101
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Vandenbon A, Kumagai Y, Lin M, Suzuki Y, Nakai K. Waves of chromatin modifications in mouse dendritic cells in response to LPS stimulation. Genome Biol 2018; 19:138. [PMID: 30231913 PMCID: PMC6146659 DOI: 10.1186/s13059-018-1524-z] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2018] [Accepted: 09/04/2018] [Indexed: 01/25/2023] Open
Abstract
BACKGROUND The importance of transcription factors (TFs) and epigenetic modifications in the control of gene expression is widely accepted. However, causal relationships between changes in TF binding, histone modifications, and gene expression during the response to extracellular stimuli are not well understood. Here, we analyze the ordering of these events on a genome-wide scale in dendritic cells in response to lipopolysaccharide (LPS) stimulation. RESULTS Using a ChIP-seq time series dataset, we find that the LPS-induced accumulation of different histone modifications follows clearly distinct patterns. Increases in H3K4me3 appear to coincide with transcriptional activation. In contrast, H3K9K14ac accumulates early after stimulation, and H3K36me3 at later time points. Integrative analysis with TF binding data reveals potential links between TF activation and dynamics in histone modifications. Especially, LPS-induced increases in H3K9K14ac and H3K4me3 are associated with binding by STAT1/2 and were severely impaired in Stat1-/- cells. CONCLUSIONS While the timing of short-term changes of some histone modifications coincides with changes in transcriptional activity, this is not the case for others. In the latter case, dynamics in modifications more likely reflect strict regulation by stimulus-induced TFs and their interactions with chromatin modifiers.
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Affiliation(s)
- Alexis Vandenbon
- Laboratory of Infection and Prevention, Institute for Frontier Life and Medical Sciences, Kyoto University, Kyoto, 606-8507, Japan.
- Institute for Liberal Arts and Sciences, Kyoto University, Kyoto, 606-8507, Japan.
| | - Yutaro Kumagai
- Quantitative Immunology Research Unit, Immunology Frontier Research Center (IFReC), Osaka University, Suita, 565-0871, Japan
- Biotechnology Research Institute for Drug Discovery, Department of Life Science and Biotechnology, National Institute of Advanced Industrial Science and Technology, Tsukuba, Ibaraki, 305-8565, Japan
| | - Mengjie Lin
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, 277-8561, Japan
| | - Yutaka Suzuki
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, 277-8561, Japan
| | - Kenta Nakai
- Laboratory of Functional Analysis in silico, The Institute of Medical Science, The University of Tokyo, Minato-ku, Tokyo, 108-8639, Japan.
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102
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Voss AK, Thomas T. Histone Lysine and Genomic Targets of Histone Acetyltransferases in Mammals. Bioessays 2018; 40:e1800078. [PMID: 30144132 DOI: 10.1002/bies.201800078] [Citation(s) in RCA: 78] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2018] [Revised: 08/01/2018] [Indexed: 01/08/2023]
Abstract
Histone acetylation has been recognized as an important post-translational modification of core nucleosomal histones that changes access to the chromatin to allow gene transcription, DNA replication, and repair. Histone acetyltransferases were initially identified as co-activators that link DNA-binding transcription factors to the general transcriptional machinery. Over the years, more chromatin-binding modes have been discovered suggesting direct interaction of histone acetyltransferases and their protein complex partners with histone proteins. While much progress has been made in characterizing histone acetyltransferase complexes biochemically, cell-free activity assay results are often at odds with in-cell histone acetyltransferase activities. In-cell studies suggest specific histone lysine targets, but broad recruitment modes, apparently not relying on specific DNA sequences, but on chromatin of a specific functional state. Here we review the evidence for general versus specific roles of individual nuclear lysine acetyltransferases in light of in vivo and in vitro data in the mammalian system.
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Affiliation(s)
- Anne K Voss
- Walter and Eliza Hall Institute of Medical Research, 3 1G Royal Parade, Parkville, Melbourne, Victoria, 3052, Australia
| | - Tim Thomas
- Department of Medical Biology, The University of Melbourne, 1G Royal Parade, Parkville, Melbourne, Victoria, 3052, Australia
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103
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Masuzawa R, Konno R, Ohsawa I, Watanabe A, Kawano F. Muscle type-specific RNA polymerase II recruitment during PGC-1α gene transcription after acute exercise in adult rats. J Appl Physiol (1985) 2018; 125:1238-1245. [PMID: 30113273 DOI: 10.1152/japplphysiol.00202.2018] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Epigenetic regulation of gene expression differs between fast- and slow-twitch skeletal muscles in adult rats, although the precise mechanisms are still unknown. The present study investigates the differences in responses of RNA polymerase II (Pol II) and histone acetylation during transcriptional activation in the plantaris and soleus muscles of adult rats after acute treadmill running. We targeted the peroxisome proliferator-activated receptor gamma coactivator 1-alpha (PGC-1α) gene to analyze epigenomic changes by chromatin immunoprecipitation. The mRNA expression of the PGC-1α-b isoform was significantly up-regulated in both plantaris and soleus muscles 2 h after acute running, although the magnitude of the up-regulation was more pronounced in the plantaris muscle. The sequences of proximal exons of the PGC-1α locus were expressed more in the plantaris muscle after acute running. Accumulation of Pol II was noted near the alternative exon 1 in both plantaris and soleus muscles in association with the enhanced distribution of acetylated histone 3. Accumulation of Pol II was also observed at the transcription start site, exon 2, and exon 3 in the plantaris muscle, but not the soleus muscle. It was noted that in the soleus muscle, acetylation of histone 3 at lysine 27 was enhanced throughout the PGC-1α locus in response to transcriptional activation, suggesting that elongating Pol II was capable of traveling through to the end of the locus. These results indicate that the mobility of Pol II during PGC-1αtranscription differed between fast- and slow-twitch skeletal muscles, affecting the strength of the transcriptional activity.
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Affiliation(s)
- Ryo Masuzawa
- Graduate School of Health Sciences, Matsumoto University
| | - Ryotaro Konno
- Department of Sports and Health Science, Faculty of Human Health Science, Matsumoto University
| | - Ikumi Ohsawa
- Department of Sports and Health Science, Faculty of Human Health and Science, Matsumoto University
| | | | - Fuminori Kawano
- Graduate School of Health Sciences, Matsumoto University, Japan
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104
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Long C, Lai Y, Li J, Huang J, Zou C. LPS promotes HBO1 stability via USP25 to modulate inflammatory gene transcription in THP-1 cells. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2018; 1861:773-782. [PMID: 30745998 DOI: 10.1016/j.bbagrm.2018.08.001] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
The histone acetyltransferase HBO1 (Histone acetyltransferase binding to origin recognition complex 1, Myst2/Kat7) participates in a range of life processes including DNA replication and tumorigenesis. Recent studies revealed that HBO1 is involved in gene transcriptional activation. However, the molecular behavior of HBO1 in inflammation is yet to be studied. Here we report that endotoxin lipopolysaccharide (LPS) elevates HBO1 protein level via up-regulating UPS25 (ubiquitin specific peptidase 25) and alters inflammatory gene transcription in THP-1 monocytes and in human primary macrophages. LPS protects HBO1 from ubiquitin proteasomal degradation without significantly altering its transcription. By immunoprecipitation, we identified that HBO1 associates with a deubiquitinating enzyme USP25 in THP-1 cells. LPS increases protein level of USP25 resulting in accumulation of HBO1 by suppression of HBO1 ubiquitination. Stabilized-HBO1 modulates inflammatory gene transcription in THP-1 cells. These findings indicate that USP25 promotes stability of HBO1 in bacterial infection thereby enhances HBO1-mediated inflammatory gene transcription.
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Affiliation(s)
- Chen Long
- Department of Minimally Invasive Surgery, the Second Xiangya Hospital, Central South University, Changsha, Hunan, China 410011.,Acute Lung Injury Center of Excellence, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA 15213
| | - Yandong Lai
- Acute Lung Injury Center of Excellence, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA 15213
| | - Jin Li
- Acute Lung Injury Center of Excellence, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA 15213
| | - Jiangsheng Huang
- Department of Minimally Invasive Surgery, the Second Xiangya Hospital, Central South University, Changsha, Hunan, China 410011
| | - Chunbin Zou
- Acute Lung Injury Center of Excellence, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA 15213
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105
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Abstract
RNA is the fundamental information transfer system in the cell. The ability to follow single messenger RNAs (mRNAs) from transcription to degradation with fluorescent probes gives quantitative information about how the information is transferred from DNA to proteins. This review focuses on the latest technological developments in the field of single-mRNA detection and their usage to study gene expression in both fixed and live cells. By describing the application of these imaging tools, we follow the journey of mRNA from transcription to decay in single cells, with single-molecule resolution. We review current theoretical models for describing transcription and translation that were generated by single-molecule and single-cell studies. These methods provide a basis to study how single-molecule interactions generate phenotypes, fundamentally changing our understating of gene expression regulation.
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Affiliation(s)
- Evelina Tutucci
- Department of Anatomy and Structural Biology, Albert Einstein College of Medicine, Bronx, New York 10461;,
| | - Nathan M. Livingston
- Center for Cell Dynamics, Johns Hopkins School of Medicine, Baltimore, Maryland 21205
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins School of Medicine, Baltimore, Maryland 21205
| | - Robert H. Singer
- Department of Anatomy and Structural Biology, Albert Einstein College of Medicine, Bronx, New York 10461;,
- Gruss-Lipper Biophotonics Center, Albert Einstein College of Medicine, Bronx, New York 10461
- Cellular Imaging Consortium, Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, Virginia 20147
| | - Bin Wu
- Center for Cell Dynamics, Johns Hopkins School of Medicine, Baltimore, Maryland 21205
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins School of Medicine, Baltimore, Maryland 21205
- The Solomon H. Snyder Department of Neuroscience, Johns Hopkins School of Medicine, Baltimore, Maryland 21205;,
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106
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Freddolino PL, Yang J, Momen-Roknabadi A, Tavazoie S. Stochastic tuning of gene expression enables cellular adaptation in the absence of pre-existing regulatory circuitry. eLife 2018; 7:e31867. [PMID: 29620524 PMCID: PMC5919758 DOI: 10.7554/elife.31867] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2017] [Accepted: 04/04/2018] [Indexed: 12/12/2022] Open
Abstract
Cells adapt to familiar changes in their environment by activating predefined regulatory programs that establish adaptive gene expression states. These hard-wired pathways, however, may be inadequate for adaptation to environments never encountered before. Here, we reveal evidence for an alternative mode of gene regulation that enables adaptation to adverse conditions without relying on external sensory information or genetically predetermined cis-regulation. Instead, individual genes achieve optimal expression levels through a stochastic search for improved fitness. By focusing on improving the overall health of the cell, the proposed stochastic tuning mechanism discovers global gene expression states that are fundamentally new and yet optimized for novel environments. We provide experimental evidence for stochastic tuning in the adaptation of Saccharomyces cerevisiae to laboratory-engineered environments that are foreign to its native gene-regulatory network. Stochastic tuning operates locally at individual gene promoters, and its efficacy is modulated by perturbations to chromatin modification machinery.
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Affiliation(s)
- Peter L Freddolino
- Department of Systems BiologyColumbia UniversityNew York CityUnited States
- Department of Biochemistry and Molecular BiophysicsColumbia UniversityNew York CityUnited States
| | - Jamie Yang
- Department of Systems BiologyColumbia UniversityNew York CityUnited States
- Department of Biochemistry and Molecular BiophysicsColumbia UniversityNew York CityUnited States
| | - Amir Momen-Roknabadi
- Department of Systems BiologyColumbia UniversityNew York CityUnited States
- Department of Biochemistry and Molecular BiophysicsColumbia UniversityNew York CityUnited States
| | - Saeed Tavazoie
- Department of Systems BiologyColumbia UniversityNew York CityUnited States
- Department of Biochemistry and Molecular BiophysicsColumbia UniversityNew York CityUnited States
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107
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Abstract
Neurons are dynamic cells that respond and adapt to stimuli throughout their long postmitotic lives. The structural and functional plasticity of neurons requires the regulated transcription of new gene products, and dysregulation of transcription in either the developing or adult brain impairs cognition. We discuss how mechanisms of chromatin regulation help to orchestrate the transcriptional programs that underlie the maturation of developing neurons and the plasticity of adult neurons. We review how chromatin regulation acts locally to modulate the expression of specific genes and more broadly to coordinate gene expression programs during transitions between cellular states. These data highlight the importance of epigenetic transcriptional mechanisms in postmitotic neurons. We suggest areas where emerging methods may advance understanding in the future.
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Affiliation(s)
- David A Gallegos
- Department of Neurobiology, Duke University School of Medicine, Durham, NC 27710, USA
| | - Urann Chan
- Department of Neurobiology, Duke University School of Medicine, Durham, NC 27710, USA
| | - Liang-Fu Chen
- Department of Neurobiology, Duke University School of Medicine, Durham, NC 27710, USA
| | - Anne E West
- Department of Neurobiology, Duke University School of Medicine, Durham, NC 27710, USA.
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108
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Goldstein I, Hager GL. The Three Ds of Transcription Activation by Glucagon: Direct, Delayed, and Dynamic. Endocrinology 2018; 159:206-216. [PMID: 29077799 PMCID: PMC6283435 DOI: 10.1210/en.2017-00521] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/05/2017] [Accepted: 10/20/2017] [Indexed: 12/13/2022]
Abstract
Upon lowered blood glucose occurring during fasting, glucagon is secreted from pancreatic islets, exerting various metabolic effects to normalize glucose levels. A considerable portion of these effects is mediated by glucagon-activated transcription factors (TFs) in liver. Glucagon directly activates several TFs via immediate cyclic adenosine monophosphate (cAMP)- and calcium-dependent signaling events. Among these TFs, cAMP response element-binding protein (CREB) is a major factor. CREB recruits histone-modifying enzymes and cooperates with other TFs on the chromatin template to increase the rate of gene transcription. In addition to direct signal transduction, the transcriptional effects of glucagon are also influenced by dynamic TF cross talk. Specifically, assisted loading of one TF by a companion TF leads to increased binding and activity. Lastly, transcriptional regulation by glucagon is also exerted by TF cascades by which a primary TF induces the gene expression of secondary TFs that bring about their activity a few hours after the initial glucagon signal. This mechanism of a delayed response may be instrumental in establishing the temporal organization of the fasting response by which distinct metabolic events separate early from prolonged fasting. In this mini-review, we summarize recent advances and critical discoveries in glucagon-dependent gene regulation with a focus on direct TF activation, dynamic TF cross talk, and TF cascades.
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Affiliation(s)
- Ido Goldstein
- Laboratory of Receptor Biology and Gene Expression, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
- Correspondence: Gordon L. Hager, PhD, Laboratory of Receptor Biology and Gene Expression, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Building 41, Room B602, Bethesda, Maryland 20892. E-mail: ; or Ido Goldstein, PhD, Laboratory of Receptor Biology and Gene Expression, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Building 41, Room B307, Bethesda, Maryland 20892. E-mail:
| | - Gordon L Hager
- Laboratory of Receptor Biology and Gene Expression, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
- Correspondence: Gordon L. Hager, PhD, Laboratory of Receptor Biology and Gene Expression, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Building 41, Room B602, Bethesda, Maryland 20892. E-mail: ; or Ido Goldstein, PhD, Laboratory of Receptor Biology and Gene Expression, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Building 41, Room B307, Bethesda, Maryland 20892. E-mail:
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109
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Huang D, Lan W, Li D, Deng B, Lin W, Ren Y, Miao Y. WHIRLY1 Occupancy Affects Histone Lysine Modification and WRKY53 Transcription in Arabidopsis Developmental Manner. FRONTIERS IN PLANT SCIENCE 2018; 9:1503. [PMID: 30405658 PMCID: PMC6202938 DOI: 10.3389/fpls.2018.01503] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/15/2018] [Accepted: 09/26/2018] [Indexed: 05/21/2023]
Abstract
Single-stranded DNA-binding proteins (SSBs) are assumed to involve in DNA replication, DNA repairmen, and gene transcription. Here, we provide the direct evidence on the functionality of an Arabidopsis SSB, WHIRLY1, by using loss- or gain-of-function lines. We show that WHIRLY1 binding to the promoter of WRKY53 represses the enrichment of H3K4me3, but enhances the enrichment of H3K9ac at the region contained WHIRLY1-binding sequences and TATA box or the translation start region of WRKY53, coincided with a recruitment of RNAPII. In vitro ChIP assays confirm that WHIRLY1 inhibits H3K4me3 enrichment at the preinitiation complex formation stage, while promotes H3K9ac enrichment and RNAPII recruitment at the elongation stage, consequently affecting the transcription of WRKY53. These results further explore the molecular actions underlying SSB-mediated gene transcription through epigenetic regulation in plant senescence.
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110
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Tycko J, Van MV, Elowitz MB, Bintu L. Advancing towards a global mammalian gene regulation model through single-cell analysis and synthetic biology. CURRENT OPINION IN BIOMEDICAL ENGINEERING 2017. [DOI: 10.1016/j.cobme.2017.10.011] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
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111
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Germier T, Kocanova S, Walther N, Bancaud A, Shaban HA, Sellou H, Politi AZ, Ellenberg J, Gallardo F, Bystricky K. Real-Time Imaging of a Single Gene Reveals Transcription-Initiated Local Confinement. Biophys J 2017; 113:1383-1394. [PMID: 28978433 PMCID: PMC5627313 DOI: 10.1016/j.bpj.2017.08.014] [Citation(s) in RCA: 110] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2017] [Revised: 07/08/2017] [Accepted: 08/04/2017] [Indexed: 11/18/2022] Open
Abstract
Genome dynamics are intimately linked to the regulation of gene expression, the most fundamental mechanism in biology, yet we still do not know whether the very process of transcription drives spatial organization at specific gene loci. Here, we have optimized the ANCHOR/ParB DNA-labeling system for real-time imaging of a single-copy, estrogen-inducible transgene in human cells. Motion of an ANCHOR3-tagged DNA locus was recorded in the same cell before and during the appearance of nascent MS2-labeled mRNA. We found that transcription initiation by RNA polymerase 2 resulted in confinement of the mRNA-producing gene domain within minutes. Transcription-induced confinement occurred in each single cell independently of initial, highly heterogeneous mobility. Constrained mobility was maintained even when inhibiting polymerase elongation. Chromatin motion at constant step size within a largely confined area hence leads to increased collisions that are compatible with the formation of gene-specific chromatin domains, and reflect the assembly of functional protein hubs and DNA processing during the rate-limiting steps of transcription.
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Affiliation(s)
- Thomas Germier
- Laboratoire de Biologie Moléculaire Eucaryote (LBME), Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, Toulouse, France
| | - Silvia Kocanova
- Laboratoire de Biologie Moléculaire Eucaryote (LBME), Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, Toulouse, France
| | - Nike Walther
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | - Aurélien Bancaud
- Laboratoire des Automatismes et Architecture des Systèmes (LAAS), CNRS, UPS, Toulouse, France
| | - Haitham Ahmed Shaban
- Laboratoire de Biologie Moléculaire Eucaryote (LBME), Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, Toulouse, France; Spectroscopy Department, Physics Division, National Research Centre, Dokki, Giza, Egypt
| | - Hafida Sellou
- Laboratoire de Biologie Moléculaire Eucaryote (LBME), Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, Toulouse, France
| | - Antonio Zaccaria Politi
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | - Jan Ellenberg
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | - Franck Gallardo
- Laboratoire de Biologie Moléculaire Eucaryote (LBME), Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, Toulouse, France; Institut des Technologies Avancées du Vivant (ITAV), Université de Toulouse, CNRS, UPS, INSA; NeoVirTech S.A., Toulouse, France
| | - Kerstin Bystricky
- Laboratoire de Biologie Moléculaire Eucaryote (LBME), Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, Toulouse, France; Institut des Technologies Avancées du Vivant (ITAV), Université de Toulouse, CNRS, UPS, INSA.
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112
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Goldstein I, Paakinaho V, Baek S, Sung MH, Hager GL. Synergistic gene expression during the acute phase response is characterized by transcription factor assisted loading. Nat Commun 2017; 8:1849. [PMID: 29185442 PMCID: PMC5707366 DOI: 10.1038/s41467-017-02055-5] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2017] [Accepted: 11/03/2017] [Indexed: 12/18/2022] Open
Abstract
The cytokines interleukin 1β and 6 (IL-1β, IL-6) mediate the acute phase response (APR). In liver, they regulate the secretion of acute phase proteins. Using RNA-seq in primary hepatocytes, we show that these cytokines regulate transcription in a bifurcated manner, leading to both synergistic and antagonistic gene expression. By mapping changes in enhancer landscape and transcription factor occupancy (using ChIP-seq), we show that synergistic gene induction is achieved by assisted loading of STAT3 on chromatin by NF-κB. With IL-6 treatment alone, STAT3 does not efficiently bind 20% of its coordinated binding sites. In the presence of IL-1β, NF-κB is activated, binds a subset of enhancers and primes their activity, as evidenced by increasing H3K27ac. This facilitates STAT3 binding and synergistic gene expression. Our findings reveal an enhancer-specific crosstalk whereby NF-κB enables STAT3 binding at some enhancers while perturbing it at others. This model reconciles seemingly contradictory reports of NF-κB-STAT3 crosstalk. The cytokines IL-1β and IL-6 mediate the systemic acute phase response (APR). Here, the authors provide evidence that these cytokines lead to both synergistic and antagonistic gene expression during APR; synergistic induction occurs by assisted loading of STAT3 on chromatin by NF-κB.
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Affiliation(s)
- Ido Goldstein
- Laboratory of Receptor Biology and Gene Expression, CCR, NCI, NIH, Bethesda, MD, 20892, USA.
| | - Ville Paakinaho
- Laboratory of Receptor Biology and Gene Expression, CCR, NCI, NIH, Bethesda, MD, 20892, USA
| | - Songjoon Baek
- Laboratory of Receptor Biology and Gene Expression, CCR, NCI, NIH, Bethesda, MD, 20892, USA
| | - Myong-Hee Sung
- Laboratory of Molecular Biology and Immunology, NIA, NIH, Baltimore, MD, 21224, USA
| | - Gordon L Hager
- Laboratory of Receptor Biology and Gene Expression, CCR, NCI, NIH, Bethesda, MD, 20892, USA.
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113
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Ha M, Hong S. Gene-regulatory interactions in embryonic stem cells represent cell-type specific gene regulatory programs. Nucleic Acids Res 2017; 45:10428-10435. [PMID: 28977540 PMCID: PMC5737473 DOI: 10.1093/nar/gkx752] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2017] [Accepted: 08/17/2017] [Indexed: 12/22/2022] Open
Abstract
Pluripotency, the ability of embryonic stem cells to differentiate into specialized cell types, is determined by ESC-specific gene regulators such as transcription factors and chromatin modification factors. It is not well understood how ESCs are poised for differentiation, however, and methods are needed for prognosis of the molecular changes in the differentiation of ESCs into specific organs. We describe a new approach to infer cell-type specific gene regulatory programs based on gene regulatory interactions in ESCs. Our method infers the molecular logic of gene regulatory mechanisms by mapping the position-specific combinatory patterns of numerous regulators in ESCs into cell-type specific gene regulations. We validate the proposed approach by recapitulating the RNA-seq and microarray data of neuronal progenitor cells, adult liver cells, and ESCs from the integrated patterns of diverse gene regulators in ESCs. We find that the collective functions of diverse gene regulators in ESCs represent distinct gene regulatory programs in specialized cell types. Our new approach expands our understanding of the differential gene regulatory information in developments encoded in regulatory networks of ESCs.
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Affiliation(s)
- Misook Ha
- Samsung Advanced Institute of Technology, Samsung Electronics Corporation, Suwon 443-803, Korea
| | - Soondo Hong
- Department of Industrial Engineering, Pusan National University, Busan 46241, South Korea
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114
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CBP Regulates Recruitment and Release of Promoter-Proximal RNA Polymerase II. Mol Cell 2017; 68:491-503.e5. [PMID: 29056321 DOI: 10.1016/j.molcel.2017.09.031] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2016] [Revised: 07/13/2017] [Accepted: 09/21/2017] [Indexed: 11/21/2022]
Abstract
Transcription activation involves RNA polymerase II (Pol II) recruitment and release from the promoter into productive elongation, but how specific chromatin regulators control these steps is unclear. Here, we identify a novel activity of the histone acetyltransferase p300/CREB-binding protein (CBP) in regulating promoter-proximal paused Pol II. We find that Drosophila CBP inhibition results in "dribbling" of Pol II from the pause site to positions further downstream but impedes transcription through the +1 nucleosome genome-wide. Promoters strongly occupied by CBP and GAGA factor have high levels of paused Pol II, a unique chromatin signature, and are highly expressed regardless of cell type. Interestingly, CBP activity is rate limiting for Pol II recruitment to these highly paused promoters through an interaction with TFIIB but for transit into elongation by histone acetylation at other genes. Thus, CBP directly stimulates both Pol II recruitment and the ability to traverse the first nucleosome, thereby promoting transcription of most genes.
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115
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Baumgart SJ, Najafova Z, Hossan T, Xie W, Nagarajan S, Kari V, Ditzel N, Kassem M, Johnsen SA. CHD1 regulates cell fate determination by activation of differentiation-induced genes. Nucleic Acids Res 2017; 45:7722-7735. [PMID: 28475736 PMCID: PMC5570082 DOI: 10.1093/nar/gkx377] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2017] [Accepted: 05/03/2017] [Indexed: 12/12/2022] Open
Abstract
The coordinated temporal and spatial activation of gene expression is essential for proper stem cell differentiation. The Chromodomain Helicase DNA-binding protein 1 (CHD1) is a chromatin remodeler closely associated with transcription and nucleosome turnover downstream of the transcriptional start site (TSS). In this study, we show that CHD1 is required for the induction of osteoblast-specific gene expression, extracellular-matrix mineralization and ectopic bone formation in vivo. Genome-wide occupancy analyses revealed increased CHD1 occupancy around the TSS of differentiation-activated genes. Furthermore, we observed that CHD1-dependent genes are mainly induced during osteoblast differentiation and are characterized by higher levels of CHD1 occupancy around the TSS. Interestingly, CHD1 depletion resulted in increased pausing of RNA Polymerase II (RNAPII) and decreased H2A.Z occupancy close to the TSS, but not at enhancer regions. These findings reveal a novel role for CHD1 during osteoblast differentiation and provide further insights into the intricacies of epigenetic regulatory mechanisms controlling cell fate determination.
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Affiliation(s)
- Simon J Baumgart
- Department of General, Visceral and Pediatric Surgery, University Medical Center Göttingen, 37075 Göttingen, Germany
| | - Zeynab Najafova
- Department of General, Visceral and Pediatric Surgery, University Medical Center Göttingen, 37075 Göttingen, Germany
| | - Tareq Hossan
- Department of General, Visceral and Pediatric Surgery, University Medical Center Göttingen, 37075 Göttingen, Germany
| | - Wanhua Xie
- Department of General, Visceral and Pediatric Surgery, University Medical Center Göttingen, 37075 Göttingen, Germany
| | - Sankari Nagarajan
- Department of General, Visceral and Pediatric Surgery, University Medical Center Göttingen, 37075 Göttingen, Germany
| | - Vijayalakshmi Kari
- Department of General, Visceral and Pediatric Surgery, University Medical Center Göttingen, 37075 Göttingen, Germany
| | - Nicholas Ditzel
- Molecular Endocrinology and Stem Cell Research Unit (KMEB), University Hospital of Odense and University of Southern Denmark, Odense 5000, Denmark
| | - Moustapha Kassem
- Molecular Endocrinology and Stem Cell Research Unit (KMEB), University Hospital of Odense and University of Southern Denmark, Odense 5000, Denmark
| | - Steven A Johnsen
- Department of General, Visceral and Pediatric Surgery, University Medical Center Göttingen, 37075 Göttingen, Germany
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Dzida T, Iqbal M, Charapitsa I, Reid G, Stunnenberg H, Matarese F, Grote K, Honkela A, Rattray M. Predicting stimulation-dependent enhancer-promoter interactions from ChIP-Seq time course data. PeerJ 2017; 5:e3742. [PMID: 28970965 PMCID: PMC5623311 DOI: 10.7717/peerj.3742] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2017] [Accepted: 08/07/2017] [Indexed: 12/31/2022] Open
Abstract
We have developed a machine learning approach to predict stimulation-dependent enhancer-promoter interactions using evidence from changes in genomic protein occupancy over time. The occupancy of estrogen receptor alpha (ERα), RNA polymerase (Pol II) and histone marks H2AZ and H3K4me3 were measured over time using ChIP-Seq experiments in MCF7 cells stimulated with estrogen. A Bayesian classifier was developed which uses the correlation of temporal binding patterns at enhancers and promoters and genomic proximity as features to predict interactions. This method was trained using experimentally determined interactions from the same system and was shown to achieve much higher precision than predictions based on the genomic proximity of nearest ERα binding. We use the method to identify a genome-wide confident set of ERα target genes and their regulatory enhancers genome-wide. Validation with publicly available GRO-Seq data demonstrates that our predicted targets are much more likely to show early nascent transcription than predictions based on genomic ERα binding proximity alone.
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Affiliation(s)
- Tomasz Dzida
- Faculty of Biology, Medicine and Health, University of Manchester, Manchester, United Kingdom
| | - Mudassar Iqbal
- Faculty of Biology, Medicine and Health, University of Manchester, Manchester, United Kingdom
| | - Iryna Charapitsa
- Chemical Biology Core Facility, European Molecular Biology Laboratory, Heidelberg, Germany
| | - George Reid
- Chemical Biology Core Facility, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Henk Stunnenberg
- Department of Molecular Life Sciences, Radboud University Nijmegen, Nijmegen, Netherlands
| | - Filomena Matarese
- Department of Molecular Life Sciences, Radboud University Nijmegen, Nijmegen, Netherlands
| | | | - Antti Honkela
- Helsinki Institute for InformationTechnology (HIIT), Department of Computer Science, University of Helsinki, Helsinki, Finland
- Department of Mathematics and Statistics, University of Helsinki, Helsinki, Finland
- Department of Public Health, University of Helsinki, Helsinki, Finland
| | - Magnus Rattray
- Faculty of Biology, Medicine and Health, University of Manchester, Manchester, United Kingdom
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117
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Atlasi Y, Stunnenberg HG. The interplay of epigenetic marks during stem cell differentiation and development. Nat Rev Genet 2017; 18:643-658. [PMID: 28804139 DOI: 10.1038/nrg.2017.57] [Citation(s) in RCA: 308] [Impact Index Per Article: 44.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Chromatin, the template for epigenetic regulation, is a highly dynamic entity that is constantly reshaped during early development and differentiation. Epigenetic modification of chromatin provides the necessary plasticity for cells to respond to environmental and positional cues, and enables the maintenance of acquired information without changing the DNA sequence. The mechanisms involve, among others, chemical modifications of chromatin, changes in chromatin constituents and reconfiguration of chromatin interactions and 3D structure. New advances in genome-wide technologies have paved the way towards an integrative view of epigenome dynamics during cell state transitions, and recent findings in embryonic stem cells highlight how the interplay between different epigenetic layers reshapes the transcriptional landscape.
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Affiliation(s)
- Yaser Atlasi
- Department of Molecular Biology, Faculty of Science, Radboud University, 6525 GA Nijmegen, The Netherlands
| | - Hendrik G Stunnenberg
- Department of Molecular Biology, Faculty of Science, Radboud University, 6525 GA Nijmegen, The Netherlands
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118
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Multi-color single-molecule tracking and subtrajectory analysis for quantification of spatiotemporal dynamics and kinetics upon T cell activation. Sci Rep 2017; 7:6994. [PMID: 28765585 PMCID: PMC5539329 DOI: 10.1038/s41598-017-06960-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2017] [Accepted: 06/20/2017] [Indexed: 11/08/2022] Open
Abstract
The dynamic properties of molecules in living cells are attracting increasing interest. We propose a new method, moving subtrajectory analysis using single-molecule tracking, and demonstrate its utility in the spatiotemporal quantification of not only dynamics but also the kinetics of interactions using single-color images. Combining this technique with three-color simultaneous single-molecule imaging, we quantified the dynamics and kinetics of molecules in spatial relation to T cell receptor (TCR) microclusters, which trigger TCR signaling. CD3ε, a component of the TCR/CD3 complex, and CD45, a phosphatase positively and negatively regulating signaling, were each found in two mobility states: faster (associated) and slower (dissociated) states. Dynamics analysis suggests that the microclusters are loosely composed of heterogeneous nanoregions, possibly surrounded by a weak barrier. Kinetics analysis quantified the association and dissociation rates of interactions with the microclusters. The associations of both CD3ε and CD45 were single-step processes. In contrast, their dissociations were each composed of two components, indicating transient and stable associated states. Inside the microclusters, the association was accelerated, and the stable association was increased. Only CD45 showed acceleration of association at the microcluster boundary, suggesting specific affinity on the boundary. Thus, this method is an innovative and versatile tool for spatiotemporal quantification.
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119
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Abstract
Epigenetic regulation in myeloid cells is crucial for cell differentiation and activation in response to developmental and environmental cues. Epigenetic control involves posttranslational modification of DNA or chromatin, and is also coupled to upstream signaling pathways and transcription factors. In this review, we summarize key epigenetic events and how dynamics in the epigenetic landscape of myeloid cells shape the development, immune activation, and innate immune memory.
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120
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Klieser E, Urbas R, Stättner S, Primavesi F, Jäger T, Dinnewitzer A, Mayr C, Kiesslich T, Holzmann K, Di Fazio P, Neureiter D, Swierczynski S. Comprehensive immunohistochemical analysis of histone deacetylases in pancreatic neuroendocrine tumors: HDAC5 as a predictor of poor clinical outcome. Hum Pathol 2017; 65:41-52. [PMID: 28235630 DOI: 10.1016/j.humpath.2017.02.009] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/21/2016] [Revised: 01/18/2017] [Accepted: 02/10/2017] [Indexed: 02/07/2023]
Abstract
Epigenetic factors contribute to carcinogenesis, tumor promotion, and chemoresistance. Histone deacetylases (HDACs) are epigenetic regulators that primarily cause chromatin compaction, leading to inaccessibility of promoter regions and eventually gene silencing. Many cancer entities feature overexpression of HDACs. Currently, the role of HDACs in pancreatic neuroendocrine tumors (pNETs) is unclear. We analyzed the expression patterns of all HDAC classes (classes I, IIA, IIB, III, and IV) in 5 human tissue microarrays representing 57 pNETs resected between 1997 and 2013 and corresponding control tissue. All pNET cases were characterized clinically and pathologically according to recent staging guidelines. The investigated cases included 32 (56.1%) female and 25 (43.9%) male pNET patients (total n=57, 47.4% immunohistochemically endocrine positive). Immunohistochemical profiling revealed a significant up-regulation of all HDAC classes in pNET versus control, with different levels of intensity and extensity ranging from 1.5- to >7-fold up-regulation. In addition, expression of several HDACs (HDAC1, HDAC2, HDAC5, HDAC11, and Sirt1) was significantly increased in G3 tumors. Correlation analysis showed a significant association between the protein expression of HDAC classes I, III, and IV and rate of the pHH3/Ki-67-associated mitotic and proliferation index. Furthermore, especially HDAC5 proved as a negative predictor of disease-free and overall survival in pNET patients. Overall, we demonstrate that specific members of all 4 HDAC classes are heterogeneously expressed in pNET. Moreover, expression of HDACs was associated with tumor grading, proliferation markers, and patient survival, therefore representing interesting new targets in pNET treatment.
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Affiliation(s)
- Eckhard Klieser
- Institute of Pathology, Paracelsus Medical University/Salzburger Landeskliniken (SALK), 5020 Salzburg, Austria.
| | - Romana Urbas
- Institute of Pathology, Paracelsus Medical University/Salzburger Landeskliniken (SALK), 5020 Salzburg, Austria.
| | - Stefan Stättner
- Department of Visceral, Transplant and Thoracic Surgery, Medical University Innsbruck, 6020 Innsbruck, Austria.
| | - Florian Primavesi
- Department of Visceral, Transplant and Thoracic Surgery, Medical University Innsbruck, 6020 Innsbruck, Austria.
| | - Tarkan Jäger
- Department of Surgery, Paracelsus Medical University/Salzburger Landeskliniken (SALK), 5020 Salzburg, Austria.
| | - Adam Dinnewitzer
- Department of Surgery, Paracelsus Medical University/Salzburger Landeskliniken (SALK), 5020 Salzburg, Austria.
| | - Christian Mayr
- Department of Internal Medicine I, Paracelsus Medical University/Salzburger Landeskliniken (SALK), 5020 Salzburg, Austria; Laboratory for Tumour Biology and Experimental Therapies, Institute of Physiology and Pathophysiology, Paracelsus Medical University, 5020 Salzburg, Austria.
| | - Tobias Kiesslich
- Department of Internal Medicine I, Paracelsus Medical University/Salzburger Landeskliniken (SALK), 5020 Salzburg, Austria; Laboratory for Tumour Biology and Experimental Therapies, Institute of Physiology and Pathophysiology, Paracelsus Medical University, 5020 Salzburg, Austria.
| | - Klaus Holzmann
- Department of Medicine I, Division: Institute of Cancer Research, Comprehensive Cancer Center, Medical University of Vienna, Vienna 1090, Austria.
| | - Pietro Di Fazio
- Department of Visceral, Thoracic and Vascular Surgery, Philipps University of Marburg, 35043 Marburg, Germany.
| | - Daniel Neureiter
- Institute of Pathology, Paracelsus Medical University/Salzburger Landeskliniken (SALK), 5020 Salzburg, Austria.
| | - Stefan Swierczynski
- Department of Surgery, Paracelsus Medical University/Salzburger Landeskliniken (SALK), 5020 Salzburg, Austria.
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121
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Developmental Control of NRAMP1 (SLC11A1) Expression in Professional Phagocytes. BIOLOGY 2017; 6:biology6020028. [PMID: 28467369 PMCID: PMC5485475 DOI: 10.3390/biology6020028] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/20/2017] [Revised: 04/25/2017] [Accepted: 04/25/2017] [Indexed: 12/11/2022]
Abstract
NRAMP1 (SLC11A1) is a professional phagocyte membrane importer of divalent metals that contributes to iron recycling at homeostasis and to nutritional immunity against infection. Analyses of data generated by several consortia and additional studies were integrated to hypothesize mechanisms restricting NRAMP1 expression to mature phagocytes. Results from various epigenetic and transcriptomic approaches were collected for mesodermal and hematopoietic cell types and compiled for combined analysis with results of genetic studies associating single nucleotide polymorphisms (SNPs) with variations in NRAMP1 expression (eQTLs). Analyses establish that NRAMP1 is part of an autonomous topologically associated domain delimited by ubiquitous CCCTC-binding factor (CTCF) sites. NRAMP1 locus contains five regulatory regions: a predicted super-enhancer (S-E) key to phagocyte-specific expression; the proximal promoter; two intronic areas, including 3' inhibitory elements that restrict expression during development; and a block of upstream sites possibly extending the S-E domain. Also the downstream region adjacent to the 3' CTCF locus boundary may regulate expression during hematopoiesis. Mobilization of the locus 14 predicted transcriptional regulatory elements occurs in three steps, beginning with hematopoiesis; at the onset of myelopoiesis and through myelo-monocytic differentiation. Basal expression level in mature phagocytes is further influenced by genetic variation, tissue environment, and in response to infections that induce various epigenetic memories depending on microorganism nature. Constitutively associated transcription factors (TFs) include CCAAT enhancer binding protein beta (C/EBPb), purine rich DNA binding protein (PU.1), early growth response 2 (EGR2) and signal transducer and activator of transcription 1 (STAT1) while hypoxia-inducible factors (HIFs) and interferon regulatory factor 1 (IRF1) may stimulate iron acquisition in pro-inflammatory conditions. Mouse orthologous locus is generally conserved; chromatin patterns typify a de novo myelo-monocytic gene whose expression is tightly controlled by TFs Pu.1, C/ebps and Irf8; Irf3 and nuclear factor NF-kappa-B p 65 subunit (RelA) regulate expression in inflammatory conditions. Functional differences in the determinants identified at these orthologous loci imply that species-specific mechanisms control gene expression.
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122
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Fujita Y, Masuda K, Bando M, Nakato R, Katou Y, Tanaka T, Nakayama M, Takao K, Miyakawa T, Tanaka T, Ago Y, Hashimoto H, Shirahige K, Yamashita T. Decreased cohesin in the brain leads to defective synapse development and anxiety-related behavior. J Exp Med 2017; 214:1431-1452. [PMID: 28408410 PMCID: PMC5413336 DOI: 10.1084/jem.20161517] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2016] [Revised: 01/14/2017] [Accepted: 03/03/2017] [Indexed: 11/21/2022] Open
Abstract
Abnormal epigenetic regulation can cause the nervous system to develop abnormally. Here, we sought to understand the mechanism by which this occurs by investigating the protein complex cohesin, which is considered to regulate gene expression and, when defective, is associated with higher-level brain dysfunction and the developmental disorder Cornelia de Lange syndrome (CdLS). We generated conditional Smc3-knockout mice and observed greater dendritic complexity and larger numbers of immature synapses in the cerebral cortex of Smc3+/- mice. Smc3+/- mice also exhibited more anxiety-related behavior, which is a symptom of CdLS. Further, a gene ontology analysis after RNA-sequencing suggested the enrichment of immune processes, particularly the response to interferons, in the Smc3+/- mice. Indeed, fewer synapses formed in their cortical neurons, and this phenotype was rescued by STAT1 knockdown. Thus, low levels of cohesin expression in the developing brain lead to changes in gene expression that in turn lead to a specific and abnormal neuronal and behavioral phenotype.
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Affiliation(s)
- Yuki Fujita
- Department of Molecular Neuroscience, Graduate School of Medicine, Osaka University, Osaka 565-0871, Japan
| | - Koji Masuda
- Research Center for Epigenetic Disease, Institute for Molecular and Cellular Biosciences, The University of Tokyo, Tokyo 113-0032, Japan
| | - Masashige Bando
- Research Center for Epigenetic Disease, Institute for Molecular and Cellular Biosciences, The University of Tokyo, Tokyo 113-0032, Japan
| | - Ryuichiro Nakato
- Research Center for Epigenetic Disease, Institute for Molecular and Cellular Biosciences, The University of Tokyo, Tokyo 113-0032, Japan
| | - Yuki Katou
- Research Center for Epigenetic Disease, Institute for Molecular and Cellular Biosciences, The University of Tokyo, Tokyo 113-0032, Japan
| | - Takashi Tanaka
- Department of Molecular Neuroscience, Graduate School of Medicine, Osaka University, Osaka 565-0871, Japan
| | - Masahiro Nakayama
- Department of Pathology, Osaka Medical Center and Research Institute for Maternal and Child Health, Osaka 594-1101, Japan
| | - Keizo Takao
- Life Science Research Center, University of Toyama, Toyama 930-0194, Japan
| | - Tsuyoshi Miyakawa
- Life Science Research Center, University of Toyama, Toyama 930-0194, Japan
- Division of Systems Medical Science, Institute for Comprehensive Medical Science, Fujita Health University, Aichi 470-1192, Japan
| | - Tatsunori Tanaka
- Laboratory of Molecular Neuropharmacology, Graduate School of Pharmaceutical Sciences, Osaka University, Osaka 565-0871, Japan
| | - Yukio Ago
- Laboratory of Molecular Neuropharmacology, Graduate School of Pharmaceutical Sciences, Osaka University, Osaka 565-0871, Japan
| | - Hitoshi Hashimoto
- Laboratory of Molecular Neuropharmacology, Graduate School of Pharmaceutical Sciences, Osaka University, Osaka 565-0871, Japan
- Division of Bioscience, Institute for Datability Science, Osaka University, Osaka 565-0871, Japan
- iPS Cell-based Research Project on Brain Neuropharmacology and Toxicology, Graduate School of Pharmaceutical Sciences, Osaka University, Osaka 565-0871, Japan
- Molecular Research Center for Children's Mental Development, United Graduate School of Child Development, Osaka University, Osaka 565-0871, Japan
| | - Katsuhiko Shirahige
- Research Center for Epigenetic Disease, Institute for Molecular and Cellular Biosciences, The University of Tokyo, Tokyo 113-0032, Japan
| | - Toshihide Yamashita
- Department of Molecular Neuroscience, Graduate School of Medicine, Osaka University, Osaka 565-0871, Japan
- Graduate School of Frontier Biosciences, Osaka University, Osaka 565-0871, Japan
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123
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Vera M, Biswas J, Senecal A, Singer RH, Park HY. Single-Cell and Single-Molecule Analysis of Gene Expression Regulation. Annu Rev Genet 2017; 50:267-291. [PMID: 27893965 DOI: 10.1146/annurev-genet-120215-034854] [Citation(s) in RCA: 83] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Recent advancements in single-cell and single-molecule imaging technologies have resolved biological processes in time and space that are fundamental to understanding the regulation of gene expression. Observations of single-molecule events in their cellular context have revealed highly dynamic aspects of transcriptional and post-transcriptional control in eukaryotic cells. This approach can relate transcription with mRNA abundance and lifetimes. Another key aspect of single-cell analysis is the cell-to-cell variability among populations of cells. Definition of heterogeneity has revealed stochastic processes, determined characteristics of under-represented cell types or transitional states, and integrated cellular behaviors in the context of multicellular organisms. In this review, we discuss novel aspects of gene expression of eukaryotic cells and multicellular organisms revealed by the latest advances in single-cell and single-molecule imaging technology.
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Affiliation(s)
- Maria Vera
- Department of Anatomy and Structural Biology, Albert Einstein College of Medicine, New York, NY 10461; , , ,
| | - Jeetayu Biswas
- Department of Anatomy and Structural Biology, Albert Einstein College of Medicine, New York, NY 10461; , , ,
| | - Adrien Senecal
- Department of Anatomy and Structural Biology, Albert Einstein College of Medicine, New York, NY 10461; , , ,
| | - Robert H Singer
- Department of Anatomy and Structural Biology, Albert Einstein College of Medicine, New York, NY 10461; , , , .,Janelia Research Campus of the HHMI, Ashburn, Virginia 20147
| | - Hye Yoon Park
- Department of Physics and Astronomy, Seoul National University, Seoul, 08826, Korea; .,Institute of Molecular Biology and Genetics, Seoul National University, Seoul, 08826, Korea
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124
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Imaging Translational and Post-Translational Gene Regulatory Dynamics in Living Cells with Antibody-Based Probes. Trends Genet 2017; 33:322-335. [PMID: 28359585 DOI: 10.1016/j.tig.2017.02.003] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2017] [Revised: 02/25/2017] [Accepted: 02/28/2017] [Indexed: 12/17/2022]
Abstract
Antibody derivatives, such as antibody fragments (Fabs) and single-chain variable fragments (scFvs), are now being used to image traditionally hard-to-see protein subpopulations, including nascent polypeptides being translated and post-translationally modified proteins. This has allowed researchers to directly image and quantify, for the first time, translation initiation and elongation kinetics with single-transcript resolution and the temporal ordering and kinetics of post-translational histone and RNA polymerase II modifications. Here, we review these developments and discuss the strengths and weaknesses of live-cell imaging with antibody-based probes. Further development of these probes will increase their versatility and open new avenues of research for dissecting complex gene regulatory dynamics.
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125
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Esnault C, Gualdrini F, Horswell S, Kelly G, Stewart A, East P, Matthews N, Treisman R. ERK-Induced Activation of TCF Family of SRF Cofactors Initiates a Chromatin Modification Cascade Associated with Transcription. Mol Cell 2017; 65:1081-1095.e5. [PMID: 28286024 PMCID: PMC5364370 DOI: 10.1016/j.molcel.2017.02.005] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2016] [Revised: 12/19/2016] [Accepted: 02/06/2017] [Indexed: 12/20/2022]
Abstract
We investigated the relationship among ERK signaling, histone modifications, and transcription factor activity, focusing on the ERK-regulated ternary complex factor family of SRF partner proteins. In MEFs, activation of ERK by TPA stimulation induced a common pattern of H3K9acS10ph, H4K16ac, H3K27ac, H3K9acK14ac, and H3K4me3 at hundreds of transcription start site (TSS) regions and remote regulatory sites. The magnitude of the increase in histone modification correlated well with changes in transcription. H3K9acS10ph preceded the other modifications. Most induced changes were TCF dependent, but TCF-independent TSSs exhibited the same hierarchy, indicating that it reflects gene activation per se. Studies with TCF Elk-1 mutants showed that TCF-dependent ERK-induced histone modifications required Elk-1 to be phosphorylated and competent to activate transcription. Analysis of direct TCF-SRF target genes and chromatin modifiers confirmed this and showed that H3S10ph required only Elk-1 phosphorylation. Induction of histone modifications following ERK stimulation is thus directed by transcription factor activation and transcription.
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Affiliation(s)
- Cyril Esnault
- Signalling and Transcription Group, Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Francesco Gualdrini
- Signalling and Transcription Group, Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Stuart Horswell
- Bioinformatics and Biostatistics STP, Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Gavin Kelly
- Bioinformatics and Biostatistics STP, Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Aengus Stewart
- Bioinformatics and Biostatistics STP, Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Phil East
- Bioinformatics and Biostatistics STP, Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Nik Matthews
- Advanced Sequencing STP, Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Richard Treisman
- Signalling and Transcription Group, Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK.
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126
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The code and beyond: transcription regulation by the RNA polymerase II carboxy-terminal domain. Nat Rev Mol Cell Biol 2017; 18:263-273. [PMID: 28248323 DOI: 10.1038/nrm.2017.10] [Citation(s) in RCA: 300] [Impact Index Per Article: 42.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The carboxy-terminal domain (CTD) extends from the largest subunit of RNA polymerase II (Pol II) as a long, repetitive and largely unstructured polypeptide chain. Throughout the transcription process, the CTD is dynamically modified by post-translational modifications, many of which facilitate or hinder the recruitment of key regulatory factors of Pol II that collectively constitute the 'CTD code'. Recent studies have revealed how the physicochemical properties of the CTD promote phase separation in the presence of other low-complexity domains. Here, we discuss the intricacies of the CTD code and how the newly characterized physicochemical properties of the CTD expand the function of the CTD beyond the code.
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127
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Shiomi T, Muto A, Hozumi S, Kimura H, Kikuchi Y. Histone H3 Lysine 27 Trimethylation Leads to Loss of Mesendodermal Competence During Gastrulation in Zebrafish Ectodermal Cells. Zoolog Sci 2017; 34:64-71. [DOI: 10.2108/zs160032] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Affiliation(s)
- Taishi Shiomi
- Department of Biological Science, Graduate School of Science, Hiroshima University, Kagamiyama 1-3-1, Higashi-Hiroshima, Hiroshima 739-8526, Japan
| | - Akihiko Muto
- Department of Biological Science, Graduate School of Science, Hiroshima University, Kagamiyama 1-3-1, Higashi-Hiroshima, Hiroshima 739-8526, Japan
| | - Shunya Hozumi
- Department of Biological Science, Graduate School of Science, Hiroshima University, Kagamiyama 1-3-1, Higashi-Hiroshima, Hiroshima 739-8526, Japan
| | - Hiroshi Kimura
- Cell Biology Unit, Institute of Innovative Research, Tokyo Institute of Technology, 4259 Nagatsuta, Midori-Ku, Yokohama 226-8501, Japan
| | - Yutaka Kikuchi
- Department of Biological Science, Graduate School of Science, Hiroshima University, Kagamiyama 1-3-1, Higashi-Hiroshima, Hiroshima 739-8526, Japan
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128
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Bose DA, Donahue G, Reinberg D, Shiekhattar R, Bonasio R, Berger SL. RNA Binding to CBP Stimulates Histone Acetylation and Transcription. Cell 2017; 168:135-149.e22. [PMID: 28086087 DOI: 10.1016/j.cell.2016.12.020] [Citation(s) in RCA: 245] [Impact Index Per Article: 35.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2016] [Revised: 10/10/2016] [Accepted: 12/14/2016] [Indexed: 12/29/2022]
Abstract
CBP/p300 are transcription co-activators whose binding is a signature of enhancers, cis-regulatory elements that control patterns of gene expression in multicellular organisms. Active enhancers produce bi-directional enhancer RNAs (eRNAs) and display CBP/p300-dependent histone acetylation. Here, we demonstrate that CBP binds directly to RNAs in vivo and in vitro. RNAs bound to CBP in vivo include a large number of eRNAs. Using steady-state histone acetyltransferase (HAT) assays, we show that an RNA binding region in the HAT domain of CBP-a regulatory motif unique to CBP/p300-allows RNA to stimulate CBP's HAT activity. At enhancers where CBP interacts with eRNAs, stimulation manifests in RNA-dependent changes in the histone acetylation mediated by CBP, such as H3K27ac, and by corresponding changes in gene expression. By interacting directly with CBP, eRNAs contribute to the unique chromatin structure at active enhancers, which, in turn, is required for regulation of target genes.
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Affiliation(s)
- Daniel A Bose
- Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Epigenetics Program, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Greg Donahue
- Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Epigenetics Program, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Danny Reinberg
- Department of Molecular Pharmacology and Biochemistry, New York University School of Medicine, New York, NY 10016, USA
| | - Ramin Shiekhattar
- Sylvester Comprehensive Cancer Center, Department of Human Genetics, University of Miami Miller School of Medicine, Biomedical Research Building, Room 719, 1501 NW 10th Avenue, Miami, FL 33136, USA
| | - Roberto Bonasio
- Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Epigenetics Program, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Shelley L Berger
- Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Epigenetics Program, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.
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129
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Maury E, Hashizume R. Epigenetic modification in chromatin machinery and its deregulation in pediatric brain tumors: Insight into epigenetic therapies. Epigenetics 2017; 12:353-369. [PMID: 28059591 DOI: 10.1080/15592294.2016.1278095] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
Malignancies are characterized by the reprogramming of epigenetic patterns. This reprogramming includes gains or losses in DNA methylation and disruption of normal patterns of covalent histone modifications, which are associated with changes in chromatin remodeling processes. This review will focus on the mechanisms underlying this reprogramming and, specifically, on the role of histone modification in chromatin machinery and the modifications in epigenetic processes occurring in brain cancer, with a specific focus on epigenetic therapies for pediatric brain tumors.
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Affiliation(s)
- Eleonore Maury
- a Department of Neurological Surgery , Northwestern University Feinberg School of Medicine , Chicago , IL , USA.,b Science in Society , Northwestern University , Evanston , IL , USA
| | - Rintaro Hashizume
- a Department of Neurological Surgery , Northwestern University Feinberg School of Medicine , Chicago , IL , USA.,c Department of Biochemistry and Molecular Genetics , Northwestern University Feinberg School of Medicine , Chicago , IL , USA
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130
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Yao J. Imaging Transcriptional Regulation of Eukaryotic mRNA Genes: Advances and Outlook. J Mol Biol 2017; 429:14-31. [DOI: 10.1016/j.jmb.2016.11.007] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2016] [Revised: 11/03/2016] [Accepted: 11/10/2016] [Indexed: 01/07/2023]
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131
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Scholes C, DePace AH, Sánchez Á. Combinatorial Gene Regulation through Kinetic Control of the Transcription Cycle. Cell Syst 2016; 4:97-108.e9. [PMID: 28041762 DOI: 10.1016/j.cels.2016.11.012] [Citation(s) in RCA: 50] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2016] [Revised: 08/09/2016] [Accepted: 11/23/2016] [Indexed: 11/20/2022]
Abstract
Cells decide when, where, and to what level to express their genes by "computing" information from transcription factors (TFs) binding to regulatory DNA. How is the information contained in multiple TF-binding sites integrated to dictate the rate of transcription? The dominant conceptual and quantitative model is that TFs combinatorially recruit one another and RNA polymerase to the promoter by direct physical interactions. Here, we develop a quantitative framework to explore kinetic control, an alternative model in which combinatorial gene regulation can result from TFs working on different kinetic steps of the transcription cycle. Kinetic control can generate a wide range of analog and Boolean computations without requiring the input TFs to be simultaneously bound to regulatory DNA. We propose experiments that will illuminate the role of kinetic control in transcription and discuss implications for deciphering the cis-regulatory "code."
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Affiliation(s)
- Clarissa Scholes
- Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA; Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138, USA
| | - Angela H DePace
- Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA.
| | - Álvaro Sánchez
- The Rowland Institute at Harvard, Harvard University, Cambridge, MA 02142, USA.
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132
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Zhao ZW, White MD, Bissiere S, Levi V, Plachta N. Quantitative imaging of mammalian transcriptional dynamics: from single cells to whole embryos. BMC Biol 2016; 14:115. [PMID: 28010727 PMCID: PMC5180410 DOI: 10.1186/s12915-016-0331-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
Probing dynamic processes occurring within the cell nucleus at the quantitative level has long been a challenge in mammalian biology. Advances in bio-imaging techniques over the past decade have enabled us to directly visualize nuclear processes in situ with unprecedented spatial and temporal resolution and single-molecule sensitivity. Here, using transcription as our primary focus, we survey recent imaging studies that specifically emphasize the quantitative understanding of nuclear dynamics in both time and space. These analyses not only inform on previously hidden physical parameters and mechanistic details, but also reveal a hierarchical organizational landscape for coordinating a wide range of transcriptional processes shared by mammalian systems of varying complexity, from single cells to whole embryos.
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Affiliation(s)
- Ziqing W Zhao
- Institute of Molecular and Cell Biology, Agency for Science, Technology and Research (A*STAR), 61 Biopolis Drive, Singapore, 138673, Singapore
| | - Melanie D White
- Institute of Molecular and Cell Biology, Agency for Science, Technology and Research (A*STAR), 61 Biopolis Drive, Singapore, 138673, Singapore
| | - Stephanie Bissiere
- Institute of Molecular and Cell Biology, Agency for Science, Technology and Research (A*STAR), 61 Biopolis Drive, Singapore, 138673, Singapore
| | - Valeria Levi
- Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Conicet, Buenos Aires, C1428EHA, Argentina
| | - Nicolas Plachta
- Institute of Molecular and Cell Biology, Agency for Science, Technology and Research (A*STAR), 61 Biopolis Drive, Singapore, 138673, Singapore.
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133
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Vaňková Hausnerová V, Lanctôt C. Chromatin decondensation is accompanied by a transient increase in transcriptional output. Biol Cell 2016; 109:65-79. [PMID: 27633335 DOI: 10.1111/boc.201600032] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2016] [Revised: 09/12/2016] [Accepted: 09/13/2016] [Indexed: 12/26/2022]
Abstract
BACKGROUND INFORMATION The levels of chromatin condensation usually correlate inversely with the levels of transcription. The mechanistic links between chromatin condensation and RNA polymerase II activity remain to be elucidated. In the present work, we sought to experimentally determine whether manipulation of chromatin condensation levels can have a direct effect on transcriptional activity. RESULTS We generated a U-2-OS cell line in which the nascent transcription of a reporter gene could be imaged alongside chromatin compaction levels in living cells. The transcripts were tagged at their 5' end with PP7 stem loops, which can be detected upon expression of a PP7 capsid protein fused to green fluorescent protein. Cycles of global chromatin hypercondensation and decondensation were performed by perfusing culture media of different osmolarities during imaging. We used the fluorescence recovery after photobleaching technique to analyse the transcriptional dynamics in both conditions. Surprisingly, we found that, despite a drop in signal intensity, nascent transcription appeared to continue at the same rate in hypercondensed chromatin. Furthermore, quantification of transcriptional profiles revealed that chromatin decondensation was accompanied by a brief and transient spike in transcriptional output. CONCLUSIONS We propose a model whereby the initiation of transcription is not impaired in condensed chromatin, but inefficient elongation in these conditions leads to the accumulation of RNA polymerase II at the transcription site. Upon chromatin decondensation, release of the RNA polymerase II halt triggers a wave of transcription, which we detect as a transient spike in activity. SIGNIFICANCE The results presented here shed light on the activity of RNA polymerase II during chromatin condensation and decondensation. As such, they point to a new level of transcriptional regulation.
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Affiliation(s)
- Viola Vaňková Hausnerová
- Institute of Cellular Biology and Pathology, First Faculty of Medicine, Charles University, Prague, Czech Republic.,BIOCEV and Department of Cell Biology, Faculty of Science, Charles University, Vestec u Prahy, 252 50, Czech Republic
| | - Christian Lanctôt
- Institute of Cellular Biology and Pathology, First Faculty of Medicine, Charles University, Prague, Czech Republic.,BIOCEV and Department of Cell Biology, Faculty of Science, Charles University, Vestec u Prahy, 252 50, Czech Republic
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134
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Hänsel-Hertsch R, Beraldi D, Lensing SV, Marsico G, Zyner K, Parry A, Di Antonio M, Pike J, Kimura H, Narita M, Tannahill D, Balasubramanian S. G-quadruplex structures mark human regulatory chromatin. Nat Genet 2016; 48:1267-72. [PMID: 27618450 DOI: 10.1038/ng.3662] [Citation(s) in RCA: 581] [Impact Index Per Article: 72.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2016] [Accepted: 08/08/2016] [Indexed: 12/14/2022]
Abstract
G-quadruplex (G4) structural motifs have been linked to transcription, replication and genome instability and are implicated in cancer and other diseases. However, it is crucial to demonstrate the bona fide formation of G4 structures within an endogenous chromatin context. Herein we address this through the development of G4 ChIP-seq, an antibody-based G4 chromatin immunoprecipitation and high-throughput sequencing approach. We find ∼10,000 G4 structures in human chromatin, predominantly in regulatory, nucleosome-depleted regions. G4 structures are enriched in the promoters and 5' UTRs of highly transcribed genes, particularly in genes related to cancer and in somatic copy number amplifications, such as MYC. Strikingly, de novo and enhanced G4 formation are associated with increased transcriptional activity, as shown by HDAC inhibitor-induced chromatin relaxation and observed in immortalized as compared to normal cellular states. Our findings show that regulatory, nucleosome-depleted chromatin and elevated transcription shape the endogenous human G4 DNA landscape.
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Affiliation(s)
| | - Dario Beraldi
- Cancer Research UK, Cambridge Institute, Li Ka Shing Centre, Cambridge, UK
| | - Stefanie V Lensing
- Cancer Research UK, Cambridge Institute, Li Ka Shing Centre, Cambridge, UK
| | - Giovanni Marsico
- Cancer Research UK, Cambridge Institute, Li Ka Shing Centre, Cambridge, UK
| | - Katherine Zyner
- Cancer Research UK, Cambridge Institute, Li Ka Shing Centre, Cambridge, UK
| | - Aled Parry
- Cancer Research UK, Cambridge Institute, Li Ka Shing Centre, Cambridge, UK
| | | | - Jeremy Pike
- Cancer Research UK, Cambridge Institute, Li Ka Shing Centre, Cambridge, UK
| | - Hiroshi Kimura
- Cell Biology Unit, Institute of Innovative Research, Tokyo Institute of Technology, Yokohama, Japan
| | - Masashi Narita
- Cancer Research UK, Cambridge Institute, Li Ka Shing Centre, Cambridge, UK
| | - David Tannahill
- Cancer Research UK, Cambridge Institute, Li Ka Shing Centre, Cambridge, UK
| | - Shankar Balasubramanian
- Cancer Research UK, Cambridge Institute, Li Ka Shing Centre, Cambridge, UK
- Department of Chemistry, University of Cambridge, Cambridge, UK
- School of Clinical Medicine, University of Cambridge, Cambridge, UK
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135
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Kozłowska M, Niedojadło K, Brzostek M, Bednarska-Kozakiewicz E. Epigenetic marks in the Hyacinthus orientalis L. mature pollen grain and during in vitro pollen tube growth. PLANT REPRODUCTION 2016; 29:251-263. [PMID: 27422435 PMCID: PMC4978762 DOI: 10.1007/s00497-016-0289-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/30/2016] [Accepted: 07/04/2016] [Indexed: 06/06/2023]
Abstract
During the sexual reproduction of flowering plants, epigenetic control of gene expression and genome integrity by DNA methylation and histone modifications plays an important role in male gametogenesis. In this study, we compared the chromatin modification patterns of the generative, sperm cells and vegetative nuclei during Hyacinthus orientalis male gametophyte development. Changes in the spatial and temporal distribution of 5-methylcytosine, acetylated histone H4 and histone deacetylase indicated potential differences in the specific epigenetic state of all analysed cells, in both the mature cellular pollen grains and the in vitro growing pollen tubes. Interestingly, we observed unique localization of chromatin modifications in the area of the generative and the vegetative nuclei located near each other in the male germ unit, indicating the precise mechanisms of gene expression regulation in this region. We discuss the differences in the patterns of the epigenetic marks along with our previous reports of nuclear metabolism and changes in chromatin organization and activity in hyacinth male gametophyte cells. We also propose that this epigenetic status of the analysed nuclei is related to the different acquired fates and biological functions of these cells.
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Affiliation(s)
- Marlena Kozłowska
- Department of Cell Biology, Faculty of Biology and Environment Protection, Nicolaus Copernicus University in Toruń, Toruń, Poland
| | - Katarzyna Niedojadło
- Department of Cell Biology, Faculty of Biology and Environment Protection, Nicolaus Copernicus University in Toruń, Toruń, Poland.
| | - Marta Brzostek
- Department of Cell Biology, Faculty of Biology and Environment Protection, Nicolaus Copernicus University in Toruń, Toruń, Poland
| | - Elżbieta Bednarska-Kozakiewicz
- Department of Cell Biology, Faculty of Biology and Environment Protection, Nicolaus Copernicus University in Toruń, Toruń, Poland
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136
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Mumby S, Gambaryan N, Meng C, Perros F, Humbert M, Wort SJ, Adcock IM. Bromodomain and extra-terminal protein mimic JQ1 decreases inflammation in human vascular endothelial cells: Implications for pulmonary arterial hypertension. Respirology 2016; 22:157-164. [PMID: 27539364 PMCID: PMC5215513 DOI: 10.1111/resp.12872] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2015] [Revised: 04/17/2016] [Accepted: 05/31/2016] [Indexed: 12/22/2022]
Abstract
Background and objective Nuclear factor kappa B (NF‐kB)‐mediated inflammatory gene expression and vascular endothelial cell proliferation/remodelling are implicated in the pathophysiology of the fatal disease, pulmonary arterial hypertension (PAH). Bromodomain and extra‐terminal (BET) proteins are essential for the expression of a subset of NF‐kB‐induced inflammatory genes. BET mimics including JQ1+ prevent binding of BETs to acetylated histones and down‐regulate the expression of selected genes. Methods The effects of JQ1+ on the proliferation of primary human pulmonary microvascular endothelial cells (HPMECs) from healthy subjects were measured by bromodeoxyuridine (BrdU) incorporation. Cell cycle progression was assessed by flow cytometry; mRNA and protein levels of cyclin‐dependent kinases (CDKs), inhibitors and cytokines were determined by reverse transcription‐quantitative PCR (RT‐qPCR), Western blotting or ELISA. Histone acetyltransferase (HAT) and deacetylase (HDAC) activities were determined in nuclear extracts from whole lung of PAH and control patients. Results JQ1+ significantly inhibited IL6 and IL8 (IL6 and CXCL8) mRNA and protein in HPMECs compared with its inactive enantiomer JQ1−. JQ1+ decreased NF‐kB p65 recruitment to native IL6 and IL8 promoters. JQ1+ showed a concentration‐dependent decrease in HPMEC proliferation compared with JQ1−‐treated cells. JQ1+ induced G1 cell cycle arrest by increasing the expression of the CDK inhibitors (CDKN) 1A (p21cip) and CDKN2D (p19INK4D) and decreasing that of CDK2, CDK4 and CDK6. JQ1+ also inhibited serum‐stimulated migration of HPMECs. Finally, HAT activity was significantly increased in the lung of PAH patients. Conclusion Inhibition of BETs in primary HPMECs decreases inflammation and remodelling. BET proteins could be a target for future therapies for PAH. Endothelial cell inflammation and proliferation are important in the pathogenesis of pulmonary arterial hypertension (PAH). Bromodomain and extra‐terminal (BET) mimics reduced inflammation and cell proliferation in primary human pulmonary vascular endothelial cells. The enhanced histone acetyltransferase (HAT) activity in PAH suggests that BET mimics may be effective in PAH although experiments in disease cells/tissues are required.
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Affiliation(s)
- Sharon Mumby
- Vascular Biology, Imperial College London, London, UK.,Airway Disease Section, National Heart and Lung Institute, Imperial College London, London, UK
| | | | - Chao Meng
- Vascular Biology, Imperial College London, London, UK
| | - Frederic Perros
- Faculty of Medicine, South Paris University, Clamart, France.,Pulmonary Hypertension: Pathophysiology and Therapeutic Innovation, INSERM Research Unit 999, Clamart, France
| | - Marc Humbert
- Faculty of Medicine, South Paris University, Clamart, France.,Pulmonary Hypertension: Pathophysiology and Therapeutic Innovation, INSERM Research Unit 999, Clamart, France.,Pulmonary Resuscitation Respiratory and Service, National Reference Centre for Pulmonary Hypertension Severe, Assistance Publique Hôpitaux de Paris, Hôpital Antoine Béclère, Paris, France
| | - S John Wort
- Vascular Biology, Imperial College London, London, UK
| | - Ian M Adcock
- Airway Disease Section, National Heart and Lung Institute, Imperial College London, London, UK
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137
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Hashimoto T, Sherwood RI, Kang DD, Rajagopal N, Barkal AA, Zeng H, Emons BJM, Srinivasan S, Jaakkola T, Gifford DK. A synergistic DNA logic predicts genome-wide chromatin accessibility. Genome Res 2016; 26:1430-1440. [PMID: 27456004 PMCID: PMC5052050 DOI: 10.1101/gr.199778.115] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2015] [Accepted: 07/20/2016] [Indexed: 01/27/2023]
Abstract
Enhancers and promoters commonly occur in accessible chromatin characterized by depleted nucleosome contact; however, it is unclear how chromatin accessibility is governed. We show that log-additive cis-acting DNA sequence features can predict chromatin accessibility at high spatial resolution. We develop a new type of high-dimensional machine learning model, the Synergistic Chromatin Model (SCM), which when trained with DNase-seq data for a cell type is capable of predicting expected read counts of genome-wide chromatin accessibility at every base from DNA sequence alone, with the highest accuracy at hypersensitive sites shared across cell types. We confirm that a SCM accurately predicts chromatin accessibility for thousands of synthetic DNA sequences using a novel CRISPR-based method of highly efficient site-specific DNA library integration. SCMs are directly interpretable and reveal that a logic based on local, nonspecific synergistic effects, largely among pioneer TFs, is sufficient to predict a large fraction of cellular chromatin accessibility in a wide variety of cell types.
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Affiliation(s)
- Tatsunori Hashimoto
- Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, Massachusetts 02142, USA
| | - Richard I Sherwood
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Daniel D Kang
- Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, Massachusetts 02142, USA
| | - Nisha Rajagopal
- Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, Massachusetts 02142, USA
| | - Amira A Barkal
- Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, Massachusetts 02142, USA; Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Haoyang Zeng
- Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, Massachusetts 02142, USA
| | - Bart J M Emons
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Sharanya Srinivasan
- Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, Massachusetts 02142, USA; Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Tommi Jaakkola
- Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, Massachusetts 02142, USA
| | - David K Gifford
- Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, Massachusetts 02142, USA
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138
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Lämke J, Brzezinka K, Bäurle I. HSFA2 orchestrates transcriptional dynamics after heat stress in Arabidopsis thaliana. Transcription 2016; 7:111-4. [PMID: 27383578 DOI: 10.1080/21541264.2016.1187550] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022] Open
Abstract
In nature, stress is typically chronic or recurring and stress exposure can prime modified responses to recurring stress. Such stress priming may occur at the level of transcription. Here, we discuss the connection between plant stress memory, transcription, and chromatin modifications using the example of recurring heat stress.
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Affiliation(s)
- Jörn Lämke
- a Institute for Biochemistry and Biology, University of Potsdam , Potsdam , Germany
| | - Krzysztof Brzezinka
- a Institute for Biochemistry and Biology, University of Potsdam , Potsdam , Germany
| | - Isabel Bäurle
- a Institute for Biochemistry and Biology, University of Potsdam , Potsdam , Germany
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139
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Puchta H. Using CRISPR/Cas in three dimensions: towards synthetic plant genomes, transcriptomes and epigenomes. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2016; 87:5-15. [PMID: 26677816 DOI: 10.1111/tpj.13100] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/06/2015] [Revised: 11/23/2015] [Accepted: 11/25/2015] [Indexed: 05/21/2023]
Abstract
It is possible to target individual sequence motives within genomes by using synthetic DNA-binding domains. This one-dimensional approach has been used successfully in plants to induce mutations or for the transcriptional regulation of single genes. When the CRISPR (clustered regularly interspaced short palindromic repeats)/Cas9 system was discovered, a tool became available allowing the extension of this approach from one to three dimensions and to construct at least partly synthetic entities on the genome, epigenome and transcriptome levels. The second dimension can be obtained by targeting the Cas9 protein to multiple unique genomic sites by applying multiple different single guiding (sg) RNAs, each defining a different DNA-binding site. Finally, the simultaneous use of phylogenetically different Cas9 proteins or sgRNAs that harbour different types of protein binding motives, allows for a third dimension of control. Thus, different types of enzyme activities - fused either to one type of Cas9 orthologue or to one type of RNA-binding domain specific to one type of sgRNA - can be targeted to multiple different genomic sites simultaneously. Thus, it should be possible to induce quantitatively different levels of expression of certain sets of genes and at the same time to repress other genes, redefining the nuclear transcriptome. Likewise, by the use of different types of histone-modifying and/or DNA (de)methylating activities, the epigenome of plants should be reprogrammable. On our way to synthetic plant genomes, the next steps will be to use complex genome engineering approaches within or between species borders to restructure and recombine natural or artificial chromosomes.
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Affiliation(s)
- Holger Puchta
- Botanical Institute II, Karlsruhe Institute of Technology, POB 6980, 76049, Karlsruhe, Germany
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140
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The Metabolic Impact on Histone Acetylation and Transcription in Ageing. Trends Biochem Sci 2016; 41:700-711. [PMID: 27283514 DOI: 10.1016/j.tibs.2016.05.008] [Citation(s) in RCA: 112] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2016] [Revised: 05/09/2016] [Accepted: 05/13/2016] [Indexed: 12/13/2022]
Abstract
Loss of cellular homeostasis during aging results in altered tissue functions and leads to a general decline in fitness and, ultimately, death. As animals age, the control of gene expression, which is orchestrated by multiple epigenetic factors, degenerates. In parallel, metabolic activity and mitochondrial protein acetylation levels also change. These two hallmarks of aging are effectively linked through the accumulating evidence that histone acetylation patterns are susceptible to alterations in key metabolites such as acetyl-CoA and NAD(+), allowing chromatin to function as a sensor of cellular metabolism. In this review we discuss experimental data supporting these connections and provide a context for the possible medical and physiological relevance.
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141
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Fan R, Toubal A, Goñi S, Drareni K, Huang Z, Alzaid F, Ballaire R, Ancel P, Liang N, Damdimopoulos A, Hainault I, Soprani A, Aron-Wisnewsky J, Foufelle F, Lawrence T, Gautier JF, Venteclef N, Treuter E. Loss of the co-repressor GPS2 sensitizes macrophage activation upon metabolic stress induced by obesity and type 2 diabetes. Nat Med 2016; 22:780-91. [PMID: 27270589 DOI: 10.1038/nm.4114] [Citation(s) in RCA: 65] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2016] [Accepted: 04/26/2016] [Indexed: 12/18/2022]
Abstract
Humans with obesity differ in their susceptibility to developing insulin resistance and type 2 diabetes (T2D). This variation may relate to the extent of adipose tissue (AT) inflammation that develops as their obesity progresses. The state of macrophage activation has a central role in determining the degree of AT inflammation and thus its dysfunction, and these states are driven by epigenomic alterations linked to gene expression. The underlying mechanisms that regulate these alterations, however, are poorly defined. Here we demonstrate that a co-repressor complex containing G protein pathway suppressor 2 (GPS2) crucially controls the macrophage epigenome during activation by metabolic stress. The study of AT from humans with and without obesity revealed correlations between reduced GPS2 expression in macrophages, elevated systemic and AT inflammation, and diabetic status. The causality of this relationship was confirmed by using macrophage-specific Gps2-knockout (KO) mice, in which inappropriate co-repressor complex function caused enhancer activation, pro-inflammatory gene expression and hypersensitivity toward metabolic-stress signals. By contrast, transplantation of GPS2-overexpressing bone marrow into two mouse models of obesity (ob/ob and diet-induced obesity) reduced inflammation and improved insulin sensitivity. Thus, our data reveal a potentially reversible disease mechanism that links co-repressor-dependent epigenomic alterations in macrophages to AT inflammation and the development of T2D.
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Affiliation(s)
- Rongrong Fan
- Karolinska Institutet, Department of Biosciences and Nutrition, Huddinge, Sweden
| | - Amine Toubal
- Sorbonne Universités, Université Pierre et Marie-Curie, Institut National de la Santé et de la Recherche Médicale (INSERM), UMR_S 1138 Cordeliers Research, Paris, France.,Institute of Cardiometabolism and Nutrition, Paris, France
| | - Saioa Goñi
- Karolinska Institutet, Department of Biosciences and Nutrition, Huddinge, Sweden
| | - Karima Drareni
- Sorbonne Universités, Université Pierre et Marie-Curie, Institut National de la Santé et de la Recherche Médicale (INSERM), UMR_S 1138 Cordeliers Research, Paris, France.,Institute of Cardiometabolism and Nutrition, Paris, France
| | - Zhiqiang Huang
- Karolinska Institutet, Department of Biosciences and Nutrition, Huddinge, Sweden
| | - Fawaz Alzaid
- Sorbonne Universités, Université Pierre et Marie-Curie, Institut National de la Santé et de la Recherche Médicale (INSERM), UMR_S 1138 Cordeliers Research, Paris, France.,Institute of Cardiometabolism and Nutrition, Paris, France
| | - Raphaelle Ballaire
- Sorbonne Universités, Université Pierre et Marie-Curie, Institut National de la Santé et de la Recherche Médicale (INSERM), UMR_S 1138 Cordeliers Research, Paris, France.,Institute of Cardiometabolism and Nutrition, Paris, France
| | - Patricia Ancel
- Institut National de la Santé et de la Recherche Médicale (INSERM), UMR 1062, INRA 1260, Aix-Marseille Université, Nutrition, Obésité et Risque Thrombotique, Marseille, France
| | - Ning Liang
- Karolinska Institutet, Department of Biosciences and Nutrition, Huddinge, Sweden
| | | | - Isabelle Hainault
- Sorbonne Universités, Université Pierre et Marie-Curie, Institut National de la Santé et de la Recherche Médicale (INSERM), UMR_S 1138 Cordeliers Research, Paris, France.,Institute of Cardiometabolism and Nutrition, Paris, France
| | - Antoine Soprani
- Sorbonne Universités, Université Pierre et Marie-Curie, Institut National de la Santé et de la Recherche Médicale (INSERM), UMR_S 1138 Cordeliers Research, Paris, France.,Clinique Geoffroy Saint-Hilaire, General de Santé, Paris, France
| | - Judith Aron-Wisnewsky
- Institute of Cardiometabolism and Nutrition, Paris, France.,Assistance Publique-Hôpitaux de Paris, Pitié-Salpêtrière Hospital, Heart and Metabolism Division, Paris, France.,Institut National de la Santé et de la Recherche Médicale (INSERM), Sorbonne Universités, Université Pierre et Marie-Curie (UPMC), UMR_S U1166, NutriOmics team, Paris, France
| | - Fabienne Foufelle
- Sorbonne Universités, Université Pierre et Marie-Curie, Institut National de la Santé et de la Recherche Médicale (INSERM), UMR_S 1138 Cordeliers Research, Paris, France.,Institute of Cardiometabolism and Nutrition, Paris, France
| | - Toby Lawrence
- Centre d'Immunologie de Marseille-Luminy (CIML), Aix-Marseille Université, UM2, Marseille, France.,Institut National de la Santé et de la Recherche Médicale (INSERM), U1104, Marseille, France.,Centre National de la Recherche Scientifique (CNRS), UMR7280, Marseille, France
| | - Jean-Francois Gautier
- Sorbonne Universités, Université Pierre et Marie-Curie, Institut National de la Santé et de la Recherche Médicale (INSERM), UMR_S 1138 Cordeliers Research, Paris, France.,Assistance Publique-Hôpitaux de Paris, Lariboisière Hospital, Department of Diabetes, Clinical Investigation Centre (CIC-9504), University Paris-Diderot, Paris, France
| | - Nicolas Venteclef
- Sorbonne Universités, Université Pierre et Marie-Curie, Institut National de la Santé et de la Recherche Médicale (INSERM), UMR_S 1138 Cordeliers Research, Paris, France.,Institute of Cardiometabolism and Nutrition, Paris, France
| | - Eckardt Treuter
- Karolinska Institutet, Department of Biosciences and Nutrition, Huddinge, Sweden
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142
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Multiplexed imaging of intracellular protein networks. Cytometry A 2016; 89:761-75. [DOI: 10.1002/cyto.a.22876] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2015] [Revised: 04/21/2016] [Accepted: 04/26/2016] [Indexed: 12/19/2022]
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143
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Morisaki T, Lyon K, DeLuca KF, DeLuca JG, English BP, Zhang Z, Lavis LD, Grimm JB, Viswanathan S, Looger LL, Lionnet T, Stasevich TJ. Real-time quantification of single RNA translation dynamics in living cells. Science 2016; 352:1425-9. [PMID: 27313040 DOI: 10.1126/science.aaf0899] [Citation(s) in RCA: 246] [Impact Index Per Article: 30.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2015] [Accepted: 04/28/2016] [Indexed: 12/14/2022]
Abstract
Although messenger RNA (mRNA) translation is a fundamental biological process, it has never been imaged in real time in vivo with single-molecule precision. To achieve this, we developed nascent chain tracking (NCT), a technique that uses multi-epitope tags and antibody-based fluorescent probes to quantify protein synthesis dynamics at the single-mRNA level. NCT reveals an elongation rate of ~10 amino acids per second, with initiation occurring stochastically every ~30 seconds. Polysomes contain ~1 ribosome every 200 to 900 nucleotides and are globular rather than elongated in shape. By developing multicolor probes, we showed that most polysomes act independently; however, a small fraction (~5%) form complexes in which two distinct mRNAs can be translated simultaneously. The sensitivity and versatility of NCT make it a powerful new tool for quantifying mRNA translation kinetics.
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Affiliation(s)
- Tatsuya Morisaki
- Department of Biochemistry and Molecular Biology and Institute for Genome Architecture and Function, Colorado State University, Fort Collins, CO, USA
| | - Kenneth Lyon
- Department of Biochemistry and Molecular Biology and Institute for Genome Architecture and Function, Colorado State University, Fort Collins, CO, USA
| | - Keith F DeLuca
- Department of Biochemistry and Molecular Biology and Institute for Genome Architecture and Function, Colorado State University, Fort Collins, CO, USA
| | - Jennifer G DeLuca
- Department of Biochemistry and Molecular Biology and Institute for Genome Architecture and Function, Colorado State University, Fort Collins, CO, USA
| | - Brian P English
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA
| | - Zhengjian Zhang
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA
| | - Luke D Lavis
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA
| | - Jonathan B Grimm
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA
| | - Sarada Viswanathan
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA
| | - Loren L Looger
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA
| | - Timothee Lionnet
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA
| | - Timothy J Stasevich
- Department of Biochemistry and Molecular Biology and Institute for Genome Architecture and Function, Colorado State University, Fort Collins, CO, USA
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144
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Abstract
The transcription cycle can be roughly divided into three stages: initiation, elongation, and termination. Understanding the molecular events that regulate all these stages requires a dynamic view of the underlying processes. The development of techniques to visualize and quantify transcription in single living cells has been essential in revealing the transcription kinetics. They have revealed that (a) transcription is heterogeneous between cells and (b) transcription can be discontinuous within a cell. In this review, we discuss the progress in our quantitative understanding of transcription dynamics in living cells, focusing on all parts of the transcription cycle. We present the techniques allowing for single-cell transcription measurements, review evidence from different organisms, and discuss how these experiments have broadened our mechanistic understanding of transcription regulation.
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Affiliation(s)
- Tineke L Lenstra
- Laboratory of Receptor Biology and Gene Expression, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland 20892;
| | - Joseph Rodriguez
- Laboratory of Receptor Biology and Gene Expression, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland 20892;
| | - Huimin Chen
- Laboratory of Receptor Biology and Gene Expression, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland 20892;
| | - Daniel R Larson
- Laboratory of Receptor Biology and Gene Expression, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland 20892;
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145
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DNA context represents transcription regulation of the gene in mouse embryonic stem cells. Sci Rep 2016; 6:24343. [PMID: 27075878 PMCID: PMC4831003 DOI: 10.1038/srep24343] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2015] [Accepted: 03/24/2016] [Indexed: 01/30/2023] Open
Abstract
Understanding gene regulatory information in DNA remains a significant challenge in biomedical research. This study presents a computational approach to infer gene regulatory programs from primary DNA sequences. Using DNA around transcription start sites as attributes, our model predicts gene regulation in the gene. We find that H3K27ac around TSS is an informative descriptor of the transcription program in mouse embryonic stem cells. We build a computational model inferring the cell-type-specific H3K27ac signatures in the DNA around TSS. A comparison of embryonic stem cell and liver cell-specific H3K27ac signatures in DNA shows that the H3K27ac signatures in DNA around TSS efficiently distinguish the cell-type specific H3K27ac peaks and the gene regulation. The arrangement of the H3K27ac signatures inferred from the DNA represents the transcription regulation of the gene in mESC. We show that the DNA around transcription start sites is associated with the gene regulatory program by specific interaction with H3K27ac.
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146
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Abstract
Chromatin regulatory processes, like all biological reactions, are dynamic and stochastic in nature but can give rise to stable and inheritable changes in gene expression patterns. A molecular understanding of those processes is key for fundamental biological insight into gene regulation, epigenetic inheritance, lineage determination, and therapeutic intervention in the case of disease. In recent years, great progress has been made in identifying important molecular players involved in key chromatin regulatory pathways. Conversely, we are only beginning to understand the dynamic interplay between protein effectors, transcription factors, and the chromatin substrate itself. Single-molecule approaches employing both highly defined chromatin substrates in vitro, as well as direct observation of complex regulatory processes in vivo, open new avenues for a molecular view of chromatin regulation. This review highlights recent applications of single-molecule methods and related techniques to investigate fundamental chromatin regulatory processes.
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Affiliation(s)
- Beat Fierz
- Laboratory
of Biophysical
Chemistry of Macromolecules, Institute of Chemical Sciences and Engineering, Ecole Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland
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147
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Nakaoka S, Sasaki K, Ito A, Nakao Y, Yoshida M. A Genetically Encoded FRET Probe to Detect Intranucleosomal Histone H3K9 or H3K14 Acetylation Using BRD4, a BET Family Member. ACS Chem Biol 2016; 11:729-33. [PMID: 25946208 DOI: 10.1021/cb501046t] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Acetylation is a well-characterized histone modification, which plays important roles in controlling epigenetic gene expression, and its malfunction is tightly associated with cancer. By taking advantage of the specific binding of BRD4 to acetylated lysine residues, we developed a FRET-based probe for visualizing histone H3 acetylation in living cells. BRD4, a protein known to be involved in acute myeloid leukemia and nuclear protein in testis midline carcinoma, recognizes the acetylation of histone H3 via its bromodomains. The probe exhibited a significant change in FRET signaling that was dependent on histone H3 acetylation. Mutagenesis studies revealed that an increase in the emission ratio reflected the acetylation of either K9 or K14 of histone H3 within the probe. Since BRD4 has increasingly drawn attention as a new anticancer drug target, we demonstrated that the developed fluorescent probe will also serve as a powerful tool to evaluate BRD4 inhibitors in living cells.
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Affiliation(s)
- Shiho Nakaoka
- Chemical
Genetics Laboratory, RIKEN, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
- Department
of Chemistry and Biochemistry, Waseda University, 3-4-1 Okubo, Shinjuku-ku, Tokyo 169-8555, Japan
| | - Kazuki Sasaki
- Chemical
Genetics Laboratory, RIKEN, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
- JST, PRESTO, 4-1-8 Honcho, Kawaguchi, Saitama 332-0012, Japan
- Chemical Genomics Research Group, RIKEN Center for
Sustainable Resource Science, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Akihiro Ito
- Chemical
Genetics Laboratory, RIKEN, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
- Chemical Genomics Research Group, RIKEN Center for
Sustainable Resource Science, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Yoichi Nakao
- Department
of Chemistry and Biochemistry, Waseda University, 3-4-1 Okubo, Shinjuku-ku, Tokyo 169-8555, Japan
| | - Minoru Yoshida
- Chemical
Genetics Laboratory, RIKEN, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
- Chemical Genomics Research Group, RIKEN Center for
Sustainable Resource Science, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
- JST, CREST Research Project, 4-1-8 Honcho, Kawaguchi, Saitama 332-0012, Japan
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148
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Kumar V, Rayan NA, Muratani M, Lim S, Elanggovan B, Xin L, Lu T, Makhija H, Poschmann J, Lufkin T, Ng HH, Prabhakar S. Comprehensive benchmarking reveals H2BK20 acetylation as a distinctive signature of cell-state-specific enhancers and promoters. Genome Res 2016; 26:612-23. [PMID: 26957309 PMCID: PMC4864461 DOI: 10.1101/gr.201038.115] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2015] [Accepted: 03/07/2016] [Indexed: 12/12/2022]
Abstract
Although over 35 different histone acetylation marks have been described, the overwhelming majority of regulatory genomics studies focus exclusively on H3K27ac and H3K9ac. In order to identify novel epigenomic traits of regulatory elements, we constructed a benchmark set of validated enhancers by performing 140 enhancer assays in human T cells. We tested 40 chromatin signatures on this unbiased enhancer set and identified H2BK20ac, a little-studied histone modification, as the most predictive mark of active enhancers. Notably, we detected a novel class of functionally distinct enhancers enriched in H2BK20ac but lacking H3K27ac, which was present in all examined cell lines and also in embryonic forebrain tissue. H2BK20ac was also unique in highlighting cell-type-specific promoters. In contrast, other acetylation marks were present in all active promoters, regardless of cell-type specificity. In stimulated microglial cells, H2BK20ac was more correlated with cell-state-specific expression changes than H3K27ac, with TGF-beta signaling decoupling the two acetylation marks at a subset of regulatory elements. In summary, our study reveals a previously unknown connection between histone acetylation and cell-type-specific gene regulation and indicates that H2BK20ac profiling can be used to uncover new dimensions of gene regulation.
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Affiliation(s)
- Vibhor Kumar
- Computational and Systems Biology, Genome Institute of Singapore, Singapore 138672, Singapore
| | - Nirmala Arul Rayan
- Computational and Systems Biology, Genome Institute of Singapore, Singapore 138672, Singapore
| | - Masafumi Muratani
- Department of Genome Biology, Faculty of Medicine, University of Tsukuba, Ibaraki, 305-8575, Japan; Stem Cell and Developmental Biology, Genome Institute of Singapore, Singapore 138672, Singapore
| | - Stefan Lim
- Computational and Systems Biology, Genome Institute of Singapore, Singapore 138672, Singapore
| | - Bavani Elanggovan
- Computational and Systems Biology, Genome Institute of Singapore, Singapore 138672, Singapore
| | - Lixia Xin
- Computational and Systems Biology, Genome Institute of Singapore, Singapore 138672, Singapore
| | - Tess Lu
- Computational and Systems Biology, Genome Institute of Singapore, Singapore 138672, Singapore
| | - Harshyaa Makhija
- Computational and Systems Biology, Genome Institute of Singapore, Singapore 138672, Singapore
| | - Jeremie Poschmann
- Computational and Systems Biology, Genome Institute of Singapore, Singapore 138672, Singapore
| | - Thomas Lufkin
- Stem Cell and Developmental Biology, Genome Institute of Singapore, Singapore 138672, Singapore; Department of Biology, Clarkson University, Potsdam, New York 13699, USA
| | - Huck Hui Ng
- Stem Cell and Developmental Biology, Genome Institute of Singapore, Singapore 138672, Singapore; Department of Biological Sciences, National University of Singapore, Singapore 117543, Singapore
| | - Shyam Prabhakar
- Computational and Systems Biology, Genome Institute of Singapore, Singapore 138672, Singapore
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149
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Li W, Notani D, Rosenfeld MG. Enhancers as non-coding RNA transcription units: recent insights and future perspectives. Nat Rev Genet 2016; 17:207-23. [PMID: 26948815 DOI: 10.1038/nrg.2016.4] [Citation(s) in RCA: 487] [Impact Index Per Article: 60.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Networks of regulatory enhancers dictate distinct cell identities and cellular responses to diverse signals by instructing precise spatiotemporal patterns of gene expression. However, 35 years after their discovery, enhancer functions and mechanisms remain incompletely understood. Intriguingly, recent evidence suggests that many, if not all, functional enhancers are themselves transcription units, generating non-coding enhancer RNAs. This observation provides a fundamental insight into the inter-regulation between enhancers and promoters, which can both act as transcription units; it also raises crucial questions regarding the potential biological roles of the enhancer transcription process and non-coding enhancer RNAs. Here, we review research progress in this field and discuss several important, unresolved questions regarding the roles and mechanisms of enhancers in gene regulation.
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Affiliation(s)
- Wenbo Li
- Howard Hughes Medical Institute, Department of Medicine, University of California San Diego, 9500 Gilman Drive, La Jolla, California 92037-0648, USA
| | - Dimple Notani
- Howard Hughes Medical Institute, Department of Medicine, University of California San Diego, 9500 Gilman Drive, La Jolla, California 92037-0648, USA
| | - Michael G Rosenfeld
- Howard Hughes Medical Institute, Department of Medicine, University of California San Diego, 9500 Gilman Drive, La Jolla, California 92037-0648, USA
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150
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Yamamoto N, Agata K, Nakashima K, Imamura T. Bidirectional promoters link cAMP signaling with irreversible differentiation through promoter-associated non-coding RNA (pancRNA) expression in PC12 cells. Nucleic Acids Res 2016; 44:5105-22. [PMID: 26945044 PMCID: PMC4914083 DOI: 10.1093/nar/gkw113] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2015] [Accepted: 02/16/2016] [Indexed: 12/14/2022] Open
Abstract
Bidirectional promoters are the major source of gene activation-associated noncoding RNA (ncRNA). PC12 cells offer an interesting model for understanding the mechanism underlying bidirectional promoter-mediated cell cycle control. Nerve growth factor (NGF)-stimulated PC12 cells elongate neurites, and are in a reversible cell-cycle-arrested state. In contrast, these cells irreversibly differentiate and cannot re-enter the normal cell cycle after NGF plus cAMP treatment. In this study, using directional RNA-seq, we found that bidirectional promoters for protein-coding genes with promoter-associated ncRNA (pancRNA) were enriched for cAMP response element consensus sequences, and were preferred targets for transcriptional regulation by the transcription factors in the cAMP-dependent pathway. A spindle-formation-associated gene, Nusap1 and pancNusap1 were among the most strictly co-transcribed pancRNA–mRNA pairs. This pancRNA–mRNA pair was specifically repressed in irreversibly differentiated PC12 cells. Knockdown (KD) and overexpression experiments showed that pancNusap1 positively regulated the Nusap1 expression in a sequence-specific manner, which was accompanied by histone acetylation at the Nusap1 promoter. Furthermore, pancNusap1 KD recapitulated the effects of cAMP on cell cycle arrest. Thus, we conclude that pancRNA-mediated histone acetylation contributes to the establishment of the cAMP-induced transcription state of the Nusap1 locus and contributes to the irreversible cell cycle exit for terminal differentiation of PC12 cells.
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Affiliation(s)
- Naoki Yamamoto
- Department of Stem Cell Biology and Medicine, Graduate School of Medical Sciences, Kyushu University, Japan Department of Biophysics, Graduate School of Science, Kyoto University, Japan
| | - Kiyokazu Agata
- Department of Biophysics, Graduate School of Science, Kyoto University, Japan
| | - Kinichi Nakashima
- Department of Stem Cell Biology and Medicine, Graduate School of Medical Sciences, Kyushu University, Japan
| | - Takuya Imamura
- Department of Stem Cell Biology and Medicine, Graduate School of Medical Sciences, Kyushu University, Japan
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