1
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Stanković D, Tain LS, Uhlirova M. Xrp1 governs the stress response program to spliceosome dysfunction. Nucleic Acids Res 2024; 52:2093-2111. [PMID: 38303573 PMCID: PMC10954486 DOI: 10.1093/nar/gkae055] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Revised: 01/03/2024] [Accepted: 01/16/2024] [Indexed: 02/03/2024] Open
Abstract
Co-transcriptional processing of nascent pre-mRNAs by the spliceosome is vital to regulating gene expression and maintaining genome integrity. Here, we show that the deficiency of functional U5 small nuclear ribonucleoprotein particles (snRNPs) in Drosophila imaginal cells causes extensive transcriptome remodeling and accumulation of highly mutagenic R-loops, triggering a robust stress response and cell cycle arrest. Despite compromised proliferative capacity, the U5 snRNP-deficient cells increased protein translation and cell size, causing intra-organ growth disbalance before being gradually eliminated via apoptosis. We identify the Xrp1-Irbp18 heterodimer as the primary driver of transcriptional and cellular stress program downstream of U5 snRNP malfunction. Knockdown of Xrp1 or Irbp18 in U5 snRNP-deficient cells attenuated JNK and p53 activity, restored normal cell cycle progression and growth, and inhibited cell death. Reducing Xrp1-Irbp18, however, did not rescue the splicing defects, highlighting the requirement of accurate splicing for cellular and tissue homeostasis. Our work provides novel insights into the crosstalk between splicing and the DNA damage response and defines the Xrp1-Irbp18 heterodimer as a critical sensor of spliceosome malfunction and mediator of the stress-induced cellular senescence program.
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Affiliation(s)
- Dimitrije Stanković
- Institute for Genetics and Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Cologne 50931, Germany
| | - Luke S Tain
- Institute for Genetics and Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Cologne 50931, Germany
| | - Mirka Uhlirova
- Institute for Genetics and Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Cologne 50931, Germany
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2
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Mitra R, Richhariya S, Hasan G. Orai-mediated calcium entry determines activity of central dopaminergic neurons by regulation of gene expression. eLife 2024; 12:RP88808. [PMID: 38289659 PMCID: PMC10945566 DOI: 10.7554/elife.88808] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2024] Open
Abstract
Maturation and fine-tuning of neural circuits frequently require neuromodulatory signals that set the excitability threshold, neuronal connectivity, and synaptic strength. Here, we present a mechanistic study of how neuromodulator-stimulated intracellular Ca2+ signals, through the store-operated Ca2+ channel Orai, regulate intrinsic neuronal properties by control of developmental gene expression in flight-promoting central dopaminergic neurons (fpDANs). The fpDANs receive cholinergic inputs for release of dopamine at a central brain tripartite synapse that sustains flight (Sharma and Hasan, 2020). Cholinergic inputs act on the muscarinic acetylcholine receptor to stimulate intracellular Ca2+ release through the endoplasmic reticulum (ER) localised inositol 1,4,5-trisphosphate receptor followed by ER-store depletion and Orai-mediated store-operated Ca2+ entry (SOCE). Analysis of gene expression in fpDANs followed by genetic, cellular, and molecular studies identified Orai-mediated Ca2+ entry as a key regulator of excitability in fpDANs during circuit maturation. SOCE activates the transcription factor trithorax-like (Trl), which in turn drives expression of a set of genes, including Set2, that encodes a histone 3 lysine 36 methyltransferase (H3K36me3). Set2 function establishes a positive feedback loop, essential for receiving neuromodulatory cholinergic inputs and sustaining SOCE. Chromatin-modifying activity of Set2 changes the epigenetic status of fpDANs and drives expression of key ion channel and signalling genes that determine fpDAN activity. Loss of activity reduces the axonal arborisation of fpDANs within the MB lobe and prevents dopamine release required for the maintenance of long flight.
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Affiliation(s)
- Rishav Mitra
- National Centre for Biological Sciences, Tata Institute of Fundamental ResearchBangaloreIndia
| | - Shlesha Richhariya
- National Centre for Biological Sciences, Tata Institute of Fundamental ResearchBangaloreIndia
- Department of Biology, Brandeis UniversityWalthamUnited States
| | - Gaiti Hasan
- National Centre for Biological Sciences, Tata Institute of Fundamental ResearchBangaloreIndia
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3
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Melnikova L, Golovnin A. Multiple Roles of dXNP and dADD1- Drosophila Orthologs of ATRX Chromatin Remodeler. Int J Mol Sci 2023; 24:16486. [PMID: 38003676 PMCID: PMC10671109 DOI: 10.3390/ijms242216486] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Revised: 11/11/2023] [Accepted: 11/16/2023] [Indexed: 11/26/2023] Open
Abstract
The Drosophila melanogaster dADD1 and dXNP proteins are orthologues of the ADD and SNF2 domains of the vertebrate ATRX (Alpha-Thalassemia with mental Retardation X-related) protein. ATRX plays a role in general molecular processes, such as regulating chromatin status and gene expression, while dADD1 and dXNP have similar functions in the Drosophila genome. Both ATRX and dADD1/dXNP interact with various protein partners and participate in various regulatory complexes. Disruption of ATRX expression in humans leads to the development of α-thalassemia and cancer, especially glioma. However, the mechanisms that allow ATRX to regulate various cellular processes are poorly understood. Studying the functioning of dADD1/dXNP in the Drosophila model may contribute to understanding the mechanisms underlying the multifunctional action of ATRX and its connection with various cellular processes. This review provides a brief overview of the currently available information in mammals and Drosophila regarding the roles of ATRX, dXNP, and dADD1. It discusses possible mechanisms of action of complexes involving these proteins.
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Affiliation(s)
- Larisa Melnikova
- Department of Drosophila Molecular Genetics, Institute of Gene Biology, Russian Academy of Sciences, 34/5 Vavilov St., 119334 Moscow, Russia
| | - Anton Golovnin
- Department of Drosophila Molecular Genetics, Institute of Gene Biology, Russian Academy of Sciences, 34/5 Vavilov St., 119334 Moscow, Russia
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4
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Chetverina D, Vorobyeva NE, Mazina MY, Fab LV, Lomaev D, Golovnina A, Mogila V, Georgiev P, Ziganshin RH, Erokhin M. Comparative interactome analysis of the PRE DNA-binding factors: purification of the Combgap-, Zeste-, Psq-, and Adf1-associated proteins. Cell Mol Life Sci 2022; 79:353. [PMID: 35676368 PMCID: PMC11072172 DOI: 10.1007/s00018-022-04383-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Revised: 04/14/2022] [Accepted: 05/08/2022] [Indexed: 01/08/2023]
Abstract
The Polycomb group (PcG) and Trithorax group (TrxG) proteins are key epigenetic regulators controlling the silenced and active states of genes in multicellular organisms, respectively. In Drosophila, PcG/TrxG proteins are recruited to the chromatin via binding to specific DNA sequences termed polycomb response elements (PREs). While precise mechanisms of the PcG/TrxG protein recruitment remain unknown, the important role is suggested to belong to sequence-specific DNA-binding factors. At the same time, it was demonstrated that the PRE DNA-binding proteins are not exclusively localized to PREs but can bind other DNA regulatory elements, including enhancers, promoters, and boundaries. To gain an insight into the PRE DNA-binding protein regulatory network, here, using ChIP-seq and immuno-affinity purification coupled to the high-throughput mass spectrometry, we searched for differences in abundance of the Combgap, Zeste, Psq, and Adf1 PRE DNA-binding proteins. While there were no conspicuous differences in co-localization of these proteins with other functional transcription factors, we show that Combgap and Zeste are more tightly associated with the Polycomb repressive complex 1 (PRC1), while Psq interacts strongly with the TrxG proteins, including the BAP SWI/SNF complex. The Adf1 interactome contained Mediator subunits as the top interactors. In addition, Combgap efficiently interacted with AGO2, NELF, and TFIID. Combgap, Psq, and Adf1 have architectural proteins in their networks. We further investigated the existence of direct interactions between different PRE DNA-binding proteins and demonstrated that Combgap-Adf1, Psq-Dsp1, and Pho-Spps can interact in the yeast two-hybrid assay. Overall, our data suggest that Combgap, Psq, Zeste, and Adf1 are associated with the protein complexes implicated in different regulatory activities and indicate their potential multifunctional role in the regulation of transcription.
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Affiliation(s)
- Darya Chetverina
- Group of Epigenetics, Institute of Gene Biology, Russian Academy of Sciences, 34/5 Vavilov Street, Moscow, 119334, Russia.
| | - Nadezhda E Vorobyeva
- Group of Dynamics of Transcriptional Complexes, Institute of Gene Biology, Russian Academy of Sciences, Moscow, Russia
| | - Marina Yu Mazina
- Group of Hormone-Dependent Transcriptional Regulation, Institute of Gene Biology, Russian Academy of Sciences, Moscow, Russia
| | - Lika V Fab
- Group of Chromatin Biology, Institute of Gene Biology, Russian Academy of Sciences, 34/5 Vavilov Street, Moscow, 119334, Russia
| | - Dmitry Lomaev
- Group of Epigenetics, Institute of Gene Biology, Russian Academy of Sciences, 34/5 Vavilov Street, Moscow, 119334, Russia
| | - Alexandra Golovnina
- Group of Epigenetics, Institute of Gene Biology, Russian Academy of Sciences, 34/5 Vavilov Street, Moscow, 119334, Russia
| | - Vladic Mogila
- Department of Control of Genetic Processes, Institute of Gene Biology, Russian Academy of Sciences, 34/5 Vavilov Street, Moscow, 119334, Russia
| | - Pavel Georgiev
- Department of Control of Genetic Processes, Institute of Gene Biology, Russian Academy of Sciences, 34/5 Vavilov Street, Moscow, 119334, Russia
| | - Rustam H Ziganshin
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, 117997, Russia
| | - Maksim Erokhin
- Group of Chromatin Biology, Institute of Gene Biology, Russian Academy of Sciences, 34/5 Vavilov Street, Moscow, 119334, Russia.
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5
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Duan J, Rieder L, Colonnetta MM, Huang A, Mckenney M, Watters S, Deshpande G, Jordan W, Fawzi N, Larschan E. CLAMP and Zelda function together to promote Drosophila zygotic genome activation. eLife 2021; 10:e69937. [PMID: 34342574 PMCID: PMC8367384 DOI: 10.7554/elife.69937] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Accepted: 08/02/2021] [Indexed: 12/22/2022] Open
Abstract
During the essential and conserved process of zygotic genome activation (ZGA), chromatin accessibility must increase to promote transcription. Drosophila is a well-established model for defining mechanisms that drive ZGA. Zelda (ZLD) is a key pioneer transcription factor (TF) that promotes ZGA in the Drosophila embryo. However, many genomic loci that contain GA-rich motifs become accessible during ZGA independent of ZLD. Therefore, we hypothesized that other early TFs that function with ZLD have not yet been identified, especially those that are capable of binding to GA-rich motifs such as chromatin-linked adaptor for male-specific lethal (MSL) proteins (CLAMP). Here, we demonstrate that Drosophila embryonic development requires maternal CLAMP to (1) activate zygotic transcription; (2) increase chromatin accessibility at promoters of specific genes that often encode other essential TFs; and (3) enhance chromatin accessibility and facilitate ZLD occupancy at a subset of key embryonic promoters. Thus, CLAMP functions as a pioneer factor that plays a targeted yet essential role in ZGA.
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Affiliation(s)
- Jingyue Duan
- Department of Molecular Biology, Cellular Biology, and Biochemistry, Brown UniversityProvidenceUnited States
| | - Leila Rieder
- Department of Biology, Emory UniversityAtlantaUnited States
| | - Megan M Colonnetta
- Department of Molecular Biology, Princeton UniversityPrincetonUnited States
| | - Annie Huang
- Department of Molecular Biology, Cellular Biology, and Biochemistry, Brown UniversityProvidenceUnited States
| | - Mary Mckenney
- Department of Molecular Biology, Cellular Biology, and Biochemistry, Brown UniversityProvidenceUnited States
| | - Scott Watters
- Department of Molecular Pharmacology, Physiology and Biotechnology, Brown UniversityProvidenceUnited States
| | - Girish Deshpande
- Department of Molecular Biology, Cellular Biology, and Biochemistry, Brown UniversityProvidenceUnited States
- Department of Molecular Biology, Princeton UniversityPrincetonUnited States
| | - William Jordan
- Department of Molecular Biology, Cellular Biology, and Biochemistry, Brown UniversityProvidenceUnited States
| | - Nicolas Fawzi
- Department of Molecular Pharmacology, Physiology and Biotechnology, Brown UniversityProvidenceUnited States
| | - Erica Larschan
- Department of Molecular Biology, Cellular Biology, and Biochemistry, Brown UniversityProvidenceUnited States
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6
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Chetverina D, Erokhin M, Schedl P. GAGA factor: a multifunctional pioneering chromatin protein. Cell Mol Life Sci 2021; 78:4125-4141. [PMID: 33528710 DOI: 10.1007/s00018-021-03776-z] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2020] [Revised: 12/08/2020] [Accepted: 01/19/2021] [Indexed: 12/27/2022]
Abstract
The Drosophila GAGA factor (GAF) is a multifunctional protein implicated in nucleosome organization and remodeling, activation and repression of gene expression, long distance enhancer-promoter communication, higher order chromosome structure, and mitosis. This broad range of activities poses questions about how a single protein can perform so many seemingly different and unrelated functions. Current studies argue that GAF acts as a "pioneer" factor, generating nucleosome-free regions of chromatin for different classes of regulatory elements. The removal of nucleosomes from regulatory elements in turn enables other factors to bind to these elements and carry out their specialized functions. Consistent with this view, GAF associates with a collection of chromatin remodelers and also interacts with proteins implicated in different regulatory functions. In this review, we summarize the known activities of GAF and the functions of its protein partners.
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Affiliation(s)
- Darya Chetverina
- Group of Epigenetics, Institute of Gene Biology, Russian Academy of Sciences, 34/5 Vavilov St., Moscow, 119334, Russia.
| | - Maksim Erokhin
- Group of Chromatin Biology, Institute of Gene Biology, Russian Academy of Sciences, 34/5 Vavilov St., Moscow, 119334, Russia
| | - Paul Schedl
- Department of Molecular Biology, Princeton University, Princeton, NJ, 08544, USA.
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7
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Ma D, Bou-Sleiman M, Joncour P, Indelicato CE, Frochaux M, Braman V, Litovchenko M, Storelli G, Deplancke B, Leulier F. Commensal Gut Bacteria Buffer the Impact of Host Genetic Variants on Drosophila Developmental Traits under Nutritional Stress. iScience 2019; 19:436-447. [PMID: 31422284 PMCID: PMC6704380 DOI: 10.1016/j.isci.2019.07.048] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2018] [Revised: 04/25/2019] [Accepted: 07/30/2019] [Indexed: 02/07/2023] Open
Abstract
Eukaryotic genomes encode several buffering mechanisms that robustly maintain invariant phenotypic outcome despite fluctuating environmental conditions. Here we show that the Drosophila gut-associated commensals, represented by a single facultative symbiont, