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Okimune K, Hataya S, Matsumoto K, Ushirogata K, Banko P, Takeda S, Takasuka TE. Histone chaperone-mediated co-expression assembly of tetrasomes and nucleosomes. FEBS Open Bio 2021; 11:2912-2920. [PMID: 34614293 PMCID: PMC8564334 DOI: 10.1002/2211-5463.13311] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2021] [Revised: 09/16/2021] [Accepted: 10/05/2021] [Indexed: 11/07/2022] Open
Abstract
The nucleosome, a basic unit of chromatin found in all eukaryotes, is thought to be assembled through the orchestrated activity of several histone chaperones and chromatin assembly factors in a stepwise manner, proceeding from tetrasome assembly, to H2A/H2B deposition, and finally to formation of the mature nucleosome. In this study, we demonstrate chaperone-mediated assembly of both tetrasomes and nucleosomes on the well-defined Widom 601 positioning sequence using a co-expression/reconstitution wheat germ cell-free system. The purified tetrasomes and nucleosomes were positioned around the center of a given sequence. The heights and diameters were measured by atomic force microscopy. Together with the reported unmodified native histones produced by the wheat germ cell-free platform, our method is expected to be useful for downstream applications in the field of chromatin research.
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Affiliation(s)
- Kei‐ichi Okimune
- Research Faculty of AgricultureHokkaido UniversitySapporoJapan
- Graduate School of Global Food ResourcesHokkaido UniversitySapporoJapan
| | - Shogo Hataya
- Research Faculty of AgricultureHokkaido UniversitySapporoJapan
- Graduate School of Global Food ResourcesHokkaido UniversitySapporoJapan
| | - Kazuki Matsumoto
- Research Faculty of AgricultureHokkaido UniversitySapporoJapan
- Graduate School of Global Food ResourcesHokkaido UniversitySapporoJapan
| | - Kanako Ushirogata
- Graduate School of Global Food ResourcesHokkaido UniversitySapporoJapan
| | - Petra Banko
- Research Faculty of AgricultureHokkaido UniversitySapporoJapan
| | - Seiji Takeda
- Faculty of Pharmaceutical SciencesHokkaido University of ScienceSapporoJapan
| | - Taichi E. Takasuka
- Research Faculty of AgricultureHokkaido UniversitySapporoJapan
- Graduate School of Global Food ResourcesHokkaido UniversitySapporoJapan
- Global Institute for Collaborative Research and EducationHokkaido UniversitySapporoJapan
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2
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Endo Y, Takemori N, Nagy SK, Okimune KI, Kamakaka R, Onouchi H, Takasuka TE. De novo reconstitution of chromatin using wheat germ cell-free protein synthesis. FEBS Open Bio 2021; 11:1552-1564. [PMID: 33960726 PMCID: PMC8167859 DOI: 10.1002/2211-5463.13178] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2021] [Revised: 04/12/2021] [Accepted: 04/21/2021] [Indexed: 01/12/2023] Open
Abstract
DNA is packaged with histones to form chromatin that impinges on all nuclear processes, including transcription, replication and repair, in the eukaryotic nucleus. A complete understanding of these molecular processes requires analysis of chromatin context in vitro. Here, Drosophila four core histones were produced in a native and unmodified form using wheat germ cell‐free protein synthesis. In the assembly reaction, four unpurified core histones and three chromatin assembly factors (dNAP‐1, dAcf1 and dISWI) were incubated with template DNA. We then assessed stoichiometry with the histones, nucleosome arrays, supercoiling and the ability of the chromatin to serve as a substrate for histone‐modifying enzymes. Overall, our method provides a new avenue to produce chromatin that can be useful in a wide range of chromatin research.
