Miguel Hernández-Consejo Superior de Investigaciones Científicas, Avenida Santiago Ramón y Cajal, s/n, Sant Joan d'Alacant, 03550, Alicante, Spain
| | - Beatriz Del Blanco
- Instituto de Neurociencias, Universidad Miguel Hernández-Consejo Superior de Investigaciones Científicas, Avenida Santiago Ramón y Cajal, s/n, Sant Joan d'Alacant, 03550, Alicante, Spain
| | - Angel Marquez-Galera
- Instituto de Neurociencias, Universidad Miguel Hernández-Consejo Superior de Investigaciones Científicas, Avenida Santiago Ramón y Cajal, s/n, Sant Joan d'Alacant, 03550, Alicante, Spain
| | - Juan Medrano-Relinque
- Instituto de Neurociencias, Universidad Miguel Hernández-Consejo Superior de Investigaciones Científicas, Avenida Santiago Ramón y Cajal, s/n, Sant Joan d'Alacant, 03550, Alicante, Spain
| | - José M Caramés
- Instituto de Neurociencias, Universidad Miguel Hernández-Consejo Superior de Investigaciones Científicas, Avenida Santiago Ramón y Cajal, s/n, Sant Joan d'Alacant, 03550, Alicante, Spain
| | - Andrzej A Szczepankiewicz
- Nencki Institute of Experimental Biology, Polish Academy of Science, 3 Pasteur Street, 02-093, Warsaw, Poland
| | - Jordi Fernandez-Albert
- Instituto de Neurociencias, Universidad Miguel Hernández-Consejo Superior de Investigaciones Científicas, Avenida Santiago Ramón y Cajal, s/n, Sant Joan d'Alacant, 03550, Alicante, Spain
| | - Carmen M Navarrón
- Instituto de Neurociencias, Universidad Miguel Hernández-Consejo Superior de Investigaciones Científicas, Avenida Santiago Ramón y Cajal, s/n, Sant Joan d'Alacant, 03550, Alicante, Spain
| | - Roman Olivares
- Instituto de Neurociencias, Universidad Miguel Hernández-Consejo Superior de Investigaciones Científicas, Avenida Santiago Ramón y Cajal, s/n, Sant Joan d'Alacant, 03550, Alicante, Spain
| | - Grzegorz M Wilczyński
- Nencki Institute of Experimental Biology, Polish Academy of Science, 3 Pasteur Street, 02-093, Warsaw, Poland
| | - Santiago Canals
- Instituto de Neurociencias, Universidad Miguel Hernández-Consejo Superior de Investigaciones Científicas, Avenida Santiago Ramón y Cajal, s/n, Sant Joan d'Alacant, 03550, Alicante, Spain
| | - Jose P Lopez-Atalaya
- Instituto de Neurociencias, Universidad Miguel Hernández-Consejo Superior de Investigaciones Científicas, Avenida Santiago Ramón y Cajal, s/n, Sant Joan d'Alacant, 03550, Alicante, Spain
| | - Angel Barco
- Instituto de Neurociencias, Universidad Miguel Hernández-Consejo Superior de Investigaciones Científicas, Avenida Santiago Ramón y Cajal, s/n, Sant Joan d'Alacant, 03550, Alicante, Spain.
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7
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Bartlett AA, Hunter RG. Chromatin Immunoprecipitation Techniques in Neuropsychiatric Research. Methods Mol Biol 2020; 2011:633-645. [PMID: 31273725 DOI: 10.1007/978-1-4939-9554-7_36] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Neuropsychiatric disorders are highly prevalent (e.g., affecting children 2-8 years old at a rate of 14%). Many of these disorders are highly heritable such as major depressive disorder and schizophrenia. Despite this, genome-wide association has failed to identify gene(s) significantly associated with diagnostic status suggesting a strong role for environmental factors and the epigenome. From a molecular standpoint, the study of DNA-protein interactions yields fruitful information regarding the regulation of cellular processes above the level of the nucleotide sequence. Understanding chromatin dynamics may continue to explain individual variation to environmental perturbation and subsequent behavioral response. Chromatin immunoprecipitation (ChIP) techniques have allowed for probing of epigenetic effectors at specific regions of the genome. The following article reviews the current techniques and considerations when incorporation ChIP into neuropsychiatric models.
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Affiliation(s)
- Andrew A Bartlett
- Department of Psychology, University of Massachusetts, Boston, Boston, MA, USA
| | - Richard G Hunter
- Department of Psychology, University of Massachusetts, Boston, Boston, MA, USA. .,Laboratory of Neuroendocrinology, The Rockefeller University, New York, NY, USA.
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8
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Huang Y, Mouttet B, Warnatz HJ, Risch T, Rietmann F, Frommelt F, Ngo QA, Dobay MP, Marovca B, Jenni S, Tsai YC, Matzk S, Amstislavskiy V, Schrappe M, Stanulla M, Gstaiger M, Bornhauser B, Yaspo ML, Bourquin JP. The Leukemogenic TCF3-HLF Complex Rewires Enhancers Driving Cellular Identity and Self-Renewal Conferring EP300 Vulnerability. Cancer Cell 2019; 36:630-644.e9. [PMID: 31735627 DOI: 10.1016/j.ccell.2019.10.004] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/09/2018] [Revised: 08/18/2019] [Accepted: 10/14/2019] [Indexed: 01/08/2023]
Abstract
The chimeric transcription factor TCF3-HLF defines an incurable acute lymphoblastic leukemia subtype. Here we decipher the regulome of endogenous TCF3-HLF and dissect its essential transcriptional components and targets by functional genomics. We demonstrate that TCF3-HLF recruits HLF binding sites at hematopoietic stem cell/myeloid lineage associated (super-) enhancers to drive lineage identity and self-renewal. Among direct targets, hijacking an HLF binding site in a MYC enhancer cluster by TCF3-HLF activates a conserved MYC-driven transformation program crucial for leukemia propagation in vivo. TCF3-HLF pioneers the cooperation with ERG and recruits histone acetyltransferase p300 (EP300), conferring susceptibility to EP300 inhibition. Our study provides a framework for targeting driving transcriptional dependencies in this fatal leukemia.
