1
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Lee Y, Choi K, Kim JE, Cha S, Nam JM. Integrating, Validating, and Expanding Information Space in Single-Molecule Surface-Enhanced Raman Spectroscopy for Biomolecules. ACS NANO 2024; 18:25359-25371. [PMID: 39228259 DOI: 10.1021/acsnano.4c09218] [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: 09/05/2024]
Abstract
Single-molecule surface-enhanced Raman spectroscopy (SM-SERS) is an ultrahigh-resolution spectroscopic method for directly obtaining the complex vibrational mode information on individual molecules. SM-SERS offers a wide range of submolecular information on the hidden heterogeneity in its functional groups and varying structures, dynamics of conformational changes, binding and reaction kinetics, and interactions with the neighboring molecule and environment. Despite the richness in information on individual molecules and potential of SM-SERS in various detection targets, including large and complex biomolecules, several issues and practical considerations remain to be addressed, such as the requirement of long integration time, challenges in forming reliable and controllable interfaces between nanostructures and biomolecules, difficulty in determining hotspot size and shape, and most importantly, insufficient signal reproducibility and stability. Moreover, utilizing and interpreting SERS spectra is challenging, mainly because of the complexity and dynamic nature of molecular fingerprint Raman spectra, and this leads to fragmentary analysis and incomplete understanding of the spectra. In this Perspective, we discuss the current challenges and future opportunities of SM-SERS in views of system approaches by integrating molecules of interest, Raman dyes, plasmonic nanostructures, and artificial intelligence, particularly for detecting and analyzing biomolecules to realize the validation and expansion of information space in SM-SERS.
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Affiliation(s)
- Yeonhee Lee
- Department of Chemistry, Seoul National University, Seoul 08826, South Korea
| | - Kyungin Choi
- Department of Chemistry, Seoul National University, Seoul 08826, South Korea
| | - Ji-Eun Kim
- Department of Chemistry, Seoul National University, Seoul 08826, South Korea
| | - Seungsang Cha
- Department of Chemistry, Seoul National University, Seoul 08826, South Korea
| | - Jwa-Min Nam
- Department of Chemistry, Seoul National University, Seoul 08826, South Korea
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2
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Hegazi E, Muir TW. The Spread of Chemical Biology into Chromatin. J Biol Chem 2024:107776. [PMID: 39276931 DOI: 10.1016/j.jbc.2024.107776] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2024] [Revised: 09/05/2024] [Accepted: 09/06/2024] [Indexed: 09/17/2024] Open
Abstract
Understanding the molecular mechanisms underlying chromatin regulation, the complexity of which seems to deepen with each passing year, requires a multidisciplinary approach. While many different tools have been brought to bear in this area, here we focus on those that have emerged from the field of chemical biology. We discuss methods that allow the generation of what is now commonly referred to as 'designer chromatin', a term that was coined by the late C. David (Dave) Allis. Among Dave's many talents was a remarkable ability to 'brand' a nascent area (or concept) such that it was immediately relatable to the broader field. This also had the entirely intentional effect of drawing more people into the area, something that as this brief review attempts to convey has certainly happened when it comes to getting chemists involved in chromatin research.
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Affiliation(s)
- Esmat Hegazi
- Department of Chemistry, Princeton University, Princeton, NJ, USA
| | - Tom W Muir
- Department of Chemistry, Princeton University, Princeton, NJ, USA.
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3
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Aguirre Rivera J, Mao G, Sabantsev A, Panfilov M, Hou Q, Lindell M, Chanez C, Ritort F, Jinek M, Deindl S. Massively parallel analysis of single-molecule dynamics on next-generation sequencing chips. Science 2024; 385:892-898. [PMID: 39172826 DOI: 10.1126/science.adn5371] [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: 12/18/2023] [Accepted: 06/12/2024] [Indexed: 08/24/2024]
Abstract
Single-molecule techniques are ideally poised to characterize complex dynamics but are typically limited to investigating a small number of different samples. However, a large sequence or chemical space often needs to be explored to derive a comprehensive understanding of complex biological processes. Here we describe multiplexed single-molecule characterization at the library scale (MUSCLE), a method that combines single-molecule fluorescence microscopy with next-generation sequencing to enable highly multiplexed observations of complex dynamics. We comprehensively profiled the sequence dependence of DNA hairpin properties and Cas9-induced target DNA unwinding-rewinding dynamics. The ability to explore a large sequence space for Cas9 allowed us to identify a number of target sequences with unexpected behaviors. We envision that MUSCLE will enable the mechanistic exploration of many fundamental biological processes.
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Affiliation(s)
- J Aguirre Rivera
- Department of Cell and Molecular Biology, Science for Life Laboratory, Uppsala University, 75105 Uppsala, Sweden
| | - G Mao
- Department of Cell and Molecular Biology, Science for Life Laboratory, Uppsala University, 75105 Uppsala, Sweden
| | - A Sabantsev
- Department of Cell and Molecular Biology, Science for Life Laboratory, Uppsala University, 75105 Uppsala, Sweden
| | - M Panfilov
- Department of Cell and Molecular Biology, Science for Life Laboratory, Uppsala University, 75105 Uppsala, Sweden
| | - Q Hou
- Department of Cell and Molecular Biology, Science for Life Laboratory, Uppsala University, 75105 Uppsala, Sweden
| | - M Lindell
- Department of Medical Sciences, Science for Life Laboratory, Uppsala University, 75144 Uppsala, Sweden
| | - C Chanez
- Department of Biochemistry, University of Zürich, 8057 Zürich, Switzerland
| | - F Ritort
- Small Biosystems Lab, Condensed Matter Physics Department, Universitat de Barcelona, 08028 Barcelona, Spain
- Institut de Nanociència i Nanotecnologia (IN2UB), Universitat de Barcelona, 08028 Barcelona, Spain
| | - M Jinek
- Department of Biochemistry, University of Zürich, 8057 Zürich, Switzerland
| | - S Deindl
- Department of Cell and Molecular Biology, Science for Life Laboratory, Uppsala University, 75105 Uppsala, Sweden
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4
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Carrothers S, Trevisan R, Jayasundara N, Pelletier N, Weeks E, Meyer JN, Di Giulio R, Weinhouse C. An epigenetic memory at the CYP1A gene in cancer-resistant, pollution-adapted killifish. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.08.14.607951. [PMID: 39185187 PMCID: PMC11343184 DOI: 10.1101/2024.08.14.607951] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 08/27/2024]
Abstract
Human exposure to polycyclic aromatic hydrocarbons (PAH) is a significant and growing public health problem. Frequent, high dose exposures are likely to increase due to a warming climate and increased frequency of large-scale wildfires. Here, we characterize an epigenetic memory at the cytochrome P450 1A ( CYP1A ) gene in a population of wild Fundulus heteroclitus that has adapted to chronic, extreme PAH pollution. In wild-type fish, CYP1A is highly induced by PAH. In PAH-tolerant fish, CYP1A induction is blunted. Since CYP1A metabolically activates PAH, this memory protects these fish from PAH-mediated cancer. However, PAH-tolerant fish reared in clean water recover CYP1A inducibility, indicating that blunted induction is a non-genetic memory of prior exposure. To explore this possibility, we bred depurated wild fish from PAH-sensitive and -tolerant populations, manually fertilized exposure-naïve embryos, and challenged them with PAH. We observed epigenetic control of the reversible memory of generational PAH stress in F 1 PAH-tolerant embryos. Specifically, we observed a bivalent domain in the CYP1A promoter enhancer comprising both activating and repressive histone post-translational modifications. Activating modifications, relative to repressive ones, showed greater increases in response to PAH in sensitive embryos, relative to tolerant, consistent with greater gene activation. Also, PAH-tolerant adult fish showed persistent induction of CYP1A long after exposure cessation, which is consistent with defective CYP1A shutoff and recovery to baseline. Since CYP1A expression is inversely correlated with cancer risk, these results indicate that PAH-tolerant fish have epigenetic protection against PAH-induced cancer in early life that degrades in response to continuous gene activation. Significance Epigenetic memory, or the inheritance across cell division within an organism or across generations, of environmental exposure response is a compelling phenomenon with limited understanding of mechanism. Here, we characterized an epigenetic memory at the CYP1A gene in pollution-adapted Fundulus heteroclitus . We found that the CYP1A promoter enhancer contains a bivalent domain, comprising both active and repressive histone modifications, that shows reduced function correlating with reduced gene induction by its pollutant activator. In early life, this memory protects fish against pollution-induced cancer. However, this reduced function carries a cost; adult fish show defective transcriptional recovery of CYP1A , which increases cancer risk later in life. These results provide an initial mechanism for a model epigenetic memory and highlight potential costs.
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5
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Algranati D, Oren R, Dassa B, Fellus-Alyagor L, Plotnikov A, Barr H, Harmelin A, London N, Ron G, Furth N, Shema E. Dual targeting of histone deacetylases and MYC as potential treatment strategy for H3-K27M pediatric gliomas. eLife 2024; 13:RP96257. [PMID: 39093942 PMCID: PMC11296706 DOI: 10.7554/elife.96257] [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] [Indexed: 08/04/2024] Open
Abstract
Diffuse midline gliomas (DMGs) are aggressive and fatal pediatric tumors of the central nervous system that are highly resistant to treatments. Lysine to methionine substitution of residue 27 on histone H3 (H3-K27M) is a driver mutation in DMGs, reshaping the epigenetic landscape of these cells to promote tumorigenesis. H3-K27M gliomas are characterized by deregulation of histone acetylation and methylation pathways, as well as the oncogenic MYC pathway. In search of effective treatment, we examined the therapeutic potential of dual targeting of histone deacetylases (HDACs) and MYC in these tumors. Treatment of H3-K27M patient-derived cells with Sulfopin, an inhibitor shown to block MYC-driven tumors in vivo, in combination with the HDAC inhibitor Vorinostat, resulted in substantial decrease in cell viability. Moreover, transcriptome and epigenome profiling revealed synergistic effect of this drug combination in downregulation of prominent oncogenic pathways such as mTOR. Finally, in vivo studies of patient-derived orthotopic xenograft models showed significant tumor growth reduction in mice treated with the drug combination. These results highlight the combined treatment with PIN1 and HDAC inhibitors as a promising therapeutic approach for these aggressive tumors.
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Affiliation(s)
- Danielle Algranati
- Department of Immunology and Regenerative Biology, Weizmann Institute of ScienceRehovotIsrael
| | - Roni Oren
- Department of Veterinary Resources, Weizmann Institute of ScienceRehovotIsrael
| | - Bareket Dassa
- Bioinformatics Unit, Department of Life Sciences Core Facilities, Faculty of Biochemistry, Weizmann Institute of ScienceRehovotIsrael
| | - Liat Fellus-Alyagor
- Department of Veterinary Resources, Weizmann Institute of ScienceRehovotIsrael
| | - Alexander Plotnikov
- Wohl Institute for Drug Discovery of the Nancy and Stephen Grand Israel National Center for Personalized Medicine, Weizmann Institute of ScienceRehovotIsrael
| | - Haim Barr
- Wohl Institute for Drug Discovery of the Nancy and Stephen Grand Israel National Center for Personalized Medicine, Weizmann Institute of ScienceRehovotIsrael
| | - Alon Harmelin
- Department of Veterinary Resources, Weizmann Institute of ScienceRehovotIsrael
| | - Nir London
- Department of Chemical and Structural Biology, Weizmann Institute of ScienceRehovotIsrael
| | - Guy Ron
- Racah Institute of Physics, Hebrew UniversityJerusalemIsrael
| | - Noa Furth
- Department of Immunology and Regenerative Biology, Weizmann Institute of ScienceRehovotIsrael
| | - Efrat Shema
- Department of Immunology and Regenerative Biology, Weizmann Institute of ScienceRehovotIsrael
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6
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Pepin AS, Schneider R. Emerging toolkits for decoding the co-occurrence of modified histones and chromatin proteins. EMBO Rep 2024; 25:3202-3220. [PMID: 39095610 PMCID: PMC11316037 DOI: 10.1038/s44319-024-00199-2] [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: 02/28/2024] [Revised: 05/10/2024] [Accepted: 06/10/2024] [Indexed: 08/04/2024] Open
Abstract
In eukaryotes, DNA is packaged into chromatin with the help of highly conserved histone proteins. Together with DNA-binding proteins, posttranslational modifications (PTMs) on these histones play crucial roles in regulating genome function, cell fate determination, inheritance of acquired traits, cellular states, and diseases. While most studies have focused on individual DNA-binding proteins, chromatin proteins, or histone PTMs in bulk cell populations, such chromatin features co-occur and potentially act cooperatively to accomplish specific functions in a given cell. This review discusses state-of-the-art techniques for the simultaneous profiling of multiple chromatin features in low-input samples and single cells, focusing on histone PTMs, DNA-binding, and chromatin proteins. We cover the origins of the currently available toolkits, compare and contrast their characteristic features, and discuss challenges and perspectives for future applications. Studying the co-occurrence of histone PTMs, DNA-binding proteins, and chromatin proteins in single cells will be central for a better understanding of the biological relevance of combinatorial chromatin features, their impact on genomic output, and cellular heterogeneity.