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Affiliation(s)
- Yaeta Endo
- Proteo-Science Center, Ehime University, Matsuyama, Japan
| | - Nobuaki Takemori
- Division of Proteomics Research Proteo-Science Center, Ehime University, Toon, Japan
| | - Szilvia K Nagy
- Department of Molecular Biology, Institute of Biochemistry and Molecular Biology, Semmelweis University, Budapest, Hungary.,Research Faculty of Agriculture, Hokkaido University, Sapporo, Japan
| | - Kei-Ichi Okimune
- Research Faculty of Agriculture, Hokkaido University, Sapporo, Japan
| | - Rohinton Kamakaka
- Department of Molecular Cell and Developmental Biology, University of California at Santa Cruz, CA, USA
| | - Hitoshi Onouchi
- Research Faculty of Agriculture, Hokkaido University, Sapporo, Japan
| | - Taichi E Takasuka
- Research Faculty of Agriculture, Hokkaido University, Sapporo, Japan.,Global Institute for Collaborative Research and Education, Hokkaido University, Sapporo, Japan
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3
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Cruz-Becerra G, Kadonaga JT. Reconstitution of Chromatin by Stepwise Salt Dialysis. Bio Protoc 2021; 11:e3977. [PMID: 33889671 DOI: 10.21769/bioprotoc.3977] [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: 10/29/2020] [Revised: 02/05/2021] [Accepted: 02/24/2021] [Indexed: 11/02/2022] Open
Abstract
Chromatin, rather than plain DNA, is the natural substrate of the molecular machines that mediate DNA-directed processes in the nucleus. Chromatin can be reconstituted in vitro by using different methodologies. The salt dialysis method yields chromatin that consists of purified histones and DNA. This biochemically pure chromatin is well-suited for a wide range of applications. Here, we describe simple and straightforward protocols for the reconstitution of chromatin by stepwise salt dialysis and the analysis of the chromatin by the micrococcal nuclease (MNase) digestion assay. Chromatin that is reconstituted with this method can be used for efficient homology-directed repair (HDR)-mediated gene edited with the CRISPR-Cas9 system as well as for biochemical studies of chromatin dynamics and function.
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Affiliation(s)
- Grisel Cruz-Becerra
- Section of Molecular Biology, University of California San Diego, La Jolla, United States
| | - James T Kadonaga
- Section of Molecular Biology, University of California San Diego, La Jolla, United States
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4
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Okimune KI, Nagy SK, Hataya S, Endo Y, Takasuka TE. Reconstitution of Drosophila and human chromatins by wheat germ cell-free co-expression system. BMC Biotechnol 2020; 20:62. [PMID: 33261588 PMCID: PMC7708258 DOI: 10.1186/s12896-020-00655-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2020] [Accepted: 11/10/2020] [Indexed: 01/10/2023] Open
Abstract
BACKGROUND Elaboration of the epigenetic regulation of chromatin is a long-standing aim in molecular and cellular biology. Hence, there is a great demand for the development of in vitro methods to reconstitute chromatin that can be used directly for biochemical assays. The widely used wheat germ cell-free protein expression method provides broad applications to investigate the function and structure of eukaryotic proteins. Such advantages, including high translation efficiency, flexibility, and possible automatization, are beneficial for achieving native-like chromatin substrates for in vitro studies. RESULTS We describe a novel, single-step in vitro chromatin assembly method by using the wheat germ cell-free protein synthesis. We demonstrated that both Drosophila and human chromatins can be reconstituted in the course of the in vitro translation of core histones by the addition of chromatin assembly factors, circular plasmid, and topoisomerase I in an ATP-dependent manner. Drosophila chromatin assembly was performed in 4 h at 26 °C, in the presence of premixed mRNAs encoding the core histones, dAcf1/dISWI chromatin remodeling complex, and nucleosome assembly protein, dNAP1. Similarly, the human chromatin was assembled by co-expressing the human core histones with Drosophila chromatin remodeling factor, dISWI, and chromatin chaperone, dNLP, for 6 h at 26 °C. The presence of reconstituted chromatin was monitored by DNA supercoiling assay, also the regular spacing of nucleosomes was assessed by Micrococcal nuclease assay. Furthermore, Drosophila linker histone H1-containing chromatin was reconstituted, affirming that the in vitro assembled chromatin is suitable for downstream applications. CONCLUSIONS The method described in this study allows the assembly of Drosophila and human chromatins, possibly in native-like form, by using a wheat germ cell-free protein expression. Although both chromatins were reconstituted successfully, there were unexpected differences with respect to the required ratio of histone-coding mRNAs and the reaction time. Overall, our new in vitro chromatin reconstitution method will aid to characterize the unrevealed structure, function, and regulation of chromatin dynamics.