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Affiliation(s)
- Yun Huang
- Division of Oncology and Children's Research Centre, University Children's Hospital Zurich, 8032 Zurich, Switzerland
| | - Brice Mouttet
- Division of Oncology and Children's Research Centre, University Children's Hospital Zurich, 8032 Zurich, Switzerland
| | - Hans-Jörg Warnatz
- Otto Warburg Laboratory Gene Regulation and Systems Biology of Cancer, Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany
| | - Thomas Risch
- Otto Warburg Laboratory Gene Regulation and Systems Biology of Cancer, Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany
| | - Fabian Rietmann
- Division of Oncology and Children's Research Centre, University Children's Hospital Zurich, 8032 Zurich, Switzerland
| | - Fabian Frommelt
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, 8093 Zurich, Switzerland
| | - Quy A Ngo
- Division of Oncology and Children's Research Centre, University Children's Hospital Zurich, 8032 Zurich, Switzerland
| | - Maria Pamela Dobay
- Division of Oncology and Children's Research Centre, University Children's Hospital Zurich, 8032 Zurich, Switzerland
| | - Blerim Marovca
- Division of Oncology and Children's Research Centre, University Children's Hospital Zurich, 8032 Zurich, Switzerland
| | - Silvia Jenni
- Division of Oncology and Children's Research Centre, University Children's Hospital Zurich, 8032 Zurich, Switzerland
| | - Yi-Chien Tsai
- Division of Oncology and Children's Research Centre, University Children's Hospital Zurich, 8032 Zurich, Switzerland
| | - Sören Matzk
- Otto Warburg Laboratory Gene Regulation and Systems Biology of Cancer, Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany
| | - Vyacheslav Amstislavskiy
- Otto Warburg Laboratory Gene Regulation and Systems Biology of Cancer, Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany
| | - Martin Schrappe
- Department of Pediatrics, Christian-Albrecht University of Kiel and University Medical Center Schleswig-Holstein, 24105 Kiel, Germany
| | - Martin Stanulla
- Pediatric Hematology and Oncology, Hannover Medical School, 30625 Hannover, Germany
| | - Matthias Gstaiger
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, 8093 Zurich, Switzerland
| | - Beat Bornhauser
- Division of Oncology and Children's Research Centre, University Children's Hospital Zurich, 8032 Zurich, Switzerland
| | - Marie-Laure Yaspo
- Otto Warburg Laboratory Gene Regulation and Systems Biology of Cancer, Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany
| | - Jean-Pierre Bourquin
- Division of Oncology and Children's Research Centre, University Children's Hospital Zurich, 8032 Zurich, Switzerland.
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9
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Bomsztyk K, Mar D, Wang Y, Denisenko O, Ware C, Frazar CD, Blattler A, Maxwell AD, MacConaghy BE, Matula TJ. PIXUL-ChIP: integrated high-throughput sample preparation and analytical platform for epigenetic studies. Nucleic Acids Res 2019; 47:e69. [PMID: 30927002 PMCID: PMC6614803 DOI: 10.1093/nar/gkz222] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2018] [Revised: 03/18/2019] [Accepted: 03/21/2019] [Indexed: 12/25/2022] Open
Abstract
Chromatin immunoprecipitation (ChIP) is the most widely used approach for identification of genome-associated proteins and their modifications. We have previously introduced a microplate-based ChIP platform, Matrix ChIP, where the entire ChIP procedure is done on the same plate without sample transfers. Compared to conventional ChIP protocols, the Matrix ChIP assay is faster and has increased throughput. However, even with microplate ChIP assays, sample preparation and chromatin fragmentation (which is required to map genomic locations) remains a major bottleneck. We have developed a novel technology (termed 'PIXUL') utilizing an array of ultrasound transducers for simultaneous shearing of samples in standard 96-well microplates. We integrated PIXUL with Matrix ChIP ('PIXUL-ChIP'), that allows for fast, reproducible, low-cost and high-throughput sample preparation and ChIP analysis of 96 samples (cell culture or tissues) in one day. Further, we demonstrated that chromatin prepared using PIXUL can be used in an existing ChIP-seq workflow. Thus, the high-throughput capacity of PIXUL-ChIP provides the means to carry out ChIP-qPCR or ChIP-seq experiments involving dozens of samples. Given the complexity of epigenetic processes, the use of PIXUL-ChIP will advance our understanding of these processes in health and disease, as well as facilitate screening of epigenetic drugs.
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Affiliation(s)
- Karol Bomsztyk
- UW Medicine South Lake Union, University of Washington, Seattle, WA 98109, USA
- Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, WA 98109, USA
- To whom correspondence should be addressed. Tel. +1 206 616 7949;
| | - Daniel Mar
- UW Medicine South Lake Union, University of Washington, Seattle, WA 98109, USA
| | - Yuliang Wang
- UW Medicine South Lake Union, University of Washington, Seattle, WA 98109, USA
- Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, WA 98109, USA
- Paul G. Allen School of Computer Science & Engineering, University of Washington, Seattle, WA 98195, USA
| | - Oleg Denisenko
- UW Medicine South Lake Union, University of Washington, Seattle, WA 98109, USA
| | - Carol Ware
- Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, WA 98109, USA
| | - Christian D Frazar
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
| | | | - Adam D Maxwell
- Department of Urology, University of Washington School of Medicine, Seattle, WA 98195, USA
- Center for Industrial and Medical Ultrasound, Applied Physics Laboratory, University of Washington, Seattle, WA 98195, USA
| | - Brian E MacConaghy
- Center for Industrial and Medical Ultrasound, Applied Physics Laboratory, University of Washington, Seattle, WA 98195, USA
| | - Thomas J Matula
- Center for Industrial and Medical Ultrasound, Applied Physics Laboratory, University of Washington, Seattle, WA 98195, USA
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10
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Zucconi BE, Makofske JL, Meyers DJ, Hwang Y, Wu M, Kuroda MI, Cole PA. Combination Targeting of the Bromodomain and Acetyltransferase Active Site of p300/CBP. Biochemistry 2019; 58:2133-2143. [PMID: 30924641 DOI: 10.1021/acs.biochem.9b00160] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
p300 and CBP are highly related histone acetyltransferase (HAT) enzymes that regulate gene expression, and their dysregulation has been linked to cancer and other diseases. p300/CBP is composed of a number of domains including a HAT domain, which is inhibited by the small molecule A-485, and an acetyl-lysine binding bromodomain, which was recently found to be selectively antagonized by the small molecule I-CBP112. Here we show that the combination of I-CBP112 and A-485 can synergize to inhibit prostate cancer cell proliferation. We find that the combination confers a dramatic reduction in p300 chromatin occupancy compared to the individual effects of blocking either domain alone. Accompanying this loss of p300 on chromatin, combination treatment leads to the reduction of specific mRNAs including androgen-dependent and pro-oncogenic prostate genes such as KLK3 (PSA) and c-Myc. Consistent with p300 directly affecting gene expression, mRNAs that are significantly reduced by combination treatment also exhibit a strong reduction in p300 chromatin occupancy at their gene promoters. The relatively few mRNAs that are up-regulated upon combination treatment show no correlation with p300 occupancy. These studies provide support for the pharmacologic advantage of concurrent targeting of two domains within one key epigenetic modification enzyme.
