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Kumar B, Navarro C, Yung PYK, Lyu J, Salazar Mantero A, Katsori AM, Schwämmle H, Martin M, Elsässer SJ. Multiplexed chromatin immunoprecipitation sequencing for quantitative study of histone modifications and chromatin factors. Nat Protoc 2024:10.1038/s41596-024-01058-z. [PMID: 39363107 DOI: 10.1038/s41596-024-01058-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2023] [Accepted: 07/29/2024] [Indexed: 10/05/2024]
Abstract
ChIP-seq is a widely used technique for studying histone post-translational modifications and DNA-binding proteins. DNA fragments associated with a specific protein or histone modification epitope are captured by using antibodies, sequenced and mapped to a reference genome. Albeit versatile and popular, performing many parallel ChIP-seq experiments to compare different conditions, replicates and epitopes is laborious, is prone to experimental variation and does not allow quantitative comparisons unless adequate spike-in chromatin is included. We present a detailed protocol for performing and analyzing a multiplexed quantitative chromatin immunoprecipitation-sequencing experiment (MINUTE-ChIP), in which multiple samples are profiled against multiple epitopes in a single workflow. Multiplexing not only dramatically increases the throughput of ChIP-seq experiments (e.g., profiling 12 samples against multiple histone modifications or DNA-binding proteins in a single experiment), but also enables accurate quantitative comparisons. The protocol consists of four parts: sample preparation (i.e., lysis, chromatin fragmentation and barcoding of native or formaldehyde-fixed material), pooling and splitting of the barcoded chromatin into parallel immunoprecipitation reactions, preparation of next-generation sequencing libraries from input and immunoprecipitated DNA and data analysis using our dedicated analysis pipeline. This pipeline autonomously generates quantitatively scaled ChIP-seq tracks for downstream analysis and visualization, alongside necessary quality control indicators. The entire workflow requires basic knowledge in molecular biology and bioinformatics and can be completed in 1 week. MINUTE-ChIP empowers biologists to perform every ChIP-seq experiment with an appropriate number of replicates and control conditions, delivering more statistically robust, exquisitely quantitative and biologically meaningful results.
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Affiliation(s)
- Banushree Kumar
- Science for Life Laboratory, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Solna, Sweden
- Ming Wai Lau Centre for Reparative Medicine, Stockholm node, Karolinska Institutet, Solna, Sweden
- Epigenica AB, A Working Lab, Solna, Sweden
| | - Carmen Navarro
- Science for Life Laboratory, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Solna, Sweden
- Ming Wai Lau Centre for Reparative Medicine, Stockholm node, Karolinska Institutet, Solna, Sweden
- Epigenica AB, A Working Lab, Solna, Sweden
| | - Philip Yuk Kwong Yung
- Science for Life Laboratory, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Solna, Sweden
- Ming Wai Lau Centre for Reparative Medicine, Stockholm node, Karolinska Institutet, Solna, Sweden
| | - Jing Lyu
- Science for Life Laboratory, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Solna, Sweden
- Ming Wai Lau Centre for Reparative Medicine, Stockholm node, Karolinska Institutet, Solna, Sweden
| | - Angelo Salazar Mantero
- Science for Life Laboratory, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Solna, Sweden
- Ming Wai Lau Centre for Reparative Medicine, Stockholm node, Karolinska Institutet, Solna, Sweden
| | - Anna-Maria Katsori
- Science for Life Laboratory, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Solna, Sweden
- Ming Wai Lau Centre for Reparative Medicine, Stockholm node, Karolinska Institutet, Solna, Sweden
| | - Hannah Schwämmle
- Science for Life Laboratory, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Solna, Sweden
- Ming Wai Lau Centre for Reparative Medicine, Stockholm node, Karolinska Institutet, Solna, Sweden
| | - Marcel Martin
- Department of Biochemistry and Biophysics, National Bioinformatics Infrastructure Sweden, Science for Life Laboratory, Stockholm University, Solna, Sweden
| | - Simon J Elsässer
- Science for Life Laboratory, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Solna, Sweden.
- Ming Wai Lau Centre for Reparative Medicine, Stockholm node, Karolinska Institutet, Solna, Sweden.
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Li M, Na X, Lin F, Liang S, Huang Y, Song J, Xu X, Yang C. DMF-ChIP-seq for Highly Sensitive and Integrated Epigenomic Profiling of Low-Input Cells. ACS APPLIED MATERIALS & INTERFACES 2024; 16:52047-52058. [PMID: 39303213 DOI: 10.1021/acsami.4c11280] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/22/2024]
Abstract
Mapping genome-wide DNA-protein interactions (DPIs) provides insights into the epigenetic landscape of complex biological systems and elucidates the mechanisms of epigenetic regulation in biological progress. However, current technologies in DPI profiling still suffer from high cell demands, low detection sensitivity, and large reagent consumption. To address these problems, we developed DMF-ChIP-seq that builds on digital microfluidic (DMF) technology to profile genome-wide DPIs in a highly efficient, cost-effective, and user-friendly way. The entire workflow including cell pretreatment, antibody recognition, pA-Tn5 tagmentation, fragment enrichment, and PCR amplification is programmatically manipulated on a single chip. Leveraging closed submicroliter reaction volumes and a superhydrophobic interface, DMF-ChIP-seq presented higher sensitivity in peak enrichment than other current methods, with high accuracy (Pearson Correlation Coefficient (PCC) > 0.86) and high repeatability (PCC > 0.92). Furthermore, DMF-ChIP-seq was capable of processing the samples with as few as 8 cells while maintaining a high signal-to-noise ratio. By applying DMF-ChIP-seq, H3K27ac histone modification of early embryonic cells during differentiation was profiled for the investigation of epigenomic landscape dynamics. With the benefits of high efficiency and sensitivity in DPI analysis, the system provides great promise in studying epigenetic regulation during various biological processes.
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Affiliation(s)
- Mingyin Li
- The MOE Key Laboratory of Spectrochemical Analysis & Instrumentation, the Key Laboratory of Chemical Biology of Fujian Province, State Key Laboratory of Physical Chemistry of Solid Surfaces, Collaborative Innovation Center of Chemistry for Energy Materials, Department of Chemical Biology, Department of Chemical Engineering, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
| | - Xing Na
- The MOE Key Laboratory of Spectrochemical Analysis & Instrumentation, the Key Laboratory of Chemical Biology of Fujian Province, State Key Laboratory of Physical Chemistry of Solid Surfaces, Collaborative Innovation Center of Chemistry for Energy Materials, Department of Chemical Biology, Department of Chemical Engineering, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
| | - Fanghe Lin
- The MOE Key Laboratory of Spectrochemical Analysis & Instrumentation, the Key Laboratory of Chemical Biology of Fujian Province, State Key Laboratory of Physical Chemistry of Solid Surfaces, Collaborative Innovation Center of Chemistry for Energy Materials, Department of Chemical Biology, Department of Chemical Engineering, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
| | - Shanshan Liang
- The MOE Key Laboratory of Spectrochemical Analysis & Instrumentation, the Key Laboratory of Chemical Biology of Fujian Province, State Key Laboratory of Physical Chemistry of Solid Surfaces, Collaborative Innovation Center of Chemistry for Energy Materials, Department of Chemical Biology, Department of Chemical Engineering, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
| | - Yuehan Huang
- School of International Education, Beijing University of Chemical Technology, Beijing, 100029, China
| | - Jia Song
- Institute for Developmental and Regenerative Cardiovascular Medicine, Xinhua Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200092, China
| | - Xing Xu
- The MOE Key Laboratory of Spectrochemical Analysis & Instrumentation, the Key Laboratory of Chemical Biology of Fujian Province, State Key Laboratory of Physical Chemistry of Solid Surfaces, Collaborative Innovation Center of Chemistry for Energy Materials, Department of Chemical Biology, Department of Chemical Engineering, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
- Department of Laboratory Medicine, Key Laboratory of Clinical Laboratory Technology for Precision Medicine, School of Medical Technology and Engineering, Fujian Medical University, Fuzhou 350005, China
| | - Chaoyong Yang
- The MOE Key Laboratory of Spectrochemical Analysis & Instrumentation, the Key Laboratory of Chemical Biology of Fujian Province, State Key Laboratory of Physical Chemistry of Solid Surfaces, Collaborative Innovation Center of Chemistry for Energy Materials, Department of Chemical Biology, Department of Chemical Engineering, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
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3
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Tomasiak A, Piński A, Milewska-Hendel A, Andreu Godall I, Borowska-Żuchowska N, Morończyk J, Moreno-Romero J, Betekhtin A. H3K4me3 changes occur in cell wall genes during the development of Fagopyrum tataricum morphogenic and non-morphogenic calli. FRONTIERS IN PLANT SCIENCE 2024; 15:1465514. [PMID: 39385990 PMCID: PMC11461221 DOI: 10.3389/fpls.2024.1465514] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/16/2024] [Accepted: 09/05/2024] [Indexed: 10/12/2024]
Abstract
Epigenetic changes accompany the dynamic changes in the cell wall composition during the development of callus cells. H3K4me3 is responsible for active gene expression and reaction to environmental cues. Chromatin immunoprecipitation (ChIP) is a powerful technique for studying the interplay between epigenetic modifications and the DNA regions of interest. In combination with sequencing, it can provide the genome-wide enrichment of the specific epigenetic mark, providing vital information on its involvement in the plethora of cellular processes. Here, we describe the genome-wide distribution of H3K4me3 in morphogenic and non-morphogenic callus of Fagopyrum tataricum. Levels of H3K4me3 were higher around the transcription start site, in agreement with the role of this mark in transcriptional activation. The global levels of methylation were higher in the non-morphogenic callus, which indicated increased gene activation compared to the morphogenic callus. We also employed ChIP to analyse the changes in the enrichment of this epigenetic mark on the cell wall-related genes in both calli types during the course of the passage. Enrichment of H3K4me3 on cell wall genes was specific for callus type, suggesting that the role of this mark in cell-wall remodelling is complex and involved in many processes related to dedifferentiation and redifferentiation. This intricacy of the cell wall composition was supported by the immunohistochemical analysis of the cell wall epitopes' distribution of pectins and extensins. Together, these data give a novel insight into the involvement of H3K4me3 in the regeneration processes in F. tataricum in vitro callus tissue culture.
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Affiliation(s)
- Alicja Tomasiak
- Institute of Biology, Biotechnology and Environmental Protection, Faculty of Natural Sciences, University of Silesia in Katowice, Katowice, Poland
| | - Artur Piński
- Institute of Biology, Biotechnology and Environmental Protection, Faculty of Natural Sciences, University of Silesia in Katowice, Katowice, Poland
| | - Anna Milewska-Hendel
- Institute of Biology, Biotechnology and Environmental Protection, Faculty of Natural Sciences, University of Silesia in Katowice, Katowice, Poland
| | - Ignasi Andreu Godall
- Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Barcelona, Spain
| | - Natalia Borowska-Żuchowska
- Institute of Biology, Biotechnology and Environmental Protection, Faculty of Natural Sciences, University of Silesia in Katowice, Katowice, Poland
| | - Joanna Morończyk
- Institute of Biology, Biotechnology and Environmental Protection, Faculty of Natural Sciences, University of Silesia in Katowice, Katowice, Poland
| | - Jordi Moreno-Romero
- Departament de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, Cerdanyola del Vallès, Barcelona, Spain
| | - Alexander Betekhtin
- Institute of Biology, Biotechnology and Environmental Protection, Faculty of Natural Sciences, University of Silesia in Katowice, Katowice, Poland
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Hu S, Liu Y, Zhang Q, Bai J, Xu C. A continuum of zinc finger transcription factor retention on native chromatin underlies dynamic genome organization. Mol Syst Biol 2024; 20:799-824. [PMID: 38745107 PMCID: PMC11220090 DOI: 10.1038/s44320-024-00038-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2023] [Revised: 04/10/2024] [Accepted: 04/15/2024] [Indexed: 05/16/2024] Open
Abstract
Transcription factor (TF) residence on chromatin translates into quantitative transcriptional or structural outcomes on genome. Commonly used formaldehyde crosslinking fixes TF-DNA interactions cumulatively and compromises the measured occupancy level. Here we mapped the occupancy level of global or individual zinc finger TFs like CTCF and MAZ, in the form of highly resolved footprints, on native chromatin. By incorporating reinforcing perturbation conditions, we established S-score, a quantitative metric to proxy the continuum of CTCF or MAZ retention across different motifs on native chromatin. The native chromatin-retained CTCF sites harbor sequence features within CTCF motifs better explained by S-score than the metrics obtained from other crosslinking or native assays. CTCF retention on native chromatin correlates with local SUMOylation level, and anti-correlates with transcriptional activity. The S-score successfully delineates the otherwise-masked differential stability of chromatin structures mediated by CTCF, or by MAZ independent of CTCF. Overall, our study established a paradigm continuum of TF retention across binding sites on native chromatin, explaining the dynamic genome organization.
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Affiliation(s)
- Siling Hu
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China
- China National Center for Bioinformation, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Yangying Liu
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China
- China National Center for Bioinformation, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Qifan Zhang
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China
- China National Center for Bioinformation, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Juan Bai
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China
- China National Center for Bioinformation, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Chenhuan Xu
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China.
- China National Center for Bioinformation, Beijing, China.
- University of Chinese Academy of Sciences, Beijing, China.
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5
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Bárcenas-Walls JR, Ansaloni F, Hervé B, Strandback E, Nyman T, Castelo-Branco G, Bartošovič M. Nano-CUT&Tag for multimodal chromatin profiling at single-cell resolution. Nat Protoc 2024; 19:791-830. [PMID: 38129675 DOI: 10.1038/s41596-023-00932-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Accepted: 10/19/2023] [Indexed: 12/23/2023]
Abstract
The ability to comprehensively analyze the chromatin state with single-cell resolution is crucial for understanding gene regulatory principles in heterogenous tissues or during development. Recently, we developed a nanobody-based single-cell CUT&Tag (nano-CT) protocol to simultaneously profile three epigenetic modalities-two histone marks and open chromatin state-from the same single cell. Nano-CT implements a new set of secondary nanobody-Tn5 fusion proteins to direct barcoded tagmentation by Tn5 transposase to genomic targets labeled by primary antibodies raised in different species. Such nanobody-Tn5 fusion proteins are currently not commercially available, and their in-house production and purification can be completed in 3-4 d by following our detailed protocol. The single-cell indexing in nano-CT is performed on a commercially available platform, making it widely accessible to the community. In comparison to other multimodal methods, nano-CT stands out in data complexity, low sample requirements and the flexibility to choose two of the three modalities. In addition, nano-CT works efficiently with fresh brain samples, generating multimodal epigenomic profiles for thousands of brain cells at single-cell resolution. The nano-CT protocol can be completed in just 3 d by users with basic skills in standard molecular biology and bioinformatics, although previous experience with single-cell assay for transposase-accessible chromatin using sequencing (scATAC-seq) is beneficial for more in-depth data analysis. As a multimodal assay, nano-CT holds immense potential to reveal interactions of various chromatin modalities, to explore epigenetic heterogeneity and to increase our understanding of the role and interplay that chromatin dynamics has in cellular development.