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Affiliation(s)
- Kei-Ichi Okimune
- Research Faculty of Agriculture, Hokkaido University, Sapporo, Japan.,Graduate School of Global Food Resources, Hokkaido University, Sapporo, Japan
| | - Szilvia K Nagy
- Research Faculty of Agriculture, Hokkaido University, Sapporo, Japan.,Department of Molecular Biology, Institute of Biochemistry and Molecular Biology, Semmelweis University, Budapest, Hungary
| | - Shogo Hataya
- Research Faculty of Agriculture, Hokkaido University, Sapporo, Japan
| | - Yaeta Endo
- Proteo-Science Center of Ehime University, Matsuyama, Japan
| | - Taichi E Takasuka
- Research Faculty of Agriculture, Hokkaido University, Sapporo, Japan. .,Graduate School of Global Food Resources, Hokkaido University, Sapporo, Japan. .,GI-CORE, Hokkaido University, Sapporo, 060-8589, Japan.
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Cruz-Becerra G, Kadonaga JT. Enhancement of homology-directed repair with chromatin donor templates in cells. eLife 2020; 9:55780. [PMID: 32343230 PMCID: PMC7244325 DOI: 10.7554/elife.55780] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2020] [Accepted: 04/28/2020] [Indexed: 12/16/2022] Open
Abstract
A key challenge in precise genome editing is the low efficiency of homology-directed repair (HDR). Here we describe a strategy for increasing the efficiency of HDR in cells by using a chromatin donor template instead of a naked DNA donor template. The use of chromatin, which is the natural form of DNA in the nucleus, increases the frequency of HDR-edited clones as well as homozygous editing. In addition, transfection of chromatin results in negligible cytotoxicity. These findings suggest that a chromatin donor template should be useful for a wide range of HDR applications such as the precise insertion or replacement of DNA fragments that contain the coding regions of genes. Genome editing is a powerful tool used across a wide range of biomedical research. There are several different techniques used, depending on the type of edit being made, and one known as homology-directed repair – or HDR for short – is a common technique for precisely inserting large sections of DNA, such as those needed to make desired proteins in cells. HDR takes advantage of the cell’s mechanisms for repairing damage to DNA if both strands of the DNA double helix are broken. The mechanism relies on a DNA template to stitch the strands back together. To insert or replace a new DNA sequence, scientists can add a customized piece of DNA of their choosing to the cell so that it might be incorporated into the genome. However, HDR is not very efficient, and the success rate is often less than a few percent. In HDR gene editing, the DNA template is typically added as purified, or ‘naked’, DNA. However, the natural form of DNA in cells, known as chromatin, is where the DNA helix is wrapped around a cluster of proteins known as histones. Cruz-Becerra and Kadonaga tested the idea that DNA in the form of chromatin might be more effective as a template for HDR than naked DNA. The two approaches were compared to see which was better at inserting a sequence at three different locations in the genome of lab-grown human cells. In these experiments, the chromatin templates were 2.3- to 7.4-fold more efficient than the naked DNA. Also, the DNA in human cells is organized as pairs of chromosomes, and chromatin was better than naked DNA for editing both copies of the chromosome pairs rather than only one of them. In addition, the chromatin is potentially less toxic to the cells. Cruz-Becerra and Kadonaga hope that this will be useful for increasing the success rate of HDR experiments and potentially other methods of gene editing in the future.
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Affiliation(s)
- Grisel Cruz-Becerra
- Section of Molecular Biology, University of California, San Diego, La Jolla, United States
| | - James T Kadonaga
- Section of Molecular Biology, University of California, San Diego, La Jolla, United States
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6
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Histone H2A isoforms: Potential implications in epigenome plasticity and diseases in eukaryotes. J Biosci 2020. [DOI: 10.1007/s12038-019-9985-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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7
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Shah S, Verma T, Rashid M, Gadewal N, Gupta S. Histone H2A isoforms: Potential implications in epigenome plasticity and diseases in eukaryotes. J Biosci 2020; 45:4. [PMID: 31965982] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Epigenetic mechanisms including the post-translational modifications of histones, incorporation of histone variants and DNA methylation have been suggested to play an important role in genome plasticity by allowing the cellular environment to define gene expression and the phenotype of an organism. Studies over the past decade have elucidated how these epigenetic mechanisms are significant in orchestrating various biological processes and contribute to different pathophysiological states. However, the role of histone isoforms and their impact on different phenotypes and physiological processes associated with diseases are not fully clear. This review is focussed on the recent advances in our understanding of the complexity of eukaryotic H2A isoforms and their roles in defining nucleosome organization. We elaborate on their potential roles in genomic complexity and regulation of gene expression, and thereby on their overall contribution towards cellular phenotype and development of diseases.