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Affiliation(s)
- Beth E Zucconi
- Division of Genetics, Department of Medicine , Brigham and Women's Hospital , Boston , Massachusetts 02115 , United States.,Department of Biological Chemistry and Molecular Pharmacology , Harvard Medical School , Boston , Massachusetts 02115 , United States
| | - Jessica L Makofske
- Division of Genetics, Department of Medicine , Brigham and Women's Hospital , Boston , Massachusetts 02115 , United States.,Department of Genetics , Harvard Medical School , Boston , Massachusetts 02115 , United States
| | - David J Meyers
- Department of Pharmacology and Molecular Sciences , Johns Hopkins School of Medicine , Baltimore , Maryland 21205 , United States
| | - Yousang Hwang
- Department of Pharmacology and Molecular Sciences , Johns Hopkins School of Medicine , Baltimore , Maryland 21205 , United States
| | - Mingxuan Wu
- Division of Genetics, Department of Medicine , Brigham and Women's Hospital , Boston , Massachusetts 02115 , United States.,Department of Biological Chemistry and Molecular Pharmacology , Harvard Medical School , Boston , Massachusetts 02115 , United States
| | - Mitzi I Kuroda
- Division of Genetics, Department of Medicine , Brigham and Women's Hospital , Boston , Massachusetts 02115 , United States.,Department of Genetics , Harvard Medical School , Boston , Massachusetts 02115 , United States
| | - Philip A Cole
- Division of Genetics, Department of Medicine , Brigham and Women's Hospital , Boston , Massachusetts 02115 , United States.,Department of Biological Chemistry and Molecular Pharmacology , Harvard Medical School , Boston , Massachusetts 02115 , United States
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11
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Janssens DH, Wu SJ, Sarthy JF, Meers MP, Myers CH, Olson JM, Ahmad K, Henikoff S. Automated in situ chromatin profiling efficiently resolves cell types and gene regulatory programs. Epigenetics Chromatin 2018; 11:74. [PMID: 30577869 PMCID: PMC6302505 DOI: 10.1186/s13072-018-0243-8] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2018] [Accepted: 12/03/2018] [Indexed: 12/22/2022] Open
Abstract
BACKGROUND Our understanding of eukaryotic gene regulation is limited by the complexity of protein-DNA interactions that comprise the chromatin landscape and by inefficient methods for characterizing these interactions. We recently introduced CUT&RUN, an antibody-targeted nuclease cleavage method that profiles DNA-binding proteins, histones and chromatin-modifying proteins in situ with exceptional sensitivity and resolution. RESULTS Here, we describe an automated CUT&RUN platform and apply it to characterize the chromatin landscapes of human cells. We find that automated CUT&RUN profiles of histone modifications crisply demarcate active and repressed chromatin regions, and we develop a continuous metric to identify cell-type-specific promoter and enhancer activities. We test the ability of automated CUT&RUN to profile frozen tumor samples and find that our method readily distinguishes two pediatric glioma xenografts by their subtype-specific gene expression programs. CONCLUSIONS The easy, cost-effective workflow makes automated CUT&RUN an attractive tool for high-throughput characterization of cell types and patient samples.
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Affiliation(s)
- Derek H Janssens
- Basic Sciences Division, Fred Hutchinson Cancer Research Center, 1100 N. Fairview Ave, Seattle, WA, 98109, USA
| | - Steven J Wu
- Basic Sciences Division, Fred Hutchinson Cancer Research Center, 1100 N. Fairview Ave, Seattle, WA, 98109, USA
- Molecular Engineering and Sciences Institute, University of Washington, Seattle, WA, 98195, USA
| | - Jay F Sarthy
- Basic Sciences Division, Fred Hutchinson Cancer Research Center, 1100 N. Fairview Ave, Seattle, WA, 98109, USA
- Cancer and Blood Disorder Center, Seattle Children's Hospital, 4800 Sand Point Way, Seattle, WA, 98105, USA
| | - Michael P Meers
- Basic Sciences Division, Fred Hutchinson Cancer Research Center, 1100 N. Fairview Ave, Seattle, WA, 98109, USA
| | - Carrie H Myers
- Clinical Research Division, Fred Hutchinson Cancer Research Center, 1100 N. Fairview Ave, Seattle, WA, 98109, USA
| | - James M Olson
- Cancer and Blood Disorder Center, Seattle Children's Hospital, 4800 Sand Point Way, Seattle, WA, 98105, USA
- Clinical Research Division, Fred Hutchinson Cancer Research Center, 1100 N. Fairview Ave, Seattle, WA, 98109, USA
| | - Kami Ahmad
- Basic Sciences Division, Fred Hutchinson Cancer Research Center, 1100 N. Fairview Ave, Seattle, WA, 98109, USA
| | - Steven Henikoff
- Basic Sciences Division, Fred Hutchinson Cancer Research Center, 1100 N. Fairview Ave, Seattle, WA, 98109, USA.
- Howard Hughes Medical Institute, Chevy Chase, MD, USA.
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12
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RELACS nuclei barcoding enables high-throughput ChIP-seq. Commun Biol 2018; 1:214. [PMID: 30534606 PMCID: PMC6281648 DOI: 10.1038/s42003-018-0219-z] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2018] [Accepted: 10/31/2018] [Indexed: 02/07/2023] Open
Abstract
Chromatin immunoprecipitation followed by deep sequencing (ChIP-seq) is an invaluable tool for mapping chromatin-associated proteins. Current barcoding strategies aim to improve assay throughput and scalability but intense sample handling and lack of standardization over cell types, cell numbers and epitopes hinder wide-spread use in the field. Here, we present a barcoding method to enable high-throughput ChIP-seq using common molecular biology techniques. The method, called RELACS (restriction enzyme-based labeling of chromatin in situ) relies on standardized nuclei extraction from any source and employs chromatin cutting and barcoding within intact nuclei. Barcoded nuclei are pooled and processed within the same ChIP reaction, for maximal comparability and workload reduction. The innovative barcoding concept is particularly user-friendly and suitable for implementation to standardized large-scale clinical studies and scarce samples. Aiming to maximize universality and scalability, RELACS can generate ChIP-seq libraries for transcription factors and histone modifications from hundreds of samples within three days. Laura Arrigoni et al. present RELACS, a method enabling high-throughput ChIP-seq which involves barcoding and processing intact nuclei in the same ChIP reaction. The method is useful for broad cell types and epitopes, robust to experimental conditions, and drastically decreases workload.