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Affiliation(s)
| | - Federico Ansaloni
- Laboratory of Molecular Neurobiology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Bastien Hervé
- Laboratory of Molecular Neurobiology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Emilia Strandback
- Protein Science Facility, Department of Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Tomas Nyman
- Protein Science Facility, Department of Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Gonçalo Castelo-Branco
- Laboratory of Molecular Neurobiology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
- Ming Wai Lau Centre for Reparative Medicine, Stockholm node, Karolinska Institutet, Stockholm, Sweden
| | - Marek Bartošovič
- Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden.
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6
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Liu Z, Wong HM, Chen X, Lin J, Zhang S, Yan S, Wang F, Li X, Wong KC. MotifHub: Detection of trans-acting DNA motif group with probabilistic modeling algorithm. Comput Biol Med 2024; 168:107753. [PMID: 38039889 DOI: 10.1016/j.compbiomed.2023.107753] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2023] [Revised: 10/30/2023] [Accepted: 11/20/2023] [Indexed: 12/03/2023]
Abstract
BACKGROUND Trans-acting factors are of special importance in transcription regulation, which is a group of proteins that can directly or indirectly recognize or bind to the 8-12 bp core sequence of cis-acting elements and regulate the transcription efficiency of target genes. The progressive development in high-throughput chromatin capture technology (e.g., Hi-C) enables the identification of chromatin-interacting sequence groups where trans-acting DNA motif groups can be discovered. The problem difficulty lies in the combinatorial nature of DNA sequence pattern matching and its underlying sequence pattern search space. METHOD Here, we propose to develop MotifHub for trans-acting DNA motif group discovery on grouped sequences. Specifically, the main approach is to develop probabilistic modeling for accommodating the stochastic nature of DNA motif patterns. RESULTS Based on the modeling, we develop global sampling techniques based on EM and Gibbs sampling to address the global optimization challenge for model fitting with latent variables. The results reflect that our proposed approaches demonstrate promising performance with linear time complexities. CONCLUSION MotifHub is a novel algorithm considering the identification of both DNA co-binding motif groups and trans-acting TFs. Our study paves the way for identifying hub TFs of stem cell development (OCT4 and SOX2) and determining potential therapeutic targets of prostate cancer (FOXA1 and MYC). To ensure scientific reproducibility and long-term impact, its matrix-algebra-optimized source code is released at http://bioinfo.cs.cityu.edu.hk/MotifHub.
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Affiliation(s)
- Zhe Liu
- Department of Computer Science, City University of Hong Kong, Kowloon Tong, Kowloon, Hong Kong, China
| | - Hiu-Man Wong
- Department of Computer Science, City University of Hong Kong, Kowloon Tong, Kowloon, Hong Kong, China
| | - Xingjian Chen
- Department of Computer Science, City University of Hong Kong, Kowloon Tong, Kowloon, Hong Kong, China
| | - Jiecong Lin
- Department of Computer Science, City University of Hong Kong, Kowloon Tong, Kowloon, Hong Kong, China
| | - Shixiong Zhang
- Department of Computer Science, City University of Hong Kong, Kowloon Tong, Kowloon, Hong Kong, China
| | - Shankai Yan
- Department of Computer Science, City University of Hong Kong, Kowloon Tong, Kowloon, Hong Kong, China
| | - Fuzhou Wang
- Department of Computer Science, City University of Hong Kong, Kowloon Tong, Kowloon, Hong Kong, China
| | - Xiangtao Li
- School of Artificial Intelligence, Jilin University, Jilin, China
| | - Ka-Chun Wong
- Department of Computer Science, City University of Hong Kong, Kowloon Tong, Kowloon, Hong Kong, China.
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7
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Xing YH, Dong R, Lee L, Rengarajan S, Riggi N, Boulay G, Rivera MN. DisP-seq reveals the genome-wide functional organization of DNA-associated disordered proteins. Nat Biotechnol 2024; 42:52-64. [PMID: 37037903 PMCID: PMC10791585 DOI: 10.1038/s41587-023-01737-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Accepted: 03/07/2023] [Indexed: 04/12/2023]
Abstract
Intrinsically disordered regions (IDRs) in DNA-associated proteins are known to influence gene regulation, but their distribution and cooperative functions in genome-wide regulatory programs remain poorly understood. Here we describe DisP-seq (disordered protein precipitation followed by DNA sequencing), an antibody-independent chemical precipitation assay that can simultaneously map endogenous DNA-associated disordered proteins genome-wide through a combination of biotinylated isoxazole precipitation and next-generation sequencing. DisP-seq profiles are composed of thousands of peaks that are associated with diverse chromatin states, are enriched for disordered transcription factors (TFs) and are often arranged in large lineage-specific clusters with high local concentrations of disordered proteins and different combinations of histone modifications linked to regulatory potential. We use DisP-seq to analyze cancer cells and reveal how disordered protein-associated islands enable IDR-dependent mechanisms that control the binding and function of disordered TFs, including oncogene-dependent sequestration of TFs through long-range interactions and the reactivation of differentiation pathways upon loss of oncogenic stimuli in Ewing sarcoma.
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Affiliation(s)
- Yu-Hang Xing
- Department of Pathology, Massachusetts General Hospital and Harvard Medical School, Charlestown, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Center for Cancer Research, Massachusetts General Hospital and Harvard Medical School, Charlestown, MA, USA
| | - Rui Dong
- Department of Pathology, Massachusetts General Hospital and Harvard Medical School, Charlestown, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Center for Cancer Research, Massachusetts General Hospital and Harvard Medical School, Charlestown, MA, USA
| | - Lukuo Lee
- Department of Pathology, Massachusetts General Hospital and Harvard Medical School, Charlestown, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Center for Cancer Research, Massachusetts General Hospital and Harvard Medical School, Charlestown, MA, USA
| | - Shruthi Rengarajan
- Department of Pathology, Massachusetts General Hospital and Harvard Medical School, Charlestown, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Center for Cancer Research, Massachusetts General Hospital and Harvard Medical School, Charlestown, MA, USA
| | - Nicolò Riggi
- Institute of Pathology, Centre Hospitalier Universitaire Vaudois, Faculty of Biology and Medicine, University of Lausanne, Lausanne, Switzerland
- Swiss Cancer Center Leman (SCCL), Centre Hospitalier Universitaire Vaudois, Faculty of Biology and Medicine, University of Lausanne, Lausanne, Switzerland
| | - Gaylor Boulay
- Department of Pathology, Massachusetts General Hospital and Harvard Medical School, Charlestown, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Center for Cancer Research, Massachusetts General Hospital and Harvard Medical School, Charlestown, MA, USA
| | - Miguel N Rivera
- Department of Pathology, Massachusetts General Hospital and Harvard Medical School, Charlestown, MA, USA.
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Center for Cancer Research, Massachusetts General Hospital and Harvard Medical School, Charlestown, MA, USA.
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Nitsch S, Schneider R. Native ChIP: Studying the Genome-Wide Distribution of Histone Modifications in Cells and Tissue. Methods Mol Biol 2024; 2846:1-16. [PMID: 39141226 DOI: 10.1007/978-1-0716-4071-5_1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/15/2024]
Abstract
For the genome-wide mapping of histone modifications, chromatin immunoprecipitation (ChIP) followed by high-throughput sequencing remains the benchmark method. While crosslinked ChIP can be used for all kinds of targets, native ChIP is predominantly used for strong and direct DNA interactors like histones and their modifications. Here we describe a native ChIP protocol that can be used for cells and tissue material.
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Affiliation(s)
- Sandra Nitsch
- Institute of Functional Epigenetics (IFE), Helmholtz Zentrum München, Neuherberg, Germany.
| | - Robert Schneider
- Institute of Functional Epigenetics (IFE), Helmholtz Zentrum München, Neuherberg, Germany
- Faculty of Biology, Ludwigs-Maximilians Universität München, Planegg-Martinsried, Munich, Germany
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9
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Lin CY, Chang YM, Tseng HY, Shih YL, Yeh HH, Liao YR, Tang HH, Hsu CL, Chen CC, Yan YT, Kao CF. Epigenetic regulator RNF20 underlies temporal hierarchy of gene expression to regulate postnatal cardiomyocyte polarization. Cell Rep 2023; 42:113416. [PMID: 37967007 DOI: 10.1016/j.celrep.2023.113416] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2022] [Revised: 09/19/2023] [Accepted: 10/25/2023] [Indexed: 11/17/2023] Open
Abstract
Differentiated cardiomyocytes (CMs) must undergo diverse morphological and functional changes during postnatal development. However, the mechanisms underlying initiation and coordination of these changes remain unclear. Here, we delineate an integrated, time-ordered transcriptional network that begins with expression of genes for cell-cell connections and leads to a sequence of structural, cell-cycle, functional, and metabolic transitions in mouse postnatal hearts. Depletion of histone H2B ubiquitin ligase RNF20 disrupts this gene network and impairs CM polarization. Subsequently, assay for transposase-accessible chromatin using sequencing (ATAC-seq) analysis confirmed that RNF20 contributes to chromatin accessibility in this context. As such, RNF20 is likely to facilitate binding of transcription factors at the promoters of genes involved in cell-cell connections and actin organization, which are crucial for CM polarization and functional integration. These results suggest that CM polarization is one of the earliest events during postnatal heart development and provide insights into how RNF20 regulates CM polarity and the postnatal gene program.
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Affiliation(s)
- Chia-Yeh Lin
- Institute of Cellular and Organismic Biology, Academia Sinica, 128, Academia Road, Section 2, Nankang, Taipei, Taiwan
| | - Yao-Ming Chang
- Institute of Biomedical Sciences, Academia Sinica, 128, Academia Road, Section 2, Nankang, Taipei, Taiwan
| | - Hsin-Yi Tseng
- Institute of Cellular and Organismic Biology, Academia Sinica, 128, Academia Road, Section 2, Nankang, Taipei, Taiwan
| | - Yen-Ling Shih
- Institute of Biomedical Sciences, Academia Sinica, 128, Academia Road, Section 2, Nankang, Taipei, Taiwan
| | - Hsiao-Hui Yeh
- Institute of Biomedical Sciences, Academia Sinica, 128, Academia Road, Section 2, Nankang, Taipei, Taiwan
| | - You-Rou Liao
- Institute of Cellular and Organismic Biology, Academia Sinica, 128, Academia Road, Section 2, Nankang, Taipei, Taiwan
| | - Han-Hsuan Tang
- Institute of Cellular and Organismic Biology, Academia Sinica, 128, Academia Road, Section 2, Nankang, Taipei, Taiwan
| | - Chia-Ling Hsu
- Institute of Cellular and Organismic Biology, Academia Sinica, 128, Academia Road, Section 2, Nankang, Taipei, Taiwan
| | - Chien-Chang Chen
- Institute of Biomedical Sciences, Academia Sinica, 128, Academia Road, Section 2, Nankang, Taipei, Taiwan
| | - Yu-Ting Yan
- Institute of Biomedical Sciences, Academia Sinica, 128, Academia Road, Section 2, Nankang, Taipei, Taiwan.
| | - Cheng-Fu Kao
- Institute of Cellular and Organismic Biology, Academia Sinica, 128, Academia Road, Section 2, Nankang, Taipei, Taiwan.
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10
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Martín-Zamora FM, Davies BE, Donnellan RD, Guynes K, Martín-Durán JM. Functional genomics in Spiralia. Brief Funct Genomics 2023; 22:487-497. [PMID: 37981859 PMCID: PMC10658182 DOI: 10.1093/bfgp/elad036] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Revised: 07/12/2023] [Accepted: 07/25/2023] [Indexed: 11/21/2023] Open
Abstract
Our understanding of the mechanisms that modulate gene expression in animals is strongly biased by studying a handful of model species that mainly belong to three groups: Insecta, Nematoda and Vertebrata. However, over half of the animal phyla belong to Spiralia, a morphologically and ecologically diverse animal clade with many species of economic and biomedical importance. Therefore, investigating genome regulation in this group is central to uncovering ancestral and derived features in genome functioning in animals, which can also be of significant societal impact. Here, we focus on five aspects of gene expression regulation to review our current knowledge of functional genomics in Spiralia. Although some fields, such as single-cell transcriptomics, are becoming more common, the study of chromatin accessibility, DNA methylation, histone post-translational modifications and genome architecture are still in their infancy. Recent efforts to generate chromosome-scale reference genome assemblies for greater species diversity and optimise state-of-the-art approaches for emerging spiralian research systems will address the existing knowledge gaps in functional genomics in this animal group.
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Affiliation(s)
- Francisco M Martín-Zamora
- School of Biological and Behavioural Sciences, Queen Mary University of London, Mile End Road, London E1 4NS, UK
| | - Billie E Davies
- School of Biological and Behavioural Sciences, Queen Mary University of London, Mile End Road, London E1 4NS, UK
| | - Rory D Donnellan
- School of Biological and Behavioural Sciences, Queen Mary University of London, Mile End Road, London E1 4NS, UK
| | - Kero Guynes
- School of Biological and Behavioural Sciences, Queen Mary University of London, Mile End Road, London E1 4NS, UK
| | - José M Martín-Durán
- School of Biological and Behavioural Sciences, Queen Mary University of London, Mile End Road, London E1 4NS, UK
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11
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Sept CE, Tak YE, Cerda-Smith CG, Hutchinson HM, Goel V, Blanchette M, Bhakta MS, Hansen AS, Joung JK, Johnstone S, Eyler CE, Aryee MJ. High-resolution CTCF footprinting reveals impact of chromatin state on cohesin extrusion dynamics. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.20.563340. [PMID: 37961446 PMCID: PMC10634716 DOI: 10.1101/2023.10.20.563340] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
Abstract
DNA looping is vital for establishing many enhancer-promoter interactions. While CTCF is known to anchor many cohesin-mediated loops, the looped chromatin fiber appears to predominantly exist in a poorly characterized actively extruding state. To better characterize extruding chromatin loop structures, we used CTCF MNase HiChIP data to determine both CTCF binding at high resolution and 3D contact information. Here we present FactorFinder, a tool that identifies CTCF binding sites at near base-pair resolution. We leverage this substantial advance in resolution to determine that the fully extruded (CTCF-CTCF) state is rare genome-wide with locus-specific variation from ~1-10%. We further investigate the impact of chromatin state on loop extrusion dynamics, and find that active enhancers and RNA Pol II impede cohesin extrusion, facilitating an enrichment of enhancer-promoter contacts in the partially extruded loop state. We propose a model of topological regulation whereby the transient, partially extruded states play active roles in transcription.
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Affiliation(s)
- Corriene E Sept
- Department of Biostatistics, Harvard T.H. Chan School of Public Health; Boston, MA 02115, USA
- Department of Data Sciences, Dana-Farber Cancer Institute; Boston, MA 02115, USA
- Broad Institute of MIT and Harvard; Cambridge, MA 02142, USA
| | - Y Esther Tak
- Molecular Pathology Unit, Massachusetts General Hospital; Charlestown, MA 02129, USA
- Department of Pathology, Harvard Medical School; Boston, MA 02115, USA
| | - Christian G Cerda-Smith
- Department of Pharmacology and Cancer Biology, Duke University School of Medicine; Durham, NC 27710, USA
| | - Haley M Hutchinson
- Department of Pharmacology and Cancer Biology, Duke University School of Medicine; Durham, NC 27710, USA
| | - Viraat Goel
- Broad Institute of MIT and Harvard; Cambridge, MA 02142, USA
- Department of Biological Engineering, Massachusetts Institute of Technology; Cambridge, MA 02139, USA
- Koch Institute for Integrative Cancer Research; Cambridge, MA 02139, USA
| | - Marco Blanchette
- Dovetail Genomics, Cantata Bio LLC, Scotts Valley, CA 95066, USA
| | - Mital S Bhakta
- Dovetail Genomics, Cantata Bio LLC, Scotts Valley, CA 95066, USA
| | - Anders S Hansen
- Broad Institute of MIT and Harvard; Cambridge, MA 02142, USA
- Department of Biological Engineering, Massachusetts Institute of Technology; Cambridge, MA 02139, USA
- Koch Institute for Integrative Cancer Research; Cambridge, MA 02139, USA
| | - J Keith Joung
- Molecular Pathology Unit, Massachusetts General Hospital; Charlestown, MA 02129, USA
- Department of Pathology, Harvard Medical School; Boston, MA 02115, USA
| | - Sarah Johnstone
- Broad Institute of MIT and Harvard; Cambridge, MA 02142, USA
- Department of Pathology, Dana-Farber Cancer Institute; Boston, MA 02215, USA
| | - Christine E Eyler
- Department of Radiation Oncology, Duke University School of Medicine; Durham, NC 27710, USA
- Duke Cancer Institute, Duke University School of Medicine; Durham, NC 27710, USA
| | - Martin J Aryee
- Department of Biostatistics, Harvard T.H. Chan School of Public Health; Boston, MA 02115, USA
- Department of Data Sciences, Dana-Farber Cancer Institute; Boston, MA 02115, USA
- Broad Institute of MIT and Harvard; Cambridge, MA 02142, USA
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12
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Pan J, Chang Z, Zhang X, Dong Q, Zhao H, Shi J, Wang G. Research progress of single-cell sequencing in tuberculosis. Front Immunol 2023; 14:1276194. [PMID: 37901241 PMCID: PMC10611525 DOI: 10.3389/fimmu.2023.1276194] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2023] [Accepted: 09/29/2023] [Indexed: 10/31/2023] Open
Abstract
Tuberculosis is a major infectious disease caused by Mycobacterium tuberculosis infection. The pathogenesis and immune mechanism of tuberculosis are not clear, and it is urgent to find new drugs, diagnosis, and treatment targets. A useful tool in the quest to reveal the enigmas related to Mycobacterium tuberculosis infection and disease is the single-cell sequencing technique. By clarifying cell heterogeneity, identifying pathogenic cell groups, and finding key gene targets, the map at the single cell level enables people to better understand the cell diversity of complex organisms and the immune state of hosts during infection. Here, we briefly reviewed the development of single-cell sequencing, and emphasized the different applications and limitations of various technologies. Single-cell sequencing has been widely used in the study of the pathogenesis and immune response of tuberculosis. We review these works summarizing the most influential findings. Combined with the multi-molecular level and multi-dimensional analysis, we aim to deeply understand the blank and potential future development of the research on Mycobacterium tuberculosis infection using single-cell sequencing technology.
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Affiliation(s)
| | | | | | | | | | - Jingwei Shi
- Key Laboratory of Pathobiology Ministry of Education, College of Basic Medical Sciences/China-Japan Union Hospital of Jilin University, Jilin University, Changchun, China
| | - Guoqing Wang
- Key Laboratory of Pathobiology Ministry of Education, College of Basic Medical Sciences/China-Japan Union Hospital of Jilin University, Jilin University, Changchun, China
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13
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Banks OGB, Harms MJ, McKnight JN, McKnight LE. Simultaneous Mapping of DNA Binding and Nucleosome Positioning with SpLiT-ChEC. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.07.03.547581. [PMID: 37461563 PMCID: PMC10349973 DOI: 10.1101/2023.07.03.547581] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 07/25/2023]
Abstract
The organization of chromatin - including the positions of nucleosomes and the binding of other proteins to DNA - helps define transcriptional profiles in eukaryotic organisms. While techniques like ChIP-Seq and MNase-Seq can map protein-DNA and nucleosome localization separately, assays designed to simultaneously capture nucleosome positions and protein-DNA interactions can produce a detailed picture of the chromatin landscape. Most assays that monitor chromatin organization and protein binding rely on antibodies, which often exhibit nonspecific binding, and/or the addition of bulky adducts to the DNA-binding protein being studied, which can affect their expression and activity. Here, we describe SpyCatcher Linked Targeting of Chromatin Endogenous Cleavage (SpLiT-ChEC), where a 13-amino acid SpyTag peptide, appended to a protein of interest, serves as a highly-specific targeting moiety for in situ enzymatic digestion. The SpyTag/SpyCatcher system forms a covalent bond, linking the target protein and a co-expressed MNase-SpyCatcher fusion construct. SpyTagged proteins are expressed from endogenous loci, whereas MNase-SpyCatcher expression is induced immediately before harvesting cultures. MNase is activated with high concentrations of calcium, which primarily digests DNA near target protein binding sites. By sequencing the DNA fragments released by targeted MNase digestion, we found that this method recovers information on protein binding and proximal nucleosome positioning. SpLiT-ChEC provides precise temporal control that we anticipate can be used to monitor chromatin under various conditions and at distinct points in the cell cycle.
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Affiliation(s)
- Orion G. B. Banks
- Institute of Molecular Biology, University of Oregon, Eugene OR 97403, USA
| | - Michael J. Harms
- Institute of Molecular Biology, University of Oregon, Eugene OR 97403, USA
- Department of Chemistry and Biochemistry, University of Oregon, Eugene OR 97403, USA
| | - Jeffrey. N. McKnight
- Institute of Molecular Biology, University of Oregon, Eugene OR 97403, USA
- Knight Campus for Accelerated Research, University of Oregon, Eugene OR 97403, USA
| | - Laura E. McKnight
- Institute of Molecular Biology, University of Oregon, Eugene OR 97403, USA
- Knight Campus for Accelerated Research, University of Oregon, Eugene OR 97403, USA
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14
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Bohm KA, Morledge-Hampton B, Stevison S, Mao P, Roberts SA, Wyrick JJ. Genome-wide maps of rare and atypical UV photoproducts reveal distinct patterns of damage formation and mutagenesis in yeast chromatin. Proc Natl Acad Sci U S A 2023; 120:e2216907120. [PMID: 36853943 PMCID: PMC10013872 DOI: 10.1073/pnas.2216907120] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2022] [Accepted: 02/03/2023] [Indexed: 03/01/2023] Open
Abstract
Ultraviolet (UV) light induces different classes of mutagenic photoproducts in DNA, namely cyclobutane pyrimidine dimers (CPDs), 6-4 photoproducts (6-4PPs), and atypical thymine-adenine photoproducts (TA-PPs). CPD formation is modulated by nucleosomes and transcription factors (TFs), which has important ramifications for Ultraviolet (UV) mutagenesis. How chromatin affects the formation of 6-4PPs and TA-PPs is unclear. Here, we use UV damage endonuclease-sequencing (UVDE-seq) to map these UV photoproducts across the yeast genome. Our results indicate that nucleosomes, the fundamental building block of chromatin, have opposing effects on photoproduct formation. Nucleosomes induce CPDs and 6-4PPs at outward rotational settings in nucleosomal DNA but suppress TA-PPs at these settings. Our data also indicate that DNA binding by different classes of yeast TFs causes lesion-specific hotspots of 6-4PPs or TA-PPs. For example, DNA binding by the TF Rap1 generally suppresses CPD and 6-4PP formation but induces a TA-PP hotspot. Finally, we show that 6-4PP formation is strongly induced at the binding sites of TATA-binding protein (TBP), which is correlated with higher mutation rates in UV-exposed yeast. These results indicate that the formation of 6-4PPs and TA-PPs is modulated by chromatin differently than CPDs and that this may have important implications for UV mutagenesis.
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Affiliation(s)
- Kaitlynne A. Bohm
- School of Molecular Biosciences, Washington State University, Pullman, WA99164
| | | | - Scott Stevison
- School of Molecular Biosciences, Washington State University, Pullman, WA99164
| | - Peng Mao
- Department of Internal Medicine, University of New Mexico Comprehensive Cancer Center, Albuquerque, NM87131
| | - Steven A. Roberts
- School of Molecular Biosciences, Washington State University, Pullman, WA99164
- Center for Reproductive Biology, Washington State University, Pullman, WA99164
| | - John J. Wyrick
- School of Molecular Biosciences, Washington State University, Pullman, WA99164
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15
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Henikoff S, Ahmad K. In situ tools for chromatin structural epigenomics. Protein Sci 2022; 31:e4458. [PMID: 36170035 PMCID: PMC9601787 DOI: 10.1002/pro.4458] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Revised: 09/19/2022] [Accepted: 09/22/2022] [Indexed: 12/14/2022]
Abstract
Technological progress over the past 15 years has fueled an explosion in genome-wide chromatin profiling tools that take advantage of low-cost short-read sequencing technologies to map particular chromatin features. Here, we survey the recent development of epigenomic tools that provide precise positions of chromatin proteins genome-wide in intact cells or nuclei. Some profiling tools are based on tethering Micrococcal Nuclease to chromatin proteins of interest in situ, whereas others similarly tether Tn5 transposase to integrate DNA sequencing adapters (tagmentation) and so eliminate the need for library preparation. These in situ cleavage and tagmentation tools have gained in popularity over the past few years, with many protocol enhancements and adaptations for single-cell and spatial chromatin profiling. The application of experimental and computational tools to address problems in gene regulation, eukaryotic development, and human disease are helping to define the emerging field of chromatin structural epigenomics.
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Affiliation(s)
- Steven Henikoff
- Fred Hutchinson Cancer CenterSeattleWashingtonUSA
- Howard Hughes Medical InstituteChevy ChaseMarylandUSA
| | - Kami Ahmad
- Fred Hutchinson Cancer CenterSeattleWashingtonUSA
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16
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Geraldes I, Fernandes M, Fraga AG, Osório NS. The impact of single-cell genomics on the field of mycobacterial infection. Front Microbiol 2022; 13:989464. [PMID: 36246265 PMCID: PMC9562642 DOI: 10.3389/fmicb.2022.989464] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Accepted: 09/14/2022] [Indexed: 11/13/2022] Open
Abstract
Genome sequencing projects of humans and other organisms reinforced that the complexity of biological systems is largely attributed to the tight regulation of gene expression at the epigenome and RNA levels. As a consequence, plenty of technological developments arose to increase the sequencing resolution to the cell dimension creating the single-cell genomics research field. Single-cell RNA sequencing (scRNA-seq) is leading the advances in this topic and comprises a vast array of different methodologies. scRNA-seq and its variants are more and more used in life science and biomedical research since they provide unbiased transcriptomic sequencing of large populations of individual cells. These methods go beyond the previous “bulk” methodologies and sculpt the biological understanding of cellular heterogeneity and dynamic transcriptomic states of cellular populations in immunology, oncology, and developmental biology fields. Despite the large burden caused by mycobacterial infections, advances in this field obtained via single-cell genomics had been comparatively modest. Nonetheless, seminal research publications using single-cell transcriptomics to study host cells infected by mycobacteria have become recently available. Here, we review these works summarizing the most impactful findings and emphasizing the different and recent single-cell methodologies used, potential issues, and problems. In addition, we aim at providing insights into current research gaps and potential future developments related to the use of single-cell genomics to study mycobacterial infection.
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Affiliation(s)
- Inês Geraldes
- Life and Health Sciences Research Institute (ICVS), School of Medicine, University of Minho, Braga, Portugal
- ICVS/3B's—PT Government Associate Laboratory, Braga, Portugal
| | - Mónica Fernandes
- Life and Health Sciences Research Institute (ICVS), School of Medicine, University of Minho, Braga, Portugal
- ICVS/3B's—PT Government Associate Laboratory, Braga, Portugal
| | - Alexandra G. Fraga
- Life and Health Sciences Research Institute (ICVS), School of Medicine, University of Minho, Braga, Portugal
- ICVS/3B's—PT Government Associate Laboratory, Braga, Portugal
| | - Nuno S. Osório
- Life and Health Sciences Research Institute (ICVS), School of Medicine, University of Minho, Braga, Portugal
- ICVS/3B's—PT Government Associate Laboratory, Braga, Portugal
- *Correspondence: Nuno S. Osório
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17
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An improved CUT&RUN method for regulation network reconstruction of low abundance transcription factor. Cell Signal 2022; 96:110361. [DOI: 10.1016/j.cellsig.2022.110361] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2022] [Accepted: 05/18/2022] [Indexed: 11/20/2022]
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18
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Kinetic principles underlying pioneer function of GAGA transcription factor in live cells. Nat Struct Mol Biol 2022; 29:665-676. [PMID: 35835866 PMCID: PMC10177624 DOI: 10.1038/s41594-022-00800-z] [Citation(s) in RCA: 31] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Accepted: 05/27/2022] [Indexed: 11/09/2022]
Abstract
How pioneer factors interface with chromatin to promote accessibility for transcription control is poorly understood in vivo. Here, we directly visualize chromatin association by the prototypical GAGA pioneer factor (GAF) in live Drosophila hemocytes. Single-particle tracking reveals that most GAF is chromatin bound, with a stable-binding fraction showing nucleosome-like confinement residing on chromatin for more than 2 min, far longer than the dynamic range of most transcription factors. These kinetic properties require the full complement of GAF's DNA-binding, multimerization and intrinsically disordered domains, and are autonomous from recruited chromatin remodelers NURF and PBAP, whose activities primarily benefit GAF's neighbors such as Heat Shock Factor. Evaluation of GAF kinetics together with its endogenous abundance indicates that, despite on-off dynamics, GAF constitutively and fully occupies major chromatin targets, thereby providing a temporal mechanism that sustains open chromatin for transcriptional responses to homeostatic, environmental and developmental signals.
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19
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Liu Z, Naler LB, Zhu Y, Deng C, Zhang Q, Zhu B, Zhou Z, Sarma M, Murray A, Xie H, Lu C. nMOWChIP-seq: low-input genome-wide mapping of non-histone targets. NAR Genom Bioinform 2022; 4:lqac030. [PMID: 35402909 PMCID: PMC8988714 DOI: 10.1093/nargab/lqac030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2021] [Revised: 03/18/2022] [Accepted: 03/25/2022] [Indexed: 11/13/2022] Open
Abstract
Genome-wide profiling of interactions between genome and various functional proteins is critical for understanding regulatory processes involved in development and diseases. Conventional assays require a large number of cells and high-quality data on tissue samples are scarce. Here we optimized a low-input chromatin immunoprecipitation followed by sequencing (ChIP-seq) technology for profiling RNA polymerase II (Pol II), transcription factor (TF), and enzyme binding at the genome scale. The new approach produces high-quality binding profiles using 1,000-50,000 cells. We used the approach to examine the binding of Pol II and two TFs (EGR1 and MEF2C) in cerebellum and prefrontal cortex of mouse brain and found that their binding profiles are highly reflective of the functional differences between the two brain regions. Our analysis reveals the potential for linking genome-wide TF or Pol II profiles with neuroanatomical origins of brain cells.
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Affiliation(s)
- Zhengzhi Liu
- Department of Biomedical Engineering and Mechanics, Virginia Tech, Blacksburg, VA, USA
| | - Lynette B Naler
- Department of Chemical Engineering, Virginia Tech, Blacksburg, VA, USA
| | - Yan Zhu
- Department of Chemical Engineering, Virginia Tech, Blacksburg, VA, USA
| | - Chengyu Deng
- Department of Chemical Engineering, Virginia Tech, Blacksburg, VA, USA
| | - Qiang Zhang
- Department of Chemical Engineering, Virginia Tech, Blacksburg, VA, USA
| | - Bohan Zhu
- Department of Chemical Engineering, Virginia Tech, Blacksburg, VA, USA
| | - Zirui Zhou
- Department of Chemical Engineering, Virginia Tech, Blacksburg, VA, USA
| | - Mimosa Sarma
- Department of Chemical Engineering, Virginia Tech, Blacksburg, VA, USA
| | - Alexander Murray
- Department of Biomedical Sciences & Pathobiology, Virginia Tech, Blacksburg, VA, USA
| | - Hehuang Xie
- Department of Biomedical Sciences & Pathobiology, Virginia Tech, Blacksburg, VA, USA
| | - Chang Lu
- Department of Chemical Engineering, Virginia Tech, Blacksburg, VA, USA
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20
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Duan M, Sivapragasam S, Antony JS, Ulibarri J, Hinz JM, Poon GMK, Wyrick JJ, Mao P. High-resolution mapping demonstrates inhibition of DNA excision repair by transcription factors. eLife 2022; 11:73943. [PMID: 35289750 PMCID: PMC8970589 DOI: 10.7554/elife.73943] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Accepted: 03/11/2022] [Indexed: 11/16/2022] Open
Abstract
DNA base damage arises frequently in living cells and needs to be removed by base excision repair (BER) to prevent mutagenesis and genome instability. Both the formation and repair of base damage occur in chromatin and are conceivably affected by DNA-binding proteins such as transcription factors (TFs). However, to what extent TF binding affects base damage distribution and BER in cells is unclear. Here, we used a genome-wide damage mapping method, N-methylpurine-sequencing (NMP-seq), and characterized alkylation damage distribution and BER at TF binding sites in yeast cells treated with the alkylating agent methyl methanesulfonate (MMS). Our data show that alkylation damage formation was mainly suppressed at the binding sites of yeast TFs ARS binding factor 1 (Abf1) and rDNA enhancer binding protein 1 (Reb1), but individual hotspots with elevated damage levels were also found. Additionally, Abf1 and Reb1 binding strongly inhibits BER in vivo and in vitro, causing slow repair both within the core motif and its adjacent DNA. Repair of ultraviolet (UV) damage by nucleotide excision repair (NER) was also inhibited by TF binding. Interestingly, TF binding inhibits a larger DNA region for NER relative to BER. The observed effects are caused by the TF–DNA interaction, because damage formation and BER can be restored by depletion of Abf1 or Reb1 protein from the nucleus. Thus, our data reveal that TF binding significantly modulates alkylation base damage formation and inhibits repair by the BER pathway. The interplay between base damage formation and BER may play an important role in affecting mutation frequency in gene regulatory regions.
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Affiliation(s)
- Mingrui Duan
- Department of Internal Medicine, University of New Mexico, Albuquerque, United States
| | - Smitha Sivapragasam
- School of Molecular Biosciences, Washington State University, Pullman, United States
| | - Jacob S Antony
- School of Molecular Biosciences, Washington State University, Pullman, United States
| | - Jenna Ulibarri
- Department of Internal Medicine, University of New Mexico, Albuquerque, United States
| | - John M Hinz
- School of Molecular Biosciences, Washington State University, Pullman, United States
| | - Gregory M K Poon
- Department of Chemistry, Georgia State University, Atlanta, United States
| | - John J Wyrick
- School of Molecular Biosciences, Washington State University, Pullman, United States
| | - Peng Mao
- Department of Internal Medicine, University of New Mexico, Albuquerque, United States
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21
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Refactoring transcription factors for metabolic engineering. Biotechnol Adv 2022; 57:107935. [PMID: 35271945 DOI: 10.1016/j.biotechadv.2022.107935] [Citation(s) in RCA: 36] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2021] [Revised: 02/04/2022] [Accepted: 03/03/2022] [Indexed: 12/19/2022]
Abstract
Due to the ability to regulate target metabolic pathways globally and dynamically, metabolic regulation systems composed of transcription factors have been widely used in metabolic engineering and synthetic biology. This review introduced the categories, action principles, prediction strategies, and related databases of transcription factors. Then, the application of global transcription machinery engineering technology and the transcription factor-based biosensors and quorum sensing systems are overviewed. In addition, strategies for optimizing the transcriptional regulatory tools' performance by refactoring transcription factors are summarized. Finally, the current limitations and prospects of constructing various regulatory tools based on transcription factors are discussed. This review will provide theoretical guidance for the rational design and construction of transcription factor-based metabolic regulation systems.
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22
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Torres-Campana D, Horard B, Denaud S, Benoit G, Loppin B, Orsi GA. Three classes of epigenomic regulators converge to hyperactivate the essential maternal gene deadhead within a heterochromatin mini-domain. PLoS Genet 2022; 18:e1009615. [PMID: 34982772 PMCID: PMC8759638 DOI: 10.1371/journal.pgen.1009615] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2021] [Revised: 01/14/2022] [Accepted: 12/10/2021] [Indexed: 11/24/2022] Open
Abstract
The formation of a diploid zygote is a highly complex cellular process that is entirely controlled by maternal gene products stored in the egg cytoplasm. This highly specialized transcriptional program is tightly controlled at the chromatin level in the female germline. As an extreme case in point, the massive and specific ovarian expression of the essential thioredoxin Deadhead (DHD) is critically regulated in Drosophila by the histone demethylase Lid and its partner, the histone deacetylase complex Sin3A/Rpd3, via yet unknown mechanisms. Here, we identified Snr1 and Mod(mdg4) as essential for dhd expression and investigated how these epigenomic effectors act with Lid and Sin3A to hyperactivate dhd. Using Cut&Run chromatin profiling with a dedicated data analysis procedure, we found that dhd is intriguingly embedded in an H3K27me3/H3K9me3-enriched mini-domain flanked by DNA regulatory elements, including a dhd promoter-proximal element essential for its expression. Surprisingly, Lid, Sin3a, Snr1 and Mod(mdg4) impact H3K27me3 and this regulatory element in distinct manners. However, we show that these effectors activate dhd independently of H3K27me3/H3K9me3, and that dhd remains silent in the absence of these marks. Together, our study demonstrates an atypical and critical role for chromatin regulators Lid, Sin3A, Snr1 and Mod(mdg4) to trigger tissue-specific hyperactivation within a unique heterochromatin mini-domain. Multicellular development depends on a tight control of gene expression in each cell type. This relies on the coordinated activities of nuclear proteins that interact with DNA or its histone scaffold to promote or restrict gene transcription. For example, we previously showed that the histone modifying enzymes Lid and Sin3A/Rpd3 are required in Drosophila ovaries for the massive expression of deadhead (dhd), a gene encoding for a thioredoxin that is essential for fertility. In this paper, we have further identified two additional dhd regulators, Snr1 and Mod(mdg4) and dissected the mechanism behind hyperactivation of this gene. Using the epigenomic profiling method Cut&Run with a dedicated data analysis approach, we unexpectedly found that dhd is embedded in an unusual chromatin mini-domain featuring repressive histone modifications H3K27me3 and H3K9me3 and flanked by two regulatory elements. However, we further showed that Lid, Sin3A, Snr1 and Mod(mdg4) behave like obligatory activators of dhd independently of this mini-domain. Our study unveils how multiple broad-acting epigenomic effectors operate in non-canonical manners to ensure a critical and specialized gene activation event. These findings challenge our knowledge on these regulatory mechanisms and their roles in development and pathology.
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Affiliation(s)
- Daniela Torres-Campana
- Laboratoire de Biologie et Modélisation de la Cellule, CNRS UMR5239, École Normale Supérieure de Lyon, University of Lyon, Lyon, France
| | - Béatrice Horard
- Laboratoire de Biologie et Modélisation de la Cellule, CNRS UMR5239, École Normale Supérieure de Lyon, University of Lyon, Lyon, France
| | - Sandrine Denaud
- Institute of Human Genetics, UMR 9002, CNRS, Université de Montpellier, Montpellier, France
| | - Gérard Benoit
- Laboratoire de Biologie et Modélisation de la Cellule, CNRS UMR5239, École Normale Supérieure de Lyon, University of Lyon, Lyon, France
| | - Benjamin Loppin
- Laboratoire de Biologie et Modélisation de la Cellule, CNRS UMR5239, École Normale Supérieure de Lyon, University of Lyon, Lyon, France
- * E-mail: (BL); (GAO)
| | - Guillermo A. Orsi
- Laboratoire de Biologie et Modélisation de la Cellule, CNRS UMR5239, École Normale Supérieure de Lyon, University of Lyon, Lyon, France
- * E-mail: (BL); (GAO)
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23
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Abstract
Mapping the epigenome is key to describe the relationship between chromatin landscapes and the control of DNA-based cellular processes such as transcription. Cleavage under targets and release using nuclease (CUT&RUN) is an in situ chromatin profiling strategy in which controlled cleavage by antibody-targeted Micrococcal Nuclease solubilizes specific protein-DNA complexes for paired-end DNA sequencing. When applied to budding yeast, CUT&RUN profiling yields precise genome-wide maps of histone modifications, histone variants, transcription factors, and ATP-dependent chromatin remodelers, while avoiding cross-linking and solubilization issues associated with the most commonly used chromatin profiling technique Chromatin Immunoprecipitation (ChIP). Furthermore, targeted chromatin complexes cleanly released by CUT&RUN can be used as input for a subsequent native immunoprecipitation step (CUT&RUN.ChIP) to simultaneously map two epitopes in single molecules genome-wide. The intrinsically low background and high resolution of CUT&RUN and CUT&RUN.ChIP allows for identification of transient genomic features such as dynamic nucleosome-remodeling intermediates. Starting from cells, one can perform CUT&RUN or CUT&RUN.ChIP and obtain purified DNA for sequencing library preparation in 2 days.
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Affiliation(s)
- Sandipan Brahma
- Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
- Howard Hughes Medical Institute, Seattle, WA, USA
| | - Steven Henikoff
- Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA.
- Howard Hughes Medical Institute, Seattle, WA, USA.
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24
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Schultz JC, Cao M, Mejia A, Zhao H. CUT&RUN Identifies Centromeric DNA Regions of Rhodotorula toruloides IFO0880. FEMS Yeast Res 2021; 21:6460484. [PMID: 34902017 DOI: 10.1093/femsyr/foab066] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2021] [Accepted: 12/10/2021] [Indexed: 11/14/2022] Open
Abstract
Rhodotorula toruloides has been increasingly explored as a host for bioproduction of lipids, fatty acid derivatives, and terpenoids. Various genetic tools have been developed, but neither a centromere nor an autonomously replicating sequence (ARS), both necessary elements for stable episomal plasmid maintenance, have yet been reported. In this study, Cleavage Under Targets and Release Using Nuclease (CUT&RUN), a method used for genome-wide mapping DNA-protein interactions, was used to identify R. toruloides IFO0880 genomic regions associated with the centromeric histone H3 protein Cse4, a marker of centromeric DNA. Fifteen putative centromeres ranging from 8 to 19 kb in length were identified and analyzed, and four were tested for, but did not show, ARS activity. These centromeric sequences contained below average GC content, corresponded to transcriptional cold-spots, were primarily nonrepetitive, and shared some vestigial transposon-related sequences but otherwise did not show significant sequence conservation. Future efforts to identify an ARS in this yeast can utilize these centromeric DNA sequences to improve the stability of episomal plasmids derived from putative ARS elements.
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Affiliation(s)
- J Carl Schultz
- Department of Chemical and Biomolecular Engineering, U.S. Department of Energy Center for Bioenergy and Bioproducts Innovation (CABBI), Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, United States
| | - Mingfeng Cao
- Department of Chemical and Biomolecular Engineering, U.S. Department of Energy Center for Bioenergy and Bioproducts Innovation (CABBI), Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, United States
| | - Andrea Mejia
- Department of Chemical and Biomolecular Engineering, U.S. Department of Energy Center for Bioenergy and Bioproducts Innovation (CABBI), Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, United States
| | - Huimin Zhao
- Department of Chemical and Biomolecular Engineering, U.S. Department of Energy Center for Bioenergy and Bioproducts Innovation (CABBI), Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, United States.,Departments of Chemistry, Biochemistry, and Bioengineering, University of Illinois at Urbana-Champaign, Urbana, IL 61801, United States
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25
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Kanapeckaitė A, Burokienė N, Mažeikienė A, Cottrell GS, Widera D. Biophysics is reshaping our perception of the epigenome: from DNA-level to high-throughput studies. BIOPHYSICAL REPORTS 2021; 1:100028. [PMID: 36425454 PMCID: PMC9680810 DOI: 10.1016/j.bpr.2021.100028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Accepted: 09/24/2021] [Indexed: 06/16/2023]
Abstract
Epigenetic research holds great promise to advance our understanding of biomarkers and regulatory processes in health and disease. An increasing number of new approaches, ranging from molecular to biophysical analyses, enable identifying epigenetic changes on the level of a single gene or the whole epigenome. The aim of this review is to highlight how the field is shifting from completely molecular-biology-driven solutions to multidisciplinary strategies including more reliance on biophysical analysis tools. Biophysics not only offers technical advancements in imaging or structure analysis but also helps to explore regulatory interactions. New computational methods are also being developed to meet the demand of growing data volumes and their processing. Therefore, it is important to capture these new directions in epigenetics from a biophysical perspective and discuss current challenges as well as multiple applications of biophysical methods and tools. Specifically, we gradually introduce different biophysical research methods by first considering the DNA-level information and eventually higher-order chromatin structures. Moreover, we aim to highlight that the incorporation of bioinformatics, machine learning, and artificial intelligence into biophysical analysis allows gaining new insights into complex epigenetic processes. The gained understanding has already proven useful in translational and clinical research providing better patient stratification options or new therapeutic insights. Together, this offers a better readiness to transform bench-top experiments into industrial high-throughput applications with a possibility to employ developed methods in clinical practice and diagnostics.
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Affiliation(s)
- Austė Kanapeckaitė
- Algorithm379, Laisvės g. 7, LT 12007, Vilnius, Lithuania
- Reading School of Pharmacy, Whiteknights, Reading, UK, RG6 6UB
| | - Neringa Burokienė
- Clinics of Internal Diseases, Family Medicine and Oncology, Institute of Clinical Medicine, Faculty of Medicine, Vilnius University, M. K. Čiurlionio str. 21/27, LT-03101 Vilnius, Lithuania
| | - Asta Mažeikienė
- Department of Physiology, Biochemistry, Microbiology and Laboratory Medicine, Institute of Biomedical Sciences, Faculty of Medicine, M. K. Čiurlionio str. 21/27, LT-03101 Vilnius, Lithuania
| | | | - Darius Widera
- Reading School of Pharmacy, Whiteknights, Reading, UK, RG6 6UB
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26
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Akdogan-Ozdilek B, Duval KL, Meng FW, Murphy PJ, Goll MG. Identification of chromatin states during zebrafish gastrulation using CUT&RUN and CUT&Tag. Dev Dyn 2021; 251:729-742. [PMID: 34647658 DOI: 10.1002/dvdy.430] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2021] [Revised: 09/29/2021] [Accepted: 10/04/2021] [Indexed: 01/04/2023] Open
Abstract
BACKGROUND Cell fate decisions are governed by interactions between sequence-specific transcription factors and a dynamic chromatin landscape. Zebrafish offer a powerful system for probing the mechanisms that drive these cell fate choices, especially in the context of early embryogenesis. However, technical challenges associated with conventional methods for chromatin profiling have slowed progress toward understanding the exact relationships between chromatin changes, transcription factor binding, and cellular differentiation during zebrafish embryogenesis. RESULTS To overcome these challenges, we adapted the chromatin profiling methods Cleavage Under Targets and Release Using Nuclease (CUT&RUN) and CUT&Tag for use in zebrafish and applied these methods to generate high-resolution enrichment maps for H3K4me3, H3K27me3, H3K9me3, RNA polymerase II, and the histone variant H2A.Z using tissue isolated from whole, mid-gastrula stage embryos. Using this data, we identify a subset of genes that may be bivalently regulated during both zebrafish and mouse gastrulation, provide evidence for an evolving H2A.Z landscape during embryo development, and demonstrate the effectiveness of CUT&RUN for detecting H3K9me3 enrichment at repetitive sequences. CONCLUSIONS Our results demonstrate the power of combining CUT&RUN and CUT&Tag methods with the strengths of the zebrafish system to define emerging chromatin landscapes in the context of vertebrate embryogenesis.
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Affiliation(s)
| | | | - Fanju W Meng
- Department of Biomedical Genetics, University of Rochester School of Medicine and Dentistry, Rochester, New York, USA
| | - Patrick J Murphy
- Department of Biomedical Genetics, University of Rochester School of Medicine and Dentistry, Rochester, New York, USA
| | - Mary G Goll
- Department of Genetics, University of Georgia, Athens, Georgia, USA
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27
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Carroll PA, Freie BW, Cheng PF, Kasinathan S, Gu H, Hedrich T, Dowdle JA, Venkataramani V, Ramani V, Wu X, Raftery D, Shendure J, Ayer DE, Muller CH, Eisenman RN. The glucose-sensing transcription factor MLX balances metabolism and stress to suppress apoptosis and maintain spermatogenesis. PLoS Biol 2021; 19:e3001085. [PMID: 34669700 PMCID: PMC8528285 DOI: 10.1371/journal.pbio.3001085] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2020] [Accepted: 09/24/2021] [Indexed: 01/02/2023] Open
Abstract
Male germ cell (GC) production is a metabolically driven and apoptosis-prone process. Here, we show that the glucose-sensing transcription factor (TF) MAX-Like protein X (MLX) and its binding partner MondoA are both required for male fertility in the mouse, as well as survival of human tumor cells derived from the male germ line. Loss of Mlx results in altered metabolism as well as activation of multiple stress pathways and GC apoptosis in the testes. This is concomitant with dysregulation of the expression of male-specific GC transcripts and proteins. Our genomic and functional analyses identify loci directly bound by MLX involved in these processes, including metabolic targets, obligate components of male-specific GC development, and apoptotic effectors. These in vivo and in vitro studies implicate MLX and other members of the proximal MYC network, such as MNT, in regulation of metabolism and differentiation, as well as in suppression of intrinsic and extrinsic death signaling pathways in both spermatogenesis and male germ cell tumors (MGCTs).
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Affiliation(s)
- Patrick A. Carroll
- Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | - Brian W. Freie
- Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | - Pei Feng Cheng
- Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | - Sivakanthan Kasinathan
- Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | - Haiwei Gu
- Department of Anesthesiology and Pain Medicine, University of Washington, Seattle, Washington, United States of America
| | - Theresa Hedrich
- Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | - James A. Dowdle
- Molecular Biology Program, Memorial Sloan Kettering Cancer Center, New York, New York, United States of America
| | - Vivek Venkataramani
- Institute of Pathology, University Medical Center Göttingen, Göttingen, Germany
| | - Vijay Ramani
- Department of Genome Sciences, University of Washington, Seattle, Washington, United States of America
| | - Xiaoying Wu
- Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | - Daniel Raftery
- Department of Anesthesiology and Pain Medicine, University of Washington, Seattle, Washington, United States of America
| | - Jay Shendure
- Department of Genome Sciences, University of Washington, Seattle, Washington, United States of America
- Howard Hughes Medical Institute, Seattle, Washington, United States of America
- Brotman Baty Institute for Precision Medicine, Seattle, Washington, United States of America
| | - Donald E. Ayer
- Huntsman Cancer Institute, Department of Oncological Sciences, University of Utah, Salt Lake City, Utah, United States of America
| | - Charles H. Muller
- Male Fertility Lab, Department of Urology, University of Washington, Seattle, Washington, United States of America
| | - Robert N. Eisenman
- Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
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28
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Su(Hw) primes 66D and 7F Drosophila chorion genes loci for amplification through chromatin decondensation. Sci Rep 2021; 11:16963. [PMID: 34417521 PMCID: PMC8379230 DOI: 10.1038/s41598-021-96488-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2021] [Accepted: 08/11/2021] [Indexed: 11/11/2022] Open
Abstract
Suppressor of Hairy wing [Su(Hw)] is an insulator protein that participates in regulating chromatin architecture and gene repression in Drosophila. In previous studies we have shown that Su(Hw) is also required for pre-replication complex (pre-RC) recruitment on Su(Hw)-bound sites (SBSs) in Drosophila S2 cells and pupa. Here, we describe the effect of Su(Hw) on developmentally regulated amplification of 66D and 7F Drosophila amplicons in follicle cells (DAFCs), widely used as models in replication studies. We show Su(Hw) binding co-localizes with all known DAFCs in Drosophila ovaries, whereas disruption of Su(Hw) binding to 66D and 7F DAFCs causes a two-fold decrease in the amplification of these loci. The complete loss of Su(Hw) binding to chromatin impairs pre-RC recruitment to all amplification regulatory regions of 66D and 7F loci at early oogenesis (prior to DAFCs amplification). These changes coincide with a considerable Su(Hw)-dependent condensation of chromatin at 66D and 7F loci. Although we observed the Brm, ISWI, Mi-2, and CHD1 chromatin remodelers at SBSs genome wide, their remodeler activity does not appear to be responsible for chromatin decondensation at the 66D and 7F amplification regulatory regions. We have discovered that, in addition to the CBP/Nejire and Chameau histone acetyltransferases, the Gcn5 acetyltransferase binds to 66D and 7F DAFCs at SBSs and this binding is dependent on Su(Hw). We propose that the main function of Su(Hw) in developmental amplification of 66D and 7F DAFCs is to establish a chromatin structure that is permissive to pre-RC recruitment.
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29
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Chawla A, Nagy C, Turecki G. Chromatin Profiling Techniques: Exploring the Chromatin Environment and Its Contributions to Complex Traits. Int J Mol Sci 2021; 22:7612. [PMID: 34299232 PMCID: PMC8305586 DOI: 10.3390/ijms22147612] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2021] [Revised: 07/09/2021] [Accepted: 07/13/2021] [Indexed: 01/04/2023] Open
Abstract
The genetic architecture of complex traits is multifactorial. Genome-wide association studies (GWASs) have identified risk loci for complex traits and diseases that are disproportionately located at the non-coding regions of the genome. On the other hand, we have just begun to understand the regulatory roles of the non-coding genome, making it challenging to precisely interpret the functions of non-coding variants associated with complex diseases. Additionally, the epigenome plays an active role in mediating cellular responses to fluctuations of sensory or environmental stimuli. However, it remains unclear how exactly non-coding elements associate with epigenetic modifications to regulate gene expression changes and mediate phenotypic outcomes. Therefore, finer interrogations of the human epigenomic landscape in associating with non-coding variants are warranted. Recently, chromatin-profiling techniques have vastly improved our understanding of the numerous functions mediated by the epigenome and DNA structure. Here, we review various chromatin-profiling techniques, such as assays of chromatin accessibility, nucleosome distribution, histone modifications, and chromatin topology, and discuss their applications in unraveling the brain epigenome and etiology of complex traits at tissue homogenate and single-cell resolution. These techniques have elucidated compositional and structural organizing principles of the chromatin environment. Taken together, we believe that high-resolution epigenomic and DNA structure profiling will be one of the best ways to elucidate how non-coding genetic variations impact complex diseases, ultimately allowing us to pinpoint cell-type targets with therapeutic potential.
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Affiliation(s)
- Anjali Chawla
- Integrated Program in Neuroscience, McGill University, 845 Sherbrooke St W, Montreal, QC H3A 0G4, Canada;
- McGill Group for Suicide Studies, Department of Psychiatry, Douglas Mental Health University Institute, McGill University, 6875 LaSalle Blvd, Verdun, QC H4H 1R3, Canada;
| | - Corina Nagy
- McGill Group for Suicide Studies, Department of Psychiatry, Douglas Mental Health University Institute, McGill University, 6875 LaSalle Blvd, Verdun, QC H4H 1R3, Canada;
- Genome Quebec Innovation Centre, Department of Human Genetics, McGill University, 845 Sherbrooke St W, Montreal, QC H3A 0G4, Canada
| | - Gustavo Turecki
- Integrated Program in Neuroscience, McGill University, 845 Sherbrooke St W, Montreal, QC H3A 0G4, Canada;
- McGill Group for Suicide Studies, Department of Psychiatry, Douglas Mental Health University Institute, McGill University, 6875 LaSalle Blvd, Verdun, QC H4H 1R3, Canada;
- Genome Quebec Innovation Centre, Department of Human Genetics, McGill University, 845 Sherbrooke St W, Montreal, QC H3A 0G4, Canada
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30
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Mitra S, Zhong J, Tran TQ, MacAlpine DM, Hartemink AJ. RoboCOP: jointly computing chromatin occupancy profiles for numerous factors from chromatin accessibility data. Nucleic Acids Res 2021; 49:7925-7938. [PMID: 34255854 PMCID: PMC8373080 DOI: 10.1093/nar/gkab553] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Revised: 05/28/2021] [Accepted: 07/08/2021] [Indexed: 01/25/2023] Open
Abstract
Chromatin is a tightly packaged structure of DNA and protein within the nucleus of a cell. The arrangement of different protein complexes along the DNA modulates and is modulated by gene expression. Measuring the binding locations and occupancy levels of different transcription factors (TFs) and nucleosomes is therefore crucial to understanding gene regulation. Antibody-based methods for assaying chromatin occupancy are capable of identifying the binding sites of specific DNA binding factors, but only one factor at a time. In contrast, epigenomic accessibility data like MNase-seq, DNase-seq, and ATAC-seq provide insight into the chromatin landscape of all factors bound along the genome, but with little insight into the identities of those factors. Here, we present RoboCOP, a multivariate state space model that integrates chromatin accessibility data with nucleotide sequence to jointly compute genome-wide probabilistic scores of nucleosome and TF occupancy, for hundreds of different factors. We apply RoboCOP to MNase-seq and ATAC-seq data to elucidate the protein-binding landscape of nucleosomes and 150 TFs across the yeast genome, and show that our model makes better predictions than existing methods. We also compute a chromatin occupancy profile of the yeast genome under cadmium stress, revealing chromatin dynamics associated with transcriptional regulation.
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Affiliation(s)
- Sneha Mitra
- Department of Computer Science, Duke University, Durham, NC 27708, USA
| | - Jianling Zhong
- Program in Computational Biology and Bioinformatics, Duke University, Durham, NC 27708, USA
| | - Trung Q Tran
- Department of Computer Science, Duke University, Durham, NC 27708, USA
| | - David M MacAlpine
- Program in Computational Biology and Bioinformatics, Duke University, Durham, NC 27708, USA.,Department of Pharmacology and Cancer Biology, Duke University Medical Center, Durham, NC 27710, USA.,Center for Genomic and Computational Biology, Duke University, Durham, NC 27708, USA
| | - Alexander J Hartemink
- Department of Computer Science, Duke University, Durham, NC 27708, USA.,Program in Computational Biology and Bioinformatics, Duke University, Durham, NC 27708, USA.,Center for Genomic and Computational Biology, Duke University, Durham, NC 27708, USA
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31
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Jordan W, Larschan E. The zinc finger protein CLAMP promotes long-range chromatin interactions that mediate dosage compensation of the Drosophila male X-chromosome. Epigenetics Chromatin 2021; 14:29. [PMID: 34187599 PMCID: PMC8240218 DOI: 10.1186/s13072-021-00399-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2021] [Accepted: 05/16/2021] [Indexed: 12/13/2022] Open
Abstract
Background Drosophila dosage compensation is an important model system for defining how active chromatin domains are formed. The male-specific lethal dosage compensation complex (MSLc) increases transcript levels of genes along the length of the single male X-chromosome to equalize with that expressed from the two female X-chromosomes. The strongest binding sites for MSLc cluster together in three-dimensional space largely independent of MSLc because clustering occurs in both sexes. CLAMP, a non-sex specific, ubiquitous zinc finger protein, binds synergistically with MSLc to enrich the occupancy of both factors on the male X-chromosome. Results Here, we demonstrate that CLAMP promotes the observed three-dimensional clustering of MSLc binding sites. Moreover, the X-enriched CLAMP protein more strongly promotes longer-range three-dimensional interactions on the X-chromosome than autosomes. Genome-wide, CLAMP promotes three-dimensional interactions between active chromatin regions together with other insulator proteins. Conclusion Overall, we define how long-range interactions which are modulated by a locally enriched ubiquitous transcription factor promote hyper-activation of the X-chromosome to mediate dosage compensation. Supplementary Information The online version contains supplementary material available at 10.1186/s13072-021-00399-3.
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Affiliation(s)
- William Jordan
- Department of Molecular Biology, Cellular Biology and Biochemistry, Brown University, Providence, RI, USA
| | - Erica Larschan
- Department of Molecular Biology, Cellular Biology and Biochemistry, Brown University, Providence, RI, USA.
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32
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Spiegel J, Cuesta SM, Adhikari S, Hänsel-Hertsch R, Tannahill D, Balasubramanian S. G-quadruplexes are transcription factor binding hubs in human chromatin. Genome Biol 2021; 22:117. [PMID: 33892767 PMCID: PMC8063395 DOI: 10.1186/s13059-021-02324-z] [Citation(s) in RCA: 120] [Impact Index Per Article: 40.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Accepted: 03/24/2021] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND The binding of transcription factors (TF) to genomic targets is critical in the regulation of gene expression. Short, double-stranded DNA sequence motifs are routinely implicated in TF recruitment, but many questions remain on how binding site specificity is governed. RESULTS Herein, we reveal a previously unappreciated role for DNA secondary structures as key features for TF recruitment. In a systematic, genome-wide study, we discover that endogenous G-quadruplex secondary structures (G4s) are prevalent TF binding sites in human chromatin. Certain TFs bind G4s with affinities comparable to double-stranded DNA targets. We demonstrate that, in a chromatin context, this binding interaction is competed out with a small molecule. Notably, endogenous G4s are prominent binding sites for a large number of TFs, particularly at promoters of highly expressed genes. CONCLUSIONS Our results reveal a novel non-canonical mechanism for TF binding whereby G4s operate as common binding hubs for many different TFs to promote increased transcription.
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Affiliation(s)
- Jochen Spiegel
- Cancer Research UK Cambridge Institute, Li Ka Shing Centre, Robinson Way, Cambridge, CB2 0RE, UK
| | - Sergio Martínez Cuesta
- Cancer Research UK Cambridge Institute, Li Ka Shing Centre, Robinson Way, Cambridge, CB2 0RE, UK
- Department of Chemistry, University of Cambridge, Cambridge, CB2 1EW, UK
- Present Address: Data Sciences and Quantitative Biology, Discovery Sciences, AstraZeneca, Cambridge, UK
| | - Santosh Adhikari
- Department of Chemistry, University of Cambridge, Cambridge, CB2 1EW, UK
| | - Robert Hänsel-Hertsch
- Cancer Research UK Cambridge Institute, Li Ka Shing Centre, Robinson Way, Cambridge, CB2 0RE, UK
- Present Address: Center for Molecular Medicine Cologne, University of Cologne, 50931, Cologne, Germany
| | - David Tannahill
- Cancer Research UK Cambridge Institute, Li Ka Shing Centre, Robinson Way, Cambridge, CB2 0RE, UK
| | - Shankar Balasubramanian
- Cancer Research UK Cambridge Institute, Li Ka Shing Centre, Robinson Way, Cambridge, CB2 0RE, UK.
- Department of Chemistry, University of Cambridge, Cambridge, CB2 1EW, UK.
- School of Clinical Medicine, University of Cambridge, Cambridge, CB2 0SP, UK.
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33
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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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34
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Rao S, Ahmad K, Ramachandran S. Cooperative binding between distant transcription factors is a hallmark of active enhancers. Mol Cell 2021; 81:1651-1665.e4. [PMID: 33705711 DOI: 10.1016/j.molcel.2021.02.014] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2020] [Revised: 02/08/2021] [Accepted: 02/09/2021] [Indexed: 12/22/2022]
Abstract
Enhancers harbor binding motifs that recruit transcription factors (TFs) for gene activation. While cooperative binding of TFs at enhancers is known to be critical for transcriptional activation of a handful of developmental enhancers, the extent of TF cooperativity genome-wide is unknown. Here, we couple high-resolution nuclease footprinting with single-molecule methylation profiling to characterize TF cooperativity at active enhancers in the Drosophila genome. Enrichment of short micrococcal nuclease (MNase)-protected DNA segments indicates that the majority of enhancers harbor two or more TF-binding sites, and we uncover protected fragments that correspond to co-bound sites in thousands of enhancers. From the analysis of co-binding, we find that cooperativity dominates TF binding in vivo at the majority of active enhancers. Cooperativity is highest between sites spaced 50 bp apart, indicating that cooperativity occurs without apparent protein-protein interactions. Our findings suggest nucleosomes promoting cooperativity because co-binding may effectively clear nucleosomes and promote enhancer function.
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Affiliation(s)
- Satyanarayan Rao
- Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, Aurora, CO 80045, USA; RNA Bioscience Initiative, University of Colorado School of Medicine, Aurora, CO 80045, USA
| | - Kami Ahmad
- Basic Sciences Division, Fred Hutchinson Cancer Research Center, 1100 Fairview Avenue North, Seattle, WA 98109, USA
| | - Srinivas Ramachandran
- Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, Aurora, CO 80045, USA; RNA Bioscience Initiative, University of Colorado School of Medicine, Aurora, CO 80045, USA.
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Chetverina D, Erokhin M, Schedl P. GAGA factor: a multifunctional pioneering chromatin protein. Cell Mol Life Sci 2021; 78:4125-4141. [PMID: 33528710 DOI: 10.1007/s00018-021-03776-z] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2020] [Revised: 12/08/2020] [Accepted: 01/19/2021] [Indexed: 12/27/2022]
Abstract
The Drosophila GAGA factor (GAF) is a multifunctional protein implicated in nucleosome organization and remodeling, activation and repression of gene expression, long distance enhancer-promoter communication, higher order chromosome structure, and mitosis. This broad range of activities poses questions about how a single protein can perform so many seemingly different and unrelated functions. Current studies argue that GAF acts as a "pioneer" factor, generating nucleosome-free regions of chromatin for different classes of regulatory elements. The removal of nucleosomes from regulatory elements in turn enables other factors to bind to these elements and carry out their specialized functions. Consistent with this view, GAF associates with a collection of chromatin remodelers and also interacts with proteins implicated in different regulatory functions. In this review, we summarize the known activities of GAF and the functions of its protein partners.
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Affiliation(s)
- Darya Chetverina
- Group of Epigenetics, Institute of Gene Biology, Russian Academy of Sciences, 34/5 Vavilov St., Moscow, 119334, Russia.
| | - Maksim Erokhin
- Group of Chromatin Biology, Institute of Gene Biology, Russian Academy of Sciences, 34/5 Vavilov St., Moscow, 119334, Russia
| | - Paul Schedl
- Department of Molecular Biology, Princeton University, Princeton, NJ, 08544, USA.
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Abstract
To persist in their dynamic human host environments, fungal pathogens must sense and adapt by modulating their gene expression to fulfill their cellular needs. Understanding transcriptional regulation on a global scale would uncover cellular processes linked to persistence and virulence mechanisms that could be targeted for antifungal therapeutics. Infections associated with the yeast Candida albicans, a highly prevalent fungal pathogen, and the multiresistant related species Candida auris are becoming a serious public health threat. To define the set of a gene regulated by a transcriptional regulator in C. albicans, chromatin immunoprecipitation (ChIP)-based techniques, including ChIP with microarray technology (ChIP-chip) or ChIP-DNA sequencing (ChIP-seq), have been widely used. Here, we describe a new set of PCR-based micrococcal nuclease (MNase)-tagging plasmids for C. albicans and other Candida spp. to determine the genome-wide location of any transcriptional regulator of interest using chromatin endogenous cleavage (ChEC) coupled to high-throughput sequencing (ChEC-seq). The ChEC procedure does not require protein-DNA cross-linking or sonication, thus avoiding artifacts related to epitope masking or the hyper-ChIPable euchromatic phenomenon. In a proof-of-concept application of ChEC-seq, we provided a high-resolution binding map of the SWI/SNF chromatin remodeling complex, a master regulator of fungal fitness in C. albicans, in addition to the transcription factor Nsi1 that is an ortholog of the DNA-binding protein Reb1 for which genome-wide occupancy was previously established in Saccharomyces cerevisiae The ChEC-seq procedure described here will allow a high-resolution genomic location definition which will enable a better understanding of transcriptional regulatory circuits that govern fungal fitness and drug resistance in these medically important fungi.IMPORTANCE Systemic fungal infections caused by Candida albicans and the "superbug" Candida auris are becoming a serious public health threat. The ability of these yeasts to cause disease is linked to their faculty to modulate the expression of genes that mediate their escape from the immune surveillance and their persistence in the different unfavorable niches within the host. Comprehensive knowledge on gene expression control of fungal fitness is consequently an interesting framework for the identification of essential infection processes that could be hindered by chemicals as potential therapeutics. Here, we expanded the use of ChEC-seq, a technique that was initially developed in the yeast model Saccharomyces cerevisiae to identify genes that are modulated by a transcriptional regulator, in pathogenic yeasts from the genus Candida This robust technique will allow a better characterization of key gene expression regulators and their contribution to virulence and antifungal resistance in these pathogenic yeasts.
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Ma S, Zhang Y. Profiling chromatin regulatory landscape: insights into the development of ChIP-seq and ATAC-seq. MOLECULAR BIOMEDICINE 2020; 1:9. [PMID: 34765994 PMCID: PMC7546943 DOI: 10.1186/s43556-020-00009-w] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2020] [Accepted: 09/04/2020] [Indexed: 12/16/2022] Open
Abstract
Chromatin regulatory landscape plays a critical role in many disease processes and embryo development. Epigenome sequencing technologies such as chromatin immunoprecipitation sequencing (ChIP-seq) and assay for transposase-accessible chromatin with high-throughput sequencing (ATAC-seq) have enabled us to dissect the pan-genomic regulatory landscape of cells and tissues in both time and space dimensions by detecting specific chromatin state and its corresponding transcription factors. Pioneered by the advancement of chromatin immunoprecipitation-chip (ChIP-chip) technology, abundant epigenome profiling technologies have become available such as ChIP-seq, DNase I hypersensitive site sequencing (DNase-seq), ATAC-seq and so on. The advent of single-cell sequencing has revolutionized the next-generation sequencing, applications in single-cell epigenetics are enriched rapidly. Epigenome sequencing technologies have evolved from low-throughput to high-throughput and from bulk sample to the single-cell scope, which unprecedentedly benefits scientists to interpret life from different angles. In this review, after briefly introducing the background knowledge of epigenome biology, we discuss the development of epigenome sequencing technologies, especially ChIP-seq & ATAC-seq and their current applications in scientific research. Finally, we provide insights into future applications and challenges.
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Affiliation(s)
- Shaoqian Ma
- School of Life Sciences, Xiamen University, Xiamen, 361102 Fujian China
| | - Yongyou Zhang
- School of Life Sciences, Xiamen University, Xiamen, 361102 Fujian China
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Kaya-Okur HS, Janssens DH, Henikoff JG, Ahmad K, Henikoff S. Efficient low-cost chromatin profiling with CUT&Tag. Nat Protoc 2020; 15:3264-3283. [PMID: 32913232 PMCID: PMC8318778 DOI: 10.1038/s41596-020-0373-x] [Citation(s) in RCA: 160] [Impact Index Per Article: 40.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2020] [Accepted: 06/05/2020] [Indexed: 02/07/2023]
Abstract
We recently introduced Cleavage Under Targets & Tagmentation (CUT&Tag), an epigenomic profiling strategy in which antibodies are bound to chromatin proteins in situ in permeabilized nuclei. These antibodies are then used to tether the cut-and-paste transposase Tn5. Activation of the transposase simultaneously cleaves DNA and adds adapters ('tagmentation') for paired-end DNA sequencing. Here, we introduce a streamlined CUT&Tag protocol that suppresses DNA accessibility artefacts to ensure high-fidelity mapping of the antibody-targeted protein and improves the signal-to-noise ratio over current chromatin profiling methods. Streamlined CUT&Tag can be performed in a single PCR tube, from cells to amplified libraries, providing low-cost genome-wide chromatin maps. By simplifying library preparation CUT&Tag requires less than a day at the bench, from live cells to sequencing-ready barcoded libraries. As a result of low background levels, barcoded and pooled CUT&Tag libraries can be sequenced for as little as $25 per sample. This enables routine genome-wide profiling of chromatin proteins and modifications and requires no special skills or equipment.
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Affiliation(s)
- Hatice S Kaya-Okur
- Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
- Altius Institute for Biomedical Sciences, Seattle, WA, USA
| | - Derek H Janssens
- Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Jorja G Henikoff
- Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Kami Ahmad
- Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Steven Henikoff
- Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA.
- Howard Hughes Medical Institute, Chevy Chase, MD, USA.
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de Jonge WJ, Brok M, Lijnzaad P, Kemmeren P, Holstege FCP. Genome-wide off-rates reveal how DNA binding dynamics shape transcription factor function. Mol Syst Biol 2020; 16:e9885. [PMID: 33280256 PMCID: PMC7586999 DOI: 10.15252/msb.20209885] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Revised: 09/06/2020] [Accepted: 09/10/2020] [Indexed: 11/25/2022] Open
Abstract
Protein-DNA interactions are dynamic, and these dynamics are an important aspect of chromatin-associated processes such as transcription or replication. Due to a lack of methods to study on- and off-rates across entire genomes, protein-DNA interaction dynamics have not been studied extensively. Here, we determine in vivo off-rates for the Saccharomyces cerevisiae chromatin organizing factor Abf1, at 191 sites simultaneously across the yeast genome. Average Abf1 residence times span a wide range, varying between 4.2 and 33 min. Sites with different off-rates are associated with different functional characteristics. This includes their transcriptional dependency on Abf1, nucleosome positioning and the size of the nucleosome-free region, as well as the ability to roadblock RNA polymerase II for termination. The results show how off-rates contribute to transcription factor function and that DIVORSEQ (Determining In Vivo Off-Rates by SEQuencing) is a meaningful way of investigating protein-DNA binding dynamics genome-wide.
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Affiliation(s)
- Wim J de Jonge
- Princess Máxima Center for Pediatric OncologyUtrechtThe Netherlands
| | - Mariël Brok
- Princess Máxima Center for Pediatric OncologyUtrechtThe Netherlands
| | - Philip Lijnzaad
- Princess Máxima Center for Pediatric OncologyUtrechtThe Netherlands
| | - Patrick Kemmeren
- Princess Máxima Center for Pediatric OncologyUtrechtThe Netherlands
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Ecdysone-Induced 3D Chromatin Reorganization Involves Active Enhancers Bound by Pipsqueak and Polycomb. Cell Rep 2020; 28:2715-2727.e5. [PMID: 31484080 PMCID: PMC6754745 DOI: 10.1016/j.celrep.2019.07.096] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2019] [Revised: 05/13/2019] [Accepted: 07/25/2019] [Indexed: 12/24/2022] Open
Abstract
Evidence suggests that Polycomb (Pc) is present at chromatin loop anchors in Drosophila. Pc is recruited to DNA through interactions with the GAGA binding factors GAF and Pipsqueak (Psq). Using HiChIP in Drosophila cells, we find that the psq gene, which has diverse roles in development and tumorigenesis, encodes distinct isoforms with unanticipated roles in genome 3D architecture. The BR-C, ttk, and bab domain (BTB)-containing Psq isoform (PsqL) colocalizes genome-wide with known architectural proteins. Conversely, Psq lacking the BTB domain (PsqS) is consistently found at Pc loop anchors and at active enhancers, including those that respond to the hormone ecdysone. After stimulation by this hormone, chromatin 3D organization is altered to connect promoters and ecdysone-responsive enhancers bound by PsqS. Our findings link Psq variants lacking the BTB domain to Pc-bound active enhancers, thus shedding light into their molecular function in chromatin changes underlying the response to hormone stimulus.
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Pasquier E, Wellinger RJ. In vivo chromatin organization on native yeast telomeric regions is independent of a cis-telomere loopback conformation. Epigenetics Chromatin 2020; 13:23. [PMID: 32443982 PMCID: PMC7243337 DOI: 10.1186/s13072-020-00344-w] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2019] [Accepted: 05/13/2020] [Indexed: 12/18/2022] Open
Abstract
Background DNA packaging into chromatin regulates all DNA-related processes and at chromosomal ends could affect both essential functions of telomeres: protection against DNA damage response and telomere replication. Despite this primordial role of chromatin, little is known about chromatin organization, and in particular about nucleosome positioning on unmodified subtelomere–telomere junctions in Saccharomyces cerevisiae. Results By ChEC experiments and indirect end-labeling, we characterized nucleosome positioning as well as specialized protein–DNA associations on most subtelomere–telomere junctions present in budding yeast. The results show that there is a relatively large nucleosome-free region at chromosome ends. Despite the absence of sequence homologies between the two major classes of subtelomere–telomere junctions (i.e.: Y’-telomeres and X-telomeres), all analyzed subtelomere–telomere junctions show a terminal nucleosome-free region just distally from the known Rap1-covered telomeric repeats. Moreover, previous evidence suggested a telomeric chromatin fold-back structure onto subtelomeric areas that supposedly was implicated in chromosome end protection. The in vivo ChEC method used herein in conjunction with several proteins in a natural context revealed no evidence for such structures in bulk chromatin. Conclusions Our study allows a structural definition of the chromatin found at chromosome ends in budding yeast. This definition, derived with direct in vivo approaches, includes a terminal area that is free of nucleosomes, certain positioned nucleosomes and conserved DNA-bound protein complexes. This organization of subtelomeric and telomeric areas however does not include a telomeric cis-loopback conformation. We propose that the observations on such fold-back structures may report rare and/or transient associations and not stable or constitutive structures.
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Affiliation(s)
- Emeline Pasquier
- Department of Microbiology and Infectious Diseases, Faculty of Medicine and Health Sciences, Université de Sherbrooke, Cancer Research Pavilion, Rm 3025, 3201, rue Jean-Mignault, Sherbrooke, QC, J1E 4K8, Canada
| | - Raymund J Wellinger
- Department of Microbiology and Infectious Diseases, Faculty of Medicine and Health Sciences, Université de Sherbrooke, Cancer Research Pavilion, Rm 3025, 3201, rue Jean-Mignault, Sherbrooke, QC, J1E 4K8, Canada.
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Hsieh THS, Cattoglio C, Slobodyanyuk E, Hansen AS, Rando OJ, Tjian R, Darzacq X. Resolving the 3D Landscape of Transcription-Linked Mammalian Chromatin Folding. Mol Cell 2020; 78:539-553.e8. [PMID: 32213323 PMCID: PMC7703524 DOI: 10.1016/j.molcel.2020.03.002] [Citation(s) in RCA: 323] [Impact Index Per Article: 80.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2019] [Revised: 01/28/2020] [Accepted: 03/02/2020] [Indexed: 01/31/2023]
Abstract
Whereas folding of genomes at the large scale of epigenomic compartments and topologically associating domains (TADs) is now relatively well understood, how chromatin is folded at finer scales remains largely unexplored in mammals. Here, we overcome some limitations of conventional 3C-based methods by using high-resolution Micro-C to probe links between 3D genome organization and transcriptional regulation in mouse stem cells. Combinatorial binding of transcription factors, cofactors, and chromatin modifiers spatially segregates TAD regions into various finer-scale structures with distinct regulatory features including stripes, dots, and domains linking promoters-to-promoters (P-P) or enhancers-to-promoters (E-P) and bundle contacts between Polycomb regions. E-P stripes extending from the edge of domains predominantly link co-expressed loci, often in the absence of CTCF and cohesin occupancy. Acute inhibition of transcription disrupts these gene-related folding features without altering higher-order chromatin structures. Our study uncovers previously obscured finer-scale genome organization, establishing functional links between chromatin folding and gene regulation.
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Affiliation(s)
- Tsung-Han S Hsieh
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA; Li Ka Shing Center for Biomedical and Health Sciences, University of California, Berkeley, Berkeley, CA 94720, USA; CIRM Center of Excellence, University of California, Berkeley, Berkeley, CA 94720, USA; Center for Computational Biology, University of California, Berkeley, Berkeley, CA 94720, USA; Howard Hughes Medical Institute, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Claudia Cattoglio
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA; Li Ka Shing Center for Biomedical and Health Sciences, University of California, Berkeley, Berkeley, CA 94720, USA; CIRM Center of Excellence, University of California, Berkeley, Berkeley, CA 94720, USA; Howard Hughes Medical Institute, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Elena Slobodyanyuk
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA; Li Ka Shing Center for Biomedical and Health Sciences, University of California, Berkeley, Berkeley, CA 94720, USA; CIRM Center of Excellence, University of California, Berkeley, Berkeley, CA 94720, USA; Howard Hughes Medical Institute, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Anders S Hansen
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA; Li Ka Shing Center for Biomedical and Health Sciences, University of California, Berkeley, Berkeley, CA 94720, USA; CIRM Center of Excellence, University of California, Berkeley, Berkeley, CA 94720, USA; Howard Hughes Medical Institute, University of California, Berkeley, Berkeley, CA 94720, USA; Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02142, USA
| | - Oliver J Rando
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Robert Tjian
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA; Li Ka Shing Center for Biomedical and Health Sciences, University of California, Berkeley, Berkeley, CA 94720, USA; CIRM Center of Excellence, University of California, Berkeley, Berkeley, CA 94720, USA; Howard Hughes Medical Institute, University of California, Berkeley, Berkeley, CA 94720, USA.
| | - Xavier Darzacq
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA; Li Ka Shing Center for Biomedical and Health Sciences, University of California, Berkeley, Berkeley, CA 94720, USA; CIRM Center of Excellence, University of California, Berkeley, Berkeley, CA 94720, USA; Center for Computational Biology, University of California, Berkeley, Berkeley, CA 94720, USA.
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Mitra S, Zhong J, MacAlpine DM, Hartemink AJ. RoboCOP: Multivariate State Space Model Integrating Epigenomic Accessibility Data to Elucidate Genome-Wide Chromatin Occupancy. RESEARCH IN COMPUTATIONAL MOLECULAR BIOLOGY : ... ANNUAL INTERNATIONAL CONFERENCE, RECOMB ... : PROCEEDINGS. RECOMB (CONFERENCE : 2005- ) 2020; 12074:136-151. [PMID: 34386808 PMCID: PMC8356533 DOI: 10.1007/978-3-030-45257-5_9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
Chromatin is the tightly packaged structure of DNA and protein within the nucleus of a cell. The arrangement of different protein complexes along the DNA modulates and is modulated by gene expression. Measuring the binding locations and level of occupancy of different transcription factors (TFs) and nucleosomes is therefore crucial to understanding gene regulation. Antibody-based methods for assaying chromatin occupancy are capable of identifying the binding sites of specific DNA binding factors, but only one factor at a time. On the other hand, epigenomic accessibility data like ATAC-seq, DNase-seq, and MNase-seq provide insight into the chromatin landscape of all factors bound along the genome, but with minimal insight into the identities of those factors. Here, we present RoboCOP, a multivariate state space model that integrates chromatin information from epigenomic accessibility data with nucleotide sequence to compute genome-wide probabilistic scores of nucleosome and TF occupancy, for hundreds of different factors at once. RoboCOP can be applied to any epigenomic dataset that provides quantitative insight into chromatin accessibility in any organism, but here we apply it to MNase-seq data to elucidate the protein-binding landscape of nucleosomes and 150 TFs across the yeast genome. Using available protein-binding datasets from the literature, we show that our model more accurately predicts the binding of these factors genome-wide.
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Affiliation(s)
- Sneha Mitra
- Department of Computer Science, Duke University, Durham, NC 27708, USA
| | - Jianling Zhong
- Program in Computational Biology and Bioinformatics, Duke University, Durham, NC 27708, USA
| | - David M MacAlpine
- Program in Computational Biology and Bioinformatics, Duke University, Durham, NC 27708, USA
- Department of Pharmacology and Cancer Biology, Duke University Medical Center, Durham, NC 27710, USA
- Center for Genomic and Computational Biology, Duke University, Durham, NC 27708, USA
| | - Alexander J Hartemink
- Department of Computer Science, Duke University, Durham, NC 27708, USA
- Program in Computational Biology and Bioinformatics, Duke University, Durham, NC 27708, USA
- Center for Genomic and Computational Biology, Duke University, Durham, NC 27708, USA
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Ramani V, Qiu R, Shendure J. High Sensitivity Profiling of Chromatin Structure by MNase-SSP. Cell Rep 2020; 26:2465-2476.e4. [PMID: 30811994 PMCID: PMC6582983 DOI: 10.1016/j.celrep.2019.02.007] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2018] [Revised: 11/07/2018] [Accepted: 02/01/2019] [Indexed: 12/11/2022] Open
Abstract
A complete view of eukaryotic gene regulation requires that we accurately delineate how transcription factors (TFs) and nucleosomes are arranged along linear DNA in a sensitive, unbiased manner. Here we introduce MNase-SSP, a single-stranded sequencing library preparation method for nuclease-digested chromatin that enables simultaneous mapping of TF and nucleosome positions. As a proof of concept, we apply MNase-SSP toward the genome-wide, high-resolution mapping of nucleosome and TF occupancy in murine embryonic stem cells (mESCs). Compared with existing MNase-seq protocols, MNase-SSP markedly enriches for short DNA fragments, enabling detection of binding by subnucleosomal particles and TFs, in addition to nucleosomes. From these same data, we identify multiple, sequence-dependent binding modes of the architectural TF Ctcf and extend this analysis to the TF Nrsf/ Rest. Looking forward, we anticipate that single stranded protocol (SSP) adaptations of any protein-DNA interaction mapping technique (e.g., ChIP-exo and CUT&RUN) will enhance the information content of the resulting data. Ramani et al. describe MNase-SSP, a single-stranded DNA sequencing library preparation method for profiling chromatin structure. MNase-SSP libraries harbor diminished sequence bias and capture shorter DNA fragments compared to traditional MNase-seq libraries. Applying MNase-SSP to murine embryonic stem cells enables simultaneous analysis of nucleosomal, subnucleosomal, and transcription factor-DNA interactions genome-wide.
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Affiliation(s)
- Vijay Ramani
- Department of Genome Sciences, University of Washington, Seattle, WA, USA; Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA, USA.
| | - Ruolan Qiu
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Jay Shendure
- Department of Genome Sciences, University of Washington, Seattle, WA, USA; Brotman-Baty Institute for Precision Medicine, Seattle, WA, USA; Howard Hughes Medical Institute, Seattle, WA, USA.
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Zhao H, Zhang W, Zhang T, Lin Y, Hu Y, Fang C, Jiang J. Genome-wide MNase hypersensitivity assay unveils distinct classes of open chromatin associated with H3K27me3 and DNA methylation in Arabidopsis thaliana. Genome Biol 2020; 21:24. [PMID: 32014062 PMCID: PMC6996174 DOI: 10.1186/s13059-020-1927-5] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2019] [Accepted: 01/06/2020] [Indexed: 12/19/2022] Open
Abstract
BACKGROUND Regulation of transcription depends on interactions between cis-regulatory elements (CREs) and regulatory proteins. Active CREs are imbedded in open chromatin that are accessible to nucleases. Several techniques, including DNase-seq, which is based on nuclease DNase I, and ATAC-seq, which is based on transposase Tn5, have been widely used to identify genomic regions associated with open chromatin. These techniques have played a key role in dissecting the regulatory networks in gene expression in both animal and plant species. RESULTS We develop a technique, named MNase hypersensitivity sequencing (MH-seq), to identify genomic regions associated with open chromatin in Arabidopsis thaliana. Genomic regions enriched with MH-seq reads are referred as MNase hypersensitive sites (MHSs). MHSs overlap with the majority (~ 90%) of the open chromatin identified previously by DNase-seq and ATAC-seq. Surprisingly, 22% MHSs are not covered by DNase-seq or ATAC-seq reads, which are referred to "specific MHSs" (sMHSs). sMHSs tend to be located away from promoters, and a substantial portion of sMHSs are derived from transposable elements. Most interestingly, genomic regions containing sMHSs are enriched with epigenetic marks, including H3K27me3 and DNA methylation. In addition, sMHSs show a number of distinct characteristics including association with transcriptional repressors. Thus, sMHSs span distinct classes of open chromatin that may not be accessible to DNase I or Tn5. We hypothesize that the small size of the MNase enzyme relative to DNase I or Tn5 allows its access to relatively more condensed chromatin domains. CONCLUSION MNase can be used to identify open chromatin regions that are not accessible to DNase I or Tn5. Thus, MH-seq provides an important tool to identify and catalog all classes of open chromatin in plants.
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Affiliation(s)
- Hainan Zhao
- Department of Plant Biology, Michigan State University, East Lansing, MI, 48824, USA
- Department of Horticulture, Michigan State University, East Lansing, MI, 48824, USA
| | - Wenli Zhang
- Department of Horticulture, University of Wisconsin-Madison, Madison, WI, 53706, USA.
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Nanjing Agriculture University, Nanjing, 210095, Jiangsu, China.
| | - Tao Zhang
- Department of Horticulture, University of Wisconsin-Madison, Madison, WI, 53706, USA
- Key Laboratory of Crop Genetics and Physiology of Jiangsu Province/Key Laboratory of Plant Functional Genomics of Ministry of Education, Yangzhou University, Yangzhou, 225009, China
| | - Yuan Lin
- Department of Plant Biology, Michigan State University, East Lansing, MI, 48824, USA
- Department of Horticulture, Michigan State University, East Lansing, MI, 48824, USA
| | - Yaodong Hu
- Department of Animal Sciences, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Chao Fang
- Department of Plant Biology, Michigan State University, East Lansing, MI, 48824, USA
- Department of Horticulture, Michigan State University, East Lansing, MI, 48824, USA
| | - Jiming Jiang
- Department of Plant Biology, Michigan State University, East Lansing, MI, 48824, USA.
- Department of Horticulture, Michigan State University, East Lansing, MI, 48824, USA.
- Department of Horticulture, University of Wisconsin-Madison, Madison, WI, 53706, USA.
- Michigan State University AgBioResearch, East Lansing, MI, 48824, USA.
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Epigenome Regulation by Dynamic Nucleosome Unwrapping. Trends Biochem Sci 2020; 45:13-26. [PMID: 31630896 PMCID: PMC10168609 DOI: 10.1016/j.tibs.2019.09.003] [Citation(s) in RCA: 55] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2019] [Revised: 09/09/2019] [Accepted: 09/13/2019] [Indexed: 12/12/2022]
Abstract
Gene regulation in eukaryotes requires the controlled access of sequence-specific transcription factors (TFs) to their sites in a chromatin landscape dominated by nucleosomes. Nucleosomes are refractory to TF binding, and often must be removed from regulatory regions. Recent genomic studies together with in vitro measurements suggest that the nucleosome barrier to TF binding is modulated by dynamic nucleosome unwrapping governed by ATP-dependent chromatin remodelers. Genome-wide occupancy and the regulation of subnucleosomal intermediates have gained recent attention with the application of high-resolution approaches for precision mapping of protein-DNA interactions. We summarize here recent findings on nucleosome substructures and TF binding dynamics, and highlight how unwrapped nucleosomal intermediates provide a novel signature of active chromatin.
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47
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Huang X, Pan Q, Lin Y, Gu T, Li Y. A native chromatin immunoprecipitation (ChIP) protocol for studying histone modifications in strawberry fruits. PLANT METHODS 2020; 16:10. [PMID: 32025237 PMCID: PMC6998251 DOI: 10.1186/s13007-020-0556-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/27/2019] [Accepted: 01/20/2020] [Indexed: 05/06/2023]
Abstract
BACKGROUND Covalent modifications of histones and histone variants have great influence on chromatin structure, which is involved in the transcriptional regulation of gene expression. Chromatin immunoprecipitation (ChIP) is a powerful tool for studying in vivo DNA-histone interactions. Strawberry is a model for Rosaceae and non-climacteric fruits, in which histone modifications have been implicated to affect fruit development and ripening. However, a validated ChIP method has not been reported in strawberry, probably due to its high levels of polysaccharides which affect the quality of prepared chromatin and the efficiency of immunoprecipitation. RESULTS We describe a native chromatin immunoprecipitation (N-ChIP) protocol suitable for strawberry by optimizing the parameters for nuclei isolation, chromatin extraction, DNA fragmentation and validation analysis using quantitative real-time PCR (qRT-PCR). The qRT-PCR results show that both the active mark H3K36me3 and the silent mark H3K9me2 are efficiently immunoprecipitated for the enriched regions. Compared to X-ChIP (cross-linked chromatin followed by immunoprecipitation), our optimized N-ChIP procedure has a higher signal-to-noise ratio and a lower background for both the active and the silent histone modifications. Furthermore, high-throughput sequencing following N-ChIP demonstrates that nearly 90% of the enriched H3K9/K14ac peaks are overlapped between biological replicates, indicating its remarkable consistency and reproducibility. CONCLUSIONS An N-ChIP method suitable for the fleshy fruit tissues of woodland strawberry Fragaria vesca is described in this study. The efficiency and reproducibility of our optimized N-ChIP protocol are validated by both qRT-PCR and high-throughput sequencing. We conclude that N-ChIP is a more suitable method for strawberry fruit tissues relative to X-ChIP, which could be combined with high-throughput sequencing to investigate the impact of histone modifications in strawberry and potentially in other fruits with high content of polysaccharides.
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Affiliation(s)
- Xiaorong Huang
- State Key Laboratory of Plant Genetics and Germplasm Enhancement and College of Horticulture, Nanjing Agricultural University, Nanjing, 210095 People’s Republic of China
- Minzhulu Primary School of Xuzhou City, Xuzhou, 221000 People’s Republic of China
| | - Qinwei Pan
- State Key Laboratory of Plant Genetics and Germplasm Enhancement and College of Horticulture, Nanjing Agricultural University, Nanjing, 210095 People’s Republic of China
| | - Ying Lin
- State Key Laboratory of Plant Genetics and Germplasm Enhancement and College of Horticulture, Nanjing Agricultural University, Nanjing, 210095 People’s Republic of China
| | - Tingting Gu
- State Key Laboratory of Plant Genetics and Germplasm Enhancement and College of Horticulture, Nanjing Agricultural University, Nanjing, 210095 People’s Republic of China
| | - Yi Li
- Department of Plant Science and Landscape, Architecture, University of Connecticut, Storrs, CT 06269 USA
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Grzybowski AT, Shah RN, Richter WF, Ruthenburg AJ. Native internally calibrated chromatin immunoprecipitation for quantitative studies of histone post-translational modifications. Nat Protoc 2019; 14:3275-3302. [PMID: 31723301 PMCID: PMC7158589 DOI: 10.1038/s41596-019-0218-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2019] [Accepted: 06/25/2019] [Indexed: 01/20/2023]
Abstract
Chromatin immunoprecipitation coupled to next-generation sequencing (ChIP-seq) has served as the central method for the study of histone modifications for the past decade. In ChIP-seq analyses, antibodies selectively capture nucleosomes bearing a modification of interest and the associated DNA is then mapped to the genome to determine the distribution of the mark. This approach has several important drawbacks: (i) ChIP interpretation necessitates the assumption of perfect antibody specificity, despite growing evidence that this is often not the case. (ii) Common methods for evaluating antibody specificity in other formats have little or no bearing on specificity within a ChIP experiment. (iii) Uncalibrated ChIP is reported as relative enrichment, which is biologically meaningless outside the experimental reference frame defined by a discrete immunoprecipitation (IP), thus preventing facile comparison across experimental conditions or modifications. (iv) Differential library amplification and loading onto next-generation sequencers, as well as computational normalization, can further compromise quantitative relationships that may exist between samples. Consequently, the researcher is presented with a series of potential pitfalls and is blind to nearly all of them. Here we provide a detailed protocol for internally calibrated ChIP (ICeChIP), a method we recently developed to resolve these problems by spike-in of defined nucleosomal standards within a ChIP procedure. This protocol is optimized for specificity and quantitative power, allowing for measurement of antibody specificity and absolute measurement of histone modification density (HMD) at genomic loci on a biologically meaningful scale enabling unambiguous comparisons. We provide guidance on optimal conditions for next-generation sequencing (NGS) and instructions for data analysis. This protocol takes between 17 and 18 h, excluding time for sequencing or bioinformatic analysis. The ICeChIP procedure enables accurate measurement of histone post-translational modifications (PTMs) genome-wide in mammalian cells as well as Drosophila melanogaster and Caenorhabditis elegans, indicating suitability for use in eukaryotic cells more broadly.
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Affiliation(s)
- Adrian T Grzybowski
- Department of Molecular Genetics and Cell Biology, The University of Chicago, Chicago, IL, USA
| | - Rohan N Shah
- Department of Molecular Genetics and Cell Biology, The University of Chicago, Chicago, IL, USA
- Division of the Biological Sciences, Pritzker School of Medicine, The University of Chicago, Chicago, IL, USA
| | - William F Richter
- Department of Molecular Genetics and Cell Biology, The University of Chicago, Chicago, IL, USA
| | - Alexander J Ruthenburg
- Department of Molecular Genetics and Cell Biology, The University of Chicago, Chicago, IL, USA.
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL, USA.
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Org T, Hensen K, Kreevan R, Mark E, Sarv O, Andreson R, Jaakma Ü, Salumets A, Kurg A. Genome-wide histone modification profiling of inner cell mass and trophectoderm of bovine blastocysts by RAT-ChIP. PLoS One 2019; 14:e0225801. [PMID: 31765427 PMCID: PMC6876874 DOI: 10.1371/journal.pone.0225801] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2019] [Accepted: 11/12/2019] [Indexed: 12/29/2022] Open
Abstract
Chromatin immunoprecipitation coupled with next-generation sequencing (ChIP-seq) has revolutionized our understanding of chromatin-related biological processes. The method, however, requires thousands of cells and has therefore limited applications in situations where cell numbers are limited. Here we describe a novel method called Restriction Assisted Tagmentation Chromatin Immunoprecipitation (RAT-ChIP) that enables global histone modification profiling from as few as 100 cells. The method is simple, cost-effective and takes a single day to complete. We demonstrate the sensitivity of the method by deriving the first genome-wide maps of histone H3K4me3 and H3K27me3 modifications of inner cell mass and trophectoderm of bovine blastocyst stage embryos.
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Affiliation(s)
- Tõnis Org
- Department of Biotechnology, Institute of Molecular and Cell Biology, University of Tartu, Tartu, Estonia
- * E-mail:
| | - Kati Hensen
- Department of Biotechnology, Institute of Molecular and Cell Biology, University of Tartu, Tartu, Estonia
| | - Rita Kreevan
- Department of Biotechnology, Institute of Molecular and Cell Biology, University of Tartu, Tartu, Estonia
| | - Elina Mark
- Chair of Animal Breeding and Biotechnology, Estonian University of Life Sciences, Tartu, Estonia
| | - Olav Sarv
- Competence Centre on Health Technologies, Tartu, Estonia
| | - Reidar Andreson
- Department of Bioinformatics, Institute of Molecular and Cell Biology, University of Tartu, Tartu, Estonia
- Institute of Genomics, University of Tartu, Tartu, Estonia
| | - Ülle Jaakma
- Chair of Animal Breeding and Biotechnology, Estonian University of Life Sciences, Tartu, Estonia
| | - Andres Salumets
- Competence Centre on Health Technologies, Tartu, Estonia
- Department of Obstetrics and Gynaecology, Institute of Clinical Medicine, University of Tartu, Tartu, Estonia
- Institute of Biomedicine and Translational Medicine, University of Tartu, Tartu, Estonia
- Department of Obstetrics and Gynaecology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
| | - Ants Kurg
- Department of Biotechnology, Institute of Molecular and Cell Biology, University of Tartu, Tartu, Estonia
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Donovan DA, Crandall JG, Banks OGB, Jensvold ZD, Truong V, Dinwiddie D, McKnight LE, McKnight JN. Engineered Chromatin Remodeling Proteins for Precise Nucleosome Positioning. Cell Rep 2019; 29:2520-2535.e4. [PMID: 31747617 PMCID: PMC6884087 DOI: 10.1016/j.celrep.2019.10.046] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2019] [Revised: 09/26/2019] [Accepted: 10/10/2019] [Indexed: 12/12/2022] Open
Abstract
Regulation of chromatin structure is essential for controlling access of DNA to factors that require association with specific DNA sequences. Here we describe the development and validation of engineered chromatin remodeling proteins (E-ChRPs) for inducing programmable changes in nucleosome positioning by design. We demonstrate that E-ChRPs function both in vitro and in vivo to specifically reposition target nucleosomes and entire nucleosomal arrays. We show that induced, systematic positioning of nucleosomes over yeast Ume6 binding sites leads to Ume6 exclusion, hyperacetylation, and transcriptional induction at target genes. We also show that programmed global loss of nucleosome-free regions at Reb1 targets is generally inhibitory with mildly repressive transcriptional effects. E-ChRPs are compatible with multiple targeting modalities, including the SpyCatcher and dCas9 moieties, resulting in high versatility and enabling diverse future applications. Thus, engineered chromatin remodeling proteins represent a simple and robust means to probe and disrupt DNA-dependent processes in different chromatin contexts.
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Affiliation(s)
- Drake A Donovan
- Institute of Molecular Biology, University of Oregon, Eugene, OR 97403, USA
| | | | - Orion G B Banks
- Institute of Molecular Biology, University of Oregon, Eugene, OR 97403, USA
| | - Zena D Jensvold
- Institute of Molecular Biology, University of Oregon, Eugene, OR 97403, USA
| | - Vi Truong
- Institute of Molecular Biology, University of Oregon, Eugene, OR 97403, USA
| | - Devin Dinwiddie
- Institute of Molecular Biology, University of Oregon, Eugene, OR 97403, USA
| | - Laura E McKnight
- Institute of Molecular Biology, University of Oregon, Eugene, OR 97403, USA
| | - Jeffrey N McKnight
- Institute of Molecular Biology, University of Oregon, Eugene, OR 97403, USA; Department of Biology, University of Oregon, Eugene, OR 97403, USA; Phil and Penny Knight Campus for Accelerating Scientific Impact, University of Oregon, Eugene, OR 97403, USA.
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