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Affiliation(s)
- Anne-Sophie Pepin
- 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, Ludwig-Maximilians-Universität München, Planegg-Martinsried, Germany.
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7
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Valsakumar D, Voigt P. Nucleosomal asymmetry: a novel mechanism to regulate nucleosome function. Biochem Soc Trans 2024; 52:1219-1232. [PMID: 38778762 PMCID: PMC11346421 DOI: 10.1042/bst20230877] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2024] [Revised: 05/07/2024] [Accepted: 05/08/2024] [Indexed: 05/25/2024]
Abstract
Nucleosomes constitute the fundamental building blocks of chromatin. They are comprised of DNA wrapped around a histone octamer formed of two copies each of the four core histones H2A, H2B, H3, and H4. Nucleosomal histones undergo a plethora of posttranslational modifications that regulate gene expression and other chromatin-templated processes by altering chromatin structure or by recruiting effector proteins. Given their symmetric arrangement, the sister histones within a nucleosome have commonly been considered to be equivalent and to carry the same modifications. However, it is now clear that nucleosomes can exhibit asymmetry, combining differentially modified sister histones or different variants of the same histone within a single nucleosome. Enabled by the development of novel tools that allow generating asymmetrically modified nucleosomes, recent biochemical and cell-based studies have begun to shed light on the origins and functional consequences of nucleosomal asymmetry. These studies indicate that nucleosomal asymmetry represents a novel regulatory mechanism in the establishment and functional readout of chromatin states. Asymmetry expands the combinatorial space available for setting up complex sets of histone marks at individual nucleosomes, regulating multivalent interactions with histone modifiers and readers. The resulting functional consequences of asymmetry regulate transcription, poising of developmental gene expression by bivalent chromatin, and the mechanisms by which oncohistones deregulate chromatin states in cancer. Here, we review recent progress and current challenges in uncovering the mechanisms and biological functions of nucleosomal asymmetry.
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Affiliation(s)
- Devisree Valsakumar
- Epigenetics Programme, Babraham Institute, Cambridge CB22 3AT, U.K
- Wellcome Centre for Cell Biology, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3BF, U.K
| | - Philipp Voigt
- Epigenetics Programme, Babraham Institute, Cambridge CB22 3AT, U.K
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8
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Stadler M, Lukauskas S, Bartke T, Müller CL. asteRIa enables robust interaction modeling between chromatin modifications and epigenetic readers. Nucleic Acids Res 2024; 52:6129-6144. [PMID: 38752495 PMCID: PMC11194111 DOI: 10.1093/nar/gkae361] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2024] [Revised: 03/15/2024] [Accepted: 04/24/2024] [Indexed: 06/25/2024] Open
Abstract
Chromatin, the nucleoprotein complex consisting of DNA and histone proteins, plays a crucial role in regulating gene expression by controlling access to DNA. Chromatin modifications are key players in this regulation, as they help to orchestrate DNA transcription, replication, and repair. These modifications recruit epigenetic 'reader' proteins, which mediate downstream events. Most modifications occur in distinctive combinations within a nucleosome, suggesting that epigenetic information can be encoded in combinatorial chromatin modifications. A detailed understanding of how multiple modifications cooperate in recruiting such proteins has, however, remained largely elusive. Here, we integrate nucleosome affinity purification data with high-throughput quantitative proteomics and hierarchical interaction modeling to estimate combinatorial effects of chromatin modifications on protein recruitment. This is facilitated by the computational workflow asteRIa which combines hierarchical interaction modeling, stability-based model selection, and replicate-consistency checks for a stable estimation of Robust Interactions among chromatin modifications. asteRIa identifies several epigenetic reader candidates responding to specific interactions between chromatin modifications. For the polycomb protein CBX8, we independently validate our results using genome-wide ChIP-Seq and bisulphite sequencing datasets. We provide the first quantitative framework for identifying cooperative effects of chromatin modifications on protein binding.
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Affiliation(s)
- Mara Stadler
- Institute of Computational Biology, Helmholtz Zentrum München, 85764 Neuherberg, Germany
- Department of Statistics, Ludwig-Maximilians-University Munich, 80539 Munich, Germany
| | - Saulius Lukauskas
- Institute of Functional Epigenetics, Helmholtz Zentrum München, 85764 Neuherberg, Germany
| | - Till Bartke
- Institute of Functional Epigenetics, Helmholtz Zentrum München, 85764 Neuherberg, Germany
| | - Christian L Müller
- Institute of Computational Biology, Helmholtz Zentrum München, 85764 Neuherberg, Germany
- Department of Statistics, Ludwig-Maximilians-University Munich, 80539 Munich, Germany
- Center for Computational Mathematics, Flatiron Institute, New York, NY 10010, USA
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9
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Menon G, Mateo-Bonmati E, Reeck S, Maple R, Wu Z, Ietswaart R, Dean C, Howard M. Proximal termination generates a transcriptional state that determines the rate of establishment of Polycomb silencing. Mol Cell 2024; 84:2255-2271.e9. [PMID: 38851186 DOI: 10.1016/j.molcel.2024.05.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Revised: 02/28/2024] [Accepted: 05/14/2024] [Indexed: 06/10/2024]
Abstract
The mechanisms and timescales controlling de novo establishment of chromatin-mediated transcriptional silencing by Polycomb repressive complex 2 (PRC2) are unclear. Here, we investigate PRC2 silencing at Arabidopsis FLOWERING LOCUS C (FLC), known to involve co-transcriptional RNA processing, histone demethylation activity, and PRC2 function, but so far not mechanistically connected. We develop and test a computational model describing proximal polyadenylation/termination mediated by the RNA-binding protein FCA that induces H3K4me1 removal by the histone demethylase FLD. H3K4me1 removal feeds back to reduce RNA polymerase II (RNA Pol II) processivity and thus enhance early termination, thereby repressing productive transcription. The model predicts that this transcription-coupled repression controls the level of transcriptional antagonism to PRC2 action. Thus, the effectiveness of this repression dictates the timescale for establishment of PRC2/H3K27me3 silencing. We experimentally validate these mechanistic model predictions, revealing that co-transcriptional processing sets the level of productive transcription at the locus, which then determines the rate of the ON-to-OFF switch to PRC2 silencing.
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Affiliation(s)
- Govind Menon
- Department of Computational and Systems Biology, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK
| | - Eduardo Mateo-Bonmati
- Department of Cell and Developmental Biology, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK
| | - Svenja Reeck
- Department of Cell and Developmental Biology, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK
| | - Robert Maple
- Department of Cell and Developmental Biology, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK
| | - Zhe Wu
- Key Laboratory of Molecular Design for Plant Cell Factory of Guangdong Higher Education Institutes, Institute of Plant and Food Science, Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, China
| | - Robert Ietswaart
- Harvard Medical School, Department of Genetics, 77 Avenue Louis Pasteur, Boston, MA 02115, USA
| | - Caroline Dean
- Department of Cell and Developmental Biology, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK.
| | - Martin Howard
- Department of Computational and Systems Biology, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK.
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10
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Rudnizky S, Murray PJ, Wolfe CH, Ha T. Single-Macromolecule Studies of Eukaryotic Genomic Maintenance. Annu Rev Phys Chem 2024; 75:209-230. [PMID: 38382570 DOI: 10.1146/annurev-physchem-090722-010601] [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: 02/23/2024]
Abstract
Genomes are self-organized and self-maintained as long, complex macromolecules of chromatin. The inherent heterogeneity, stochasticity, phase separation, and chromatin dynamics of genome operation make it challenging to study genomes using ensemble methods. Various single-molecule force-, fluorescent-, and sequencing-based techniques rooted in different disciplines have been developed to fill critical gaps in the capabilities of bulk measurements, each providing unique, otherwise inaccessible, insights into the structure and maintenance of the genome. Capable of capturing molecular-level details about the organization, conformational changes, and packaging of genetic material, as well as processive and stochastic movements of maintenance factors, a single-molecule toolbox provides an excellent opportunity for collaborative research to understand how genetic material functions in health and malfunctions in disease. In this review, we discuss novel insights brought to genomic sciences by single-molecule techniques and their potential to continue to revolutionize the field-one molecule at a time.
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Affiliation(s)
- Sergei Rudnizky
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Peter J Murray
- Department of Biology, Johns Hopkins University, Baltimore, Maryland, USA
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, Massachusetts, USA;
| | - Clara H Wolfe
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Taekjip Ha
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, Massachusetts, USA;
- Department of Pediatrics, Harvard Medical School, Boston, Massachusetts, USA
- Howard Hughes Medical Institute, Boston Children's Hospital, Boston, Massachusetts, USA
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11
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Cohen LRZ, Meshorer E. The many faces of H3.3 in regulating chromatin in embryonic stem cells and beyond. Trends Cell Biol 2024:S0962-8924(24)00052-7. [PMID: 38614918 DOI: 10.1016/j.tcb.2024.03.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2024] [Revised: 03/12/2024] [Accepted: 03/14/2024] [Indexed: 04/15/2024]
Abstract
H3.3 is a highly conserved nonreplicative histone variant. H3.3 is enriched in promoters and enhancers of active genes, but it is also found within suppressed heterochromatin, mostly around telomeres. Accordingly, H3.3 is associated with seemingly contradicting functions: It is involved in development, differentiation, reprogramming, and cell fate, as well as in heterochromatin formation and maintenance, and the silencing of developmental genes. The emerging view is that different cellular contexts and histone modifications can promote opposing functions for H3.3. Here, we aim to provide an update with a focus on H3.3 functions in early mammalian development, considering the context of embryonic stem cell maintenance and differentiation, to finally conclude with emerging roles in cancer development and cell fate transition and maintenance.
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Affiliation(s)
- Lea R Z Cohen
- Department of Genetics, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel; The Edmond and Lily Safra Center for Brain Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Eran Meshorer
- Department of Genetics, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel; The Edmond and Lily Safra Center for Brain Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel.
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12
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Lukauskas S, Tvardovskiy A, Nguyen NV, Stadler M, Faull P, Ravnsborg T, Özdemir Aygenli B, Dornauer S, Flynn H, Lindeboom RGH, Barth TK, Brockers K, Hauck SM, Vermeulen M, Snijders AP, Müller CL, DiMaggio PA, Jensen ON, Schneider R, Bartke T. Decoding chromatin states by proteomic profiling of nucleosome readers. Nature 2024; 627:671-679. [PMID: 38448585 PMCID: PMC10954555 DOI: 10.1038/s41586-024-07141-5] [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: 05/10/2021] [Accepted: 01/31/2024] [Indexed: 03/08/2024]
Abstract
DNA and histone modifications combine into characteristic patterns that demarcate functional regions of the genome1,2. While many 'readers' of individual modifications have been described3-5, how chromatin states comprising composite modification signatures, histone variants and internucleosomal linker DNA are interpreted is a major open question. Here we use a multidimensional proteomics strategy to systematically examine the interaction of around 2,000 nuclear proteins with over 80 modified dinucleosomes representing promoter, enhancer and heterochromatin states. By deconvoluting complex nucleosome-binding profiles into networks of co-regulated proteins and distinct nucleosomal features driving protein recruitment or exclusion, we show comprehensively how chromatin states are decoded by chromatin readers. We find highly distinctive binding responses to different features, many factors that recognize multiple features, and that nucleosomal modifications and linker DNA operate largely independently in regulating protein binding to chromatin. Our online resource, the Modification Atlas of Regulation by Chromatin States (MARCS), provides in-depth analysis tools to engage with our results and advance the discovery of fundamental principles of genome regulation by chromatin states.
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Affiliation(s)
- Saulius Lukauskas
- Institute of Functional Epigenetics, Helmholtz Zentrum München, Neuherberg, Germany
- MRC Laboratory of Medical Sciences (LMS), London, UK
- Department of Chemical Engineering, Imperial College London, London, UK
| | - Andrey Tvardovskiy
- Institute of Functional Epigenetics, Helmholtz Zentrum München, Neuherberg, Germany
| | - Nhuong V Nguyen
- MRC Laboratory of Medical Sciences (LMS), London, UK
- Institute of Clinical Sciences (ICS), Faculty of Medicine, Imperial College London, London, UK
| | - Mara Stadler
- Institute of Functional Epigenetics, Helmholtz Zentrum München, Neuherberg, Germany
- Institute of Computational Biology, Helmholtz Zentrum München, Neuherberg, Germany
- Department of Statistics, Ludwig Maximilian University Munich, Munich, Germany
| | - Peter Faull
- MRC Laboratory of Medical Sciences (LMS), London, UK
- Proteomic Sciences Technology Platform, The Francis Crick Institute, London, UK
- Northwestern Proteomics Core Facility, Northwestern University, Chicago, IL, USA
| | - Tina Ravnsborg
- VILLUM Center for Bioanalytical Sciences and Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark
| | | | - Scarlett Dornauer
- Institute of Functional Epigenetics, Helmholtz Zentrum München, Neuherberg, Germany
| | - Helen Flynn
- Proteomic Sciences Technology Platform, The Francis Crick Institute, London, UK
| | - Rik G H Lindeboom
- Department of Molecular Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Oncode Institute, Radboud University Nijmegen, Nijmegen, The Netherlands
- The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Teresa K Barth
- Metabolomics and Proteomics Core, Helmholtz Zentrum München, Munich, Germany
- Clinical Protein Analysis Unit (ClinZfP), Biomedical Center (BMC), Faculty of Medicine, Ludwig Maximilian University Munich, Martinsried, Germany
| | - Kevin Brockers
- Institute of Functional Epigenetics, Helmholtz Zentrum München, Neuherberg, Germany
| | - Stefanie M Hauck
- Metabolomics and Proteomics Core, Helmholtz Zentrum München, Munich, Germany
| | - Michiel Vermeulen
- Department of Molecular Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Oncode Institute, Radboud University Nijmegen, Nijmegen, The Netherlands
- The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | | | - Christian L Müller
- Institute of Computational Biology, Helmholtz Zentrum München, Neuherberg, Germany
- Department of Statistics, Ludwig Maximilian University Munich, Munich, Germany
- Center for Computational Mathematics, Flatiron Institute, New York, NY, USA
| | - Peter A DiMaggio
- Department of Chemical Engineering, Imperial College London, London, UK
| | - Ole N Jensen
- VILLUM Center for Bioanalytical Sciences and Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark
| | - Robert Schneider
- Institute of Functional Epigenetics, Helmholtz Zentrum München, Neuherberg, Germany
- Faculty of Biology, Ludwig Maximilian University Munich, Martinsried, Germany
- German Center for Diabetes Research (DZD), Neuherberg, Germany
| | - Till Bartke
- Institute of Functional Epigenetics, Helmholtz Zentrum München, Neuherberg, Germany.
- MRC Laboratory of Medical Sciences (LMS), London, UK.
- Institute of Clinical Sciences (ICS), Faculty of Medicine, Imperial College London, London, UK.
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13
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Glancy E, Choy N, Eckersley-Maslin MA. Bivalent chromatin: a developmental balancing act tipped in cancer. Biochem Soc Trans 2024; 52:217-229. [PMID: 38385532 PMCID: PMC10903468 DOI: 10.1042/bst20230426] [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: 11/21/2023] [Revised: 02/05/2024] [Accepted: 02/07/2024] [Indexed: 02/23/2024]
Abstract
Bivalent chromatin is defined by the co-occurrence of otherwise opposing H3K4me3 and H3K27me3 modifications and is typically located at unmethylated promoters of lowly transcribed genes. In embryonic stem cells, bivalent chromatin has been proposed to poise developmental genes for future activation, silencing or stable repression upon lineage commitment. Normally, bivalent chromatin is kept in tight balance in cells, in part through the activity of the MLL/COMPASS-like and Polycomb repressive complexes that deposit the H3K4me3 and H3K27me3 modifications, respectively, but also emerging novel regulators including DPPA2/4, QSER1, BEND3, TET1 and METTL14. In cancers, both the deregulation of existing domains and the creation of de novo bivalent states is associated with either the activation or silencing of transcriptional programmes. This may facilitate diverse aspects of cancer pathology including epithelial-to-mesenchymal plasticity, chemoresistance and immune evasion. Here, we review current methods for detecting bivalent chromatin and discuss the factors involved in the formation and fine-tuning of bivalent domains. Finally, we examine how the deregulation of chromatin bivalency in the context of cancer could facilitate and/or reflect cancer cell adaptation. We propose a model in which bivalent chromatin represents a dynamic balance between otherwise opposing states, where the underlying DNA sequence is primed for the future activation or repression. Shifting this balance in any direction disrupts the tight equilibrium and tips cells into an altered epigenetic and phenotypic space, facilitating both developmental and cancer processes.
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Affiliation(s)
- Eleanor Glancy
- Peter MacCallum Cancer Centre, Melbourne, Victoria 3000, Australia
- Sir Peter MacCallum Department of Oncology, The University of Melbourne, Melbourne, Victoria 3010, Australia
| | - Natalie Choy
- Peter MacCallum Cancer Centre, Melbourne, Victoria 3000, Australia
- Sir Peter MacCallum Department of Oncology, The University of Melbourne, Melbourne, Victoria 3010, Australia
| | - Melanie A. Eckersley-Maslin
- Peter MacCallum Cancer Centre, Melbourne, Victoria 3000, Australia
- Sir Peter MacCallum Department of Oncology, The University of Melbourne, Melbourne, Victoria 3010, Australia
- Department of Anatomy and Physiology, The University of Melbourne, Melbourne, Victoria 3010, Australia
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14
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Yagci ZB, Kelkar GR, Johnson TJ, Sen D, Keung AJ. Designing Epigenome Editors: Considerations of Biochemical and Locus Specificities. Methods Mol Biol 2024; 2842:23-55. [PMID: 39012589 DOI: 10.1007/978-1-0716-4051-7_2] [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: 07/17/2024]
Abstract
The advent of locus-specific protein recruitment technologies has enabled a new class of studies in chromatin biology. Epigenome editors (EEs) enable biochemical modifications of chromatin at almost any specific endogenous locus. Their locus-specificity unlocks unique information including the functional roles of distinct modifications at specific genomic loci. Given the growing interest in using these tools for biological and translational studies, there are many specific design considerations depending on the scientific question or clinical need. Here, we present and discuss important design considerations and challenges regarding the biochemical and locus specificities of epigenome editors. These include how to: account for the complex biochemical diversity of chromatin; control for potential interdependency of epigenome editors and their resultant modifications; avoid sequestration effects; quantify the locus specificity of epigenome editors; and improve locus-specificity by considering concentration, affinity, avidity, and sequestration effects.
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Affiliation(s)
- Z Begum Yagci
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC, USA
| | - Gautami R Kelkar
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC, USA
| | - Tyler J Johnson
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC, USA
| | - Dilara Sen
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC, USA
| | - Albert J Keung
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC, USA.
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15
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Meers MP, Llagas G, Janssens DH, Codomo CA, Henikoff S. Multifactorial profiling of epigenetic landscapes at single-cell resolution using MulTI-Tag. Nat Biotechnol 2023; 41:708-716. [PMID: 36316484 PMCID: PMC10188359 DOI: 10.1038/s41587-022-01522-9] [Citation(s) in RCA: 23] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Accepted: 09/21/2022] [Indexed: 11/09/2022]
Abstract
Chromatin profiling at locus resolution uncovers gene regulatory features that define cell types and developmental trajectories, but it remains challenging to map and compare different chromatin-associated proteins in the same sample. Here we describe Multiple Target Identification by Tagmentation (MulTI-Tag), an antibody barcoding approach for profiling multiple chromatin features simultaneously in single cells. We optimized MulTI-Tag to retain high sensitivity and specificity, and we demonstrate detection of up to three histone modifications in the same cell: H3K27me3, H3K4me1/2 and H3K36me3. We apply MulTI-Tag to resolve distinct cell types and developmental trajectories; to distinguish unique, coordinated patterns of active and repressive element regulatory usage associated with differentiation outcomes; and to uncover associations between histone marks. Multifactorial epigenetic profiling holds promise for comprehensively characterizing cell-specific gene regulatory landscapes in development and disease.
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Affiliation(s)
- Michael P Meers
- Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
- Department of Genetics, Washington University School of Medicine in St. Louis, St. Louis, MO, USA
| | - Geneva Llagas
- Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Derek H Janssens
- Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Christine A Codomo
- Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, 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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16
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González-Ramírez M, Blanco E, Di Croce L. A computational pipeline to learn gene expression predictive models from epigenetic information at enhancers or promoters. STAR Protoc 2023; 4:101948. [PMID: 36583961 PMCID: PMC9816966 DOI: 10.1016/j.xpro.2022.101948] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Revised: 11/01/2022] [Accepted: 11/28/2022] [Indexed: 12/31/2022] Open
Abstract
Here, we present a computational pipeline to obtain quantitative models that characterize the relationship of gene expression with the epigenetic marking at enhancers or promoters in mouse embryonic stem cells. Our protocol consists of (i) generating predictive models of gene expression from epigenetic information (such as histone modification ChIP-seq) at enhancers or promoters and (ii) assessing the performance of these predictive models. This protocol could be applied to other biological scenarios or other types of epigenetic data. For complete details on the use and execution of this protocol, please refer to Gonzalez-Ramirez et al. (2021).1.
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Affiliation(s)
- Mar González-Ramírez
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Dr. Aiguader 88, 08003 Barcelona, Spain.
| | - Enrique Blanco
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Dr. Aiguader 88, 08003 Barcelona, Spain
| | - Luciano Di Croce
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Dr. Aiguader 88, 08003 Barcelona, Spain; Universitat Pompeu Fabra (UPF), Barcelona, Spain; Institució Catalana de Recerca i Estudis Avançats (ICREA), Pg. Lluis Companys 23, 08010 Barcelona, Spain.
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17
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Multiplexed, single-molecule, epigenetic analysis of plasma-isolated nucleosomes for cancer diagnostics. Nat Biotechnol 2023; 41:212-221. [PMID: 36076083 DOI: 10.1038/s41587-022-01447-3] [Citation(s) in RCA: 23] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2021] [Accepted: 07/25/2022] [Indexed: 11/08/2022]
Abstract
The analysis of cell-free DNA (cfDNA) in plasma provides information on pathological processes in the body. Blood cfDNA is in the form of nucleosomes, which maintain their tissue- and cancer-specific epigenetic state. We developed a single-molecule multiparametric assay to comprehensively profile the epigenetics of plasma-isolated nucleosomes (EPINUC), DNA methylation and cancer-specific protein biomarkers. Our system allows for high-resolution detection of six active and repressive histone modifications and their ratios and combinatorial patterns on millions of individual nucleosomes by single-molecule imaging. In addition, our system provides sensitive and quantitative data on plasma proteins, including detection of non-secreted tumor-specific proteins, such as mutant p53. EPINUC analysis of a cohort of 63 colorectal cancer, 10 pancreatic cancer and 33 healthy plasma samples detected cancer with high accuracy and sensitivity, even at early stages. Finally, combining EPINUC with direct single-molecule DNA sequencing revealed the tissue of origin of colorectal, pancreatic, lung and breast tumors. EPINUC provides multilayered information of potential clinical relevance from limited (<1 ml) liquid biopsy material.
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18
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Marklund E, Ke Y, Greenleaf WJ. High-throughput biochemistry in RNA sequence space: predicting structure and function. Nat Rev Genet 2023; 24:401-414. [PMID: 36635406 DOI: 10.1038/s41576-022-00567-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/08/2022] [Indexed: 01/14/2023]
Abstract
RNAs are central to fundamental biological processes in all known organisms. The set of possible intramolecular interactions of RNA nucleotides defines the range of alternative structural conformations of a specific RNA that can coexist, and these structures enable functional catalytic properties of RNAs and/or their productive intermolecular interactions with other RNAs or proteins. However, the immense combinatorial space of potential RNA sequences has precluded predictive mapping between RNA sequence and molecular structure and function. Recent advances in high-throughput approaches in vitro have enabled quantitative thermodynamic and kinetic measurements of RNA-RNA and RNA-protein interactions, across hundreds of thousands of sequence variations. In this Review, we explore these techniques, how they can be used to understand RNA function and how they might form the foundations of an accurate model to predict the structure and function of an RNA directly from its nucleotide sequence. The experimental techniques and modelling frameworks discussed here are also highly relevant for the sampling of sequence-structure-function space of DNAs and proteins.
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Affiliation(s)
- Emil Marklund
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
| | - Yuxi Ke
- Department of Bioengineering, Stanford University, Stanford, CA, USA
| | - William J Greenleaf
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA.
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19
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Epigenetic factor competition reshapes the EMT landscape. Proc Natl Acad Sci U S A 2022; 119:e2210844119. [PMID: 36215492 PMCID: PMC9586264 DOI: 10.1073/pnas.2210844119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The emergence of and transitions between distinct phenotypes in isogenic cells can be attributed to the intricate interplay of epigenetic marks, external signals, and gene-regulatory elements. These elements include chromatin remodelers, histone modifiers, transcription factors, and regulatory RNAs. Mathematical models known as gene-regulatory networks (GRNs) are an increasingly important tool to unravel the workings of such complex networks. In such models, epigenetic factors are usually proposed to act on the chromatin regions directly involved in the expression of relevant genes. However, it has been well-established that these factors operate globally and compete with each other for targets genome-wide. Therefore, a perturbation of the activity of a regulator can redistribute epigenetic marks across the genome and modulate the levels of competing regulators. In this paper, we propose a conceptual and mathematical modeling framework that incorporates both local and global competition effects between antagonistic epigenetic regulators, in addition to local transcription factors, and show the counterintuitive consequences of such interactions. We apply our approach to recent experimental findings on the epithelial-mesenchymal transition (EMT). We show that it can explain the puzzling experimental data, as well as provide verifiable predictions.
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20
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Ford BR, Vignali PDA, Rittenhouse NL, Scharping NE, Peralta R, Lontos K, Frisch AT, Delgoffe GM, Poholek AC. Tumor microenvironmental signals reshape chromatin landscapes to limit the functional potential of exhausted T cells. Sci Immunol 2022; 7:eabj9123. [PMID: 35930654 PMCID: PMC9851604 DOI: 10.1126/sciimmunol.abj9123] [Citation(s) in RCA: 39] [Impact Index Per Article: 19.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Response rates to immunotherapy in solid tumors remain low due in part to the elevated prevalence of terminally exhausted T cells, a hypofunctional differentiation state induced through persistent antigen and stress signaling. However, the mechanisms promoting progression to terminal exhaustion in the tumor remain undefined. Using the low-input chromatin immunoprecipitation sequencing method CUT&RUN, we profiled the histone modification landscape of tumor-infiltrating CD8+ T cells throughout differentiation. We found that terminally exhausted T cells had unexpected chromatin features that limit their transcriptional potential. Terminally exhausted T cells had a substantial fraction of active chromatin, including active enhancers enriched for bZIP/AP-1 transcription factor motifs that lacked correlated gene expression, which was restored by immunotherapeutic costimulatory signaling. Reduced transcriptional potential was also driven by an increase in histone bivalency, which we linked directly to hypoxia exposure. Enforced expression of the hypoxia-insensitive histone demethylase Kdm6b was sufficient to overcome hypoxia, increase function, and promote antitumor immunity. Our study reveals the specific epigenetic changes mediated by histone modifications during T cell differentiation that support exhaustion in cancer, highlighting that their altered function is driven by improper costimulatory signals and environmental factors. These data suggest that even terminally exhausted T cells may remain competent for transcription in settings of increased costimulatory signaling and reduced hypoxia.
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Affiliation(s)
- B. Rhodes Ford
- Division of Pediatric Rheumatology, Department of Pediatrics, University of Pittsburgh, Pittsburgh, PA 15260, USA.,Department of Immunology, University of Pittsburgh, Pittsburgh, PA 15260, USA
| | - Paolo D. A. Vignali
- Department of Immunology, University of Pittsburgh, Pittsburgh, PA 15260, USA.,Tumor Microenvironment Center, UPMC Hillman Cancer Center, University of Pittsburgh, Pittsburgh, PA 15260, USA
| | - Natalie L. Rittenhouse
- Division of Pediatric Rheumatology, Department of Pediatrics, University of Pittsburgh, Pittsburgh, PA 15260, USA
| | - Nicole E. Scharping
- Department of Immunology, University of Pittsburgh, Pittsburgh, PA 15260, USA.,Tumor Microenvironment Center, UPMC Hillman Cancer Center, University of Pittsburgh, Pittsburgh, PA 15260, USA
| | - Ronal Peralta
- Department of Immunology, University of Pittsburgh, Pittsburgh, PA 15260, USA.,Tumor Microenvironment Center, UPMC Hillman Cancer Center, University of Pittsburgh, Pittsburgh, PA 15260, USA
| | - Konstantinos Lontos
- Tumor Microenvironment Center, UPMC Hillman Cancer Center, University of Pittsburgh, Pittsburgh, PA 15260, USA.,Department of Oncology, University of Pittsburgh Medical Center, Pittsburgh, PA 15260, USA
| | - Andrew T. Frisch
- Department of Immunology, University of Pittsburgh, Pittsburgh, PA 15260, USA.,Tumor Microenvironment Center, UPMC Hillman Cancer Center, University of Pittsburgh, Pittsburgh, PA 15260, USA
| | - Greg M. Delgoffe
- Department of Immunology, University of Pittsburgh, Pittsburgh, PA 15260, USA.,Tumor Microenvironment Center, UPMC Hillman Cancer Center, University of Pittsburgh, Pittsburgh, PA 15260, USA.,Corresponding author. (G.M.D.); (A.C.P.)
| | - Amanda C. Poholek
- Division of Pediatric Rheumatology, Department of Pediatrics, University of Pittsburgh, Pittsburgh, PA 15260, USA.,Department of Immunology, University of Pittsburgh, Pittsburgh, PA 15260, USA.,Corresponding author. (G.M.D.); (A.C.P.)
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21
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Single-cell epigenetic analysis reveals principles of chromatin states in H3.3-K27M gliomas. Mol Cell 2022; 82:2696-2713.e9. [PMID: 35716669 DOI: 10.1016/j.molcel.2022.05.023] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Revised: 03/28/2022] [Accepted: 05/18/2022] [Indexed: 11/23/2022]
Abstract
Cancer cells are highly heterogeneous at the transcriptional level and epigenetic state. Methods to study epigenetic heterogeneity are limited in throughput and information obtained per cell. Here, we adapted cytometry by time-of-flight (CyTOF) to analyze a wide panel of histone modifications in primary tumor-derived lines of diffused intrinsic pontine glioma (DIPG). DIPG is a lethal glioma, driven by a histone H3 lysine 27 mutation (H3-K27M). We identified two epigenetically distinct subpopulations in DIPG, reflecting inherent heterogeneity in expression of the mutant histone. These two subpopulations are robust across tumor lines derived from different patients and show differential proliferation capacity and expression of stem cell and differentiation markers. Moreover, we demonstrate the use of these high-dimensional data to elucidate potential interactions between histone modifications and epigenetic alterations during the cell cycle. Our work establishes new concepts for the analysis of epigenetic heterogeneity in cancer that could be applied to diverse biological systems.
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22
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Furth N, Algranati D, Dassa B, Beresh O, Fedyuk V, Morris N, Kasper LH, Jones D, Monje M, Baker SJ, Shema E. H3-K27M-mutant nucleosomes interact with MLL1 to shape the glioma epigenetic landscape. Cell Rep 2022; 39:110836. [PMID: 35584667 DOI: 10.1016/j.celrep.2022.110836] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Revised: 03/01/2022] [Accepted: 04/27/2022] [Indexed: 01/08/2023] Open
Abstract
Cancer-associated mutations in genes encoding histones dramatically reshape chromatin and support tumorigenesis. Lysine to methionine substitution of residue 27 on histone H3 (K27M) is a driver mutation in high-grade pediatric gliomas, known to abrogate polycomb repressive complex 2 (PRC2) activity. We applied single-molecule systems to image individual nucleosomes and delineate the combinatorial epigenetic patterns associated with H3-K27M expression. We found that chromatin marks on H3-K27M-mutant nucleosomes are dictated both by their incorporation preferences and by intrinsic properties of the mutation. Mutant nucleosomes not only preferentially bind PRC2 but also directly interact with MLL1, leading to genome-wide redistribution of H3K4me3. H3-K27M-mediated deregulation of repressive and active chromatin marks leads to unbalanced "bivalent" chromatin, which may support a poorly differentiated cellular state. This study provides evidence for a direct effect of H3-K27M oncohistone on the MLL1-H3K4me3 pathway and highlights the capability of single-molecule tools to reveal mechanisms of chromatin deregulation in cancer.
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Affiliation(s)
- Noa Furth
- Department of Biological Regulation, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Danielle Algranati
- Department of Biological Regulation, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Bareket Dassa
- Bioinformatics Unit, Department of Life Sciences Core Facilities, Faculty of Biochemistry, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Olga Beresh
- Department of Biological Regulation, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Vadim Fedyuk
- Department of Biological Regulation, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Natasha Morris
- Department of Biological Regulation, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Lawryn H Kasper
- Department of Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | | | - Michelle Monje
- Department of Neurology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Suzanne J Baker
- Department of Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Efrat Shema
- Department of Biological Regulation, Weizmann Institute of Science, Rehovot 76100, Israel.
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23
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Furth N, Shema E. It's all in the combination: decoding the epigenome for cancer research and diagnostics. Curr Opin Genet Dev 2022; 73:101899. [PMID: 35091256 PMCID: PMC9168437 DOI: 10.1016/j.gde.2022.101899] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2021] [Revised: 12/20/2021] [Accepted: 12/28/2021] [Indexed: 12/14/2022]
Abstract
Genome regulation is governed by the dynamics of chromatin modifications. The extensive and diverse array of DNA and histone modifications allow multiple elements to act combinatorically and direct tissue-specific and cell-specific outcomes. Yet, our ability to elucidate these complex combinations and link them to normal genome regulation, as well as understand their deregulation in cancer, has been hindered by the lack of suitable technologies. Here, we describe recent findings indicating the importance of the combinatorial epigenome, and novel methodologies to measure and characterize these combinations. These complementary methods span multiple disciplines, providing a means to decode epigenetic combinations and link them to biological outcomes. Finally, we discuss the promise of harnessing the rich combinatorial epigenetic information to improve cancer diagnostics and monitoring.
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Affiliation(s)
- Noa Furth
- Department of Biological Regulation, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Efrat Shema
- Department of Biological Regulation, Weizmann Institute of Science, Rehovot 76100, Israel.
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24
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Tost J. Current and Emerging Technologies for the Analysis of the Genome-Wide and Locus-Specific DNA Methylation Patterns. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2022; 1389:395-469. [DOI: 10.1007/978-3-031-11454-0_16] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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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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Kumar D, Cinghu S, Oldfield AJ, Yang P, Jothi R. Decoding the function of bivalent chromatin in development and cancer. Genome Res 2021; 31:2170-2184. [PMID: 34667120 PMCID: PMC8647824 DOI: 10.1101/gr.275736.121] [Citation(s) in RCA: 50] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2021] [Accepted: 10/15/2021] [Indexed: 12/12/2022]
Abstract
Bivalent chromatin is characterized by the simultaneous presence of H3K4me3 and H3K27me3, histone modifications generally associated with transcriptionally active and repressed chromatin, respectively. Prevalent in embryonic stem cells (ESCs), bivalency is postulated to poise/prime lineage-controlling developmental genes for rapid activation during embryogenesis while maintaining a transcriptionally repressed state in the absence of activation cues; however, this hypothesis remains to be directly tested. Most gene promoters DNA hypermethylated in adult human cancers are bivalently marked in ESCs, and it was speculated that bivalency predisposes them for aberrant de novo DNA methylation and irreversible silencing in cancer, but evidence supporting this model is largely lacking. Here, we show that bivalent chromatin does not poise genes for rapid activation but protects promoters from de novo DNA methylation. Genome-wide studies in differentiating ESCs reveal that activation of bivalent genes is no more rapid than that of other transcriptionally silent genes, challenging the premise that H3K4me3 is instructive for transcription. H3K4me3 at bivalent promoters-a product of the underlying DNA sequence-persists in nearly all cell types irrespective of gene expression and confers protection from de novo DNA methylation. Bivalent genes in ESCs that are frequent targets of aberrant hypermethylation in cancer are particularly strongly associated with loss of H3K4me3/bivalency in cancer. Altogether, our findings suggest that bivalency protects reversibly repressed genes from irreversible silencing and that loss of H3K4me3 may make them more susceptible to aberrant DNA methylation in diseases such as cancer. Bivalency may thus represent a distinct regulatory mechanism for maintaining epigenetic plasticity.
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Affiliation(s)
- Dhirendra Kumar
- Epigenetics and Stem Cell Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, North Carolina 27709, USA
| | - Senthilkumar Cinghu
- Epigenetics and Stem Cell Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, North Carolina 27709, USA
| | - Andrew J Oldfield
- Epigenetics and Stem Cell Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, North Carolina 27709, USA
| | - Pengyi Yang
- Epigenetics and Stem Cell Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, North Carolina 27709, USA
| | - Raja Jothi
- Epigenetics and Stem Cell Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, North Carolina 27709, USA
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27
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Makasheva K, Bryan LC, Anders C, Panikulam S, Jinek M, Fierz B. Multiplexed Single-Molecule Experiments Reveal Nucleosome Invasion Dynamics of the Cas9 Genome Editor. J Am Chem Soc 2021; 143:16313-16319. [PMID: 34597515 PMCID: PMC8517959 DOI: 10.1021/jacs.1c06195] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2021] [Indexed: 12/29/2022]
Abstract
Single-molecule measurements provide detailed mechanistic insights into molecular processes, for example in genome regulation where DNA access is controlled by nucleosomes and the chromatin machinery. However, real-time single-molecule observations of nuclear factors acting on defined chromatin substrates are challenging to perform quantitatively and reproducibly. Here we present XSCAN (multiplexed single-molecule detection of chromatin association), a method to parallelize single-molecule experiments by simultaneous imaging of a nucleosome library, where each nucleosome type carries an identifiable DNA sequence within its nucleosomal DNA. Parallel experiments are subsequently spatially decoded, via the detection of specific binding of dye-labeled DNA probes. We use this method to reveal how the Cas9 nuclease overcomes the nucleosome barrier when invading chromatinized DNA as a function of PAM position.
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Affiliation(s)
- Kristina Makasheva
- Laboratory
of Biophysical Chemistry of Macromolecules, Institute of Chemical
Sciences and Engineering (ISIC), École
Polytechnique Fédérale de Lausanne (EPFL), Station 6, 1015 Lausanne, Switzerland
| | - Louise C. Bryan
- Laboratory
of Biophysical Chemistry of Macromolecules, Institute of Chemical
Sciences and Engineering (ISIC), École
Polytechnique Fédérale de Lausanne (EPFL), Station 6, 1015 Lausanne, Switzerland
| | - Carolin Anders
- Department
of Biochemistry, University of Zurich, Winterthurerstr. 190, 8057 Zurich, Switzerland
| | - Sherin Panikulam
- Department
of Biochemistry, University of Zurich, Winterthurerstr. 190, 8057 Zurich, Switzerland
| | - Martin Jinek
- Department
of Biochemistry, University of Zurich, Winterthurerstr. 190, 8057 Zurich, Switzerland
| | - Beat Fierz
- Laboratory
of Biophysical Chemistry of Macromolecules, Institute of Chemical
Sciences and Engineering (ISIC), École
Polytechnique Fédérale de Lausanne (EPFL), Station 6, 1015 Lausanne, Switzerland
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28
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González-Ramírez M, Ballaré C, Mugianesi F, Beringer M, Santanach A, Blanco E, Di Croce L. Differential contribution to gene expression prediction of histone modifications at enhancers or promoters. PLoS Comput Biol 2021; 17:e1009368. [PMID: 34473698 PMCID: PMC8443064 DOI: 10.1371/journal.pcbi.1009368] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2021] [Revised: 09/15/2021] [Accepted: 08/21/2021] [Indexed: 12/31/2022] Open
Abstract
The ChIP-seq signal of histone modifications at promoters is a good predictor of gene expression in different cellular contexts, but whether this is also true at enhancers is not clear. To address this issue, we develop quantitative models to characterize the relationship of gene expression with histone modifications at enhancers or promoters. We use embryonic stem cells (ESCs), which contain a full spectrum of active and repressed (poised) enhancers, to train predictive models. As many poised enhancers in ESCs switch towards an active state during differentiation, predictive models can also be trained on poised enhancers throughout differentiation and in development. Remarkably, we determine that histone modifications at enhancers, as well as promoters, are predictive of gene expression in ESCs and throughout differentiation and development. Importantly, we demonstrate that their contribution to the predictive models varies depending on their location in enhancers or promoters. Moreover, we use a local regression (LOESS) to normalize sequencing data from different sources, which allows us to apply predictive models trained in a specific cellular context to a different one. We conclude that the relationship between gene expression and histone modifications at enhancers is universal and different from promoters. Our study provides new insight into how histone modifications relate to gene expression based on their location in enhancers or promoters. Gene expression can be properly predicted by the ChIP-seq signal of histone modifications at promoters, but whether this is also true at enhancers is unclear. In this study we develop predictive models of gene expression that demonstrate the predictive power of histone modifications at enhancers in the context of mouse embryonic stem cells, during differentiation, and in animal development. Moreover, by assessing the contribution of each histone modification, we found that enhancer predictive models and promoter predictive models have different histone modification requirement. Therefore, different histone modifications relate better to enhancer or promoter function(s). Finally, by applying predictive models trained in a specific cellular context to a different one, we concluded that the relationship between gene expression and histone modifications at enhancers is universal.
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Affiliation(s)
- Mar González-Ramírez
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
| | - Cecilia Ballaré
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
| | - Francesca Mugianesi
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Malte Beringer
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
| | - Alexandra Santanach
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
| | - Enrique Blanco
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
| | - Luciano Di Croce
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
- ICREA, Pg. Barcelona, Spain
- * E-mail:
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29
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Mitchener MM, Muir TW. Janus Bioparticles: Asymmetric Nucleosomes and Their Preparation Using Chemical Biology Approaches. Acc Chem Res 2021; 54:3215-3227. [PMID: 34319695 DOI: 10.1021/acs.accounts.1c00313] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
The fundamental repeating unit of chromatin, the nucleosome, is composed of DNA wrapped around two copies each of four canonical histone proteins. Nucleosomes possess 2-fold pseudo-symmetry that is subject to disruption in cellular contexts. For example, the post-translational modification (PTM) of histones plays an essential role in epigenetic regulation, and the introduction of a PTM on only one of the two "sister" histone copies in a given nucleosome eliminates the inherent symmetry of the complex. Similarly, the removal or swapping of histones for variants or the introduction of a histone mutant may render the two faces of the nucleosome asymmetric, creating, if you will, a type of "Janus" bioparticle. Over the past decade, many groups have detailed the discovery of asymmetric species in chromatin isolated from numerous cell types. However, in vitro biochemical and biophysical investigation of asymmetric nucleosomes has proven synthetically challenging. Whereas symmetric nucleosomes are readily formed via a stochastic combination of their histone and DNA components, asymmetric nucleosome assembly demands the selective incorporation of a single modified/mutant histone copy alongside its wild-type counterpart.Herein we describe the chemical biology tools that we and others have developed in recent years for investigating nucleosome asymmetry. Such approaches, each with its own benefits and shortcomings, fall into five broad categories. First, we discuss affinity tag-based purification methods. These enable the assembly of theoretically any asymmetric nucleosome of interest but are frequently labor-intensive and suffer from low yields. Second, we detail transient cross-linking strategies that are amenable to the preparation of histone H3- or H4-modified/mutant asymmetric species. These yield asymmetric nucleosomes in a traceless fashion, albeit through the use of more complicated synthesis techniques. Third, we describe a synthetic biology technique based on the generation of bump-hole mutant H3 histones that selectively heterodimerize. Although currently developed only for H3 and a related isoform, this method uniquely allows for the interrogation of nucleosome asymmetry in yeast. Fourth, we outline a method for generating H2A- or H2B-modified/mutant asymmetric nucleosomes that relies on the differential DNA-histone contact strength inherent in the Widom 601 DNA sequence. This technique involves the initial formation of hexasomes which are then complemented with distinct H2A/H2B dimers. Finally, we review an approach that utilizes split intein technology to isolate asymmetric H2A- or H2B-modified/mutant nucleosomes. This method shares steps in common with the former but exploits tagged, intein-fused dimers for the facile purification of asymmetric products.Throughout the Account, we highlight various biological questions that drove the development of these methods and ultimately were answered by them. Though each technique has its own shortcomings, collectively these chemical biology tools provide a means to biochemically interrogate a plethora of asymmetric nucleosome species. We conclude with a discussion of remaining challenges, particularly that of endogenous asymmetric nucleosome detection.
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Affiliation(s)
- Michelle M. Mitchener
- Department of Chemistry, Princeton University, Princeton, New Jersey 08544, United States
| | - Tom W. Muir
- Department of Chemistry, Princeton University, Princeton, New Jersey 08544, United States
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30
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Furth N, Shilo S, Cohen N, Erez N, Fedyuk V, Schrager AM, Weinberger A, Dror AA, Zigron A, Shehadeh M, Sela E, Srouji S, Amit S, Levy I, Segal E, Dahan R, Jones D, Douek DC, Shema E. Unified platform for genetic and serological detection of COVID-19 with single-molecule technology. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2021. [PMID: 34075385 PMCID: PMC8168389 DOI: 10.1101/2021.05.25.21257501] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
The COVID-19 pandemic raises the need for diverse diagnostic approaches to rapidly detect different stages of viral infection. The flexible and quantitative nature of single-molecule imaging technology renders it optimal for development of new diagnostic tools. Here we present a proof-of-concept for a single-molecule based, enzyme-free assay for detection of SARS-CoV-2. The unified platform we developed allows direct detection of the viral genetic material from patients' samples, as well as their immune response consisting of IgG and IgM antibodies. Thus, it establishes a platform for diagnostics of COVID-19, which could also be adjusted to diagnose additional pathogens.
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Affiliation(s)
- Noa Furth
- Department of Biological Regulation, Weizmann Institute of Science, Rehovot, Israel
| | - Shay Shilo
- Department of Biological Regulation, Weizmann Institute of Science, Rehovot, Israel
| | - Niv Cohen
- Department of Biological Regulation, Weizmann Institute of Science, Rehovot, Israel
| | - Nir Erez
- Department of Biological Regulation, Weizmann Institute of Science, Rehovot, Israel
| | - Vadim Fedyuk
- Department of Biological Regulation, Weizmann Institute of Science, Rehovot, Israel
| | - Alexander M Schrager
- Human Immunology Section, Vaccine Research Center, National Institutes of Health, Bethesda, MD, USA
| | - Adina Weinberger
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Amiel A Dror
- Department of Otolaryngology, Head and Neck Surgery, Galilee Medical Center, Nahariya, Israel.,The Azrieli Faculty of Medicine, Bar-Ilan University, Safed, Israel
| | - Asaf Zigron
- Oral and Maxillofacial Department, Galilee Medical Center, Nahariya, Israel.,The Azrieli Faculty of Medicine, Bar-Ilan University, Safed, Israel
| | - Mona Shehadeh
- Clinical Laboratories division, Clinical Biochemistry and Endocrinology laboratory, Galilee Medical Center, Naharia, Israel.,The Azrieli Faculty of Medicine, Bar-Ilan University, Safed, Israel
| | - Eyal Sela
- Department of Otolaryngology, Head and Neck Surgery, Galilee Medical Center, Nahariya, Israel.,The Azrieli Faculty of Medicine, Bar-Ilan University, Safed, Israel
| | - Samer Srouji
- Oral and Maxillofacial Department, Galilee Medical Center, Nahariya, Israel.,The Azrieli Faculty of Medicine, Bar-Ilan University, Safed, Israel
| | | | - Itzchak Levy
- Sheba Medical Center, Ramat Gan, Israel.,Sackler Medical School, Tel Aviv university, Tel Aviv, Israel
| | - Eran Segal
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Rony Dahan
- Department of Immunology, Weizmann Institute of Science, Rehovot, Israel
| | | | - Daniel C Douek
- Human Immunology Section, Vaccine Research Center, National Institutes of Health, Bethesda, MD, USA
| | - Efrat Shema
- Department of Biological Regulation, Weizmann Institute of Science, Rehovot, Israel
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31
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Furth N, Shilo S, Cohen N, Erez N, Fedyuk V, Schrager AM, Weinberger A, Dror AA, Zigron A, Shehadeh M, Sela E, Srouji S, Amit S, Levy I, Segal E, Dahan R, Jones D, Douek DC, Shema E. Unified platform for genetic and serological detection of COVID-19 with single-molecule technology. PLoS One 2021; 16:e0255096. [PMID: 34310620 PMCID: PMC8312974 DOI: 10.1371/journal.pone.0255096] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Accepted: 07/10/2021] [Indexed: 11/26/2022] Open
Abstract
The COVID-19 pandemic raises the need for diverse diagnostic approaches to rapidly detect different stages of viral infection. The flexible and quantitative nature of single-molecule imaging technology renders it optimal for development of new diagnostic tools. Here we present a proof-of-concept for a single-molecule based, enzyme-free assay for detection of SARS-CoV-2. The unified platform we developed allows direct detection of the viral genetic material from patients' samples, as well as their immune response consisting of IgG and IgM antibodies. Thus, it establishes a platform for diagnostics of COVID-19, which could also be adjusted to diagnose additional pathogens.
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Affiliation(s)
- Noa Furth
- Department of Biological Regulation, Weizmann Institute of Science, Rehovot, Israel
| | - Shay Shilo
- Department of Biological Regulation, Weizmann Institute of Science, Rehovot, Israel
| | - Niv Cohen
- Department of Biological Regulation, Weizmann Institute of Science, Rehovot, Israel
| | - Nir Erez
- Department of Biological Regulation, Weizmann Institute of Science, Rehovot, Israel
| | - Vadim Fedyuk
- Department of Biological Regulation, Weizmann Institute of Science, Rehovot, Israel
| | - Alexander M. Schrager
- Human Immunology Section, Vaccine Research Center, National Institutes of Health, Bethesda, MD, United States of America
| | - Adina Weinberger
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Amiel A. Dror
- Department of Otolaryngology, Head and Neck Surgery, Galilee Medical Center, Nahariya, Israel
- The Azrieli Faculty of Medicine, Bar-Ilan University, Safed, Israel
| | - Asaf Zigron
- The Azrieli Faculty of Medicine, Bar-Ilan University, Safed, Israel
- Oral and Maxillofacial Department, Galilee Medical Center, Nahariya, Israel
| | - Mona Shehadeh
- The Azrieli Faculty of Medicine, Bar-Ilan University, Safed, Israel
- Clinical Laboratories Division, Clinical Biochemistry and Endocrinology Laboratory, Galilee Medical Center, Naharia, Israel
| | - Eyal Sela
- Department of Otolaryngology, Head and Neck Surgery, Galilee Medical Center, Nahariya, Israel
- The Azrieli Faculty of Medicine, Bar-Ilan University, Safed, Israel
| | - Samer Srouji
- The Azrieli Faculty of Medicine, Bar-Ilan University, Safed, Israel
- Oral and Maxillofacial Department, Galilee Medical Center, Nahariya, Israel
| | | | - Itzchak Levy
- Sheba Medical Center, Ramat Gan, Israel
- Sackler Medical School, Tel Aviv university, Tel Aviv, Israel
| | - Eran Segal
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Rony Dahan
- Department of Immunology, Weizmann Institute of Science, Rehovot, Israel
| | - Dan Jones
- SeqLL, Woburn, MA, United States of America
| | - Daniel C. Douek
- Human Immunology Section, Vaccine Research Center, National Institutes of Health, Bethesda, MD, United States of America
| | - Efrat Shema
- Department of Biological Regulation, Weizmann Institute of Science, Rehovot, Israel
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32
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Zhao W, Qiao L, Yan S, Nie Q, Zhang L. Mathematical modeling of histone modifications reveals the formation mechanism and function of bivalent chromatin. iScience 2021; 24:102732. [PMID: 34278251 PMCID: PMC8261666 DOI: 10.1016/j.isci.2021.102732] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Revised: 05/23/2021] [Accepted: 06/08/2021] [Indexed: 01/09/2023] Open
Abstract
Bivalent chromatin is characterized by occupation of both activating and repressive histone modifications. Here, we develop a mathematical model that involves antagonistic histone modifications H3K4me3 and H3K27me3 to capture the key features of bivalent chromatin. Three necessary conditions for the emergence of bivalent chromatin are identified, including advantageous methylating activity over demethylating activity, frequent noise conversions of modifications, and sufficient nonlinearity. The first condition is further confirmed by analyzing the existing experimental data. Investigation of the composition of bivalent chromatin reveals that bivalent nucleosomes carrying both H3K4me3 and H3K27me3 account for no more than half of nucleosomes at the bivalent chromatin domain. We identify that bivalent chromatin not only allows transitions to multiple states but also serves as a stepping stone to facilitate a stepwise transition between repressive chromatin state and activating chromatin state and thus elucidate crucial roles of bivalent chromatin in mediating phenotypical plasticity during cell fate determination. Emergence of bivalency needs advantageous writing activity over erasing activity Emergence of bivalency is facilitated by noise and nonlinearity The proportion of bivalent nucleosomes at bivalent chromatin is no more than 50% Bivalent chromatin facilitates chromatin state transitions
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Affiliation(s)
- Wei Zhao
- Beijing International Center for Mathematical Research, Peking University, Beijing 100871, China.,Center for Quantitative Biology, Peking University, Beijing 100871, China
| | - Lingxia Qiao
- Beijing International Center for Mathematical Research, Peking University, Beijing 100871, China
| | - Shiyu Yan
- Center for Quantitative Biology, Peking University, Beijing 100871, China
| | - Qing Nie
- Department of Mathematics and Department of Developmental and Cell Biology, University of California Irvine, Irvine, CA 92697, USA
| | - Lei Zhang
- Beijing International Center for Mathematical Research, Peking University, Beijing 100871, China.,Center for Quantitative Biology, Peking University, Beijing 100871, China
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33
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Fiskus W, Mill CP, Nabet B, Perera D, Birdwell C, Manshouri T, Lara B, Kadia TM, DiNardo C, Takahashi K, Daver N, Bose P, Masarova L, Pemmaraju N, Kornblau S, Borthakur G, Montalban-Bravo G, Manero GG, Sharma S, Stubbs M, Su X, Green MR, Coarfa C, Verstovsek S, Khoury JD, Vakoc CR, Bhalla KN. Superior efficacy of co-targeting GFI1/KDM1A and BRD4 against AML and post-MPN secondary AML cells. Blood Cancer J 2021; 11:98. [PMID: 34016956 PMCID: PMC8138012 DOI: 10.1038/s41408-021-00487-3] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2021] [Revised: 04/20/2021] [Accepted: 04/30/2021] [Indexed: 12/15/2022] Open
Abstract
There is an unmet need to overcome nongenetic therapy-resistance to improve outcomes in AML, especially post-myeloproliferative neoplasm (MPN) secondary (s) AML. Studies presented describe effects of genetic knockout, degradation or small molecule targeted-inhibition of GFI1/LSD1 on active enhancers, altering gene-expressions and inducing differentiation and lethality in AML and (MPN) sAML cells. A protein domain-focused CRISPR screen in LSD1 (KDM1A) inhibitor (i) treated AML cells, identified BRD4, MOZ, HDAC3 and DOT1L among the codependencies. Our findings demonstrate that co-targeting LSD1 and one of these co-dependencies exerted synergistic in vitro lethality in AML and post-MPN sAML cells. Co-treatment with LSD1i and the JAKi ruxolitinib was also synergistically lethal against post-MPN sAML cells. LSD1i pre-treatment induced GFI1, PU.1 and CEBPα but depleted c-Myc, overcoming nongenetic resistance to ruxolitinib, or to BETi in post-MPN sAML cells. Co-treatment with LSD1i and BETi or ruxolitinib exerted superior in vivo efficacy against post-MPN sAML cells. These findings highlight LSD1i-based combinations that merit testing for clinical efficacy, especially to overcome nongenetic therapy-resistance in AML and post-MPN sAML.
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Affiliation(s)
- Warren Fiskus
- The University of Texas M.D. Anderson Cancer Center, Houston, TX, USA
| | | | - Behnam Nabet
- Department of Cancer Biology, Dana-Farber Cancer Institute and Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Dimuthu Perera
- Department of Molecular and Cellular Biology Baylor College of Medicine, Houston, TX, USA
| | | | - Taghi Manshouri
- The University of Texas M.D. Anderson Cancer Center, Houston, TX, USA
| | - Bernardo Lara
- The University of Texas M.D. Anderson Cancer Center, Houston, TX, USA
| | - Tapan M Kadia
- The University of Texas M.D. Anderson Cancer Center, Houston, TX, USA
| | - Courtney DiNardo
- The University of Texas M.D. Anderson Cancer Center, Houston, TX, USA
| | - Koichi Takahashi
- The University of Texas M.D. Anderson Cancer Center, Houston, TX, USA
| | - Naval Daver
- The University of Texas M.D. Anderson Cancer Center, Houston, TX, USA
| | - Prithviraj Bose
- The University of Texas M.D. Anderson Cancer Center, Houston, TX, USA
| | - Lucia Masarova
- The University of Texas M.D. Anderson Cancer Center, Houston, TX, USA
| | - Naveen Pemmaraju
- The University of Texas M.D. Anderson Cancer Center, Houston, TX, USA
| | - Steven Kornblau
- The University of Texas M.D. Anderson Cancer Center, Houston, TX, USA
| | - Gautam Borthakur
- The University of Texas M.D. Anderson Cancer Center, Houston, TX, USA
| | | | | | - Sunil Sharma
- The Translational Genomics Research Institute (TGen), Phoenix, AZ, USA
| | | | - Xiaoping Su
- The University of Texas M.D. Anderson Cancer Center, Houston, TX, USA
| | - Michael R Green
- The University of Texas M.D. Anderson Cancer Center, Houston, TX, USA
| | - Cristian Coarfa
- Department of Molecular and Cellular Biology Baylor College of Medicine, Houston, TX, USA
| | - Srdan Verstovsek
- The University of Texas M.D. Anderson Cancer Center, Houston, TX, USA
| | - Joseph D Khoury
- The University of Texas M.D. Anderson Cancer Center, Houston, TX, USA
| | | | - Kapil N Bhalla
- The University of Texas M.D. Anderson Cancer Center, Houston, TX, USA.
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34
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Alajem A, Roth H, Ratgauzer S, Bavli D, Motzik A, Lahav S, Peled I, Ram O. DNA methylation patterns expose variations in enhancer-chromatin modifications during embryonic stem cell differentiation. PLoS Genet 2021; 17:e1009498. [PMID: 33844685 PMCID: PMC8062104 DOI: 10.1371/journal.pgen.1009498] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2020] [Revised: 04/22/2021] [Accepted: 03/19/2021] [Indexed: 12/15/2022] Open
Abstract
In mammals, cellular identity is defined through strict regulation of chromatin modifications and DNA methylation that control gene expression. Methylation of cytosines at CpG sites in the genome is mainly associated with suppression; however, the reason for enhancer-specific methylation is not fully understood. We used sequential ChIP-bisulfite-sequencing for H3K4me1 and H3K27ac histone marks. By collecting data from the same genomic region, we identified enhancers differentially methylated between these two marks. We observed a global gain of CpG methylation primarily in H3K4me1-marked nucleosomes during mouse embryonic stem cell differentiation. This gain occurred largely in enhancer regions that regulate genes critical for differentiation. The higher levels of DNA methylation in H3K4me1- versus H3K27ac-marked enhancers, despite it being the same genomic region, indicates cellular heterogeneity of enhancer states. Analysis of single-cell RNA-seq profiles demonstrated that this heterogeneity correlates with gene expression during differentiation. Furthermore, heterogeneity of enhancer methylation correlates with transcription start site methylation. Our results provide insights into enhancer-based functional variation in complex biological systems. Cellular dynamics are underlined by numerous regulatory layers. The regulatory mechanism of interest in this work are enhancers. Enhancers are regulatory regions responsible, mainly, for increasing the possibility of transcription of a certain gene. Enhancers are marked by two distinct chemical groups-H3K4me1 and H3K27ac on the tail of histones. Histones are the proteins responsible for DNA packaging into condensed chromatin structure. In contrast, DNA methylation is a chemical modification often found on enhancers, and is traditionally associated with repression. A long-debated question revolves around the functional relevance of DNA methylation in the context of enhancers. Here, we combined the two regulatory layers, histone marks and DNA methylation, to a single measurement that can highlight DNA methylation separately on each histone mark but at the same genomic region. When isolated with H3K4me1, enhancers showed higher levels of methylation compared to H3K27ac. As we measured the same genomic locations, we show that differences of DNA methylation between these marks can only be explained by cellular heterogeneity. We also demonstrated that these enhancers tend to play roles in stem cell differentiation and expression levels of the genes they control correlate with cell-to-cell variation.
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Affiliation(s)
- Adi Alajem
- Department of Biological Chemistry, Alexander Silberman Institute of Life Sciences, The Hebrew University, Jerusalem, Israel
| | - Hava Roth
- Department of Biological Chemistry, Alexander Silberman Institute of Life Sciences, The Hebrew University, Jerusalem, Israel
| | - Sofia Ratgauzer
- Department of Biological Chemistry, Alexander Silberman Institute of Life Sciences, The Hebrew University, Jerusalem, Israel
| | - Danny Bavli
- Department of Biological Chemistry, Alexander Silberman Institute of Life Sciences, The Hebrew University, Jerusalem, Israel
| | - Alex Motzik
- Department of Biological Chemistry, Alexander Silberman Institute of Life Sciences, The Hebrew University, Jerusalem, Israel
| | - Shlomtzion Lahav
- Department of Biological Chemistry, Alexander Silberman Institute of Life Sciences, The Hebrew University, Jerusalem, Israel
| | - Itay Peled
- Department of Biological Chemistry, Alexander Silberman Institute of Life Sciences, The Hebrew University, Jerusalem, Israel
| | - Oren Ram
- Department of Biological Chemistry, Alexander Silberman Institute of Life Sciences, The Hebrew University, Jerusalem, Israel
- * E-mail:
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35
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Using computational modelling to reveal mechanisms of epigenetic Polycomb control. Biochem Soc Trans 2021; 49:71-77. [PMID: 33616630 PMCID: PMC7925002 DOI: 10.1042/bst20190955] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2020] [Revised: 01/29/2021] [Accepted: 02/01/2021] [Indexed: 11/17/2022]
Abstract
The Polycomb system is essential for stable gene silencing in many organisms. This regulation is achieved in part through addition of the histone modifications H3K27me2/me3 by Polycomb Repressive Complex 2 (PRC2). These modifications are believed to be the causative epigenetic memory elements of PRC2-mediated silencing. As these marks are stored locally in the chromatin, PRC2-based memory is a cis-acting system. A key feature of stable epigenetic memory in cis is PRC2-mediated, self-reinforcing feedback from K27-methylated histones onto nearby histones in a read-write paradigm. However, it was not clear under what conditions such feedback can lead to stable memory, able, for example, to survive the perturbation of histone dilution at DNA replication. In this context, computational modelling has allowed a rigorous exploration of possible underlying memory mechanisms and has also greatly accelerated our understanding of switching between active and silenced states. Specifically, modelling has predicted that switching and memory at Polycomb loci is digital, with a locus being either active or inactive, rather than possessing intermediate, smoothly varying levels of activation. Here, we review recent advances in models of Polycomb control, focusing on models of epigenetic switching through nucleation and spreading of H3K27me2/me3. We also examine models that incorporate transcriptional feedback antagonism and those including bivalent chromatin states. With more quantitative experimental data on histone modification kinetics, as well as single-cell resolution data on transcription and protein levels for PRC2 targets, we anticipate an expanded need for modelling to help dissect increasingly interconnected and complex memory mechanisms.
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36
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Stelman CR, Smith BM, Chandra B, Roberts-Galbraith RH. CBP/p300 homologs CBP2 and CBP3 play distinct roles in planarian stem cell function. Dev Biol 2021; 473:130-143. [PMID: 33607113 DOI: 10.1016/j.ydbio.2021.02.004] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Revised: 02/08/2021] [Accepted: 02/09/2021] [Indexed: 11/19/2022]
Abstract
Chromatin modifications function as critical regulators of gene expression and cellular identity, especially in the regulation and maintenance of the pluripotent state. However, many studies of chromatin modification in stem cells-and pluripotent stem cells in particular-are performed in mammalian stem cell culture, an in vitro condition mimicking a very transient state during mammalian development. Thus, new models for studying pluripotent stem cells in vivo could be helpful for understanding the roles of chromatin modification, for confirming prior in vitro studies, and for exploring evolution of the pluripotent state. The freshwater flatworm, Schmidtea mediterranea, is an excellent model for studying adult pluripotent stem cells, particularly in the context of robust, whole-body regeneration. To identify chromatin modifying and remodeling enzymes critical for planarian regeneration and stem cell maintenance, we took a candidate approach and screened planarian homologs of 25 genes known to regulate chromatin biology in other organisms. Through our study, we identified six genes with novel functions in planarian homeostasis, regeneration, and behavior. Of the list of genes characterized, we identified five planarian homologs of the mammalian CREB-Binding Protein (CBP) and p300 family of histone acetyltransferases, representing an expansion of this family in planarians. We find that two planarian CBP family members are required for planarian survival, with knockdown of Smed-CBP2 and Smed-CBP3 causing distinct defects in stem cell maintenance or function. Loss of CBP2 causes a quick, dramatic loss of stem cells, while knockdown of CBP3 affects stem cells more narrowly, influencing differentiation of several cell types that include neuronal subtypes and cells of the eye. Further, we find that Smed-CBP1 is required for planarian fissioning behavior. We propose that the division of labor among a diversified CBP family in planarians presents an opportunity to dissect specific functions of a broadly important histone acetyltransferase family.
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Affiliation(s)
- Clara R Stelman
- Department of Molecular and Cellular Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Britessia M Smith
- Department of Cellular Biology, University of Georgia, Athens, GA, USA
| | - Bidushi Chandra
- Department of Cellular Biology, University of Georgia, Athens, GA, USA
| | - Rachel H Roberts-Galbraith
- Department of Molecular and Cellular Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA; Department of Cellular Biology, University of Georgia, Athens, GA, USA.
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37
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Mass Spectrometry to Study Chromatin Compaction. BIOLOGY 2020; 9:biology9060140. [PMID: 32604817 PMCID: PMC7345930 DOI: 10.3390/biology9060140] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/01/2020] [Revised: 06/19/2020] [Accepted: 06/23/2020] [Indexed: 12/26/2022]
Abstract
Chromatin accessibility is a major regulator of gene expression. Histone writers/erasers have a critical role in chromatin compaction, as they “flag” chromatin regions by catalyzing/removing covalent post-translational modifications on histone proteins. Anomalous chromatin decondensation is a common phenomenon in cells experiencing aging and viral infection. Moreover, about 50% of cancers have mutations in enzymes regulating chromatin state. Numerous genomics methods have evolved to characterize chromatin state, but the analysis of (in)accessible chromatin from the protein perspective is not yet in the spotlight. We present an overview of the most used approaches to generate data on chromatin accessibility and then focus on emerging methods that utilize mass spectrometry to quantify the accessibility of histones and the rest of the chromatin bound proteome. Mass spectrometry is currently the method of choice to quantify entire proteomes in an unbiased large-scale manner; accessibility on chromatin of proteins and protein modifications adds an extra quantitative layer to proteomics dataset that assist more informed data-driven hypotheses in chromatin biology. We speculate that this emerging new set of methods will enhance predictive strength on which proteins and histone modifications are critical in gene regulation, and which proteins occupy different chromatin states in health and disease.
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38
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Abstract
Predicting regulatory potential from primary DNA sequences or transcription factor binding patterns is not possible. However, the annotation of the genome by chromatin proteins, histone modifications, and differential compaction is largely sufficient to reveal the locations of genes and their differential activity states. The Polycomb Group (PcG) and Trithorax Group (TrxG) proteins are the central players in this cell type-specific chromatin organization. PcG function was originally viewed as being solely repressive and irreversible, as observed at the homeotic loci in flies and mammals. However, it is now clear that modular and reversible PcG function is essential at most developmental genes. Focusing mainly on recent advances, we review evidence for how PcG and TrxG patterns change dynamically during cell type transitions. The ability to implement cell type-specific transcriptional programming with exquisite fidelity is essential for normal development.
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Affiliation(s)
- Mitzi I Kuroda
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts 02115, USA; ,
| | - Hyuckjoon Kang
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts 02115, USA; ,
| | - Sandip De
- Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland 20892, USA; ,
| | - Judith A Kassis
- Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland 20892, USA; ,
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39
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Khan KA, Ng MK, Cheung P. The Use of Mononucleosome Immunoprecipitation for Analysis of Combinatorial Histone Post-translational Modifications and Purification of Nucleosome-Interacting Proteins. Front Cell Dev Biol 2020; 8:331. [PMID: 32457909 PMCID: PMC7225312 DOI: 10.3389/fcell.2020.00331] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2020] [Accepted: 04/16/2020] [Indexed: 01/05/2023] Open
Abstract
The nucleosome is the principal structural unit of chromatin. Although many studies focus on individual histone post-translational modifications (PTMs) in isolation, it is important to recognize that multiple histone PTMs can function together or cross-regulate one another within the nucleosome context. In addition, different modifications or histone-binding surfaces can synergize to stabilize the binding of nuclear factors to nucleosomes. To facilitate these types of studies, we present here a step-by-step protocol for isolating high yields of mononucleosomes for biochemical analyses. Furthermore, we discuss differences and variations of the basic protocol used in different publications and characterize the relative abundance of selected histone PTMs and chromatin-binding proteins in the different chromatin fractions obtained by this method.
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Affiliation(s)
| | - Marlee K Ng
- Department of Biology, York University, Toronto, ON, Canada
| | - Peter Cheung
- Department of Biology, York University, Toronto, ON, Canada
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40
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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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41
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Guidotti N, Fierz B. Semisynthesis and Reconstitution of Nucleosomes Carrying Asymmetric Histone Modifications. Methods Mol Biol 2020; 2133:263-291. [PMID: 32144672 DOI: 10.1007/978-1-0716-0434-2_13] [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: 06/10/2023]
Abstract
Nucleosomes, the basic unit of chromatin, contain a protein core of histone proteins, which are heavily posttranslationally modified. These modifications form a combinatorial language which defines the functional state of the underlying genome. As each histone type exists in two copies in a nucleosome, the modification patterns can differ between the individual histones, resulting in asymmetry and increasing combinatorial complexity. To systematically explore the regulation of chromatin regulatory enzymes (writers, erasers, or readers), chemically defined nucleosomes are required. We have developed strategies to chemically modify histones and control nucleosome assembly, thereby enabling the reconstitution of asymmetric histone modification patterns. Here, we report a detailed protocol for the modular assembly of such nucleosomes. Employing a three-segment ligation strategy for the semisynthesis of H3, coupled with the use of the protease cleavable "lnc-tag," we provide an efficient and traceless method for the controlled semisynthesis and reconstitution of asymmetrically modified nucleosomes.
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Affiliation(s)
- Nora Guidotti
- École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Beat Fierz
- École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland.
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42
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Cao H, Salazar-García L, Gao F, Wahlestedt T, Wu CL, Han X, Cai Y, Xu D, Wang F, Tang L, Ricciardi N, Cai D, Wang H, Chin MPS, Timmons JA, Wahlestedt C, Kapranov P. Novel approach reveals genomic landscapes of single-strand DNA breaks with nucleotide resolution in human cells. Nat Commun 2019; 10:5799. [PMID: 31862872 PMCID: PMC6925131 DOI: 10.1038/s41467-019-13602-7] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2019] [Accepted: 11/11/2019] [Indexed: 12/20/2022] Open
Abstract
Single-strand breaks (SSBs) represent the major form of DNA damage, yet techniques to map these lesions genome-wide with nucleotide-level precision are limited. Here, we present a method, termed SSiNGLe, and demonstrate its utility to explore the distribution and dynamic changes in genome-wide SSBs in response to different biological and environmental stimuli. We validate SSiNGLe using two very distinct sequencing techniques and apply it to derive global profiles of SSBs in different biological states. Strikingly, we show that patterns of SSBs in the genome are non-random, specific to different biological states, enriched in regulatory elements, exons, introns, specific types of repeats and exhibit differential preference for the template strand between exons and introns. Furthermore, we show that breaks likely contribute to naturally occurring sequence variants. Finally, we demonstrate strong links between SSB patterns and age. Overall, SSiNGLe provides access to unexplored realms of cellular biology, not obtainable with current approaches.
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Affiliation(s)
- Huifen Cao
- Institute of Genomics, School of Biomedical Sciences, Huaqiao University, 668 Jimei Road, Xiamen, 361021, China
| | - Lorena Salazar-García
- Institute of Genomics, School of Biomedical Sciences, Huaqiao University, 668 Jimei Road, Xiamen, 361021, China
| | - Fan Gao
- Institute of Genomics, School of Biomedical Sciences, Huaqiao University, 668 Jimei Road, Xiamen, 361021, China
| | - Thor Wahlestedt
- Institute of Genomics, School of Biomedical Sciences, Huaqiao University, 668 Jimei Road, Xiamen, 361021, China
| | - Chun-Lin Wu
- Department of Pathology, Second Affiliated Hospital of Fujian Medical University, Quanzhou, 362000, China
| | - Xueer Han
- Institute of Genomics, School of Biomedical Sciences, Huaqiao University, 668 Jimei Road, Xiamen, 361021, China
| | - Ye Cai
- Institute of Genomics, School of Biomedical Sciences, Huaqiao University, 668 Jimei Road, Xiamen, 361021, China
| | - Dongyang Xu
- Institute of Genomics, School of Biomedical Sciences, Huaqiao University, 668 Jimei Road, Xiamen, 361021, China
| | - Fang Wang
- Institute of Genomics, School of Biomedical Sciences, Huaqiao University, 668 Jimei Road, Xiamen, 361021, China
| | - Lu Tang
- Institute of Genomics, School of Biomedical Sciences, Huaqiao University, 668 Jimei Road, Xiamen, 361021, China
| | - Natalie Ricciardi
- Center for Therapeutic Innovation and Department of Psychiatry and Behavioral Sciences, University of Miami Miller School of Medicine, 1501 NW 10th Ave, Miami, FL, 33136, USA
| | - DingDing Cai
- Institute of Genomics, School of Biomedical Sciences, Huaqiao University, 668 Jimei Road, Xiamen, 361021, China
| | - Huifang Wang
- Institute of Genomics, School of Biomedical Sciences, Huaqiao University, 668 Jimei Road, Xiamen, 361021, China
| | - Mario P S Chin
- Institute of Genomics, School of Biomedical Sciences, Huaqiao University, 668 Jimei Road, Xiamen, 361021, China
| | - James A Timmons
- Augur Precision Medicine LTD, Scion House, Stirling University Innovation Park, Stirling, FK9 4NF, UK
| | - Claes Wahlestedt
- Center for Therapeutic Innovation and Department of Psychiatry and Behavioral Sciences, University of Miami Miller School of Medicine, 1501 NW 10th Ave, Miami, FL, 33136, USA.
| | - Philipp Kapranov
- Institute of Genomics, School of Biomedical Sciences, Huaqiao University, 668 Jimei Road, Xiamen, 361021, China.
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43
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Abstract
The epigenetic modifications of histones are versatile marks that are intimately connected to development and disease pathogenesis including human cancers. In this review, we will discuss the many different types of histone modifications and the biological processes with which they are involved. Specifically, we review the enzymatic machineries and modifications that are involved in cancer development and progression, and how to apply currently available small molecule inhibitors for histone modifiers as tool compounds to study the functional significance of histone modifications and their clinical implications.
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Affiliation(s)
- Zibo Zhao
- Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Simpson Querrey 7th Floor 303 E. Superior Street, Chicago, IL 60611 USA
- Simpson Querrey Center for Epigenetics, Northwestern University Feinberg School of Medicine, Chicago, IL 60611 USA
| | - Ali Shilatifard
- Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Simpson Querrey 7th Floor 303 E. Superior Street, Chicago, IL 60611 USA
- Simpson Querrey Center for Epigenetics, Northwestern University Feinberg School of Medicine, Chicago, IL 60611 USA
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44
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Garoli D, Yamazaki H, Maccaferri N, Wanunu M. Plasmonic Nanopores for Single-Molecule Detection and Manipulation: Toward Sequencing Applications. NANO LETTERS 2019; 19:7553-7562. [PMID: 31587559 DOI: 10.1021/acs.nanolett.9b02759] [Citation(s) in RCA: 77] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
Solid-state nanopore-based sensors are promising platforms for next-generation sequencing technologies, featuring label-free single-molecule sensitivity, rapid detection, and low-cost manufacturing. In recent years, solid-state nanopores have been explored due to their miscellaneous fabrication methods and their use in a wide range of sensing applications. Here, we highlight a novel family of solid-state nanopores which have recently appeared, namely plasmonic nanopores. The use of plasmonic nanopores to engineer electromagnetic fields around a nanopore sensor allows for enhanced optical spectroscopies, local control over temperature, thermophoresis of molecules and ions to/from the sensor, and trapping of entities. This Mini Review offers a comprehensive understanding of the current state-of-the-art plasmonic nanopores for single-molecule detection and biomolecular sequencing applications and discusses the latest advances and future perspectives on plasmonic nanopore-based technologies.
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Affiliation(s)
- Denis Garoli
- Istituto Italiano di Tecnologia , via Morego 30 , I-16163 , Genova , Italy
| | - Hirohito Yamazaki
- Department of Physics , Northeastern University , 360 Huntington Avenue , Boston , Massachusetts 02115 , United States
| | - Nicolò Maccaferri
- Physics and Materials Science Research Unit , University of Luxembourg , 162a avenue de la Faïencerie , L-1511 Luxembourg , Luxembourg
| | - Meni Wanunu
- Department of Physics , Northeastern University , 360 Huntington Avenue , Boston , Massachusetts 02115 , United States
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45
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Zheng D, Trynda J, Sun Z, Li Z. NUCLIZE for quantifying epigenome: generating histone modification data at single-nucleosome resolution using genuine nucleosome positions. BMC Genomics 2019; 20:541. [PMID: 31266464 PMCID: PMC6604165 DOI: 10.1186/s12864-019-5932-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2019] [Accepted: 06/24/2019] [Indexed: 01/06/2023] Open
Abstract
Background Defining histone modification at single-nucleosome resolution provides accurate epigenomic information in individual nucleosomes. However, most of histone modification data deposited in current databases, such as ENCODE and Roadmap, have low resolution with peaks of several kilo-base pairs (kb), which due to the technical defects of regular ChIP-Seq technology. Results To generate histone modification data at single-nucleosome resolution, we developed a novel approach, NUCLIZE, using synergistic analyses of histone modification data from ChIP-Seq and high-resolution nucleosome mapping data from native MNase-Seq. With this approach, we generated quantitative epigenomics data of single and multivalent histone modification marks in each nucleosome. We found that the dominant trivalent histone mark (H3K4me3/H3K9ac/H3K27ac) and others showed defined and specific patterns near each TSS, indicating potential epigenetic codes regulating gene transcription. Conclusions Single-nucleosome histone modification data render epigenomic data become quantitative, which is essential for investigating dynamic changes of epigenetic regulation in the biological process or for functional epigenomics studies. Thus, NUCLIZE turns current epigenomic mapping studies into genuine functional epigenomics studies with quantitative epigenomic data. Electronic supplementary material The online version of this article (10.1186/s12864-019-5932-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Daoshan Zheng
- Department of Cancer Biology and Mayo Clinic Comprehensive Cancer Center, Mayo Clinic, 4500 San Pablo Road, Griffin 210, Jacksonville, FL, 32224, USA
| | - Justyna Trynda
- Department of Cancer Biology and Mayo Clinic Comprehensive Cancer Center, Mayo Clinic, 4500 San Pablo Road, Griffin 210, Jacksonville, FL, 32224, USA
| | - Zhifu Sun
- Bioinformatics Core and Mayo Clinic Comprehensive Cancer Center, Mayo Clinic, 4500 San Pablo Road, Griffin 210, Jacksonville, FL, 32224, USA
| | - Zhaoyu Li
- Department of Cancer Biology and Mayo Clinic Comprehensive Cancer Center, Mayo Clinic, 4500 San Pablo Road, Griffin 210, Jacksonville, FL, 32224, USA.
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46
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Abstract
Understanding chromatin regulation holds enormous promise for controlling gene regulation, predicting cellular identity, and developing diagnostics and cellular therapies. However, the dynamic nature of chromatin, together with cell-to-cell heterogeneity in its structure, limits our ability to extract its governing principles. Single cell mapping of chromatin modifications, in conjunction with expression measurements, could help overcome these limitations. Here, we review recent advances in single cell-based measurements of chromatin modifications, including optimization to reduce DNA loss, improved DNA sequencing, barcoding, and antibody engineering. We also highlight several applications of these techniques that have provided insights into cell-type classification, mapping modification co-occurrence and heterogeneity, and monitoring chromatin dynamics.
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Affiliation(s)
- Connor H Ludwig
- Department of Bioengineering, Stanford University, Shriram Center, 443 Via Ortega, Rm 042, Stanford, CA 94305, USA
| | - Lacramioara Bintu
- Department of Bioengineering, Stanford University, Shriram Center, 443 Via Ortega, Rm 042, Stanford, CA 94305, USA
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47
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Sneppen K, Ringrose L. Theoretical analysis of Polycomb-Trithorax systems predicts that poised chromatin is bistable and not bivalent. Nat Commun 2019; 10:2133. [PMID: 31086177 PMCID: PMC6513952 DOI: 10.1038/s41467-019-10130-2] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2018] [Accepted: 04/12/2019] [Indexed: 12/15/2022] Open
Abstract
Polycomb (PcG) and Trithorax (TrxG) group proteins give stable epigenetic memory of silent and active gene expression states, but also allow poised states in pluripotent cells. Here we systematically address the relationship between poised, active and silent chromatin, by integrating 73 publications on PcG/TrxG biochemistry into a mathematical model comprising 144 nucleosome modification states and 8 enzymatic reactions. Our model predicts that poised chromatin is bistable and not bivalent. Bivalent chromatin, containing opposing active and silent modifications, is present as an unstable background population in all system states, and different subtypes co-occur with active and silent chromatin. In contrast, bistability, in which the system switches frequently between stable active and silent states, occurs under a wide range of conditions at the transition between monostable active and silent system states. By proposing that bistability and not bivalency is associated with poised chromatin, this work has implications for understanding the molecular nature of pluripotency. Polycomb and Trithorax group proteins regulate silent and active gene expression states, but also allow poised states in pluripotent cells. Here the authors present a mathematical model that integrates data on Polycomb/ Trithorax biochemistry into a single coherent framework which predicts that poised chromatin is not bivalent as previously proposed, but is bistable, meaning that the system switches frequently between stable active and silent states.
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Affiliation(s)
- Kim Sneppen
- Center for Models of Life, Niels Bohr Institute, University of Copenhagen, Blegdamsvej 17, 2100, Copenhagen, Denmark.
| | - Leonie Ringrose
- Integrated Research Institute for Life Sciences, Humboldt-Universität zu Berlin, Philippstrasse 13, Haus 22, 10115, Berlin, Germany.
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48
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49
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Choudhury R, Singh S, Arumugam S, Roguev A, Stewart AF. The Set1 complex is dimeric and acts with Jhd2 demethylation to convey symmetrical H3K4 trimethylation. Genes Dev 2019; 33:550-564. [PMID: 30842216 PMCID: PMC6499330 DOI: 10.1101/gad.322222.118] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2018] [Accepted: 02/15/2019] [Indexed: 12/19/2022]
Abstract
In this study, Choudhury et al. report that yeast Set1C/COMPASS is dimeric and, consequently, symmetrically trimethylates histone 3 Lys4 (H3K4me3) on promoter nucleosomes. This presents a new paradigm for the establishment of epigenetic detail, in which dimeric methyltransferase and monomeric demethylase cooperate to eliminate asymmetry and focus symmetrical H3K4me3 onto selected nucleosomes. Epigenetic modifications can maintain or alter the inherent symmetry of the nucleosome. However, the mechanisms that deposit and/or propagate symmetry or asymmetry are not understood. Here we report that yeast Set1C/COMPASS (complex of proteins associated with Set1) is dimeric and, consequently, symmetrically trimethylates histone 3 Lys4 (H3K4me3) on promoter nucleosomes. Mutation of the dimer interface to make Set1C monomeric abolished H3K4me3 on most promoters. The most active promoters, particularly those involved in the oxidative phase of the yeast metabolic cycle, displayed H3K4me2, which is normally excluded from active promoters, and a subset of these also displayed H3K4me3. In wild-type yeast, deletion of the sole H3K4 demethylase, Jhd2, has no effect. However, in monomeric Set1C yeast, Jhd2 deletion increased H3K4me3 levels on the H3K4me2 promoters. Notably, the association of Set1C with the elongating polymerase was not perturbed by monomerization. These results imply that symmetrical H3K4 methylation is an embedded consequence of Set1C dimerism and that Jhd2 demethylates asymmetric H3K4me3. Consequently, rather than methylation and demethylation acting in opposition as logic would suggest, a dimeric methyltransferase and monomeric demethylase cooperate to eliminate asymmetry and focus symmetrical H3K4me3 onto selected nucleosomes. This presents a new paradigm for the establishment of epigenetic detail.
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Affiliation(s)
- Rupam Choudhury
- Genomics, Biotechnology Center, Center for Molecular and Cellular Bioengineering, University of Technology Dresden, 01307 Dresden, Germany
| | - Sukhdeep Singh
- Genomics, Biotechnology Center, Center for Molecular and Cellular Bioengineering, University of Technology Dresden, 01307 Dresden, Germany
| | - Senthil Arumugam
- European Molecular Biology Laboratory Australia Node for Single Molecule Science, ARC Centre of Excellence in Advanced Molecular Imaging, School of Medical Sciences, University of New South Wales, Sydney 2052, Australia
| | - Assen Roguev
- Genomics, Biotechnology Center, Center for Molecular and Cellular Bioengineering, University of Technology Dresden, 01307 Dresden, Germany.,Department of Cellular and Molecular Pharmacology, University of California at San Francisco, San Francisco, California 94518, USA
| | - A Francis Stewart
- Genomics, Biotechnology Center, Center for Molecular and Cellular Bioengineering, University of Technology Dresden, 01307 Dresden, Germany
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50
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Abstract
The advent of locus-specific protein recruitment technologies has enabled a new class of studies in chromatin biology. Epigenome editors enable biochemical modifications of chromatin at almost any specific endogenous locus. Their locus specificity unlocks unique information including the functional roles of distinct modifications at specific genomic loci. Given the growing interest in using these tools for biological and translational studies, there are many specific design considerations depending on the scientific question or clinical need. Here we present and discuss important design considerations and challenges regarding the biochemical and locus specificities of epigenome editors. These include how to account for the complex biochemical diversity of chromatin; control for potential interdependency of epigenome editors and their resultant modifications; avoid sequestration effects; quantify the locus specificity of epigenome editors; and improve locus specificity by considering concentration, affinity, avidity, and sequestration effects.
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