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Affiliation(s)
- Sanket Shah
- Epigenetics and Chromatin Biology Group, Caner Research Institute, Advanced Centre for Treatment, Research and Education in Cancer, Tata Memorial Centre, Kharghar, Navi Mumbai 410 210, India
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Chavez C, Cruz-Becerra G, Fei J, Kassavetis GA, Kadonaga JT. The tardigrade damage suppressor protein binds to nucleosomes and protects DNA from hydroxyl radicals. eLife 2019; 8:47682. [PMID: 31571581 PMCID: PMC6773438 DOI: 10.7554/elife.47682] [Citation(s) in RCA: 49] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2019] [Accepted: 08/29/2019] [Indexed: 12/21/2022] Open
Abstract
Tardigrades, also known as water bears, are animals that can survive extreme conditions. The tardigrade Ramazzottius varieornatus contains a unique nuclear protein termed Dsup, for damage suppressor, which can increase the resistance of human cells to DNA damage under conditions, such as ionizing radiation or hydrogen peroxide treatment, that generate hydroxyl radicals. Here we find that R. varieornatus Dsup is a nucleosome-binding protein that protects chromatin from hydroxyl radicals. Moreover, a Dsup ortholog from the tardigrade Hypsibius exemplaris similarly binds to nucleosomes and protects DNA from hydroxyl radicals. Strikingly, a conserved region in Dsup proteins exhibits sequence similarity to the nucleosome-binding domain of vertebrate HMGN proteins and is functionally important for nucleosome binding and hydroxyl radical protection. These findings suggest that Dsup promotes the survival of tardigrades under diverse conditions by a direct mechanism that involves binding to nucleosomes and protecting chromosomal DNA from hydroxyl radicals. Tardigrades, also known as water bears and moss piglets, are small animals found in many different environments on land and sea. These animals have the remarkable ability to survive extremes including very low temperatures, high levels of radiation and exposure to chemicals that are harmful to other forms of life. Tardigrades have even been found to survive the harsh conditions of outer space. X-rays are a type of radiation naturally produced by lightning strikes and are also found in cosmic rays from outer space. High doses of X-rays can cause genetic mutations that may lead to serious illness or death. This is because when X-rays come into contact with water they split the water molecules to make particles known as hydroxyl radicals, which in turn damage the DNA inside cells. The genomes of animals and plants are made of DNA, which is packaged into a structure called chromatin. Previous studies identified a protein named Dsup in a tardigrade called Ramazzottius varieornatus that can protect human cells from damage by X-rays. However, it was not known whether Dsup binds directly to chromatin or plays a more indirect role in protecting DNA. Chavez, Cruz-Becerra, Fei, Kassavetis et al. used biochemical approaches to study Dsup. Their experiments revealed that Dsup from R. varieornatus binds to chromatin to protect the DNA from damage by hydroxyl radicals, and that the Dsup protein in another tardigrade species also works in a similar way. Further analysis showed that a region of Dsup that is needed to bind to chromatin is very similar to a region that had been previously found only in chromatin-binding proteins from humans and other vertebrates (animals with backbones). This connection between Dsup and vertebrate chromatin-binding proteins remains a mystery. The new findings about tardigrade Dsup may help researchers develop animal cells that live longer under normal or extreme environmental conditions. In this manner, Dsup could be used to expand the range of applications of cells in biotechnology. It could also increase the effectiveness of current methods, such as the production of some pharmaceuticals, that depend upon the use of cultured cells.
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Affiliation(s)
- Carolina Chavez
- Section of Molecular Biology, University of California, San Diego, San Diego, United States
| | - Grisel Cruz-Becerra
- Section of Molecular Biology, University of California, San Diego, San Diego, United States
| | - Jia Fei
- Section of Molecular Biology, University of California, San Diego, San Diego, United States
| | - George A Kassavetis
- Section of Molecular Biology, University of California, San Diego, San Diego, United States
| | - James T Kadonaga
- Section of Molecular Biology, University of California, San Diego, San Diego, United States
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9
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The transformation of the DNA template in RNA polymerase II transcription: a historical perspective. Nat Struct Mol Biol 2019; 26:766-770. [PMID: 31439939 DOI: 10.1038/s41594-019-0278-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2019] [Accepted: 07/10/2019] [Indexed: 11/08/2022]
Abstract
The discovery of RNA polymerases I, II, and III opened up a new era in gene expression. Here I provide a personal retrospective account of the transformation of the DNA template, as it evolved from naked DNA to chromatin, in the biochemical analysis of transcription by RNA polymerase II. These studies have revealed new insights into the mechanisms by which transcription factors function with chromatin to regulate gene expression.