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13
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Visual Servoing-Based Nanorobotic System for Automated Electrical Characterization of Nanotubes inside SEM. SENSORS 2018; 18:s18041137. [PMID: 29642495 PMCID: PMC5948737 DOI: 10.3390/s18041137] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/01/2018] [Revised: 03/25/2018] [Accepted: 03/26/2018] [Indexed: 11/23/2022]
Abstract
The maneuvering and electrical characterization of nanotubes inside a scanning electron microscope (SEM) has historically been time-consuming and laborious for operators. Before the development of automated nanomanipulation-enabled techniques for the performance of pick-and-place and characterization of nanoobjects, these functions were still incomplete and largely operated manually. In this paper, a dual-probe nanomanipulation system vision-based feedback was demonstrated to automatically perform 3D nanomanipulation tasks, to investigate the electrical characterization of nanotubes. The XY-position of Atomic Force Microscope (AFM) cantilevers and individual carbon nanotubes (CNTs) were precisely recognized via a series of image processing operations. A coarse-to-fine positioning strategy in the Z-direction was applied through the combination of the sharpness-based depth estimation method and the contact-detection method. The use of nanorobotic magnification-regulated speed aided in improving working efficiency and reliability. Additionally, we proposed automated alignment of manipulator axes by visual tracking the movement trajectory of the end effector. The experimental results indicate the system’s capability for automated measurement electrical characterization of CNTs. Furthermore, the automated nanomanipulation system has the potential to be extended to other nanomanipulation tasks.
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14
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Steube A, Schenk T, Tretyakov A, Saluz HP. High-intensity UV laser ChIP-seq for the study of protein-DNA interactions in living cells. Nat Commun 2017; 8:1303. [PMID: 29101361 PMCID: PMC5670203 DOI: 10.1038/s41467-017-01251-7] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2016] [Accepted: 08/31/2017] [Indexed: 01/10/2023] Open
Abstract
Genome-wide mapping of transcription factor binding is generally performed by chemical protein–DNA crosslinking, followed by chromatin immunoprecipitation and deep sequencing (ChIP-seq). Here we present the ChIP-seq technique based on photochemical crosslinking of protein–DNA interactions by high-intensity ultraviolet (UV) laser irradiation in living mammalian cells (UV-ChIP-seq). UV laser irradiation induces an efficient and instant formation of covalent “zero-length” crosslinks exclusively between nucleic acids and proteins that are in immediate contact, thus resulting in a “snapshot” of direct protein–DNA interactions in their natural environment. Here we show that UV-ChIP-seq, applied for genome-wide profiling of the sequence-specific transcriptional repressor B-cell lymphoma 6 (BCL6) in human diffuse large B-cell lymphoma (DLBCL) cells, produces sensitive and precise protein–DNA binding profiles, highly enriched with canonical BCL6 DNA sequence motifs. Using this technique, we also found numerous previously undetectable direct BCL6 binding sites, particularly in condensed, inaccessible areas of chromatin. Chromatin immunoprecipitation followed by DNA sequencing (ChIP-seq) can map transcription factor binding to a given genome. Here, Steube and colleagues devise a ChIP-seq technique based on photochemical crosslinking by high-intensity ultraviolet laser irradiation, and describe its utility.
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Affiliation(s)
- Arndt Steube
- Department of Cell and Molecular Biology, Leibniz Institute for Natural Product Research and Infection Biology-Hans Knöll Institute (HKI), Jena, 07745, Germany. .,Department of Internal Medicine IV, Jena University Hospital, Friedrich Schiller University, Jena, 07747, Germany. .,Friedrich Schiller University, Jena, 07737, Germany.
| | - Tino Schenk
- Friedrich Schiller University, Jena, 07737, Germany. .,Department of Hematology and Medical Oncology, Clinic of Internal Medicine II, Jena University Hospital, Jena, 07747, Germany. .,Institute of Molecular Cell Biology, Center for Molecular Biomedicine Jena (CMB), Jena University Hospital, Jena, 07745, Germany.
| | - Alexander Tretyakov
- Department of Cell and Molecular Biology, Leibniz Institute for Natural Product Research and Infection Biology-Hans Knöll Institute (HKI), Jena, 07745, Germany
| | - Hans Peter Saluz
- Department of Cell and Molecular Biology, Leibniz Institute for Natural Product Research and Infection Biology-Hans Knöll Institute (HKI), Jena, 07745, Germany. .,Friedrich Schiller University, Jena, 07737, Germany.
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15
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Seuter S, Neme A, Carlberg C. Epigenomic PU.1-VDR crosstalk modulates vitamin D signaling. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2017; 1860:405-415. [PMID: 28232093 DOI: 10.1016/j.bbagrm.2017.02.005] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/11/2016] [Revised: 02/07/2017] [Accepted: 02/12/2017] [Indexed: 01/15/2023]
Abstract
The ETS-domain transcription factor PU.1 acts as a pioneer factor for other transcription factors including nuclear receptors. In this study, we report that in THP-1 human monocytes the PU.1 cistrome comprises 122,319 genomic sites. Interestingly, at 6498 (5.3%) of these loci PU.1 binding was significantly modulated by the vitamin D receptor (VDR) ligand 1α,25-dihydroxyvitamin D3 (1,25(OH)2D3). In most cases 1,25(OH)2D3 increased PU.1 association, which correlated strongly with VDR co-location and overlap ratios for canonical DR3-type VDR binding sites. Genome-wide 6488 sites associating both with PU.1 and VDR as well as 5649 non-VDR overlapping, 1,25(OH)2D3-sensitive PU.1 loci represent the PU.1-VDR crosstalk and can be described by four gene regulatory scenarios, each. Chromatin accessibility was the major discriminator between these models. The location of the PU.1 binding loci in open chromatin coincided with a significantly smaller mean distance to the closest 1,25(OH)2D3 target gene. PU.1 knockdown indicated that the pioneer factor is relevant for the transcriptional activation of 1,25(OH)2D3 target genes but its impact differed in magnitude and orientation. In conclusion, PU.1 is an important modulator of VDR signaling in monocytes, including but also exceeding its role as a pioneer factor, but we found no evidence for a direct interaction of both proteins.
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Affiliation(s)
- Sabine Seuter
- School of Medicine, Institute of Biomedicine, University of Eastern Finland, FI-70211 Kuopio, Finland
| | - Antonio Neme
- School of Medicine, Institute of Biomedicine, University of Eastern Finland, FI-70211 Kuopio, Finland
| | - Carsten Carlberg
- School of Medicine, Institute of Biomedicine, University of Eastern Finland, FI-70211 Kuopio, Finland.
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16
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Zhou P, Gu F, Zhang L, Akerberg BN, Ma Q, Li K, He A, Lin Z, Stevens SM, Zhou B, Pu WT. Mapping cell type-specific transcriptional enhancers using high affinity, lineage-specific Ep300 bioChIP-seq. eLife 2017; 6:22039. [PMID: 28121289 PMCID: PMC5295818 DOI: 10.7554/elife.22039] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2016] [Accepted: 01/23/2017] [Indexed: 12/31/2022] Open
Abstract
Understanding the mechanisms that regulate cell type-specific transcriptional programs requires developing a lexicon of their genomic regulatory elements. We developed a lineage-selective method to map transcriptional enhancers, regulatory genomic regions that activate transcription, in mice. Since most tissue-specific enhancers are bound by the transcriptional co-activator Ep300, we used Cre-directed, lineage-specific Ep300 biotinylation and pulldown on immobilized streptavidin followed by next generation sequencing of co-precipitated DNA to identify lineage-specific enhancers. By driving this system with lineage-specific Cre transgenes, we mapped enhancers active in embryonic endothelial cells/blood or skeletal muscle. Analysis of these enhancers identified new transcription factor heterodimer motifs that likely regulate transcription in these lineages. Furthermore, we identified candidate enhancers that regulate adult heart- or lung- specific endothelial cell specialization. Our strategy for tissue-specific protein biotinylation opens new avenues for studying lineage-specific protein-DNA and protein-protein interactions.
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Affiliation(s)
- Pingzhu Zhou
- Department of Cardiology, Boston Children's Hospital, Boston, United States
| | - Fei Gu
- Department of Cardiology, Boston Children's Hospital, Boston, United States
| | - Lina Zhang
- Department of Biochemistry, Institute of Basic Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Brynn N Akerberg
- Department of Cardiology, Boston Children's Hospital, Boston, United States
| | - Qing Ma
- Department of Cardiology, Boston Children's Hospital, Boston, United States
| | - Kai Li
- Department of Cardiology, Boston Children's Hospital, Boston, United States
| | - Aibin He
- Institute of Molecular Medicine, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China
| | - Zhiqiang Lin
- Department of Cardiology, Boston Children's Hospital, Boston, United States
| | - Sean M Stevens
- Department of Cardiology, Boston Children's Hospital, Boston, United States
| | - Bin Zhou
- State Key Laboratory of Cell Biology, CAS center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai, China
| | - William T Pu
- Department of Cardiology, Boston Children's Hospital, Boston, United States.,Harvard Stem Cell Institute, Harvard University, Cambridge, United States
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17
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Abstract
Functional elements in the genome express their function through physical association with particular proteins: transcription factors, components of the transcription machinery, specific histone modifications, and others. The genome-wide characterization of the protein-DNA interaction landscape of these proteins is thus a key approach toward the identification of candidate genomic regulatory regions. ChIP-seq (Chromatin Immunoprecipitation coupled with high-throughput sequencing) has emerged as the primary experimental methods for carrying out this task. Here, the ChIP-seq protocol is described together with some of the most important considerations for applying it in practice.
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18
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Dirks RAM, Stunnenberg HG, Marks H. Genome-wide epigenomic profiling for biomarker discovery. Clin Epigenetics 2016; 8:122. [PMID: 27895806 PMCID: PMC5117701 DOI: 10.1186/s13148-016-0284-4] [Citation(s) in RCA: 50] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2016] [Accepted: 11/02/2016] [Indexed: 12/24/2022] Open
Abstract
A myriad of diseases is caused or characterized by alteration of epigenetic patterns, including changes in DNA methylation, post-translational histone modifications, or chromatin structure. These changes of the epigenome represent a highly interesting layer of information for disease stratification and for personalized medicine. Traditionally, epigenomic profiling required large amounts of cells, which are rarely available with clinical samples. Also, the cellular heterogeneity complicates analysis when profiling clinical samples for unbiased genome-wide biomarker discovery. Recent years saw great progress in miniaturization of genome-wide epigenomic profiling, enabling large-scale epigenetic biomarker screens for disease diagnosis, prognosis, and stratification on patient-derived samples. All main genome-wide profiling technologies have now been scaled down and/or are compatible with single-cell readout, including: (i) Bisulfite sequencing to determine DNA methylation at base-pair resolution, (ii) ChIP-Seq to identify protein binding sites on the genome, (iii) DNaseI-Seq/ATAC-Seq to profile open chromatin, and (iv) 4C-Seq and HiC-Seq to determine the spatial organization of chromosomes. In this review we provide an overview of current genome-wide epigenomic profiling technologies and main technological advances that allowed miniaturization of these assays down to single-cell level. For each of these technologies we evaluate their application for future biomarker discovery. We will focus on (i) compatibility of these technologies with methods used for clinical sample preservation, including methods used by biobanks that store large numbers of patient samples, and (ii) automation of these technologies for robust sample preparation and increased throughput.
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Affiliation(s)
- René A M Dirks
- Department of Molecular Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Radboud University, 6500HB Nijmegen, The Netherlands
| | - Hendrik G Stunnenberg
- Department of Molecular Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Radboud University, 6500HB Nijmegen, The Netherlands
| | - Hendrik Marks
- Department of Molecular Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Radboud University, 6500HB Nijmegen, The Netherlands
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19
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Mita P, Lhakhang T, Li D, Eichinger DJ, Fenyo D, Boeke JD. Fluorescence ImmunoPrecipitation (FLIP): a Novel Assay for High-Throughput IP. Biol Proced Online 2016; 18:16. [PMID: 27528826 PMCID: PMC4983793 DOI: 10.1186/s12575-016-0046-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2016] [Accepted: 07/13/2016] [Indexed: 01/27/2023] Open
Abstract
Background The immunoprecipitation (IP) assay is a valuable molecular biology tool applied across a breadth of fields. The standard assay couples IP to immunoblotting (IP/IB), a procedure severely limited as it is not easily scaled for high-throughput analysis. Results Here we describe and characterize a new methodology for fast and reliable evaluation of an immunoprecipitation reaction. FLIP (FLuorescence IP) relies on the expression of the target protein as a chromophore-tagged protein and couples IP with the measurement of fluorescent signal coating agarose beads. We show here that FLIP displays similar sensitivity to the standard IP/IB procedure but is amenable to high-throughput analysis. We applied FLIP to the screening of mouse monoclonal antibodies of unknown behavior in IP procedures. The parallel analysis of the considered antibodies using FLIP and IP/western shows good correlation between the two procedures. We also show application of FLIP using unpurified antibodies (hybridoma supernatant) and we developed a publicly available tool for the easy analysis and quantification of FLIP signals. Conclusions Altogether, our characterizations of this new methodology show that FLIP is an appealing and reliable tool for any application of high-throughput IP. Electronic supplementary material The online version of this article (doi:10.1186/s12575-016-0046-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Paolo Mita
- Institute of Systems Genetics (ISG), Department of Biochemistry and Molecular Pharmacology, NYU Langone Medical Center, ACLSW Room 560, 430 East 29th Street, New York, NY 10016 USA ; High Throughput Biology Center, Johns Hopkins University School of Medicine, Baltimore, MD 21205 USA
| | - Tenzin Lhakhang
- Center for Health Informatics and Bioinformatics, and Department of Biochemistry and Molecular Pharmacology, NYU Langone Medical Center, New York, NY USA
| | - Donghui Li
- Institute of Systems Genetics (ISG), Department of Biochemistry and Molecular Pharmacology, NYU Langone Medical Center, ACLSW Room 560, 430 East 29th Street, New York, NY 10016 USA ; McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205 USA ; High Throughput Biology Center, Johns Hopkins University School of Medicine, Baltimore, MD 21205 USA
| | | | - David Fenyo
- Center for Health Informatics and Bioinformatics, and Department of Biochemistry and Molecular Pharmacology, NYU Langone Medical Center, New York, NY USA
| | - Jef D Boeke
- Institute of Systems Genetics (ISG), Department of Biochemistry and Molecular Pharmacology, NYU Langone Medical Center, ACLSW Room 560, 430 East 29th Street, New York, NY 10016 USA ; High Throughput Biology Center, Johns Hopkins University School of Medicine, Baltimore, MD 21205 USA
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20
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Shang W, Lu H, Wan W, Fukuda T, Shen Y. Vision-based Nano Robotic System for High-throughput Non-embedded Cell Cutting. Sci Rep 2016; 6:22534. [PMID: 26941071 PMCID: PMC4778025 DOI: 10.1038/srep22534] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2015] [Accepted: 02/17/2016] [Indexed: 12/25/2022] Open
Abstract
Cell cutting is a significant task in biology study, but the highly productive non-embedded cell cutting is still a big challenge for current techniques. This paper proposes a vision-based nano robotic system and then realizes automatic non-embedded cell cutting with this system. First, the nano robotic system is developed and integrated with a nanoknife inside an environmental scanning electron microscopy (ESEM). Then, the positions of the nanoknife and the single cell are recognized, and the distance between them is calculated dynamically based on image processing. To guarantee the positioning accuracy and the working efficiency, we propose a distance-regulated speed adapting strategy, in which the moving speed is adjusted intelligently based on the distance between the nanoknife and the target cell. The results indicate that the automatic non-embedded cutting is able to be achieved within 1–2 mins with low invasion benefiting from the high precise nanorobot system and the sharp edge of nanoknife. This research paves a way for the high-throughput cell cutting at cell’s natural condition, which is expected to make significant impact on the biology studies, especially for the in-situ analysis at cellular and subcellular scale, such as cell interaction investigation, neural signal transduction and low invasive cell surgery.
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Affiliation(s)
- Wanfeng Shang
- Mechanical Engineering Department, Xi'an University of Science and Technology, Xi'an 710054, China
| | - Haojian Lu
- Department of Mechanical and Biomedical Engineering, City University of Hong Kong, Hong Kong, China
| | - Wenfeng Wan
- Department of Mechanical and Biomedical Engineering, City University of Hong Kong, Hong Kong, China
| | - Toshio Fukuda
- School of Mechatronic Engineering, Beijing Institute of Technology, Beijing 100081, China
| | - Yajing Shen
- Department of Mechanical and Biomedical Engineering, City University of Hong Kong, Hong Kong, China.,City University of Hong Kong Shenzhen Research Institute, Shen Zhen 518057, China
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21
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Turner KB, Naciri J, Liu JL, Anderson GP, Goldman ER, Zabetakis D. Next-Generation Sequencing of a Single Domain Antibody Repertoire Reveals Quality of Phage Display Selected Candidates. PLoS One 2016; 11:e0149393. [PMID: 26895405 PMCID: PMC4760936 DOI: 10.1371/journal.pone.0149393] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2015] [Accepted: 02/01/2016] [Indexed: 11/18/2022] Open
Abstract
Next-Generation Sequencing and bioinformatics are powerful tools for analyzing the large number of DNA sequences present in an immune library. In this work, we constructed a cDNA library of single domain antibodies from a llama immunized with staphylococcal enterotoxin B. The resulting library was sequenced, resulting in approximately 8.5 million sequences with 5.4 million representing intact, useful sequences. The sequenced library was interrogated using sequences of known SEB-binding single domain antibodies from the library obtained through phage display panning methods in a previous study. New antibodies were identified, produced, and characterized, and were shown to have affinities and melting temperatures comparable to those obtained by traditional panning methods. This demonstrates the utility of using NGS as a complementary tool to phage-displayed biopanning as a means for rapidly obtaining additional antibodies from an immune library. It also shows that phage display, using a library of high diversity, is able to select high quality antibodies even when they are low in frequency.
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Affiliation(s)
- Kendrick B. Turner
- American Society for Engineering Education, Postdoctoral Fellow at the US Naval Research Laboratory, Washington, DC, United States of America
| | - Jennifer Naciri
- American Society for Engineering Education, Science and Engineering Apprenticeship Participant at US Naval Research Laboratory, Washington, DC, United States of America
| | - Jinny L. Liu
- Center for Bio/molecular Science and Engineering, US Naval Research Laboratory, Washington, DC, United States of America
| | - George P. Anderson
- Center for Bio/molecular Science and Engineering, US Naval Research Laboratory, Washington, DC, United States of America
| | - Ellen R. Goldman
- Center for Bio/molecular Science and Engineering, US Naval Research Laboratory, Washington, DC, United States of America
| | - Dan Zabetakis
- Center for Bio/molecular Science and Engineering, US Naval Research Laboratory, Washington, DC, United States of America
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22
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Arrigoni L, Richter AS, Betancourt E, Bruder K, Diehl S, Manke T, Bönisch U. Standardizing chromatin research: a simple and universal method for ChIP-seq. Nucleic Acids Res 2015; 44:e67. [PMID: 26704968 PMCID: PMC4838356 DOI: 10.1093/nar/gkv1495] [Citation(s) in RCA: 68] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2015] [Accepted: 12/09/2015] [Indexed: 01/18/2023] Open
Abstract
Chromatin immunoprecipitation followed by next generation sequencing (ChIP-seq) is a key technique in chromatin research. Although heavily applied, existing ChIP-seq protocols are often highly fine-tuned workflows, optimized for specific experimental requirements. Especially the initial steps of ChIP-seq, particularly chromatin shearing, are deemed to be exceedingly cell-type-specific, thus impeding any protocol standardization efforts. Here we demonstrate that harmonization of ChIP-seq workflows across cell types and conditions is possible when obtaining chromatin from properly isolated nuclei. We established an ultrasound-based nuclei extraction method (NEXSON: Nuclei EXtraction by SONication) that is highly effective across various organisms, cell types and cell numbers. The described method has the potential to replace complex cell-type-specific, but largely ineffective, nuclei isolation protocols. By including NEXSON in ChIP-seq workflows, we completely eliminate the need for extensive optimization and sample-dependent adjustments. Apart from this significant simplification, our approach also provides the basis for a fully standardized ChIP-seq and yields highly reproducible transcription factor and histone modifications maps for a wide range of different cell types. Even small cell numbers (∼10 000 cells per ChIP) can be easily processed without application of modified chromatin or library preparation protocols.
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Affiliation(s)
- Laura Arrigoni
- Max Planck Institute of Immunobiology and Epigenetics, Stübeweg 51, Freiburg, 79108, Germany
| | - Andreas S Richter
- Max Planck Institute of Immunobiology and Epigenetics, Stübeweg 51, Freiburg, 79108, Germany
| | - Emily Betancourt
- Max Planck Institute of Immunobiology and Epigenetics, Stübeweg 51, Freiburg, 79108, Germany
| | - Kerstin Bruder
- Max Planck Institute of Immunobiology and Epigenetics, Stübeweg 51, Freiburg, 79108, Germany
| | - Sarah Diehl
- Luxembourg Centre for Systems Biomedicine, Université du Luxembourg, avenue du Swing 6, Belvaux, 4366, Luxembourg
| | - Thomas Manke
- Max Planck Institute of Immunobiology and Epigenetics, Stübeweg 51, Freiburg, 79108, Germany
| | - Ulrike Bönisch
- Max Planck Institute of Immunobiology and Epigenetics, Stübeweg 51, Freiburg, 79108, Germany
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23
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Occupancy of RNA Polymerase II Phosphorylated on Serine 5 (RNAP S5P) and RNAP S2P on Varicella-Zoster Virus Genes 9, 51, and 66 Is Independent of Transcript Abundance and Polymerase Location within the Gene. J Virol 2015; 90:1231-43. [PMID: 26559844 DOI: 10.1128/jvi.02617-15] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2015] [Accepted: 11/05/2015] [Indexed: 02/07/2023] Open
Abstract
UNLABELLED Regulation of gene transcription in varicella-zoster virus (VZV), a ubiquitous human neurotropic alphaherpesvirus, requires coordinated binding of multiple host and virus proteins onto specific regions of the virus genome. Chromatin immunoprecipitation (ChIP) is widely used to determine the location of specific proteins along a genomic region. Since the size range of sheared virus DNA fragments governs the limit of accurate protein localization, particularly for compact herpesvirus genomes, we used a quantitative PCR (qPCR)-based assay to determine the efficiency of VZV DNA shearing before ChIP, after which the assay was used to determine the relationship between transcript abundance and the occupancy of phosphorylated RNA polymerase II (RNAP) on the gene promoter, body, and terminus of VZV genes 9, 51, and 66. The abundance of VZV gene 9, 51, and 66 transcripts in VZV-infected human fetal lung fibroblasts was determined by reverse transcription-linked quantitative PCR. Our results showed that the C-terminal domain of RNAP is hyperphosphorylated at serine 5 (S5(P)) on VZV genes 9, 51, and 66 independently of transcript abundance and the location within the virus gene at both 1 and 3 days postinfection (dpi). In contrast, phosphorylated serine 2 (S2(P))-modified RNAP was not detected at any virus gene location at 3 dpi and was detected at levels only slightly above background levels at 1 dpi. IMPORTANCE Regulation of herpesvirus gene transcription is an elaborate choreography between proteins and DNA that is revealed by chromatin immunoprecipitation (ChIP). We used a quantitative PCR-based assay to determine fragment size after DNA shearing, a critical parameter in ChIP assays, and exposed a basic difference in the mechanism of transcription between mammalian cells and VZV. We found that hyperphosphorylation at serine 5 of the C-terminal domain of RNAP along the lengths of VZV genes (the promoter, body, and transcription termination site) was independent of mRNA abundance. In contrast, little to no enrichment of serine 3 phosphorylation of RNAP was detected at these virus gene regions. This is distinct from the findings for RNAP at highly regulated host genes, where RNAP S5(P) occupancy decreased and S2(P) levels increased as the polymerase transited through the gene. Overall, these results suggest that RNAP associates with human and virus transcriptional units through different mechanisms.
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Leung YT, Shi L, Maurer K, Song L, Zhang Z, Petri M, Sullivan KE. Interferon regulatory factor 1 and histone H4 acetylation in systemic lupus erythematosus. Epigenetics 2015; 10:191-9. [PMID: 25611806 DOI: 10.1080/15592294.2015.1009764] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Histone acetylation modulates gene expression and has been described as increased in systemic lupus erythematosus (SLE). We investigated interferon regulatory factor 1 (IRF1) interactions that influence H4 acetylation (H4ac) in SLE. Intracellular flow cytometry for H4 acetylated lysine (K) 5, K8, K12, and K16 was performed. Histone acetylation was defined in monocytes and T cells from controls and SLE patients. RNA-Seq studies were performed on monocytes to look for an imbalance in histone acetyltransferases and histone deacetylase enzyme expression. Expression levels were validated using real-time quantitative RT-PCR. IRF1 induction of H4ac was evaluated using D54MG cells overexpressing IRF1. IRF1 protein interactions were studied using co-immunoprecipitation assays. IRF1-dependent recruitment of histone acetyltransferases to target genes was examined by ChIP assays using p300 antibody. Flow cytometry data showed significantly increased H4K5, H4K8, H4K12, and H4K16 acetylation in SLE monocytes. HDAC3 and HDAC11 gene expression were decreased in SLE monocytes. PCAF showed significantly higher gene expression in SLE than controls. IRF1-overexpressing D54MG cells were associated with significantly increased H4K5, H4K8, and H4K12 acetylation compared to vector-control D54MG cells both globally and at specific target genes. Co-immunoprecipitation studies using D54MG cells revealed IRF1 protein-protein interactions with PCAF, P300, CBP, GCN5, ATF2, and HDAC3. ChIP experiments demonstrated increased p300 recruitment to known IRF1 targets in D54MG cells overexpressing IRF1. In contrast, p300 binding to IRF1 targets decreased in D54MG cells with IRF1 knockdown. SLE appears to be associated with an imbalance in histone acetyltransferases and histone deacetylase enzymes favoring pathologic H4 acetylation. Furthermore, IRF1 directly interacts with chromatin modifying enzymes, supporting a model where recruitment to specific target genes is mediated in part by IRF1.
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Affiliation(s)
- Yiu Tak Leung
- a Division of Rheumatology ; University of Pennsylvania Perelman School of Medicine ; Philadelphia , PA USA
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Mundade R, Ozer HG, Wei H, Prabhu L, Lu T. Role of ChIP-seq in the discovery of transcription factor binding sites, differential gene regulation mechanism, epigenetic marks and beyond. Cell Cycle 2015; 13:2847-52. [PMID: 25486472 PMCID: PMC4614920 DOI: 10.4161/15384101.2014.949201] [Citation(s) in RCA: 88] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Many biologically significant processes, such as cell differentiation and cell cycle progression, gene transcription and DNA replication, chromosome stability and epigenetic silencing etc. depend on the crucial interactions between cellular proteins and DNA. Chromatin immunoprecipitation (ChIP) is an important experimental technique for studying interactions between specific proteins and DNA in the cell and determining their localization on a specific genomic locus. In recent years, the combination of ChIP with second generation DNA-sequencing technology (ChIP-seq) allows precise genomic functional assay. This review addresses the important applications of ChIP-seq with an emphasis on its role in genome-wide mapping of transcription factor binding sites, the revelation of underlying molecular mechanisms of differential gene regulation that are governed by specific transcription factors, and the identification of epigenetic marks. Furthermore, we also describe the ChIP-seq data analysis workflow and a perspective for the exciting potential advancement of ChIP-seq technology in the future.
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Affiliation(s)
- Rasika Mundade
- a Department of Pharmacology and Toxicology ; Indiana University School of Medicine ; Indianapolis , IN USA
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26
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Wallerman O, Nord H, Bysani M, Borghini L, Wadelius C. lobChIP: from cells to sequencing ready ChIP libraries in a single day. Epigenetics Chromatin 2015. [PMID: 26195988 PMCID: PMC4507313 DOI: 10.1186/s13072-015-0017-5] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
BACKGROUND ChIP-seq is the method of choice for genome-wide studies of protein-DNA interactions. We describe a new method for ChIP-seq sample preparation, termed lobChIP, where the library reactions are performed on cross-linked ChIP fragments captured on beads. RESULTS The lobChIP method was found both to reduce time and cost and to simplify the processing of many samples in parallel. lobChIP has an early incorporation of barcoded sequencing adaptors that minimizes the risk of sample cross-contamination and can lead to reduced amount of adaptor dimers in the sequencing libraries, while allowing for direct decross-linking and amplification of the sample. CONCLUSIONS With results for histone modifications and transcription factors, we show that lobChIP performs equal to or better than standard protocols and that it makes it possible to go from cells to sequencing ready libraries within a single day.
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Affiliation(s)
- Ola Wallerman
- Science for Life Laboratory, Department of Immunology, Genetics and Pathology, BMC, Uppsala University, Box 815, 75108 Uppsala, Sweden ; Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Helena Nord
- Science for Life Laboratory, Department of Immunology, Genetics and Pathology, BMC, Uppsala University, Box 815, 75108 Uppsala, Sweden
| | - Madhusudhan Bysani
- Science for Life Laboratory, Department of Immunology, Genetics and Pathology, BMC, Uppsala University, Box 815, 75108 Uppsala, Sweden ; Department of Clinical Sciences, CRC, Lund University Diabetes Center, Malmö, Sweden
| | - Lisa Borghini
- Science for Life Laboratory, Department of Immunology, Genetics and Pathology, BMC, Uppsala University, Box 815, 75108 Uppsala, Sweden ; Human Genetics, Genome Institute of Singapore, Singapore, Singapore
| | - Claes Wadelius
- Science for Life Laboratory, Department of Immunology, Genetics and Pathology, BMC, Uppsala University, Box 815, 75108 Uppsala, Sweden
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Wardle FC, Tan H. A ChIP on the shoulder? Chromatin immunoprecipitation and validation strategies for ChIP antibodies. F1000Res 2015; 4:235. [PMID: 26594335 PMCID: PMC4648227 DOI: 10.12688/f1000research.6719.1] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 07/02/2015] [Indexed: 12/18/2022] Open
Abstract
Chromatin immunoprecipitation (ChIP) is a technique widely used in the study of epigenetics and transcriptional regulation of gene expression. However, its antibody-centric nature exposes it to similar challenges faced by other antibody-based procedures, of which the most prominent are issues of specificity and affinity in antigen recognition. As with other techniques that make use of antibodies, recent studies have shown the need for validation of ChIP antibodies in order to be sure they recognize the advertised protein or epitope. We summarize here the issues surrounding ChIP antibody usage, and highlight the toolkit of validation methods that can be employed by investigators looking to appraise these reagents.
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Affiliation(s)
- Fiona C Wardle
- Randall Division of Cell and Molecular Biophysics, New Hunt's House, King's College London, Guy's Campus, London, SE1 1UL, UK
| | - Haihan Tan
- Randall Division of Cell and Molecular Biophysics, New Hunt's House, King's College London, Guy's Campus, London, SE1 1UL, UK
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Imam S, Schäuble S, Brooks AN, Baliga NS, Price ND. Data-driven integration of genome-scale regulatory and metabolic network models. Front Microbiol 2015; 6:409. [PMID: 25999934 PMCID: PMC4419725 DOI: 10.3389/fmicb.2015.00409] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2015] [Accepted: 04/20/2015] [Indexed: 12/21/2022] Open
Abstract
Microbes are diverse and extremely versatile organisms that play vital roles in all ecological niches. Understanding and harnessing microbial systems will be key to the sustainability of our planet. One approach to improving our knowledge of microbial processes is through data-driven and mechanism-informed computational modeling. Individual models of biological networks (such as metabolism, transcription, and signaling) have played pivotal roles in driving microbial research through the years. These networks, however, are highly interconnected and function in concert-a fact that has led to the development of a variety of approaches aimed at simulating the integrated functions of two or more network types. Though the task of integrating these different models is fraught with new challenges, the large amounts of high-throughput data sets being generated, and algorithms being developed, means that the time is at hand for concerted efforts to build integrated regulatory-metabolic networks in a data-driven fashion. In this perspective, we review current approaches for constructing integrated regulatory-metabolic models and outline new strategies for future development of these network models for any microbial system.
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Affiliation(s)
- Saheed Imam
- Institute for Systems Biology Seattle, WA, USA
| | - Sascha Schäuble
- Institute for Systems Biology Seattle, WA, USA ; Jena University Language and Information Engineering Lab, Friedrich-Schiller-University Jena Jena, Germany
| | | | - Nitin S Baliga
- Institute for Systems Biology Seattle, WA, USA ; Departments of Biology and Microbiology, University of Washington Seattle, WA, USA ; Molecular and Cellular Biology Program, University of Washington Seattle, WA, USA ; Lawrence Berkeley National Lab Berkeley, CA, USA
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