601
|
Hajheidari M, Koncz C, Bucher M. Chromatin Evolution-Key Innovations Underpinning Morphological Complexity. FRONTIERS IN PLANT SCIENCE 2019; 10:454. [PMID: 31031789 PMCID: PMC6474313 DOI: 10.3389/fpls.2019.00454] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/10/2019] [Accepted: 03/26/2019] [Indexed: 05/20/2023]
Abstract
The history of life consists of a series of major evolutionary transitions, including emergence and radiation of complex multicellular eukaryotes from unicellular ancestors. The cells of multicellular organisms, with few exceptions, contain the same genome, however, their organs are composed of a variety of cell types that differ in both structure and function. This variation is largely due to the transcriptional activity of different sets of genes in different cell types. This indicates that complex transcriptional regulation played a key role in the evolution of complexity in eukaryotes. In this review, we summarize how gene duplication and subsequent evolutionary innovations, including the structural evolution of nucleosomes and chromatin-related factors, contributed to the complexity of the transcriptional system and provided a basis for morphological diversity.
Collapse
Affiliation(s)
- Mohsen Hajheidari
- Botanical Institute, Cologne Biocenter, Cluster of Excellence on Plant Sciences, University of Cologne, Cologne, Germany
| | - Csaba Koncz
- Department of Plant Developmental Biology, Max Planck Institute for Plant Breeding Research, Cologne, Germany
- Biological Research Center, Institute of Plant Biology, Hungarian Academy of Sciences, Szeged, Hungary
| | - Marcel Bucher
- Botanical Institute, Cologne Biocenter, Cluster of Excellence on Plant Sciences, University of Cologne, Cologne, Germany
| |
Collapse
|
602
|
Kweon SM, Chen Y, Moon E, Kvederaviciutė K, Klimasauskas S, Feldman DE. An Adversarial DNA N 6-Methyladenine-Sensor Network Preserves Polycomb Silencing. Mol Cell 2019; 74:1138-1147.e6. [PMID: 30982744 PMCID: PMC6591016 DOI: 10.1016/j.molcel.2019.03.018] [Citation(s) in RCA: 99] [Impact Index Per Article: 19.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2018] [Revised: 11/12/2018] [Accepted: 03/18/2019] [Indexed: 02/07/2023]
Abstract
Adenine N6 methylation in DNA (6mA) is widespread among bacteria and phage and is detected in mammalian genomes, where its function is largely unexplored. Here we show that 6mA deposition and removal are catalyzed by the Mettl4 methyltransferase and Alkbh4 dioxygenase, respectively, and that 6mA accumulation in genic elements corresponds with transcriptional silencing. Inactivation of murine Mettl4 depletes 6mA and causes sublethality and craniofacial dysmorphism in incross progeny. We identify distinct 6mA sensor domains of prokaryotic origin within the MPND deubiquitinase and ASXL1, a component of the Polycomb repressive deubiquitinase (PR-DUB) complex, both of which act to remove monoubiquitin from histone H2A (H2A-K119Ub), a repressive mark. Deposition of 6mA by Mettl4 triggers the proteolytic destruction of both sensor proteins, preserving genome-wide H2A-K119Ub levels. Expression of the bacterial 6mA methyltransferase Dam, in contrast, fails to destroy either sensor. These findings uncover a native, adversarial 6mA network architecture that preserves Polycomb silencing. 6mA deposition and erasure by mammalian Mettl4 and Alkbh4, respectively Mettl4-deficient mice display craniofacial dysmorphism 6mA triggers proteolysis of its cognate sensor proteins ASXL1 and MPND Adversarial 6mA network architecture preserves Polycomb silencing
Collapse
Affiliation(s)
- Soo-Mi Kweon
- Department of Pathology, Keck School of Medicine of USC, Los Angeles, CA 90033, USA
| | - Yibu Chen
- Bioinformatics Service, Department of Health Sciences Libraries, Keck School of Medicine of USC, Los Angeles, CA 90033, USA
| | - Eugene Moon
- Department of Pathology, Keck School of Medicine of USC, Los Angeles, CA 90033, USA
| | - Kotryna Kvederaviciutė
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius LT-10257, Lithuania
| | - Saulius Klimasauskas
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius LT-10257, Lithuania
| | - Douglas E Feldman
- Department of Pathology, Keck School of Medicine of USC, Los Angeles, CA 90033, USA.
| |
Collapse
|
603
|
Shields EJ, Petracovici AF, Bonasio R. lncRedibly versatile: biochemical and biological functions of long noncoding RNAs. Biochem J 2019; 476:1083-1104. [PMID: 30971458 PMCID: PMC6745715 DOI: 10.1042/bcj20180440] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2018] [Revised: 02/28/2019] [Accepted: 03/19/2019] [Indexed: 02/07/2023]
Abstract
Long noncoding RNAs (lncRNAs) are transcripts that do not code for proteins, but nevertheless exert regulatory effects on various biochemical pathways, in part via interactions with proteins, DNA, and other RNAs. LncRNAs are thought to regulate transcription and other biological processes by acting, for example, as guides that target proteins to chromatin, scaffolds that facilitate protein-protein interactions and complex formation, and orchestrators of phase-separated compartments. The study of lncRNAs has reached an exciting time, as recent advances in experimental and computational methods allow for genome-wide interrogation of biochemical and biological mechanisms of these enigmatic transcripts. A better appreciation for the biochemical versatility of lncRNAs has allowed us to begin closing gaps in our knowledge of how they act in diverse cellular and organismal contexts, including development and disease.
Collapse
Affiliation(s)
- Emily J Shields
- Epigenetics Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, U.S.A
- Graduate Group in Genomics and Computational Biology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, U.S.A
| | - Ana F Petracovici
- Epigenetics Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, U.S.A
- Graduate Group in Genetics and Epigenetics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, U.S.A
| | - Roberto Bonasio
- Epigenetics Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, U.S.A.
- Department of Cell and Developmental Biology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, U.S.A
| |
Collapse
|
604
|
Over-expression of Hsp83 in grossly depleted hsrω lncRNA background causes synthetic lethality and l(2)gl phenocopy in Drosophila. J Biosci 2019. [DOI: 10.1007/s12038-019-9852-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
|
605
|
Brand M, Nakka K, Zhu J, Dilworth FJ. Polycomb/Trithorax Antagonism: Cellular Memory in Stem Cell Fate and Function. Cell Stem Cell 2019; 24:518-533. [PMID: 30951661 PMCID: PMC6866673 DOI: 10.1016/j.stem.2019.03.005] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Stem cells are continuously challenged with the decision to either self-renew or adopt a new fate. Self-renewal is regulated by a system of cellular memory, which must be bypassed for differentiation. Previous studies have identified Polycomb group (PcG) and Trithorax group (TrxG) proteins as key modulators of cellular memory. In this Perspective, we draw from embryonic and adult stem cell studies to discuss the complex roles played by PcG and TrxG in maintaining cell identity while allowing for microenvironment-mediated alterations in cell fate. Finally, we discuss the potential for targeting these proteins as a therapeutic approach in cancer.
Collapse
Affiliation(s)
- Marjorie Brand
- Sprott Center for Stem Cell Research, Ottawa Hospital Research Institute, Ottawa, ON, Canada K1H 8L6; Department of Cellular and Molecular Medicine, University of Ottawa, Ottawa, ON, Canada K1H 8L6.
| | - Kiran Nakka
- Sprott Center for Stem Cell Research, Ottawa Hospital Research Institute, Ottawa, ON, Canada K1H 8L6; Department of Cellular and Molecular Medicine, University of Ottawa, Ottawa, ON, Canada K1H 8L6
| | - Jiayu Zhu
- Sprott Center for Stem Cell Research, Ottawa Hospital Research Institute, Ottawa, ON, Canada K1H 8L6; Department of Cellular and Molecular Medicine, University of Ottawa, Ottawa, ON, Canada K1H 8L6
| | - F Jeffrey Dilworth
- Sprott Center for Stem Cell Research, Ottawa Hospital Research Institute, Ottawa, ON, Canada K1H 8L6; Department of Cellular and Molecular Medicine, University of Ottawa, Ottawa, ON, Canada K1H 8L6.
| |
Collapse
|
606
|
Laugesen A, Højfeldt JW, Helin K. Molecular Mechanisms Directing PRC2 Recruitment and H3K27 Methylation. Mol Cell 2019; 74:8-18. [PMID: 30951652 PMCID: PMC6452890 DOI: 10.1016/j.molcel.2019.03.011] [Citation(s) in RCA: 354] [Impact Index Per Article: 70.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2018] [Revised: 02/12/2019] [Accepted: 03/05/2019] [Indexed: 02/07/2023]
Abstract
The polycomb repressive complex 2 (PRC2) is a chromatin-associated methyltransferase catalyzing mono-, di-, and trimethylation of lysine 27 on histone H3 (H3K27). This activity is required for normal organismal development and maintenance of gene expression patterns to uphold cell identity. PRC2 function is often deregulated in disease and is a promising candidate for therapeutic targeting in cancer. In this review, we discuss the molecular mechanisms proposed to take part in modulating PRC2 recruitment and shaping H3K27 methylation patterns across the genome. This includes consideration of factors influencing PRC2 residence time on chromatin and PRC2 catalytic activity with a focus on the mechanisms giving rise to regional preferences and differential deposition of H3K27 methylation. We further discuss existing evidence for functional diversity between distinct subsets of PRC2 complexes with the aim of extracting key concepts and highlighting major open questions toward a more complete understanding of PRC2 function.
Collapse
Affiliation(s)
- Anne Laugesen
- Biotech Research and Innovation Centre (BRIC), University of Copenhagen, Ole Maaløes Vej 5, DK-2200 Copenhagen N, Denmark; The Novo Nordisk Foundation Center for Stem Cell Biology (DanStem), University of Copenhagen, Blegdamsvej 3, DK-2200 Copenhagen N, Denmark
| | - Jonas Westergaard Højfeldt
- Biotech Research and Innovation Centre (BRIC), University of Copenhagen, Ole Maaløes Vej 5, DK-2200 Copenhagen N, Denmark; The Novo Nordisk Foundation Center for Stem Cell Biology (DanStem), University of Copenhagen, Blegdamsvej 3, DK-2200 Copenhagen N, Denmark
| | - Kristian Helin
- Biotech Research and Innovation Centre (BRIC), University of Copenhagen, Ole Maaløes Vej 5, DK-2200 Copenhagen N, Denmark; The Novo Nordisk Foundation Center for Stem Cell Biology (DanStem), University of Copenhagen, Blegdamsvej 3, DK-2200 Copenhagen N, Denmark; Cell Biology Program and Center for Epigenetics Research, Memorial Sloan Kettering Cancer Center (MSKCC), 1275 York Avenue, New York, NY 10065, USA.
| |
Collapse
|
607
|
Zhang Y, Koppula P, Gan B. Regulation of H2A ubiquitination and SLC7A11 expression by BAP1 and PRC1. Cell Cycle 2019; 18:773-783. [PMID: 30907299 DOI: 10.1080/15384101.2019.1597506] [Citation(s) in RCA: 82] [Impact Index Per Article: 16.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
SLC7A11 (or xCT) imports extracellular cystine into cells to promote glutathione synthesis, thus inhibiting ferroptosis. SLC7A11 expression is tightly controlled in normal cells and its dysregulation results in aberrant expression of SLC7A11 in human cancers. We recently discovered that tumor suppressor BAP1, a H2A deubiquitinase, represses SLC7A11 expression by reducing H2A ubiquitination (H2Aub) on the SLC7A11 promoter. BAP1 inactivation in cancer cells leads to SLC7A11 de-repression, ferroptosis resistance, and tumor development. Here we show that BAP1 promotes ferroptosis induced by class I ferroptosis inducer (FIN) erastin but not by class II FIN RSL3, further supporting that BAP1 regulates ferroptosis through SLC7A11. In addition, we studied how BAP1 coordinates with other transcription factors to regulate SLC7A11 expression and show that BAP1-mediated SLC7A11 repression does not require NRF2 and ATF4 transcription factors. Finally, we show that, while BAP1 decreases whereas PRC1 (a major H2Aub ubiquitin ligase) increases H2Aub binding on the SLC7A11 promoter, both BAP1 and PRC1 represses SLC7A11 expression, suggesting that a dynamic regulation of H2Aub is important for SLC7A11 repression. Together, our data provide additional insights on epigenetic regulation of SLC7A11 expression in cancer cells.
Collapse
Affiliation(s)
- Yilei Zhang
- a Department of Experimental Radiation Oncology , the University of Texas MD Anderson Cancer Center , Houston , TX , USA
| | - Pranavi Koppula
- a Department of Experimental Radiation Oncology , the University of Texas MD Anderson Cancer Center , Houston , TX , USA.,b Department of Experimental Radiation Oncology , The University of Texas MD Anderson UTHealth Graduate School of Biomedical Sciences , Houston , TX , USA
| | - Boyi Gan
- a Department of Experimental Radiation Oncology , the University of Texas MD Anderson Cancer Center , Houston , TX , USA.,b Department of Experimental Radiation Oncology , The University of Texas MD Anderson UTHealth Graduate School of Biomedical Sciences , Houston , TX , USA
| |
Collapse
|
608
|
Nava M, Dutta P, Farias-Eisner R, Vadgama JV, Wu Y. Utilization of NGS technologies to investigate transcriptomic and epigenomic mechanisms in trastuzumab resistance. Sci Rep 2019; 9:5141. [PMID: 30914750 PMCID: PMC6435657 DOI: 10.1038/s41598-019-41672-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2018] [Accepted: 03/08/2019] [Indexed: 12/14/2022] Open
Abstract
NGS (Next Generation Sequencing) technologies allows us to determine key gene expression signatures that correlate with resistance (and responsiveness) to anti-cancer therapeutics. We have undertaken a transcriptomic and chromatin immunoprecipitation followed by sequencing (ChIP-seq) approach to describe differences in gene expression and the underlying chromatin landscape between two representative HER2+ cell lines, one of which is sensitive (SKBR3) and the other which is resistant (JIMT1) to trastuzumab. We identified differentially expressed genes (DEGs) and differentially expressed transcripts (DETs) between SKBR3 and JIMT1 cells. Several of the DEGs are components of the Polycomb Repressing Complex 2 (PRC2), and they are expressed higher in JIMT1 cells. In addition, we utilized ChIP-seq to identify H3K18ac, H3K27ac and H3K27me3 histone modifications genome-wide. We identified key differences of H3K18ac and H3K27ac enrichment in regulatory regions, found a correlation between these modifications and differential gene expression and identified a transcription factor binding motif for LRF near these modifications in both cell lines. Lastly, we found a small subset of genes that contain repressive H3K27me3 marks near the gene body in SKBR3 cells but are absent in JIMT1. Taken together, our data suggests that differential gene expression and trastuzumab responsiveness in JIMT1 and SKBR3 is determined by epigenetic mechanisms.
Collapse
Affiliation(s)
- Miguel Nava
- Division of Cancer Research and Training, Department of Medicine, Charles R. Drew University of Medicine and Science, Los Angeles, USA
- Jonsson Comprehensive Cancer Center, David Geffen School of Medicine, University of California at Los Angeles, Los Angeles, CA, USA
| | - Pranabananda Dutta
- Division of Cancer Research and Training, Department of Medicine, Charles R. Drew University of Medicine and Science, Los Angeles, USA
| | - Robin Farias-Eisner
- Jonsson Comprehensive Cancer Center, David Geffen School of Medicine, University of California at Los Angeles, Los Angeles, CA, USA
| | - Jaydutt V Vadgama
- Division of Cancer Research and Training, Department of Medicine, Charles R. Drew University of Medicine and Science, Los Angeles, USA.