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10
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Gottesfeld JM. Milestones in transcription and chromatin published in the Journal of Biological Chemistry. J Biol Chem 2019; 294:1652-1660. [PMID: 30710013 DOI: 10.1074/jbc.tm118.004162] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
During Herbert Tabor's tenure as Editor-in-Chief from 1971 to 2010, JBC has published many seminal papers in the fields of chromatin structure, epigenetics, and regulation of transcription in eukaryotes. As of this writing, more than 21,000 studies on gene transcription at the molecular level have been published in JBC since 1971. This brief review will attempt to highlight some of these ground-breaking discoveries and show how early studies published in JBC have influenced current research. Papers published in the Journal have reported the initial discovery of multiple forms of RNA polymerase in eukaryotes, identification and purification of essential components of the transcription machinery, and identification and mechanistic characterization of various transcriptional activators and repressors and include studies on chromatin structure and post-translational modifications of the histone proteins. The large body of literature published in the Journal has inspired current research on how chromatin organization and epigenetics impact regulation of gene expression.
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Affiliation(s)
- Joel M Gottesfeld
- Departments of Molecular Medicine and Chemistry, The Scripps Research Institute, La Jolla, California 92037.
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11
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Il’ina IA, Konev AY. The role of aTp-dependent chromatin remodeling factors in chromatin assembly in vivo. Vavilovskii Zhurnal Genet Selektsii 2019. [DOI: 10.18699/vj19.476] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Chromatin assembly is a fundamental process essential for chromosome duplication subsequent to DNA replication. In addition, histone removal and incorporation take place constantly throughout the cell cycle in the course of DNA-utilizing processes, such as transcription, damage repair or recombination. In vitro studies have revealed that nucleosome assembly relies on the combined action of core histone chaperones and ATP-utilizing molecular motor proteins such as ACF or CHD1. Despite extensive biochemical characterization of ATP-dependent chromatin assembly and remodeling factors, it has remained unclear to what extent nucleosome assembly is an ATP-dependent process in vivo. Our original and published data about the functions of ATP-dependent chromatin assembly and remodeling factors clearly demonstrated that these proteins are important for nucleosome assembly and histone exchange in vivo. During male pronucleus reorganization after fertilization CHD1 has a critical role in the genomescale, replication-independent nucleosome assembly involving the histone variant H3.3. Thus, the molecular motor proteins, such as CHD1, function not only in the remodeling of existing nucleosomes but also in de novo nucleosome assembly from DNA and histones in vivo. ATP-dependent chromatin assembly and remodeling factors have been implicated in the process of histone exchange during transcription and DNA repair, in the maintenance of centromeric chromatin and in the loading and remodeling of nucleosomes behind a replication fork. Thus, chromatin remodeling factors are involved in the processes of both replication-dependent and replication-independent chromatin assembly. The role of these proteins is especially prominent in the processes of large-scale chromatin reorganization; for example, during male pronucleus formation or in DNA repair. Together, ATP-dependent chromatin assembly factors, histone chaperones and chromatin modifying enzymes form a “chromatin integrity network” to ensure proper maintenance and propagation of chromatin landscape.
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Affiliation(s)
- Iu. A. Il’ina
- Petersburg Nuclear Physics Institute named by B.P. Konstantinov of National Research Centre “Kurchatov Institute”
| | - A. Yu. Konev
- Petersburg Nuclear Physics Institute named by B.P. Konstantinov of National Research Centre “Kurchatov Institute”
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12
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Tekel SJ, Barrett C, Vargas D, Haynes KA. Design, Construction, and Validation of Histone-Binding Effectors in Vitro and in Cells. Biochemistry 2018; 57:4707-4716. [PMID: 29791133 DOI: 10.1021/acs.biochem.8b00327] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Chromatin is a system of nuclear proteins and nucleic acids that plays a pivotal role in gene expression and cell behavior and is therefore the subject of intense study for cell development and cancer research. Biochemistry, crystallography, and reverse genetics have elucidated the macromolecular interactions that drive chromatin regulation. One of the central mechanisms is the recognition of post-translational modifications (PTMs) on histone proteins by a family of nuclear proteins known as "readers". This knowledge has launched a wave of activity around the rational design of proteins that interact with histone PTMs. Useful molecular tools have emerged from this work, enabling researchers to probe and manipulate chromatin states in live cells. Chromatin-based proteins represent a vast design space that remains underexplored. Therefore, we have developed a rapid prototyping platform to identify engineered fusion proteins that bind histone PTMs in vitro and regulate genes near the same histone PTMs in living cells. We have used our system to build gene activators with strong avidity for the gene silencing-associated histone PTM H3K27me3. Here, we describe procedures and data for cell-free production of fluorescently tagged fusion proteins, enzyme-linked immunosorbent assay-based measurement of histone PTM binding, and a live cell assay to demonstrate that the fusion proteins modulate transcriptional activation at a site that carries the target histone PTM. This pipeline will be useful for synthetic biologists who are interested in designing novel histone PTM-binding actuators and probes.
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Affiliation(s)
- Stefan J Tekel
- School of Biological and Health Systems Engineering , Arizona State University , Tempe , Arizona 85287 , United States
| | - Cassandra Barrett
- School of Biological and Health Systems Engineering , Arizona State University , Tempe , Arizona 85287 , United States
| | - Daniel Vargas
- School of Biological and Health Systems Engineering , Arizona State University , Tempe , Arizona 85287 , United States
| | - Karmella A Haynes
- School of Biological and Health Systems Engineering , Arizona State University , Tempe , Arizona 85287 , United States
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13
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Fei J, Ishii H, Hoeksema MA, Meitinger F, Kassavetis GA, Glass CK, Ren B, Kadonaga JT. NDF, a nucleosome-destabilizing factor that facilitates transcription through nucleosomes. Genes Dev 2018; 32:682-694. [PMID: 29759984 PMCID: PMC6004073 DOI: 10.1101/gad.313973.118] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2018] [Accepted: 04/11/2018] [Indexed: 12/22/2022]
Abstract
Our understanding of transcription by RNA polymerase II (Pol II) is limited by our knowledge of the factors that mediate this critically important process. Here we describe the identification of NDF, a nucleosome-destabilizing factor that facilitates Pol II transcription in chromatin. NDF has a PWWP motif, interacts with nucleosomes near the dyad, destabilizes nucleosomes in an ATP-independent manner, and facilitates transcription by Pol II through nucleosomes in a purified and defined transcription system as well as in cell nuclei. Upon transcriptional induction, NDF is recruited to the transcribed regions of thousands of genes and colocalizes with a subset of H3K36me3-enriched regions. Notably, the recruitment of NDF to gene bodies is accompanied by an increase in the transcript levels of many of the NDF-enriched genes. In addition, the global loss of NDF results in a decrease in the RNA levels of many genes. In humans, NDF is present at high levels in all tested tissue types, is essential in stem cells, and is frequently overexpressed in breast cancer. These findings indicate that NDF is a nucleosome-destabilizing factor that is recruited to gene bodies during transcriptional activation and facilitates Pol II transcription through nucleosomes.
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Affiliation(s)
- Jia Fei
- Section of Molecular Biology, University of California at San Diego, La Jolla, California 92093, USA
| | - Haruhiko Ishii
- Ludwig Institute for Cancer Research, San Diego Branch, La Jolla, California 92093, USA
| | - Marten A Hoeksema
- Department of Cellular and Molecular Medicine, University of California at San Diego, La Jolla, California 92093, USA
- Department of Medicine, University of California at San Diego, La Jolla, California 92093, USA
| | - Franz Meitinger
- Ludwig Institute for Cancer Research, San Diego Branch, La Jolla, California 92093, USA
| | - George A Kassavetis
- Section of Molecular Biology, University of California at San Diego, La Jolla, California 92093, USA
| | - Christopher K Glass
- Department of Cellular and Molecular Medicine, University of California at San Diego, La Jolla, California 92093, USA
- Department of Medicine, University of California at San Diego, La Jolla, California 92093, USA
| | - Bing Ren
- Ludwig Institute for Cancer Research, San Diego Branch, La Jolla, California 92093, USA
- Department of Cellular and Molecular Medicine, University of California at San Diego, La Jolla, California 92093, USA
- Center for Epigenomics, Institute of Genome Medicine, Moores Cancer Center, University of California at San Diego, La Jolla, California 92093, USA
| | - James T Kadonaga
- Section of Molecular Biology, University of California at San Diego, La Jolla, California 92093, USA
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