- Jonsson Comprehensive Cancer Center, David Geffen School of Medicine, University of California at Los Angeles, Los Angeles, CA, USA.
| | - Yanyuan Wu
- Division of Cancer Research and Training, Department of Medicine, Charles R. Drew University of Medicine and Science, Los Angeles, USA.
- Jonsson Comprehensive Cancer Center, David Geffen School of Medicine, University of California at Los Angeles, Los Angeles, CA, USA.
| |
Collapse
|
609
|
Fukushima HS, Takeda H, Nakamura R. Targeted in vivo epigenome editing of H3K27me3. Epigenetics Chromatin 2019; 12:17. [PMID: 30871638 PMCID: PMC6419334 DOI: 10.1186/s13072-019-0263-z] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2018] [Accepted: 03/07/2019] [Indexed: 01/10/2023] Open
Abstract
BACKGROUND Epigenetic modifications have a central role in transcriptional regulation. While several studies using next-generation sequencing have revealed genome-wide associations between epigenetic modifications and transcriptional states, a direct causal relationship at specific genomic loci has not been fully demonstrated, due to a lack of technology for targeted manipulation of epigenetic modifications. Recently, epigenome editing techniques based on the CRISPR-Cas9 system have been reported to directly manipulate specific modifications at precise genomic regions. However, the number of editable modifications as well as studies applying these techniques in vivo is still limited. RESULTS Here, we report direct modification of the epigenome in medaka (Japanese killifish, Oryzias latipes) embryos. Specifically, we developed a method to ectopically induce the repressive histone modification, H3K27me3 in a locus-specific manner, using a fusion construct of Oryzias latipes H3K27 methyltransferase Ezh2 (olEzh2) and dCas9 (dCas9-olEzh2). Co-injection of dCas9-olEzh2 mRNA with single guide RNAs (sgRNAs) into one-cell-stage embryos induced specific H3K27me3 accumulation at the targeted loci and induced downregulation of gene expression. CONCLUSION In this study, we established the in vivo epigenome editing of H3K27me3 using medaka embryos. The locus-specific manipulation of the epigenome in living organisms will lead to a previously inaccessible understanding of the role of epigenetic modifications in development and disease.
Collapse
Affiliation(s)
- Hiroto S. Fukushima
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Hongo 7-3-1, Bunkyo-ku, Tokyo 113-0033 Japan
| | - Hiroyuki Takeda
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Hongo 7-3-1, Bunkyo-ku, Tokyo 113-0033 Japan
| | - Ryohei Nakamura
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Hongo 7-3-1, Bunkyo-ku, Tokyo 113-0033 Japan
| |
Collapse
|
610
|
Abstract
Epigenetic gene regulation ensures the mitotically or meiotically stable heritability (or both) of gene expression or protein activity states and maintains repetitive element repression and cellular identities. The repressive Polycomb-group (PcG) proteins consist of several large complexes that control cellular memory by acting on chromatin and are antagonized by the Trithorax-group proteins. Especially, Polycomb repressive complex 2 (PRC2) is highly conserved in plants and animals but its function in unicellular eukaryotes and during land plant evolution is less understood. Additional PcG complexes and associated proteins are only partially conserved and have evolved in a lineage-specific manner. In this review, I will focus on recent advances in the understanding of PcG function in the green lineage and its contribution to land plant evolution.
Collapse
Affiliation(s)
- Daniel Schubert
- Department of Biology, Epigenetics of Plants, Freie Universität Berlin, Berlin, Germany
| |
Collapse
|
611
|
Zhang Q, McKenzie NJ, Warneford-Thomson R, Gail EH, Flanigan SF, Owen BM, Lauman R, Levina V, Garcia BA, Schittenhelm RB, Bonasio R, Davidovich C. RNA exploits an exposed regulatory site to inhibit the enzymatic activity of PRC2. Nat Struct Mol Biol 2019; 26:237-247. [PMID: 30833789 DOI: 10.1038/s41594-019-0197-y] [Citation(s) in RCA: 78] [Impact Index Per Article: 15.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2018] [Accepted: 01/29/2019] [Indexed: 12/18/2022]
Abstract
Polycomb repressive complex 2 (PRC2) is a histone methyltransferase that maintains cell identity during development in multicellular organisms by marking repressed genes and chromatin domains. In addition to four core subunits, PRC2 comprises multiple accessory subunits that vary in their composition during cellular differentiation and define two major holo-PRC2 complexes: PRC2.1 and PRC2.2. PRC2 binds to RNA, which inhibits its enzymatic activity, but the mechanism of RNA-mediated inhibition of holo-PRC2 is poorly understood. Here we present in vivo and in vitro protein-RNA interaction maps and identify an RNA-binding patch within the allosteric regulatory site of human and mouse PRC2, adjacent to the methyltransferase center. RNA-mediated inhibition of holo-PRC2 is relieved by allosteric activation of PRC2 by H3K27me3 and JARID2-K116me3 peptides. Both holo-PRC2.1 and holo-PRC2.2 bind RNA, providing a unified model to explain how RNA and allosteric stimuli antagonistically regulate the enzymatic activity of PRC2.
Collapse
Affiliation(s)
- Qi Zhang
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Faculty of Medicine, Nursing and Health Sciences, Monash University, Clayton, Victoria, Australia
| | - Nicholas J McKenzie
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Faculty of Medicine, Nursing and Health Sciences, Monash University, Clayton, Victoria, Australia
| | - Robert Warneford-Thomson
- Epigenetics Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA.,Graduate Group in Biochemistry and Biophysics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Emma H Gail
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Faculty of Medicine, Nursing and Health Sciences, Monash University, Clayton, Victoria, Australia
| | - Sarena F Flanigan
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Faculty of Medicine, Nursing and Health Sciences, Monash University, Clayton, Victoria, Australia
| | - Brady M Owen
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Faculty of Medicine, Nursing and Health Sciences, Monash University, Clayton, Victoria, Australia
| | - Richard Lauman
- Epigenetics Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA.,Graduate Group in Biochemistry and Biophysics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Vitalina Levina
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Faculty of Medicine, Nursing and Health Sciences, Monash University, Clayton, Victoria, Australia
| | - Benjamin A Garcia
- Epigenetics Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA.,Department of Biochemistry and Biophysics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Ralf B Schittenhelm
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Faculty of Medicine, Nursing and Health Sciences, Monash University, Clayton, Victoria, Australia.,Monash Biomedical Proteomics Facility, Monash Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia
| | - Roberto Bonasio
- Epigenetics Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA. .,Department of Cell and Developmental Biology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA.
| | - Chen Davidovich
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Faculty of Medicine, Nursing and Health Sciences, Monash University, Clayton, Victoria, Australia. .,EMBL-Australia and the ARC Centre of Excellence in Advanced Molecular Imaging, Clayton, Victoria, Australia.
| |
Collapse
|
612
|
Dorafshan E, Kahn TG, Glotov A, Savitsky M, Walther M, Reuter G, Schwartz YB. Ash1 counteracts Polycomb repression independent of histone H3 lysine 36 methylation. EMBO Rep 2019; 20:embr.201846762. [PMID: 30833342 DOI: 10.15252/embr.201846762] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2018] [Revised: 01/31/2019] [Accepted: 02/05/2019] [Indexed: 12/11/2022] Open
Abstract
Polycomb repression is critical for metazoan development. Equally important but less studied is the Trithorax system, which safeguards Polycomb target genes from the repression in cells where they have to remain active. It was proposed that the Trithorax system acts via methylation of histone H3 at lysine 4 and lysine 36 (H3K36), thereby inhibiting histone methyltransferase activity of the Polycomb complexes. Here we test this hypothesis by asking whether the Trithorax group protein Ash1 requires H3K36 methylation to counteract Polycomb repression. We show that Ash1 is the only Drosophila H3K36-specific methyltransferase necessary to prevent excessive Polycomb repression of homeotic genes. Unexpectedly, our experiments reveal no correlation between the extent of H3K36 methylation and the resistance to Polycomb repression. Furthermore, we find that complete substitution of the zygotic histone H3 with a variant in which lysine 36 is replaced by arginine does not cause excessive repression of homeotic genes. Our results suggest that the model, where the Trithorax group proteins methylate histone H3 to inhibit the histone methyltransferase activity of the Polycomb complexes, needs revision.
Collapse
Affiliation(s)
| | - Tatyana G Kahn
- Department of Molecular Biology, Umeå University, Umeå, Sweden
| | | | | | - Matthias Walther
- Institute of Developmental Genetics, Martin-Luther University of Halle-Wittenberg, Halle, Germany.,Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
| | - Gunter Reuter
- Institute of Developmental Genetics, Martin-Luther University of Halle-Wittenberg, Halle, Germany
| | - Yuri B Schwartz
- Department of Molecular Biology, Umeå University, Umeå, Sweden
| |
Collapse
|
613
|
Loubiere V, Martinez AM, Cavalli G. Cell Fate and Developmental Regulation Dynamics by Polycomb Proteins and 3D Genome Architecture. Bioessays 2019; 41:e1800222. [PMID: 30793782 DOI: 10.1002/bies.201800222] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2018] [Revised: 12/22/2018] [Indexed: 12/14/2022]
Abstract
Targeted transitions in chromatin states at thousands of genes are essential drivers of eukaryotic development. Therefore, understanding the in vivo dynamics of epigenetic regulators is crucial for deciphering the mechanisms underpinning cell fate decisions. This review illustrates how, in addition to its cell memory function, the Polycomb group of transcriptional regulators orchestrates temporal, cell and tissue-specific expression of master genes during development. These highly sophisticated developmental transitions are dependent on the context- and tissue-specific assembly of the different types of Polycomb Group (PcG) complexes, which regulates their targeting and/or activities on chromatin. Here, an overview is provided of how PcG complexes function at multiple scales to regulate transcription, local chromatin environment, and higher order structures that support normal differentiation and are perturbed in tumorigenesis.
Collapse
Affiliation(s)
- Vincent Loubiere
- Institute of Human Genetics, UMR 9002, CNRS and University of Montpellier, 34396, Montpellier, France
| | - Anne-Marie Martinez
- Institute of Human Genetics, UMR 9002, CNRS and University of Montpellier, 34396, Montpellier, France
| | - Giacomo Cavalli
- Institute of Human Genetics, UMR 9002, CNRS and University of Montpellier, 34396, Montpellier, France
| |
Collapse
|
614
|
Abstract
Ubiquitously transcribed tetratricopeptide repeat on chromosome X (UTX, encoded by KDM6A) is a histone demethylase that targets di- and tri-methylated histone H3 lysine 27 (H3K27). UTX function has been linked to homeotic gene expression, embryonic development, and cellular reprogramming. UTX and its protein interactors within the COMPASS family, including the MLL3 and MLL4 lysine methyltransferases, are frequently mutated in multiple human cancers; however, the molecular basis of how these mutations contribute to oncogenesis remains unclear. Here, we discuss catalytic-dependent and -independent functions of UTX and its partners MLL3 and MLL4 as part of the COMPASS family during development and in oncogenesis.
Collapse
Affiliation(s)
- Lu Wang
- Simpson Querrey Center for Epigenetics, Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Searle 6-512, 320 E. Superior St., Chicago, IL 60611, USA
| | - Ali Shilatifard
- Simpson Querrey Center for Epigenetics, Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Searle 6-512, 320 E. Superior St., Chicago, IL 60611, USA.
| |
Collapse
|
615
|
Schulz WA, Lang A, Koch J, Greife A. The histone demethylase UTX/KDM6A in cancer: Progress and puzzles. Int J Cancer 2019; 145:614-620. [PMID: 30628063 DOI: 10.1002/ijc.32116] [Citation(s) in RCA: 59] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2018] [Revised: 12/11/2018] [Accepted: 01/07/2019] [Indexed: 01/01/2023]
Abstract
The lysine-specific demethylase 6A/UTX (gene name KDM6A) acts as a component of the COMPASS complex to control gene activation. UTX demethylates H3K27me2/3 at genes and enhancers. Deleterious mutations in KDM6A are found in many cancer types, prominently urothelial carcinoma and certain T-cell leukemias. In certain cancers, however, UTX supports oncogenic transcription factors, e.g. steroid hormone receptors in breast and prostate cancer. In fetal development, UTX regulates lineage choice and cell differentiation. Analogously, loss of UTX function in cancer may lead to metaplasia or impede differentiation. Likely because its function is contingent on its interacting transcription factors, the effects of UTX inactivation are not uniform and require detailed investigation in each cancer type. In urothelial carcinoma, in particular, the functional consequences of the frequent mutations in KDM6A and other COMPASS component genes are poorly understood. Nevertheless, UTX inactivation appears to sensitize many cancers to inhibitors of the H3K27 methyltransferase EZH2. Conversely, inhibitors of UTX enzymatic activity may be applicable in cancers with an oncogenic UTX function. Intriguingly, the fact that KDM6A is localized on the X-chromosome, but both copies are expressed, may account for gender-specific differences in cancer susceptibility. In conclusion, despite recent progress, many open questions need to be addressed, most importantly, the detailed mechanisms by which KDM6A inactivation promotes various cancers, but also with which proteins UTX interacts in and apart from the COMPASS complex, and to which extent its catalytic function is required for its tumor-suppressive function.
Collapse
Affiliation(s)
- Wolfgang A Schulz
- Department of Urology, Medical Faculty, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Alexander Lang
- Department of Urology, Medical Faculty, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Julian Koch
- Department of Molecular Physical Chemistry, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Annemarie Greife
- Department of Molecular Physical Chemistry, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| |
Collapse
|
616
|
Agrawal Singh S, Lerdrup M, Gomes ALR, van de Werken HJG, Vilstrup Johansen J, Andersson R, Sandelin A, Helin K, Hansen K. PLZF targets developmental enhancers for activation during osteogenic differentiation of human mesenchymal stem cells. eLife 2019; 8:e40364. [PMID: 30672466 PMCID: PMC6344081 DOI: 10.7554/elife.40364] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2018] [Accepted: 12/13/2018] [Indexed: 12/14/2022] Open
Abstract
The PLZF transcription factor is essential for osteogenic differentiation of hMSCs; however, its regulation and molecular function during this process is not fully understood. Here, we revealed that the ZBTB16 locus encoding PLZF, is repressed by Polycomb (PcG) and H3K27me3 in naive hMSCs. At the pre-osteoblast stage of differentiation, the locus lost PcG binding and H3K27me3, gained JMJD3 recruitment, and H3K27ac resulting in high expression of PLZF. Subsequently, PLZF was recruited to osteogenic enhancers, influencing H3K27 acetylation and expression of nearby genes important for osteogenic function. Furthermore, we identified a latent enhancer within the ZBTB16/PLZF locus itself that became active, gained PLZF, p300 and Mediator binding and looped to the promoter of the nicotinamide N-methyltransferase (NNMT) gene. The increased expression of NNMT correlated with a decline in SAM levels, which is dependent on PLZF and is required for osteogenic differentiation.
Collapse
Affiliation(s)
- Shuchi Agrawal Singh
- Biotech Research and Innovation Centre (BRIC), Faculty of Health and Medical SciencesUniversity of CopenhagenCopenhagenDenmark
- Department of HematologyCambridge Institute for Medical Research and Welcome Trust/MRC Stem Cell Institute, University of CambridgeCambridgeUnited Kingdom
- Centre for Epigenetics, Faculty of Health and Medical SciencesUniversity of CopenhagenCopenhagenDenmark
| | - Mads Lerdrup
- Biotech Research and Innovation Centre (BRIC), Faculty of Health and Medical SciencesUniversity of CopenhagenCopenhagenDenmark
- Centre for Epigenetics, Faculty of Health and Medical SciencesUniversity of CopenhagenCopenhagenDenmark
| | - Ana-Luisa R Gomes
- Biotech Research and Innovation Centre (BRIC), Faculty of Health and Medical SciencesUniversity of CopenhagenCopenhagenDenmark
- Centre for Epigenetics, Faculty of Health and Medical SciencesUniversity of CopenhagenCopenhagenDenmark
| | - Harmen JG van de Werken
- Department of Cell BiologyUniversity Medical CenterRotterdamNetherlands
- Cancer Computational Biology Center, University Medical CenterRotterdamNetherlands
- Department of UrologyUniversity Medical CenterRotterdamNetherlands
| | - Jens Vilstrup Johansen
- Biotech Research and Innovation Centre (BRIC), Faculty of Health and Medical SciencesUniversity of CopenhagenCopenhagenDenmark
- Centre for Epigenetics, Faculty of Health and Medical SciencesUniversity of CopenhagenCopenhagenDenmark
- Department of Biology, The Bioinformatics CentreUniversity of CopenhagenCopenhagenDenmark
| | - Robin Andersson
- Biotech Research and Innovation Centre (BRIC), Faculty of Health and Medical SciencesUniversity of CopenhagenCopenhagenDenmark
- Centre for Epigenetics, Faculty of Health and Medical SciencesUniversity of CopenhagenCopenhagenDenmark
- Department of Biology, The Bioinformatics CentreUniversity of CopenhagenCopenhagenDenmark
| | - Albin Sandelin
- Biotech Research and Innovation Centre (BRIC), Faculty of Health and Medical SciencesUniversity of CopenhagenCopenhagenDenmark
- Centre for Epigenetics, Faculty of Health and Medical SciencesUniversity of CopenhagenCopenhagenDenmark
- Department of Biology, The Bioinformatics CentreUniversity of CopenhagenCopenhagenDenmark
| | - Kristian Helin
- The Novo Nordisk Center for Stem Cell Biology, Faculty of Health and Medical Sciences University of CopenhagenCopenhagenDenmark
- Cell Biology ProgramMemorial Sloan Kettering Cancer CenterNew YorkUnited States
- Center for Epigenetics ResearchMemorial Sloan Kettering Cancer CenterNew YorkUnited States
| | - Klaus Hansen
- Biotech Research and Innovation Centre (BRIC), Faculty of Health and Medical SciencesUniversity of CopenhagenCopenhagenDenmark
- Centre for Epigenetics, Faculty of Health and Medical SciencesUniversity of CopenhagenCopenhagenDenmark
| |
Collapse
|
617
|
Chory EJ, Calarco JP, Hathaway NA, Bell O, Neel DS, Crabtree GR. Nucleosome Turnover Regulates Histone Methylation Patterns over the Genome. Mol Cell 2019; 73:61-72.e3. [PMID: 30472189 PMCID: PMC6510544 DOI: 10.1016/j.molcel.2018.10.028] [Citation(s) in RCA: 52] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2018] [Revised: 09/04/2018] [Accepted: 10/16/2018] [Indexed: 12/18/2022]
Abstract
Recent studies have indicated that nucleosome turnover is rapid, occurring several times per cell cycle. To access the effect of nucleosome turnover on the epigenetic landscape, we investigated H3K79 methylation, which is produced by a single methyltransferase (Dot1l) with no known demethylase. Using chemical-induced proximity (CIP), we find that the valency of H3K79 methylation (mono-, di-, and tri-) is determined by nucleosome turnover rates. Furthermore, propagation of this mark is predicted by nucleosome turnover simulations over the genome and accounts for the asymmetric distribution of H3K79me toward the transcriptional unit. More broadly, a meta-analysis of other conserved histone modifications demonstrates that nucleosome turnover models predict both valency and chromosomal propagation of methylation marks. Based on data from worms, flies, and mice, we propose that the turnover of modified nucleosomes is a general means of propagation of epigenetic marks and a determinant of methylation valence.
Collapse
Affiliation(s)
- Emma J Chory
- Department of Chemical Engineering, Stanford University, Stanford, CA 94305, USA; Departments of Pathology and Developmental Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Joseph P Calarco
- Departments of Pathology and Developmental Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Nathaniel A Hathaway
- Division of Chemical Biology and Medicinal Chemistry, Center for Integrative Chemical Biology and Drug Discovery, UNC Eshelman School of Pharmacy, Chapel Hill, NC 27599, USA
| | - Oliver Bell
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna Biocenter (VBC), 1030 Vienna, Austria; Department of Biochemistry and Molecular Medicine and the Norris Comprehensive Cancer Center, Keck School of Medicine of the University of Southern California, Los Angeles, CA 90089-9601, USA
| | - Dana S Neel
- Departments of Pathology and Developmental Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Gerald R Crabtree
- Departments of Pathology and Developmental Biology, Stanford University School of Medicine, Stanford, CA 94305, USA; Howard Hughes Medical Institute, Chevy Chase, MD, USA.
| |
Collapse
|
618
|
Moore-Morris T, van Vliet PP, Andelfinger G, Puceat M. Role of Epigenetics in Cardiac Development and Congenital Diseases. Physiol Rev 2019; 98:2453-2475. [PMID: 30156497 DOI: 10.1152/physrev.00048.2017] [Citation(s) in RCA: 55] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
The heart is the first organ to be functional in the fetus. Heart formation is a complex morphogenetic process regulated by both genetic and epigenetic mechanisms. Congenital heart diseases (CHD) are the most prominent congenital diseases. Genetics is not sufficient to explain these diseases or the impact of them on patients. Epigenetics is more and more emerging as a basis for cardiac malformations. This review brings the essential knowledge on cardiac biology of development. It further provides a broad background on epigenetics with a focus on three-dimensional conformation of chromatin. Then, we summarize the current knowledge of the impact of epigenetics on cardiac cell fate decision. We further provide an update on the epigenetic anomalies in the genesis of CHD.
Collapse
Affiliation(s)
- Thomas Moore-Morris
- Université Aix-Marseille, INSERM UMR- 1251, Marseille , France ; Cardiovascular Genetics, Department of Pediatrics, CHU Sainte-Justine, Montreal, Quebec , Canada ; Université de Montréal, Montreal, Quebec , Canada ; and Laboratoire International Associé INSERM, Marseille France-CHU Ste Justine, Quebec, Canada
| | - Patrick Piet van Vliet
- Université Aix-Marseille, INSERM UMR- 1251, Marseille , France ; Cardiovascular Genetics, Department of Pediatrics, CHU Sainte-Justine, Montreal, Quebec , Canada ; Université de Montréal, Montreal, Quebec , Canada ; and Laboratoire International Associé INSERM, Marseille France-CHU Ste Justine, Quebec, Canada
| | - Gregor Andelfinger
- Université Aix-Marseille, INSERM UMR- 1251, Marseille , France ; Cardiovascular Genetics, Department of Pediatrics, CHU Sainte-Justine, Montreal, Quebec , Canada ; Université de Montréal, Montreal, Quebec , Canada ; and Laboratoire International Associé INSERM, Marseille France-CHU Ste Justine, Quebec, Canada
| | - Michel Puceat
- Université Aix-Marseille, INSERM UMR- 1251, Marseille , France ; Cardiovascular Genetics, Department of Pediatrics, CHU Sainte-Justine, Montreal, Quebec , Canada ; Université de Montréal, Montreal, Quebec , Canada ; and Laboratoire International Associé INSERM, Marseille France-CHU Ste Justine, Quebec, Canada
| |
Collapse
|
619
|
Pais MS. Somatic Embryogenesis Induction in Woody Species: The Future After OMICs Data Assessment. FRONTIERS IN PLANT SCIENCE 2019; 10:240. [PMID: 30984207 PMCID: PMC6447717 DOI: 10.3389/fpls.2019.00240] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/17/2018] [Accepted: 02/12/2019] [Indexed: 05/15/2023]
Abstract
Very early somatic embryogenesis has been recognized as a powerful method to propagate plants in vitro. For some woody species and in particular for some coniferous trees, somatic embryogenesis induction has become a routine procedure. For the majority, the application of this technology presents yet many limitations especially due to the genotype, the induction conditions, the number of embryos produced, maturation, and conversion, among other factors that compromise the systematic use of somatic embryogenesis for commercial purposes especially of woody species and forest trees in particular. The advancements obtained on somatic embryogenesis in Arabidopsis and the development of OMIC technologies allowed the characterization of genes and the corresponding proteins that are conserved in woody species. This knowledge will help in understanding the molecular mechanisms underlying the complex regulatory networks that control somatic embryogenesis in woody plants. In this revision, we report on developments of OMICs (genomics, transcriptomics, metabolomics, and proteomics) applied to somatic embryogenesis induction and its contribution for understanding the change of fate giving rise to the expression of somatic embryogenesis competence.
Collapse
|
620
|
Fonseca S, Rubio V. Arabidopsis CRL4 Complexes: Surveying Chromatin States and Gene Expression. FRONTIERS IN PLANT SCIENCE 2019; 10:1095. [PMID: 31608079 PMCID: PMC6761389 DOI: 10.3389/fpls.2019.01095] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/07/2019] [Accepted: 08/09/2019] [Indexed: 05/10/2023]
Abstract
CULLIN4 (CUL4) RING ligase (CRL4) complexes contain a CUL4 scaffold protein, associated to RBX1 and to DDB1 proteins and have traditionally been associated to protein degradation events. Through DDB1, these complexes can associate with numerous DCAF proteins, which directly interact with specific targets promoting their ubiquitination and subsequent degradation by the proteasome. A characteristic feature of the majority of DCAF proteins that associate with DDB1 is the presence of the DWD motif. DWD-containing proteins sum up to 85 in the plant model species Arabidopsis. In the last decade, numerous Arabidopsis DWD proteins have been studied and their molecular functions uncovered. Independently of whether their association with CRL4 has been confirmed or not, DWD proteins are often found as components of additional multimeric protein complexes that play key roles in essential nuclear events. For most of them, the significance of their complex partnership is still unexplored. Here, we summarize recent findings involving both confirmed and putative CRL4-associated DCAF proteins in regulating nuclei architecture remodelling, DNA damage repair, histone post-translational modification, mRNA processing and export, and ribosome biogenesis, that definitely have an impact in gene expression and de novo protein synthesis. We hypothesized that, by maintaining accurate levels of regulatory proteins through targeted degradation and transcriptional control, CRL4 complexes help to surveil nuclear processes essential for plant development and survival.
Collapse
|
621
|
Decourcelle A, Leprince D, Dehennaut V. Regulation of Polycomb Repression by O-GlcNAcylation: Linking Nutrition to Epigenetic Reprogramming in Embryonic Development and Cancer. Front Endocrinol (Lausanne) 2019; 10:117. [PMID: 30873122 PMCID: PMC6400832 DOI: 10.3389/fendo.2019.00117] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/10/2018] [Accepted: 02/08/2019] [Indexed: 11/25/2022] Open
Abstract
Epigenetic modifications are major actors of early embryogenesis and carcinogenesis and are sensitive to nutritional environment. In recent years, the nutritional sensor O-GlcNAcylation has been recognized as a key regulator of chromatin remodeling. In this review, we summarize and discuss recent clues that OGT and O-GlcNAcylation intimately regulate the functions of the Polycomb group proteins at different levels especially during Drosophila melanogaster embryonic development and in human cancer cell lines. These observations define an additional connection between nutrition and epigenetic reprogramming associated to embryonic development and cancer.
Collapse
|
622
|
Abstract
Epigenetic mechanisms, including DNA and histone modifications, are pivotal for normal brain development and functions by modulating spatial and temporal gene expression. Dysregulation of the epigenetic machinery can serve as a causal role in numerous brain disorders. Proper mammalian brain development and functions depend on the precise expression of neuronal-specific genes, transcription factors and epigenetic modifications. Antagonistic polycomb and trithorax proteins form multimeric complexes and play important roles in these processes by epigenetically controlling gene repression or activation through various molecular mechanisms. Aberrant expression or disruption of either protein group can contribute to neurodegenerative diseases. This review focus on the current progress of Polycomb and Trithorax complexes in brain development and disease, and provides a future outlook of the field.
Collapse
|
623
|
Watanabe S, Shimada S, Akiyama Y, Ishikawa Y, Ogura T, Ogawa K, Ono H, Mitsunori Y, Ban D, Kudo A, Yamaoka S, Tanabe M, Tanaka S. Loss of KDM6A characterizes a poor prognostic subtype of human pancreatic cancer and potentiates HDAC inhibitor lethality. Int J Cancer 2018; 145:192-205. [PMID: 30556125 DOI: 10.1002/ijc.32072] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2018] [Accepted: 12/05/2018] [Indexed: 01/03/2023]
Abstract
Although genomic analysis have recently discovered the malignant subtype of human pancreatic ductal adenocarcinoma (PDAC) characterized by frequent mutations of histone demethylase KDM6A, the biological and molecular roles still remain obscure. We herein elucidated the clinical and biological impacts of KDM6A deficiency on human PDAC and identified the therapeutic potential by pathological and molecular evaluation. Immunohistochemical analysis suggested that loss of KDM6A in cancerous tissues was an independent prognostic factor for both recurrence-free and overall survival in the 103 tumor specimens surgically resected from patients with PDAC. We established KDM6A knocked out cells by using the CRISPR/Cas9 system and KDM6A-expressed cells by doxycycline-inducible system from each two human PDAC cell lines, respectively. KDM6A knockout enhanced aggressive traits of human PDAC cell lines, whereas KDM6A overexpression suppressed them. Microarray analysis revealed reduced expression of 22 genes including five well-known tumor suppressors, such as CDKN1A, and ChIP-PCR analysis displayed depleted enrichment of histone H3 lysine 27 acetylation (H3K27ac) at the promoter regions of the five candidates. The epigenetic alterations were induced by the impaired recruitment of histone acetyltransferase p300, which cooperatively interacted with KDM6A. Consistent with these results, the KDM6A knockout cells demonstrated higher vulnerability to histone deacetylase (HDAC) inhibitors through the reactivation of CDKN1A in vitro and in vivo than the KDM6A wild-type. In conclusion, KDM6A exhibited essential roles in human PDAC as a tumor suppressor and KDM6A deficiency could be a promising biomarker for unfavorable outcome in PDAC patients and a potential surrogate marker for response to HDAC inhibitors.
Collapse
Affiliation(s)
- Shuichi Watanabe
- Department of Molecular Oncology, Graduate School of Medicine, Tokyo Medical and Dental University, Tokyo, Japan.,Department of Hepato-Biliary-Pancreatic Surgery, Graduate School of Medicine, Tokyo Medical and Dental University, Tokyo, Japan
| | - Shu Shimada
- Department of Molecular Oncology, Graduate School of Medicine, Tokyo Medical and Dental University, Tokyo, Japan
| | - Yoshimitsu Akiyama
- Department of Molecular Oncology, Graduate School of Medicine, Tokyo Medical and Dental University, Tokyo, Japan
| | - Yoshiya Ishikawa
- Department of Molecular Oncology, Graduate School of Medicine, Tokyo Medical and Dental University, Tokyo, Japan.,Department of Hepato-Biliary-Pancreatic Surgery, Graduate School of Medicine, Tokyo Medical and Dental University, Tokyo, Japan
| | - Toshiro Ogura
- Department of Hepato-Biliary-Pancreatic Surgery, Graduate School of Medicine, Tokyo Medical and Dental University, Tokyo, Japan
| | - Kosuke Ogawa
- Department of Hepato-Biliary-Pancreatic Surgery, Graduate School of Medicine, Tokyo Medical and Dental University, Tokyo, Japan
| | - Hiroaki Ono
- Department of Hepato-Biliary-Pancreatic Surgery, Graduate School of Medicine, Tokyo Medical and Dental University, Tokyo, Japan
| | - Yusuke Mitsunori
- Department of Hepato-Biliary-Pancreatic Surgery, Graduate School of Medicine, Tokyo Medical and Dental University, Tokyo, Japan
| | - Daisuke Ban
- Department of Hepato-Biliary-Pancreatic Surgery, Graduate School of Medicine, Tokyo Medical and Dental University, Tokyo, Japan
| | - Atsushi Kudo
- Department of Hepato-Biliary-Pancreatic Surgery, Graduate School of Medicine, Tokyo Medical and Dental University, Tokyo, Japan
| | - Shoji Yamaoka
- Department of Molecular Virology, Graduate School of Medicine, Tokyo Medical and Dental University, Tokyo, Japan
| | - Minoru Tanabe
- Department of Hepato-Biliary-Pancreatic Surgery, Graduate School of Medicine, Tokyo Medical and Dental University, Tokyo, Japan
| | - Shinji Tanaka
- Department of Molecular Oncology, Graduate School of Medicine, Tokyo Medical and Dental University, Tokyo, Japan.,Department of Hepato-Biliary-Pancreatic Surgery, Graduate School of Medicine, Tokyo Medical and Dental University, Tokyo, Japan
| |
Collapse
|
624
|
Weinman LM, Running KLD, Carey NS, Stevenson EJ, Swaney DL, Chow BY, Krogan NJ, Krogan NT. TCO, a Putative Transcriptional Regulator in Arabidopsis, Is a Target of the Protein Kinase CK2. Int J Mol Sci 2018; 20:ijms20010099. [PMID: 30597831 PMCID: PMC6337506 DOI: 10.3390/ijms20010099] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2018] [Revised: 12/26/2018] [Accepted: 12/26/2018] [Indexed: 11/16/2022] Open
Abstract
As multicellular organisms grow, spatial and temporal patterns of gene expression are strictly regulated to ensure that developmental programs are invoked at appropriate stages. In this work, we describe a putative transcriptional regulator in Arabidopsis, TACO LEAF (TCO), whose overexpression results in the ectopic activation of reproductive genes during vegetative growth. Isolated as an activation-tagged allele, tco-1D displays gene misexpression and phenotypic abnormalities, such as curled leaves and early flowering, characteristic of chromatin regulatory mutants. A role for TCO in this mode of transcriptional regulation is further supported by the subnuclear accumulation patterns of TCO protein and genetic interactions between tco-1D and chromatin modifier mutants. The endogenous expression pattern of TCO and gene misregulation in tco loss-of-function mutants indicate that this factor is involved in seed development. We also demonstrate that specific serine residues of TCO protein are targeted by the ubiquitous kinase CK2. Collectively, these results identify TCO as a novel regulator of gene expression whose activity is likely influenced by phosphorylation, as is the case with many chromatin regulators.
Collapse
Affiliation(s)
- Laina M Weinman
- Department of Biology, American University, 4400 Massachusetts Avenue NW, Washington, DC 20016, USA.
| | - Katherine L D Running
- Department of Biology, American University, 4400 Massachusetts Avenue NW, Washington, DC 20016, USA.
| | - Nicholas S Carey
- Department of Biology, American University, 4400 Massachusetts Avenue NW, Washington, DC 20016, USA.
| | - Erica J Stevenson
- Gladstone Institute of Data Science and Biotechnology, J. David Gladstone Institutes, San Francisco, CA 94158, USA.
| | - Danielle L Swaney
- Gladstone Institute of Data Science and Biotechnology, J. David Gladstone Institutes, San Francisco, CA 94158, USA.
- Quantitative Biosciences Institute (QBI), University of California, San Francisco, CA 94158, USA.
| | - Brenda Y Chow
- Department of Biology, American University, 4400 Massachusetts Avenue NW, Washington, DC 20016, USA.
| | - Nevan J Krogan
- Gladstone Institute of Data Science and Biotechnology, J. David Gladstone Institutes, San Francisco, CA 94158, USA.
- Quantitative Biosciences Institute (QBI), University of California, San Francisco, CA 94158, USA.
| | - Naden T Krogan
- Department of Biology, American University, 4400 Massachusetts Avenue NW, Washington, DC 20016, USA.
| |
Collapse
|
625
|
Zhao Z, Wang L, Volk AG, Birch NW, Stoltz KL, Bartom ET, Marshall SA, Rendleman EJ, Nestler CM, Shilati J, Schiltz GE, Crispino JD, Shilatifard A. Regulation of MLL/COMPASS stability through its proteolytic cleavage by taspase1 as a possible approach for clinical therapy of leukemia. Genes Dev 2018; 33:61-74. [PMID: 30573454 PMCID: PMC6317322 DOI: 10.1101/gad.319830.118] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2018] [Accepted: 11/02/2018] [Indexed: 12/24/2022]
Abstract
In this study, Zhao et al. investigated the biological significance of MLL1 cleavage by the endopeptidase taspase1. They demonstrate that taspase1-dependent cleavage of MLL1 results in the destabilization of MLL, and thus their findings provide insights into the direct regulation of the stability of MLL1 through its cleavage by taspase1. Chromosomal translocations of the Mixed-lineage leukemia 1 (MLL1) gene generate MLL chimeras that drive the pathogenesis of acute myeloid and lymphoid leukemia. The untranslocated MLL1 is a substrate for proteolytic cleavage by the endopeptidase threonine aspartase 1 (taspase1); however, the biological significance of MLL1 cleavage by this endopeptidase remains unclear. Here, we demonstrate that taspase1-dependent cleavage of MLL1 results in the destabilization of MLL. Upon loss of taspase1, MLL1 association with chromatin is markedly increased due to the stabilization of its unprocessed version, and this stabilization of the uncleaved MLL1 can result in the displacement of MLL chimeras from chromatin in leukemic cells. Casein kinase II (CKII) phosphorylates MLL1 proximal to the taspase1 cleavage site, facilitating its cleavage, and pharmacological inhibition of CKII blocks taspase1-dependent MLL1 processing, increases MLL1 stability, and results in the displacement of the MLL chimeras from chromatin. Accordingly, inhibition of CKII in a MLL-AF9 mouse model of leukemia delayed leukemic progression in vivo. This study provides insights into the direct regulation of the stability of MLL1 through its cleavage by taspase1, which can be harnessed for targeted therapeutic approaches for the treatment of aggressive leukemia as the result of MLL translocations.
Collapse
Affiliation(s)
- Zibo Zhao
- Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Chicago, Illinois 60611, USA.,Simpson Querrey Center for Epigenetics, Northwestern University Feinberg School of Medicine, Chicago, Illinois 60611, USA
| | - Lu Wang
- Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Chicago, Illinois 60611, USA.,Simpson Querrey Center for Epigenetics, Northwestern University Feinberg School of Medicine, Chicago, Illinois 60611, USA
| | - Andrew G Volk
- Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Chicago, Illinois 60611, USA.,Simpson Querrey Center for Epigenetics, Northwestern University Feinberg School of Medicine, Chicago, Illinois 60611, USA.,Division of Hematology/Oncology, Northwestern University Feinberg School of Medicine, Chicago, Illinois 60611, USA.,Robert H. Lurie Comprehensive Cancer Center, Northwestern University Feinberg School of Medicine, Chicago, Illinois 60611, USA
| | - Noah W Birch
- Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Chicago, Illinois 60611, USA.,Simpson Querrey Center for Epigenetics, Northwestern University Feinberg School of Medicine, Chicago, Illinois 60611, USA
| | - Kristen L Stoltz
- Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Chicago, Illinois 60611, USA.,Simpson Querrey Center for Epigenetics, Northwestern University Feinberg School of Medicine, Chicago, Illinois 60611, USA.,Center for Molecular Innovation and Drug Discovery, Northwestern University, Evanston, Illinois 60208, USA
| | - Elizabeth T Bartom
- Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Chicago, Illinois 60611, USA
| | - Stacy A Marshall
- Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Chicago, Illinois 60611, USA.,Simpson Querrey Center for Epigenetics, Northwestern University Feinberg School of Medicine, Chicago, Illinois 60611, USA
| | - Emily J Rendleman
- Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Chicago, Illinois 60611, USA.,Simpson Querrey Center for Epigenetics, Northwestern University Feinberg School of Medicine, Chicago, Illinois 60611, USA
| | - Carson M Nestler
- Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Chicago, Illinois 60611, USA.,Simpson Querrey Center for Epigenetics, Northwestern University Feinberg School of Medicine, Chicago, Illinois 60611, USA
| | - Joseph Shilati
- Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Chicago, Illinois 60611, USA.,Simpson Querrey Center for Epigenetics, Northwestern University Feinberg School of Medicine, Chicago, Illinois 60611, USA
| | - Gary E Schiltz
- Robert H. Lurie Comprehensive Cancer Center, Northwestern University Feinberg School of Medicine, Chicago, Illinois 60611, USA.,Center for Molecular Innovation and Drug Discovery, Northwestern University, Evanston, Illinois 60208, USA.,Department of Pharmacology, Northwestern University Feinberg School of Medicine, Chicago, Illinois 60611, USA
| | - John D Crispino
- Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Chicago, Illinois 60611, USA.,Simpson Querrey Center for Epigenetics, Northwestern University Feinberg School of Medicine, Chicago, Illinois 60611, USA.,Division of Hematology/Oncology, Northwestern University Feinberg School of Medicine, Chicago, Illinois 60611, USA.,Robert H. Lurie Comprehensive Cancer Center, Northwestern University Feinberg School of Medicine, Chicago, Illinois 60611, USA
| | - Ali Shilatifard
- Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Chicago, Illinois 60611, USA.,Simpson Querrey Center for Epigenetics, Northwestern University Feinberg School of Medicine, Chicago, Illinois 60611, USA.,Robert H. Lurie Comprehensive Cancer Center, Northwestern University Feinberg School of Medicine, Chicago, Illinois 60611, USA
| |
Collapse
|
626
|
Cohen I, Zhao D, Menon G, Nakayama M, Koseki H, Zheng D, Ezhkova E. PRC1 preserves epidermal tissue integrity independently of PRC2. Genes Dev 2018; 33:55-60. [PMID: 30567998 PMCID: PMC6317312 DOI: 10.1101/gad.319939.118] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2018] [Accepted: 11/05/2018] [Indexed: 12/21/2022]
Abstract
Cohen et al. show that, despite extensive genomic cobinding, PRC1 is essential for epidermal integrity, whereas PRC2 is dispensable. Polycomb-repressive complex 1 (PRC1) and PRC2 are critical chromatin regulators of gene expression and tissue development. Here, we show that despite extensive genomic cobinding, PRC1 is essential for epidermal integrity, whereas PRC2 is dispensable. Loss of PRC1 resulted in blistering skin, reminiscent of human skin fragility syndromes. Conversely, PRC1 does not restrict epidermal stratification during skin morphogenesis, whereas PRC2 does. Molecular dissection demonstrated that PRC1 functions with PRC2 to silence/dampen expression of adhesion genes. In contrast, PRC1 promotes expression of critical epidermal adhesion genes independently of PRC2-mediated H3K27me3. Together, we demonstrate a functional link between epigenetic regulation and skin diseases.
Collapse
Affiliation(s)
- Idan Cohen
- Black Family Stem Cell Institute, Department of Cell, Developmental, and Regenerative Biology, Icahn School of Medicine at Mount Sinai, New York, New York 10029, USA
| | - Dejian Zhao
- Department of Genetics, Albert Einstein College of Medicine, Bronx, New York 10461, USA
| | - Gopinathan Menon
- California Academy of Sciences, San Francisco, California 94118, USA
| | - Manabu Nakayama
- Department of Frontier Research and Development, Kazusa DNA Research Institute, Kisarazu, Chiba 292-0818, Japan
| | - Haruhiko Koseki
- Laboratory for Developmental Genetics, RIKEN Center for Integrative Medical Sciences (RIKEN-IMS) Tsurumi-ku, Yokohama 230-0045, Japan.,Advanced Research and Development Programs for Medical Innovation (AMED-CREST), Tsurumi-ku, Yokohama 230-0045, Japan
| | - Deyou Zheng
- Department of Genetics, Albert Einstein College of Medicine, Bronx, New York 10461, USA.,Department of Neurology, Albert Einstein College of Medicine, Bronx, New York 10461, USA.,Department of Neuroscience, Albert Einstein College of Medicine, Bronx, New York 10461, USA
| | - Elena Ezhkova
- Black Family Stem Cell Institute, Department of Cell, Developmental, and Regenerative Biology, Icahn School of Medicine at Mount Sinai, New York, New York 10029, USA
| |
Collapse
|
627
|
Onodera A, Kokubo K, Nakayama T. Epigenetic and Transcriptional Regulation in the Induction, Maintenance, Heterogeneity, and Recall-Response of Effector and Memory Th2 Cells. Front Immunol 2018; 9:2929. [PMID: 30619290 PMCID: PMC6299044 DOI: 10.3389/fimmu.2018.02929] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2018] [Accepted: 11/29/2018] [Indexed: 12/24/2022] Open
Abstract
Antigen-primed T cells respond to restimulation much faster than naïve T cells and form the cellular basis of immunological memory. The formation of memory Th2 cells starts when naïve CD4 T cells are transformed into effector Th2 cells and is completed after antigen clearance and a long-term resting phase accompanied by epigenetic changes in the Th2 signature genes. Memory Th2 cells maintain their functions and acquired heterogeneity through epigenetic machinery, on which the recall-response of memory Th2 cells is also dependent. We provide an overview of the epigenetics in the whole Th2 cell cycle, mainly focusing on two different histone lysine methyltransferase complexes: the Polycomb and Trithorax groups. We finally discuss the pathophysiology and potential therapeutic strategies for the treatment of Th2-mediated inflammatory diseases in mice and humans.
Collapse
Affiliation(s)
- Atsushi Onodera
- Department of Immunology, Graduate School of Medicine, Chiba University, Chiba, Japan.,Institue for Global Prominent Research, Chiba University, Chiba, Japan
| | - Kota Kokubo
- Department of Immunology, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Toshinori Nakayama
- Department of Immunology, Graduate School of Medicine, Chiba University, Chiba, Japan
| |
Collapse
|
628
|
Hinohara K, Wu HJ, Vigneau S, McDonald TO, Igarashi KJ, Yamamoto KN, Madsen T, Fassl A, Egri SB, Papanastasiou M, Ding L, Peluffo G, Cohen O, Kales SC, Lal-Nag M, Rai G, Maloney DJ, Jadhav A, Simeonov A, Wagle N, Brown M, Meissner A, Sicinski P, Jaffe JD, Jeselsohn R, Gimelbrant AA, Michor F, Polyak K. KDM5 Histone Demethylase Activity Links Cellular Transcriptomic Heterogeneity to Therapeutic Resistance. Cancer Cell 2018; 34:939-953.e9. [PMID: 30472020 PMCID: PMC6310147 DOI: 10.1016/j.ccell.2018.10.014] [Citation(s) in RCA: 147] [Impact Index Per Article: 24.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/22/2017] [Revised: 08/17/2018] [Accepted: 10/25/2018] [Indexed: 12/30/2022]
Abstract
Members of the KDM5 histone H3 lysine 4 demethylase family are associated with therapeutic resistance, including endocrine resistance in breast cancer, but the underlying mechanism is poorly defined. Here we show that genetic deletion of KDM5A/B or inhibition of KDM5 activity increases sensitivity to anti-estrogens by modulating estrogen receptor (ER) signaling and by decreasing cellular transcriptomic heterogeneity. Higher KDM5B expression levels are associated with higher transcriptomic heterogeneity and poor prognosis in ER+ breast tumors. Single-cell RNA sequencing, cellular barcoding, and mathematical modeling demonstrate that endocrine resistance is due to selection for pre-existing genetically distinct cells, while KDM5 inhibitor resistance is acquired. Our findings highlight the importance of cellular phenotypic heterogeneity in therapeutic resistance and identify KDM5A/B as key regulators of this process.
Collapse
Affiliation(s)
- Kunihiko Hinohara
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Medicine, Harvard Medical School, Boston, MA 02115, USA
| | - Hua-Jun Wu
- Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Biostatistics, Harvard T. H. Chan School of Public Health, Boston, MA 02115, USA; Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA
| | - Sébastien Vigneau
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Thomas O McDonald
- Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Biostatistics, Harvard T. H. Chan School of Public Health, Boston, MA 02115, USA; Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA; Center for Cancer Evolution, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Kyomi J Igarashi
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Kimiyo N Yamamoto
- Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Biostatistics, Harvard T. H. Chan School of Public Health, Boston, MA 02115, USA; Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA
| | - Thomas Madsen
- Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Biostatistics, Harvard T. H. Chan School of Public Health, Boston, MA 02115, USA; Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA
| | - Anne Fassl
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Shawn B Egri
- The Eli and Edythe L Broad Institute of MIT and Harvard, Cambridge, MA 02139, USA
| | | | - Lina Ding
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Medicine, Harvard Medical School, Boston, MA 02115, USA
| | - Guillermo Peluffo
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Medicine, Harvard Medical School, Boston, MA 02115, USA
| | - Ofir Cohen
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; The Eli and Edythe L Broad Institute of MIT and Harvard, Cambridge, MA 02139, USA
| | - Stephen C Kales
- National Center for Advancing Translational Sciences, Bethesda, MD 20892, USA
| | - Madhu Lal-Nag
- National Center for Advancing Translational Sciences, Bethesda, MD 20892, USA
| | - Ganesha Rai
- National Center for Advancing Translational Sciences, Bethesda, MD 20892, USA
| | - David J Maloney
- National Center for Advancing Translational Sciences, Bethesda, MD 20892, USA
| | - Ajit Jadhav
- National Center for Advancing Translational Sciences, Bethesda, MD 20892, USA
| | - Anton Simeonov
- National Center for Advancing Translational Sciences, Bethesda, MD 20892, USA
| | - Nikhil Wagle
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Medicine, Harvard Medical School, Boston, MA 02115, USA; The Eli and Edythe L Broad Institute of MIT and Harvard, Cambridge, MA 02139, USA
| | - Myles Brown
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Medicine, Harvard Medical School, Boston, MA 02115, USA; Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Ludwig Center at Harvard, Boston, MA 02215, USA
| | - Alexander Meissner
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA; The Eli and Edythe L Broad Institute of MIT and Harvard, Cambridge, MA 02139, USA
| | - Piotr Sicinski
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Jacob D Jaffe
- The Eli and Edythe L Broad Institute of MIT and Harvard, Cambridge, MA 02139, USA
| | - Rinath Jeselsohn
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Medicine, Harvard Medical School, Boston, MA 02115, USA
| | - Alexander A Gimelbrant
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Franziska Michor
- Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Biostatistics, Harvard T. H. Chan School of Public Health, Boston, MA 02115, USA; Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA; Center for Cancer Evolution, Dana-Farber Cancer Institute, Boston, MA 02215, USA; The Eli and Edythe L Broad Institute of MIT and Harvard, Cambridge, MA 02139, USA; Ludwig Center at Harvard, Boston, MA 02215, USA.
| | - Kornelia Polyak
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Medicine, Harvard Medical School, Boston, MA 02115, USA; Center for Cancer Evolution, Dana-Farber Cancer Institute, Boston, MA 02215, USA; The Eli and Edythe L Broad Institute of MIT and Harvard, Cambridge, MA 02139, USA; Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Ludwig Center at Harvard, Boston, MA 02215, USA.
| |
Collapse
|
629
|
Tatavosian R, Kent S, Brown K, Yao T, Duc HN, Huynh TN, Zhen CY, Ma B, Wang H, Ren X. Nuclear condensates of the Polycomb protein chromobox 2 (CBX2) assemble through phase separation. J Biol Chem 2018; 294:1451-1463. [PMID: 30514760 DOI: 10.1074/jbc.ra118.006620] [Citation(s) in RCA: 233] [Impact Index Per Article: 38.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2018] [Revised: 11/28/2018] [Indexed: 01/01/2023] Open
Abstract
Polycomb group (PcG) proteins repress master regulators of development and differentiation through organization of chromatin structure. Mutation and dysregulation of PcG genes cause developmental defects and cancer. PcG proteins form condensates in the cell nucleus, and these condensates are the physical sites of PcG-targeted gene silencing via formation of facultative heterochromatin. However, the physiochemical principles underlying the formation of PcG condensates remain unknown, and their determination could shed light on how these condensates compact chromatin. Using fluorescence live-cell imaging, we observed that the Polycomb repressive complex 1 (PRC1) protein chromobox 2 (CBX2), a member of the CBX protein family, undergoes phase separation to form condensates and that the CBX2 condensates exhibit liquid-like properties. Using site-directed mutagenesis, we demonstrated that the conserved residues of CBX2 within the intrinsically disordered region (IDR), which is the region for compaction of chromatin in vitro, promote the condensate formation both in vitro and in vivo We showed that the CBX2 condensates concentrate DNA and nucleosomes. Using genetic engineering, we report that trimethylation of Lys-27 at histone H3 (H3K27me3), a marker of heterochromatin formation produced by PRC2, had minimal effects on the CBX2 condensate formation. We further demonstrated that the CBX2 condensate formation does not require CBX2-PRC1 subunits; however, the condensate formation of CBX2-PRC1 subunits depends on CBX2, suggesting a mechanism underlying the assembly of CBX2-PRC1 condensates. In summary, our results reveal that PcG condensates assemble through liquid-liquid phase separation (LLPS) and suggest that phase-separated condensates can organize PcG-bound chromatin.
Collapse
Affiliation(s)
- Roubina Tatavosian
- Department of Chemistry, University of Colorado, Denver, Colorado 80217-3364
| | - Samantha Kent
- Department of Chemistry, University of Colorado, Denver, Colorado 80217-3364
| | - Kyle Brown
- Department of Chemistry, University of Colorado, Denver, Colorado 80217-3364
| | - Tingting Yao
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, Colorado 80523
| | - Huy Nguyen Duc
- Department of Chemistry, University of Colorado, Denver, Colorado 80217-3364
| | - Thao Ngoc Huynh
- Department of Chemistry, University of Colorado, Denver, Colorado 80217-3364
| | - Chao Yu Zhen
- Department of Chemistry, University of Colorado, Denver, Colorado 80217-3364
| | - Brian Ma
- Department of Chemistry, University of Colorado, Denver, Colorado 80217-3364
| | - Haobin Wang
- Department of Chemistry, University of Colorado, Denver, Colorado 80217-3364
| | - Xiaojun Ren
- Department of Chemistry, University of Colorado, Denver, Colorado 80217-3364.
| |
Collapse
|
630
|
Kasinath V, Poepsel S, Nogales E. Recent Structural Insights into Polycomb Repressive Complex 2 Regulation and Substrate Binding. Biochemistry 2018; 58:346-354. [PMID: 30451485 PMCID: PMC6438374 DOI: 10.1021/acs.biochem.8b01064] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Polycomb group proteins are transcriptional repressors controlling gene expression patterns and maintaining cell type identity. The chemical modifications of histones and DNA caused by the regulated activity of chromatin-modifying enzymes such as Polycomb help establish and maintain such expression patterns. Polycomb repressive complex 2 (PRC2) is the only known methyltransferase specific for histone H3 lysine 27 (H3K27) and catalyzes its trimethylation leading to the repressive H3K27me3 mark. Structural biology has made important contributions to our understanding of the molecular mechanisms that ensure the spatiotemporal regulation of PRC2 activity and the establishment of inactive chromatin domains marked by H3K27me3. In this review, we discuss the recent structural studies that have advanced our understanding of PRC2 function, in particular the roles of intersubunit interactions in complex assembly and the regulation of methyltransferase activity, as well as the mechanism of local H3K27me3 spreading leading to repressive domains.
Collapse
Affiliation(s)
- Vignesh Kasinath
- California Institute for Quantitative Biosciences (QB3) , University of California , Berkeley , California 94720 , United States.,Molecular Biophysics and Integrated Bioimaging Division , Lawrence Berkeley National Laboratory , Berkeley , California 94720 , United States
| | - Simon Poepsel
- California Institute for Quantitative Biosciences (QB3) , University of California , Berkeley , California 94720 , United States.,Molecular Biophysics and Integrated Bioimaging Division , Lawrence Berkeley National Laboratory , Berkeley , California 94720 , United States
| | - Eva Nogales
- California Institute for Quantitative Biosciences (QB3) , University of California , Berkeley , California 94720 , United States.,Molecular Biophysics and Integrated Bioimaging Division , Lawrence Berkeley National Laboratory , Berkeley , California 94720 , United States.,Department of Molecular and Cellular Biology , University of California , Berkeley , California 94720 , United States.,Howard Hughes Medical Institute , University of California , Berkeley , California 94720 , United States
| |
Collapse
|
631
|
Urban EA, Johnston RJ. Buffering and Amplifying Transcriptional Noise During Cell Fate Specification. Front Genet 2018; 9:591. [PMID: 30555516 PMCID: PMC6282114 DOI: 10.3389/fgene.2018.00591] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2018] [Accepted: 11/15/2018] [Indexed: 11/29/2022] Open
Abstract
The molecular processes that drive gene transcription are inherently noisy. This noise often manifests in the form of transcriptional bursts, producing fluctuations in gene activity over time. During cell fate specification, this noise is often buffered to ensure reproducible developmental outcomes. However, sometimes noise is utilized as a “bet-hedging” mechanism to diversify functional roles across a population of cells. Studies of bacteria, yeast, and cultured cells have provided insights into the nature and roles of noise in transcription, yet we are only beginning to understand the mechanisms by which noise influences the development of multicellular organisms. Here we discuss the sources of transcriptional noise and the mechanisms that either buffer noise to drive reproducible fate choices or amplify noise to randomly specify fates.
Collapse
Affiliation(s)
- Elizabeth A Urban
- Department of Biology, Johns Hopkins University, Baltimore, MD, United States
| | - Robert J Johnston
- Department of Biology, Johns Hopkins University, Baltimore, MD, United States
| |
Collapse
|
632
|
Castiglioni I, Caccia R, Garcia-Manteiga JM, Ferri G, Caretti G, Molineris I, Nishioka K, Gabellini D. The Trithorax protein Ash1L promotes myoblast fusion by activating Cdon expression. Nat Commun 2018; 9:5026. [PMID: 30487570 PMCID: PMC6262021 DOI: 10.1038/s41467-018-07313-8] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2018] [Accepted: 10/24/2018] [Indexed: 12/17/2022] Open
Abstract
Myoblast fusion (MF) is required for muscle growth and repair, and its alteration contributes to muscle diseases. The mechanisms governing this process are incompletely understood, and no epigenetic regulator has been previously described. Ash1L is an epigenetic activator belonging to the Trithorax group of proteins and is involved in FSHD muscular dystrophy, autism and cancer. Its physiological role in skeletal muscle is unknown. Here we report that Ash1L expression is positively correlated with MF and reduced in Duchenne muscular dystrophy. In vivo, ex vivo and in vitro experiments support a selective and evolutionary conserved requirement for Ash1L in MF. RNA- and ChIP-sequencing indicate that Ash1L is required to counteract Polycomb repressive activity to allow activation of selected myogenesis genes, in particular the key MF gene Cdon. Our results promote Ash1L as an important epigenetic regulator of MF and suggest that its activity could be targeted to improve cell therapy for muscle diseases. Myoblast fusion in skeletal muscle is a complex process but how this is regulated is unclear. Here, the authors identify Ash1L, a histone methyltransferase, as modulating myoblast fusion via activation of the myogenesis gene Cdon, and observe decreased Ash1L expression in Duchenne muscular dystrophy.
Collapse
Affiliation(s)
- Ilaria Castiglioni
- Division of Genetics and Cell Biology, IRCCS San Raffaele Scientific Institute, via Olgettina 60, Milano, 20132, Italy
| | - Roberta Caccia
- Division of Genetics and Cell Biology, IRCCS San Raffaele Scientific Institute, via Olgettina 60, Milano, 20132, Italy
| | - Jose Manuel Garcia-Manteiga
- Center for Translational Genomics and BioInformatics, IRCCS San Raffaele Scientific Institute, via Olgettina 60, Milano, 20132, Italy
| | - Giulia Ferri
- Division of Genetics and Cell Biology, IRCCS San Raffaele Scientific Institute, via Olgettina 60, Milano, 20132, Italy
| | - Giuseppina Caretti
- Department of Biosciences, University of Milan, via Celoria 26, Milano, 20133, Italy
| | - Ivan Molineris
- Center for Translational Genomics and BioInformatics, IRCCS San Raffaele Scientific Institute, via Olgettina 60, Milano, 20132, Italy
| | - Kenichi Nishioka
- Department of Biomolecular Sciences, Division of Molecular Genetics and Epigenetics, Faculty of Medicine, Saga University, Saga, Japan.,Laboratory for Developmental Genetics, RIKEN IMS, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama City, Kanagawa, 230-0045, Japan
| | - Davide Gabellini
- Division of Genetics and Cell Biology, IRCCS San Raffaele Scientific Institute, via Olgettina 60, Milano, 20132, Italy.
| |
Collapse
|
633
|
Bicocca VT, Ormsby T, Adhvaryu KK, Honda S, Selker EU. ASH1-catalyzed H3K36 methylation drives gene repression and marks H3K27me2/3-competent chromatin. eLife 2018; 7:41497. [PMID: 30468429 PMCID: PMC6251624 DOI: 10.7554/elife.41497] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2018] [Accepted: 10/31/2018] [Indexed: 12/31/2022] Open
Abstract
Methylation of histone H3 at lysine 36 (H3K36me), a widely-distributed chromatin mark, largely results from association of the lysine methyltransferase (KMT) SET-2 with RNA polymerase II (RNAPII), but most eukaryotes also have additional H3K36me KMTs that act independently of RNAPII. These include the orthologs of ASH1, which are conserved in animals, plants, and fungi but whose function and control are poorly understood. We found that Neurospora crassa has just two H3K36 KMTs, ASH1 and SET-2, and were able to explore the function and distribution of each enzyme independently. While H3K36me deposited by SET-2 marks active genes, inactive genes are modified by ASH1 and its activity is critical for their repression. ASH1-marked chromatin can be further modified by methylation of H3K27, and ASH1 catalytic activity modulates the accumulation of H3K27me2/3 both positively and negatively. These findings provide new insight into ASH1 function, H3K27me2/3 establishment, and repression in facultative heterochromatin. Not all genes in a cell’s DNA are active all the time. There are several ways to control this activity. One is by altering how the DNA is packaged into cells. DNA strands are wrapped around proteins called histones to form nucleosomes. Nucleosomes can then be packed together tightly, to restrict access to the DNA at genes that are not active, or loosely to allow access to the DNA of active genes. Chemical marks, such as methyl groups, can be attached to particular sites on histones to influence how they pack together. One important site for such marks is known as position 36 on histone H3, or H3K36 for short. Correctly adding methyl groups to this site is critical for normal development, and when this process goes wrong it can lead to diseases like cancer. An enzyme called SET-2 oversees the methylation of H3K36 in fungi, plants and animals. However, many species have several other enzymes that can also add methyl groups to H3K36, and their roles are less clear. A type of fungus called Neurospora crassa contains just two enzymes that can add methyl groups to H3K36: SET-2, and another enzyme called ASH1. By performing experiments that inactivated SET-2 and ASH1 in this fungus, Bicocca et al. found that each enzyme works on a different set of genes. Genes in regions marked by SET-2 were accessible for the cell to use, while genes marked by ASH1 were inaccessible. ASH1 also affects whether a methyl group is added to another site on histone H3. This mark is important for controlling the activity of genes that are critical for development. ASH1 is found in many other organisms, including humans. The results presented by Bicocca et al. could therefore be built upon to understand the more complicated systems for regulating H3K36 methylation in other species. From there, we can investigate how to intervene when things go wrong during developmental disorders and cancer.
Collapse
Affiliation(s)
- Vincent T Bicocca
- Institute of Molecular Biology, University of Oregon, Eugene, United States
| | - Tereza Ormsby
- Department of Biochemistry Faculty of Science, Charles University, Prague, Czech Republic
| | | | - Shinji Honda
- Faculty of Medical Sciences, University of Fukui, Fukui, Japan
| | - Eric U Selker
- Institute of Molecular Biology, University of Oregon, Eugene, United States
| |
Collapse
|
634
|
Ferguson JW, Devarajan M, Atit RP. Stage-specific roles of Ezh2 and Retinoic acid signaling ensure calvarial bone lineage commitment. Dev Biol 2018; 443:173-187. [PMID: 30222957 PMCID: PMC6217976 DOI: 10.1016/j.ydbio.2018.09.014] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2018] [Revised: 09/07/2018] [Accepted: 09/13/2018] [Indexed: 01/10/2023]
Abstract
Development of the skull bones requires the coordination of two stem progenitor populations, the cranial neural crest cells (CNCC) and head paraxial mesoderm (PM), to ensure cell fate selection and morphogenesis. The epigenetic methyltransferase, Ezh2, plays a role in skull bone formation, but the spatiotemporal function of Ezh2 between the CNCC- and PM-derived bone formation in vivo remains undefined. Here, using a temporally-inducible conditional deletion of Ezh2 in both the CNCC- and PM- derived cranial mesenchyme between E8.5 and E9.5, we find a reduction of the CNCC-derived calvarial bones and a near complete loss of the PM-derived calvarial bones due to an arrest in calvarial bone fate commitment. In contrast, deletion of Ezh2 after E9.5 permits PM-derived skull bone development, suggesting that Ezh2 is required early to guide calvarial bone progenitor commitment. Furthermore, exposure to all-trans Retinoic acid at E10.0 can mimic the Ezh2 mutant calvarial phenotype, and administration of the pan retinoic acid receptor (RAR) antagonist, BMS-453, to Ezh2 mutants partially restores the commitment to the calvarial bone lineage and PM-derived bone development in vivo. Exogenous RA signaling activation in the Ezh2 mutants leads to synergistic activation of the anti-osteogenic factors in the cranial mesenchyme in vivo. Thus, RA signaling and EZH2 can function in parallel to guide calvarial bone progenitor commitment by balancing the suppression of anti-osteogenic factors.
Collapse
Affiliation(s)
- James W Ferguson
- Department of Biology, Case Western Reserve University, Cleveland, OH 44106, United States
| | - Mahima Devarajan
- Department of Biology, Case Western Reserve University, Cleveland, OH 44106, United States
| | - Radhika P Atit
- Department of Biology, Case Western Reserve University, Cleveland, OH 44106, United States; Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, OH 44106, United States; Department of Dermatology, Case Western Reserve University, Cleveland, OH 44106, United States.
| |
Collapse
|
635
|
Riddle NC, Elgin SCR. The Drosophila Dot Chromosome: Where Genes Flourish Amidst Repeats. Genetics 2018; 210:757-772. [PMID: 30401762 PMCID: PMC6218221 DOI: 10.1534/genetics.118.301146] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2018] [Accepted: 08/17/2018] [Indexed: 11/18/2022] Open
Abstract
The F element of the Drosophila karyotype (the fourth chromosome in Drosophila melanogaster) is often referred to as the "dot chromosome" because of its appearance in a metaphase chromosome spread. This chromosome is distinct from other Drosophila autosomes in possessing both a high level of repetitious sequences (in particular, remnants of transposable elements) and a gene density similar to that found in the other chromosome arms, ∼80 genes distributed throughout its 1.3-Mb "long arm." The dot chromosome is notorious for its lack of recombination and is often neglected as a consequence. This and other features suggest that the F element is packaged as heterochromatin throughout. F element genes have distinct characteristics (e.g, low codon bias, and larger size due both to larger introns and an increased number of exons), but exhibit expression levels comparable to genes found in euchromatin. Mapping experiments show the presence of appropriate chromatin modifications for the formation of DNaseI hypersensitive sites and transcript initiation at the 5' ends of active genes, but, in most cases, high levels of heterochromatin proteins are observed over the body of these genes. These various features raise many interesting questions about the relationships of chromatin structures with gene and chromosome function. The apparent evolution of the F element as an autosome from an ancestral sex chromosome also raises intriguing questions. The findings argue that the F element is a unique chromosome that occupies its own space in the nucleus. Further study of the F element should provide new insights into chromosome structure and function.
Collapse
Affiliation(s)
- Nicole C Riddle
- Department of Biology, The University of Alabama at Birmingham, Alabama 35294
| | - Sarah C R Elgin
- Department of Biology, Washington University in St. Louis, Missouri 63130
| |
Collapse
|
636
|
Di Carlo V, Mocavini I, Di Croce L. Polycomb complexes in normal and malignant hematopoiesis. J Cell Biol 2018; 218:55-69. [PMID: 30341152 PMCID: PMC6314559 DOI: 10.1083/jcb.201808028] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2018] [Revised: 09/21/2018] [Accepted: 10/04/2018] [Indexed: 12/13/2022] Open
Abstract
Di Carlo et al. discuss how the regulation/dysregulation of Polycomb group proteins contributes to hematopoiesis and hematological disorders. Epigenetic mechanisms are crucial for sustaining cell type–specific transcription programs. Among the distinct factors, Polycomb group (PcG) proteins are major negative regulators of gene expression in mammals. These proteins play key roles in regulating the proliferation, self-renewal, and differentiation of stem cells. During hematopoietic differentiation, many PcG proteins are fundamental for proper lineage commitment, as highlighted by the fact that a lack of distinct PcG proteins results in embryonic lethality accompanied by differentiation biases. Correspondingly, proteins of these complexes are frequently dysregulated in hematological diseases. In this review, we present an overview of the role of PcG proteins in normal and malignant hematopoiesis, focusing on the compositional complexity of PcG complexes, and we briefly discuss the ongoing clinical trials for drugs targeting these factors.
Collapse
Affiliation(s)
- Valerio Di Carlo
- Centre for Genomic Regulation, The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Ivano Mocavini
- Centre for Genomic Regulation, The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Luciano Di Croce
- Centre for Genomic Regulation, The Barcelona Institute of Science and Technology, Barcelona, Spain .,Universitat Pompeu Fabra, Barcelona, Spain.,Institucio Catalana de Recerca i Estudis Avançats, Barcelona, Spain
| |
Collapse
|
637
|
Reverón-Gómez N, González-Aguilera C, Stewart-Morgan KR, Petryk N, Flury V, Graziano S, Johansen JV, Jakobsen JS, Alabert C, Groth A. Accurate Recycling of Parental Histones Reproduces the Histone Modification Landscape during DNA Replication. Mol Cell 2018; 72:239-249.e5. [PMID: 30146316 PMCID: PMC6202308 DOI: 10.1016/j.molcel.2018.08.010] [Citation(s) in RCA: 149] [Impact Index Per Article: 24.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2018] [Revised: 06/25/2018] [Accepted: 08/07/2018] [Indexed: 12/22/2022]
Abstract
Chromatin organization is disrupted genome-wide during DNA replication. On newly synthesized DNA, nucleosomes are assembled from new naive histones and old modified histones. It remains unknown whether the landscape of histone post-translational modifications (PTMs) is faithfully copied during DNA replication or the epigenome is perturbed. Here we develop chromatin occupancy after replication (ChOR-seq) to determine histone PTM occupancy immediately after DNA replication and across the cell cycle. We show that H3K4me3, H3K36me3, H3K79me3, and H3K27me3 positional information is reproduced with high accuracy on newly synthesized DNA through histone recycling. Quantitative ChOR-seq reveals that de novo methylation to restore H3K4me3 and H3K27me3 levels occurs across the cell cycle with mark- and locus-specific kinetics. Collectively, this demonstrates that accurate parental histone recycling preserves positional information and allows PTM transmission to daughter cells while modification of new histones gives rise to complex epigenome fluctuations across the cell cycle that could underlie cell-to-cell heterogeneity.
Collapse
Affiliation(s)
- Nazaret Reverón-Gómez
- Biotech Research and Innovation Centre (BRIC), University of Copenhagen, Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen, Denmark; The Novo Nordisk Center for Protein Research (CPR), University of Copenhagen, Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Cristina González-Aguilera
- Biotech Research and Innovation Centre (BRIC), University of Copenhagen, Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Kathleen R Stewart-Morgan
- Biotech Research and Innovation Centre (BRIC), University of Copenhagen, Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen, Denmark; The Novo Nordisk Center for Protein Research (CPR), University of Copenhagen, Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Nataliya Petryk
- Biotech Research and Innovation Centre (BRIC), University of Copenhagen, Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen, Denmark; The Novo Nordisk Center for Protein Research (CPR), University of Copenhagen, Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Valentin Flury
- Biotech Research and Innovation Centre (BRIC), University of Copenhagen, Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen, Denmark; The Novo Nordisk Center for Protein Research (CPR), University of Copenhagen, Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Simona Graziano
- Biotech Research and Innovation Centre (BRIC), University of Copenhagen, Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen, Denmark; The Novo Nordisk Center for Protein Research (CPR), University of Copenhagen, Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Jens Vilstrup Johansen
- Biotech Research and Innovation Centre (BRIC), University of Copenhagen, Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Janus Schou Jakobsen
- Biotech Research and Innovation Centre (BRIC), University of Copenhagen, Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Constance Alabert
- Biotech Research and Innovation Centre (BRIC), University of Copenhagen, Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Anja Groth
- Biotech Research and Innovation Centre (BRIC), University of Copenhagen, Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen, Denmark; The Novo Nordisk Center for Protein Research (CPR), University of Copenhagen, Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen, Denmark.
| |
Collapse
|
638
|
Li M, Ma Z, Roy S, Patel SK, Lane DC, Duffy CR, Cai HN. Selective interactions between diverse STEs organize the ANT-C Hox cluster. Sci Rep 2018; 8:15158. [PMID: 30310129 PMCID: PMC6181975 DOI: 10.1038/s41598-018-33588-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2018] [Accepted: 10/01/2018] [Indexed: 11/09/2022] Open
Abstract
The three-dimensional organization of the eukaryotic genome is important for its structure and function. Recent studies indicate that hierarchies of chromatin loops underlie important aspects of both genomic organization and gene regulation. Looping between insulator or boundary elements interferes with enhancer-promoter communications and limits the spread active or repressive organized chromatin. We have used the SF1 insulator in the Drosophila Antennapedia homeotic gene complex (ANT-C) as a model to study the mechanism and regulation of chromatin looping events. We reported previously that SF1 tethers a transient chromatin loop in the early embryo that insulates the Hox gene Sex comb reduce from the neighbor non-Hox gene fushi tarazu for their independent regulation. To further probe the functional range and connectivity of SF1, we used high-resolution chromosomal conformation capture (3C) to search for SF1 looping partners across ANT-C. We report here the identification of three distal SF1 Tether Elements (STEs) located in the labial, Deformed and Antennapedia Hox gene regions, extending the range of SF1 looping network to the entire complex. These novel STEs are bound by four different combinations of insulator proteins and exhibit distinct behaviors in enhancer block, enhancer-bypass and boundary functions. Significantly, the six STEs we identified so far map to all but one of the major boundaries between repressive and active histone domains, underlining the functional relevance of these long-range chromatin loops in organizing the Hox complex. Importantly, SF1 selectively captured with only 5 STEs out of ~20 sites that display similar insulator binding profiles, indicating that presence of insulator proteins alone is not sufficient to determine looping events. These findings suggest that selective interaction among diverse STE insulators organize the Drosophila Hox genes in the 3D nuclear space.
Collapse
Affiliation(s)
- Mo Li
- Department of Cellular Biology, University of Georgia, Athens, GA, 30602, USA
| | - Zhibo Ma
- Department of Cellular Biology, University of Georgia, Athens, GA, 30602, USA
| | - Sharmila Roy
- Department of Cellular Biology, University of Georgia, Athens, GA, 30602, USA
| | - Sapna K Patel
- Department of Cellular Biology, University of Georgia, Athens, GA, 30602, USA
| | - Derrick C Lane
- Department of Cellular Biology, University of Georgia, Athens, GA, 30602, USA
| | - Carly R Duffy
- Department of Cellular Biology, University of Georgia, Athens, GA, 30602, USA
| | - Haini N Cai
- Department of Cellular Biology, University of Georgia, Athens, GA, 30602, USA.
| |
Collapse
|
639
|
Yin B, Yu F, Wang C, Li B, Liu M, Ye L. Epigenetic Control of Mesenchymal Stem Cell Fate Decision via Histone Methyltransferase Ash1l. Stem Cells 2018; 37:115-127. [PMID: 30270478 DOI: 10.1002/stem.2918] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2018] [Revised: 08/18/2018] [Accepted: 08/28/2018] [Indexed: 02/06/2023]
Abstract
Previous research indicates that knocking out absent, small, or homeotic-like (Ash1l) in mice, a histone 3 lysine 4 (H3K4) trimethyltransferase, can result in arthritis with more severe cartilage and bone destruction. Research has documented the essential role of Ash1l in stem cell fate decision such as hematopoietic stem cells and the progenitors of keratinocytes. Following up on those insights, our research seeks to document the function of Ash1l in skeletal formation, specifically whether it controls the fate decision of mesenchymal progenitor cells. Our findings indicate that in osteoporotic bones, Ash1l was significantly decreased, indicating a positive correlation between bone mass and the expression of Ash1l. Silencing of Ash1l that had been markedly upregulated in differentiated C3H10T1/2 (C3) cells hampered osteogenesis and chondrogenesis but promoted adipogenesis. Consistently, overexpression of an Ash1l SET domain-containing fragment 3 rather than Ash1lΔN promoted osteogenic and chondrogenic differentiation of C3 cells and simultaneously inhibited adipogenic differentiation. This indicates that the role of Ash1l in regulating the differentiation of C3 cells is linked to its histone methyltransferase activity. Subcutaneous ex vivo transplantation experiments confirmed the role of Ash1l in the promotion of osteogenesis. Further experiments proved that Ash1l can epigenetically affect the expression of essential osteogenic and chondrogenic transcription factors. It exerts this impact via modifications in the enrichment of H3K4me3 on their promoter regions. Considering the promotional action of Ash1l on bone, it could potentially prompt new therapeutic strategy to promote osteogenesis. Stem Cells 2019;37:115-127.
Collapse
Affiliation(s)
- Bei Yin
- State Key Laboratory of Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, People's Republic of China.,West China School of Stomatology, Sichuan University, Chengdu, People's Republic of China
| | - Fanyuan Yu
- State Key Laboratory of Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, People's Republic of China.,West China School of Stomatology, Sichuan University, Chengdu, People's Republic of China
| | - Chenglin Wang
- State Key Laboratory of Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, People's Republic of China.,West China School of Stomatology, Sichuan University, Chengdu, People's Republic of China
| | - Boer Li
- State Key Laboratory of Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, People's Republic of China.,West China School of Stomatology, Sichuan University, Chengdu, People's Republic of China
| | - Mengyu Liu
- State Key Laboratory of Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, People's Republic of China.,West China School of Stomatology, Sichuan University, Chengdu, People's Republic of China
| | - Ling Ye
- State Key Laboratory of Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, People's Republic of China.,West China School of Stomatology, Sichuan University, Chengdu, People's Republic of China
| |
Collapse
|
640
|
Bellec M, Radulescu O, Lagha M. Remembering the past: Mitotic bookmarking in a developing embryo. ACTA ACUST UNITED AC 2018; 11:41-49. [PMID: 30417158 PMCID: PMC6218673 DOI: 10.1016/j.coisb.2018.08.003] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
During development, transcriptional properties of progenitor cells are stably propagated across multiple cellular divisions. Yet, at each division, chromatin faces structural constraints imposed by the important nuclear re-organization operating during mitosis. It is now clear that not all transcriptional regulators are ejected during mitosis, but rather that a subset of transcription factors, chromatin regulators and epigenetic histone marks are able to ‘bookmark’ specific loci, thereby providing a mitotic memory. Here we review mechanisms of mitotic bookmarking and discuss their impact on transcriptional dynamics in the context of multicellular developing embryos. We document recent discoveries and technological advances, and present current mathematical models of short-term transcriptional memory. Mitotically retained factors are able to ‘bookmark’ specific loci during embryogenesis. Mitotic bookmarking can elicit rapid post-mitotic transcriptional re-activation. Mathematical models relating transcriptional memory predict that efficient memory requires slow dynamics. Mitotic memory leads to a spectrum of consequences: stability, flexibility or plasticity.
Collapse
Affiliation(s)
- Maelle Bellec
- Institut de Genetique Moleculaire de Montpellier, University of Montpellier, CNRS, Montpellier, France
| | - Ovidiu Radulescu
- DIMNP, UMR CNRS 5235, University of Montpellier, Montpellier, France
| | - Mounia Lagha
- Institut de Genetique Moleculaire de Montpellier, University of Montpellier, CNRS, Montpellier, France
- Corresponding author: Lagha, Mounia
| |
Collapse
|
641
|
Du J, Kirk B, Zeng J, Ma J, Wang Q. Three classes of response elements for human PRC2 and MLL1/2-Trithorax complexes. Nucleic Acids Res 2018; 46:8848-8864. [PMID: 29992232 PMCID: PMC6158500 DOI: 10.1093/nar/gky595] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2018] [Revised: 06/19/2018] [Accepted: 06/21/2018] [Indexed: 12/15/2022] Open
Abstract
Polycomb group (PcG) and Trithorax group (TrxG) proteins are essential for maintaining epigenetic memory in both embryonic stem cells and differentiated cells. To date, how they are localized to hundreds of specific target genes within a vertebrate genome had remained elusive. Here, by focusing on short cis-acting DNA elements of single functions, we discovered three classes of response elements in human genome: Polycomb response elements (PREs), Trithorax response elements (TREs) and Polycomb/Trithorax response elements (P/TREs). In particular, the four PREs (PRE14, 29, 39 and 48) are the first set of, to our knowledge, bona fide vertebrate PREs ever discovered, while many previously reported Drosophila or vertebrate PREs are likely P/TREs. We further demonstrated that YY1 and CpG islands are specifically enriched in the four TREs (PRE30, 41, 44 and 55), but not in the PREs. The three classes of response elements as unraveled in this study should guide further global investigation and open new doors for a deeper understanding of PcG and TrxG mechanisms in vertebrates.
Collapse
Affiliation(s)
- Junqing Du
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA
| | - Brian Kirk
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA
| | - Jia Zeng
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA
| | - Jianpeng Ma
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA
- Department of Bioengineering, Rice University, 6500 Main Street, Houston, TX 77030, USA
| | - Qinghua Wang
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA
| |
Collapse
|
642
|
Cheutin T, Cavalli G. Loss of PRC1 induces higher-order opening of Hox loci independently of transcription during Drosophila embryogenesis. Nat Commun 2018; 9:3898. [PMID: 30254245 PMCID: PMC6156336 DOI: 10.1038/s41467-018-05945-4] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2018] [Accepted: 07/30/2018] [Indexed: 12/14/2022] Open
Abstract
Polycomb-group proteins are conserved chromatin factors that maintain the silencing of key developmental genes, notably the Hox gene clusters, outside of their expression domains. Depletion of Polycomb repressive complex 1 (PRC1) proteins typically results in chromatin unfolding, as well as ectopic transcription. To disentangle these two phenomena, here we analyze the temporal function of two PRC1 proteins, Polyhomeotic (Ph) and Polycomb (Pc), on Hox gene clusters during Drosophila embryogenesis. We show that the absence of Ph or Pc affects the higher-order chromatin folding of Hox clusters prior to ectopic Hox gene transcription, demonstrating that PRC1 primary function during early embryogenesis is to compact its target chromatin. Moreover, the differential effects of Ph and Pc on Hox cluster folding match the differences in ectopic Hox gene expression observed in these two mutants. Our data suggest that PRC1 maintains gene silencing by folding chromatin domains and impose architectural layer to gene regulation. Loss of Polycomb repressive complex 1 (PRC1) proteins usually results in both chromatin unfolding and ectopic transcription. Here, the authors analyze the temporal function of two PRC1 proteins during Drosophila embryogenesis and provide evidence that PRC1 maintains gene silencing by folding chromatin domains.
Collapse
Affiliation(s)
- Thierry Cheutin
- Institute of Human Genetics, CNRS and the University of Montpellier, Montpellier, France.
| | - Giacomo Cavalli
- Institute of Human Genetics, CNRS and the University of Montpellier, Montpellier, France.
| |
Collapse
|
643
|
Mandal M, Maienschein-Cline M, Maffucci P, Veselits M, Kennedy DE, McLean KC, Okoreeh MK, Karki S, Cunningham-Rundles C, Clark MR. BRWD1 orchestrates epigenetic landscape of late B lymphopoiesis. Nat Commun 2018; 9:3888. [PMID: 30250168 PMCID: PMC6155124 DOI: 10.1038/s41467-018-06165-6] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2017] [Accepted: 08/20/2018] [Indexed: 12/30/2022] Open
Abstract
Transcription factor (TF) networks determine cell fate in hematopoiesis. However, how TFs cooperate with other regulatory mechanisms to instruct transcription remains poorly understood. Here we show that in small pre-B cells, the lineage restricted epigenetic reader BRWD1 closes early development enhancers and opens the enhancers of late B lymphopoiesis to TF binding. BRWD1 regulates over 7000 genes to repress proliferative and induce differentiation programs. However, BRWD1 does not regulate the expression of TFs required for B lymphopoiesis. Hypogammaglobulinemia patients with BRWD1 mutations have B-cell transcriptional profiles and enhancer landscapes similar to those observed in Brwd1-/- mice. These data indicate that, in both mice and humans, BRWD1 is a master orchestrator of enhancer accessibility that cooperates with TF networks to drive late B-cell development. B-cell development is tightly regulated by transcription programs that are coordinated by transcription factors (TF) and locus accessibility. Here the authors show that, in mice and humans, the epigenetic reader BRWD1 inhibits and promotes the accessibility of enhancers for early and late B lymphopoiesis, respectively.
Collapse
Affiliation(s)
- Malay Mandal
- Department of Medicine, Section of Rheumatology and Gwen Knapp Center for Lupus and Immunology Research, University of Chicago, Chicago, Illinois, USA.
| | - Mark Maienschein-Cline
- Core for Research Informatics, University of Illinois at Chicago, Chicago, Illinois, USA
| | - Patrick Maffucci
- Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA.,Division of Clinical Immunology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Margaret Veselits
- Department of Medicine, Section of Rheumatology and Gwen Knapp Center for Lupus and Immunology Research, University of Chicago, Chicago, Illinois, USA
| | - Domenick E Kennedy
- Department of Medicine, Section of Rheumatology and Gwen Knapp Center for Lupus and Immunology Research, University of Chicago, Chicago, Illinois, USA
| | - Kaitlin C McLean
- Department of Medicine, Section of Rheumatology and Gwen Knapp Center for Lupus and Immunology Research, University of Chicago, Chicago, Illinois, USA
| | - Michael K Okoreeh
- Department of Medicine, Section of Rheumatology and Gwen Knapp Center for Lupus and Immunology Research, University of Chicago, Chicago, Illinois, USA
| | - Sophiya Karki
- Department of Research Biology, Genentech, South San Francisco, California, USA
| | - Charlotte Cunningham-Rundles
- Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA.,Division of Clinical Immunology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Marcus R Clark
- Department of Medicine, Section of Rheumatology and Gwen Knapp Center for Lupus and Immunology Research, University of Chicago, Chicago, Illinois, USA.
| |
Collapse
|
644
|
Koohy H, Bolland DJ, Matheson LS, Schoenfelder S, Stellato C, Dimond A, Várnai C, Chovanec P, Chessa T, Denizot J, Manzano Garcia R, Wingett SW, Freire-Pritchett P, Nagano T, Hawkins P, Stephens L, Elderkin S, Spivakov M, Fraser P, Corcoran AE, Varga-Weisz PD. Genome organization and chromatin analysis identify transcriptional downregulation of insulin-like growth factor signaling as a hallmark of aging in developing B cells. Genome Biol 2018; 19:126. [PMID: 30180872 PMCID: PMC6124017 DOI: 10.1186/s13059-018-1489-y] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2018] [Accepted: 07/20/2018] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND Aging is characterized by loss of function of the adaptive immune system, but the underlying causes are poorly understood. To assess the molecular effects of aging on B cell development, we profiled gene expression and chromatin features genome-wide, including histone modifications and chromosome conformation, in bone marrow pro-B and pre-B cells from young and aged mice. RESULTS Our analysis reveals that the expression levels of most genes are generally preserved in B cell precursors isolated from aged compared with young mice. Nonetheless, age-specific expression changes are observed at numerous genes, including microRNA encoding genes. Importantly, these changes are underpinned by multi-layered alterations in chromatin structure, including chromatin accessibility, histone modifications, long-range promoter interactions, and nuclear compartmentalization. Previous work has shown that differentiation is linked to changes in promoter-regulatory element interactions. We find that aging in B cell precursors is accompanied by rewiring of such interactions. We identify transcriptional downregulation of components of the insulin-like growth factor signaling pathway, in particular downregulation of Irs1 and upregulation of Let-7 microRNA expression, as a signature of the aged phenotype. These changes in expression are associated with specific alterations in H3K27me3 occupancy, suggesting that Polycomb-mediated repression plays a role in precursor B cell aging. CONCLUSIONS Changes in chromatin and 3D genome organization play an important role in shaping the altered gene expression profile of aged precursor B cells. Components of the insulin-like growth factor signaling pathways are key targets of epigenetic regulation in aging in bone marrow B cell precursors.
Collapse
Affiliation(s)
- Hashem Koohy
- Nuclear Dynamics Programme, Babraham Institute, Cambridge, UK
- Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Daniel J Bolland
- Nuclear Dynamics Programme, Babraham Institute, Cambridge, UK
- Laboratory of Lymphocyte Signalling and Development, Babraham Institute, Cambridge, UK
| | - Louise S Matheson
- Nuclear Dynamics Programme, Babraham Institute, Cambridge, UK
- Laboratory of Lymphocyte Signalling and Development, Babraham Institute, Cambridge, UK
| | | | | | - Andrew Dimond
- Nuclear Dynamics Programme, Babraham Institute, Cambridge, UK
| | - Csilla Várnai
- Nuclear Dynamics Programme, Babraham Institute, Cambridge, UK
| | - Peter Chovanec
- Nuclear Dynamics Programme, Babraham Institute, Cambridge, UK
- Laboratory of Lymphocyte Signalling and Development, Babraham Institute, Cambridge, UK
| | | | - Jeremy Denizot
- Nuclear Dynamics Programme, Babraham Institute, Cambridge, UK
- Present address: Université Clermont Auvergne, Inserm U1071, M2iSH, USC-INRA 2018, F-, 63000, Clermont-Ferrand, France
| | | | - Steven W Wingett
- Nuclear Dynamics Programme, Babraham Institute, Cambridge, UK
- Bioinformatics, Babraham Institute, Cambridge, UK
| | - Paula Freire-Pritchett
- Nuclear Dynamics Programme, Babraham Institute, Cambridge, UK
- Division of Cell Biology, Medical Research Council Laboratory of Molecular Biology, Cambridge, CB2 0QH, UK
| | - Takashi Nagano
- Nuclear Dynamics Programme, Babraham Institute, Cambridge, UK
| | | | | | - Sarah Elderkin
- Nuclear Dynamics Programme, Babraham Institute, Cambridge, UK
| | - Mikhail Spivakov
- Nuclear Dynamics Programme, Babraham Institute, Cambridge, UK
- Functional Gene Control Group, MRC London Institute of Medical Sciences (LMS), Du Cane Road, London, W12 0NN, UK
| | - Peter Fraser
- Nuclear Dynamics Programme, Babraham Institute, Cambridge, UK
- Department of Biological Science, Florida State University, Tallahassee, FL, USA
| | - Anne E Corcoran
- Nuclear Dynamics Programme, Babraham Institute, Cambridge, UK.
- Laboratory of Lymphocyte Signalling and Development, Babraham Institute, Cambridge, UK.
| | - Patrick D Varga-Weisz
- Nuclear Dynamics Programme, Babraham Institute, Cambridge, UK.
- School of Biological Sciences, University of Essex, Colchester, UK.
| |
Collapse
|
645
|
Epigenetic and non-epigenetic functions of the RYBP protein in development and disease. Mech Ageing Dev 2018; 174:111-120. [DOI: 10.1016/j.mad.2018.03.011] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2017] [Revised: 03/22/2018] [Accepted: 03/26/2018] [Indexed: 12/30/2022]
|
646
|
Nakagawa T, Yoneda M, Higashi M, Ohkuma Y, Ito T. Enhancer function regulated by combinations of transcription factors and cofactors. Genes Cells 2018; 23:808-821. [PMID: 30092612 DOI: 10.1111/gtc.12634] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2018] [Revised: 07/23/2018] [Accepted: 07/24/2018] [Indexed: 12/11/2022]
Abstract
Regulation of the expression of diverse genes is essential for making possible the complexity of higher organisms, and the temporal and spatial regulation of gene expression allows for the alteration of cell types and growth patterns. A critical component of this regulation is the DNA sequence-specific binding of transcription factors (TFs). However, most TFs do not independently participate in gene transcriptional regulation, because they lack an effector function. Instead, TFs are thought to work by recruiting cofactors, including Mediator complex (Mediator), chromatin-remodeling complexes (CRCs), and histone-modifying complexes (HMCs). Mediator associates with the majority of transcribed genes and acts as an integrator of multiple signals. On the other hand, CRCs and HMCs are selectively recruited by TFs. Although all the pairings between TFs and CRCs or HMCs are not fully known, there are a growing number of established TF-CRC and TF-HMC combinations. In this review, we focused on the most important of these pairings and discuss how they control gene expression.
Collapse
Affiliation(s)
- Takeya Nakagawa
- Department of Biochemistry, Nagasaki University School of Medicine, Nagasaki, Japan
| | - Mitsuhiro Yoneda
- Department of Biochemistry, Nagasaki University School of Medicine, Nagasaki, Japan
| | - Miki Higashi
- Department of Biochemistry, Nagasaki University School of Medicine, Nagasaki, Japan
| | - Yoshiaki Ohkuma
- Department of Biochemistry, Nagasaki University School of Medicine, Nagasaki, Japan
| | - Takashi Ito
- Department of Biochemistry, Nagasaki University School of Medicine, Nagasaki, Japan
| |
Collapse
|
647
|
Meller B, Kuźnicki D, Arasimowicz-Jelonek M, Deckert J, Floryszak-Wieczorek J. BABA-Primed Histone Modifications in Potato for Intergenerational Resistance to Phytophthora infestans. FRONTIERS IN PLANT SCIENCE 2018; 9:1228. [PMID: 30233606 PMCID: PMC6135045 DOI: 10.3389/fpls.2018.01228] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/21/2018] [Accepted: 08/02/2018] [Indexed: 05/23/2023]
Abstract
In this paper we analyzed β-aminobutyric acid (BABA)-primed epigenetic adjustment of potato cv. "Sarpo Mira" to Phytophthora infestans. The first stress-free generation of the potato genotype obtained from BABA-primed parent plants via tubers and seeds showed pronounced resistance to the pathogen, which was tuned with the transcriptional memory of SA-responsive genes. During the early priming phase before the triggering stress, we found robust bistable deposition of histone marks (H3K4me2 and H3K27me3) on the NPR1 (Non-expressor of PR genes) and the SNI1 gene (Suppressor of NPR1, Inducible), in which transcription antagonized silencing. Switchable chromatin states of these adverse systemic acquired resistance (SAR) regulators probably reprogrammed responsiveness of the PR1 and PR2 genes and contributed to stress imprinting. The elevated levels of heritable H3K4me2 tag in the absence of transcription on SA-dependent genes in BABA-primed (F0) and its vegetative and generative progeny (F1) before pathogen challenge provided evidence for the epigenetic mark for intergenerational memory in potato. Moreover, our study revealed that histone acetylation was not critical for maintaining BABA-primed defense information until the plants were triggered with the virulent pathogen when rapid and boosted PRs gene expression probably required histone acetyltransferase (HAT) activity both in F0 and F1 progeny.
Collapse
Affiliation(s)
- Barbara Meller
- Department of Plant Physiology, Poznań University of Life Sciences, Poznań, Poland
| | - Daniel Kuźnicki
- Department of Plant Physiology, Poznań University of Life Sciences, Poznań, Poland
| | | | - Joanna Deckert
- Department of Plant Ecophysiology, Faculty of Biology, Adam Mickiewicz University in Poznań, Poznań, Poland
| | | |
Collapse
|
648
|
Chan HL, Beckedorff F, Zhang Y, Garcia-Huidobro J, Jiang H, Colaprico A, Bilbao D, Figueroa ME, LaCava J, Shiekhattar R, Morey L. Polycomb complexes associate with enhancers and promote oncogenic transcriptional programs in cancer through multiple mechanisms. Nat Commun 2018; 9:3377. [PMID: 30139998 PMCID: PMC6107513 DOI: 10.1038/s41467-018-05728-x] [Citation(s) in RCA: 94] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2017] [Accepted: 07/25/2018] [Indexed: 12/16/2022] Open
Abstract
Polycomb repressive complex 1 (PRC1) plays essential roles in cell fate decisions and development. However, its role in cancer is less well understood. Here, we show that RNF2, encoding RING1B, and canonical PRC1 (cPRC1) genes are overexpressed in breast cancer. We find that cPRC1 complexes functionally associate with ERα and its pioneer factor FOXA1 in ER+ breast cancer cells, and with BRD4 in triple-negative breast cancer cells (TNBC). While cPRC1 still exerts its repressive function, it is also recruited to oncogenic active enhancers. RING1B regulates enhancer activity and gene transcription not only by promoting the expression of oncogenes but also by regulating chromatin accessibility. Functionally, RING1B plays a divergent role in ER+ and TNBC metastasis. Finally, we show that concomitant recruitment of RING1B to active enhancers occurs across multiple cancers, highlighting an under-explored function of cPRC1 in regulating oncogenic transcriptional programs in cancer. The role of Polycomb Repressive Complex 1 (PRC1) is well described in development. Here, the authors investigate canonical PRC1’s regulation of transcriptional programs in breast cancer where, in addition to its repressive function, it is also recruited to oncogenic active enhancers to regulate enhancer activity and chromatin accessibility.
Collapse
Affiliation(s)
- Ho Lam Chan
- Sylvester Comprehensive Cancer Center, Biomedical Research Building, 1501 NW 10th Avenue, Miami, FL, 33136, USA.,Department of Human Genetics, University of Miami Miller School of Medicine, Miami, FL, 33136, USA
| | - Felipe Beckedorff
- Sylvester Comprehensive Cancer Center, Biomedical Research Building, 1501 NW 10th Avenue, Miami, FL, 33136, USA.,Department of Human Genetics, University of Miami Miller School of Medicine, Miami, FL, 33136, USA
| | - Yusheng Zhang
- Sylvester Comprehensive Cancer Center, Biomedical Research Building, 1501 NW 10th Avenue, Miami, FL, 33136, USA.,Department of Human Genetics, University of Miami Miller School of Medicine, Miami, FL, 33136, USA
| | - Jenaro Garcia-Huidobro
- Sylvester Comprehensive Cancer Center, Biomedical Research Building, 1501 NW 10th Avenue, Miami, FL, 33136, USA.,Department of Human Genetics, University of Miami Miller School of Medicine, Miami, FL, 33136, USA.,Centro de Investigaciones Médicas (CIM), Núcleo Científico Multidisciplinario, Escuela de Medicina, Universidad de Talca, Avenida Lircay S/N, Talca, 3460000, Chile
| | - Hua Jiang
- Laboratory of Cellular and Structural Biology, The Rockefeller University, New York, NY, 10065, USA
| | - Antonio Colaprico
- Sylvester Comprehensive Cancer Center, Biomedical Research Building, 1501 NW 10th Avenue, Miami, FL, 33136, USA.,Department of Human Genetics, University of Miami Miller School of Medicine, Miami, FL, 33136, USA
| | - Daniel Bilbao
- Sylvester Comprehensive Cancer Center, Biomedical Research Building, 1501 NW 10th Avenue, Miami, FL, 33136, USA
| | - Maria E Figueroa
- Sylvester Comprehensive Cancer Center, Biomedical Research Building, 1501 NW 10th Avenue, Miami, FL, 33136, USA.,Department of Human Genetics, University of Miami Miller School of Medicine, Miami, FL, 33136, USA
| | - John LaCava
- Laboratory of Cellular and Structural Biology, The Rockefeller University, New York, NY, 10065, USA.,Institute for Systems Genetics and Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, NY, 10016, USA
| | - Ramin Shiekhattar
- Sylvester Comprehensive Cancer Center, Biomedical Research Building, 1501 NW 10th Avenue, Miami, FL, 33136, USA.,Department of Human Genetics, University of Miami Miller School of Medicine, Miami, FL, 33136, USA
| | - Lluis Morey
- Sylvester Comprehensive Cancer Center, Biomedical Research Building, 1501 NW 10th Avenue, Miami, FL, 33136, USA. .,Department of Human Genetics, University of Miami Miller School of Medicine, Miami, FL, 33136, USA.
| |
Collapse
|
649
|
Kyrchanova O, Kurbidaeva A, Sabirov M, Postika N, Wolle D, Aoki T, Maksimenko O, Mogila V, Schedl P, Georgiev P. The bithorax complex iab-7 Polycomb response element has a novel role in the functioning of the Fab-7 chromatin boundary. PLoS Genet 2018; 14:e1007442. [PMID: 30110328 PMCID: PMC6110506 DOI: 10.1371/journal.pgen.1007442] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2018] [Revised: 08/27/2018] [Accepted: 07/30/2018] [Indexed: 12/22/2022] Open
Abstract
Expression of the three bithorax complex homeotic genes is orchestrated by nine parasegment-specific regulatory domains. Autonomy of each domain is conferred by boundary elements (insulators). Here, we have used an in situ replacement strategy to reanalyze the sequences required for the functioning of one of the best-characterized fly boundaries, Fab-7. It was initially identified by a deletion, Fab-71, that transformed parasegment (PS) 11 into a duplicate copy of PS12. Fab-71 deleted four nuclease hypersensitive sites, HS*, HS1, HS2, and HS3, located between the iab-6 and iab-7 regulatory domains. Transgenic and P-element excision experiments mapped the boundary to HS*+HS1+HS2, while HS3 was shown to be the iab-7 Polycomb response element (PRE). Recent replacement experiments showed that HS1 is both necessary and sufficient for boundary activity when HS3 is also present in the replacement construct. Surprisingly, while HS1+HS3 combination has full boundary activity, we discovered that HS1 alone has only minimal function. Moreover, when combined with HS3, only the distal half of HS1, dHS1, is needed. A ~1,000 kD multiprotein complex containing the GAF protein, called the LBC, binds to the dHS1 sequence and we show that mutations in dHS1, that disrupt LBC binding in nuclear extracts, eliminate boundary activity and GAF binding in vivo. HS3 has binding sites for GAF and Pho proteins that are required for PRE silencing. In contrast, HS3 boundary activity only requires the GAF binding sites. LBC binding with HS3 in nuclear extracts, and GAF association in vivo, depend upon the HS3 GAF sites, but not the Pho sites. Consistent with a role for the LBC in HS3 boundary activity, the boundary function of the dHS1+HS3mPho combination is lost when the flies are heterozygous for a mutation in the GAF gene. Taken together, these results reveal a novel function for the iab-7 PREs in chromosome architecture. Polycomb group proteins (PcG) are important epigenetic regulators of developmental genes in all higher eukaryotes. In Drosophila, these proteins are bound to specific regulatory DNA elements called Polycomb group Response Elements (PREs). Drosophila PREs are made up of binding sites for a complex array of DNA binding proteins, including GAF and Pho. In the regulatory region of the bithorax complex (BX-C), the boundary/insulator elements organize the autonomous regulatory domains, and their active or repressed states are regulated by PREs. Here, we studied functional properties of sequences that constitute the Fab-7 boundary and the adjacent iab-7 PRE. It was previously thought that the sole function of the iab-7 PRE is to recruit PcG proteins in parasegments anterior to PS12 and silence the iab-7 domain. However, we found that the iab-7 PRE also functions as a component of the Fab-7 boundary. The boundary activity of the iab-7 PRE sequence depends upon a large complex called the LBC. We show that it is possible to reconstitute a fully functional boundary by combining the LBC binding sequences in HS1 with the iab-7 PRE. Moreover, its boundary function is independent of its PcG silencing activity.
Collapse
Affiliation(s)
- Olga Kyrchanova
- Department of the Control of Genetic Processes, Institute of Gene Biology, Russian Academy of Sciences, Moscow, Russia
| | - Amina Kurbidaeva
- Laboratory of Gene Expression Regulation in Development, Institute of Gene Biology, Russian Academy of Sciences, Moscow, Russia
- Department of Molecular Biology, Princeton University, Princeton, NJ, United States of America
| | - Marat Sabirov
- Group of Molecular Organization of Genome, Institute of Gene Biology, Russian Acsademy of Sciences, Moscow, Russia
| | - Nikolay Postika
- Department of the Control of Genetic Processes, Institute of Gene Biology, Russian Academy of Sciences, Moscow, Russia
| | - Daniel Wolle
- Department of Molecular Biology, Princeton University, Princeton, NJ, United States of America
| | - Tsutomu Aoki
- Department of Molecular Biology, Princeton University, Princeton, NJ, United States of America
| | - Oksana Maksimenko
- Group of Molecular Organization of Genome, Institute of Gene Biology, Russian Acsademy of Sciences, Moscow, Russia
| | - Vladic Mogila
- Laboratory of Gene Expression Regulation in Development, Institute of Gene Biology, Russian Academy of Sciences, Moscow, Russia
| | - Paul Schedl
- Laboratory of Gene Expression Regulation in Development, Institute of Gene Biology, Russian Academy of Sciences, Moscow, Russia
- Department of Molecular Biology, Princeton University, Princeton, NJ, United States of America
- * E-mail: (PS); (PG)
| | - Pavel Georgiev
- Department of the Control of Genetic Processes, Institute of Gene Biology, Russian Academy of Sciences, Moscow, Russia
- * E-mail: (PS); (PG)
| |
Collapse
|
650
|
Unbiased shRNA screening, using a combination of FACS and high-throughput sequencing, enables identification of novel modifiers of Polycomb silencing. Sci Rep 2018; 8:12128. [PMID: 30108332 PMCID: PMC6092423 DOI: 10.1038/s41598-018-30649-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2017] [Accepted: 08/03/2018] [Indexed: 12/19/2022] Open
Abstract
Polycomb silencing is an important and rapidly growing field that is relevant to a broad range of aspects of human health, including cancer and stem cell biology. To date, the regulatory mechanisms for the fine-tuning of Polycomb silencing remain unclear, but it is likely that there is a series of unidentified factors that functionally modify or balance the silencing. However, a practical gene screening strategy for identifying such factors has not yet been developed. The failure of screening strategies used thus far is probably due to the effect of the loss-of-function phenotypes of these factors on cell cycle progression. Here, by applying fluorescence-activated cell sorter (FACS) and high-throughput sequencing (HTS) technology in a large-scale lentivirus-mediated shRNA screening, we obtained a consecutive dataset from all shRNAs tested, which highlighted a substantial number of genes that may control Polycomb silencing. We consider that this unbiased strategy can readily be applied to a wide range of studies to uncover novel regulatory layers for expression of genes of interest.
Collapse
|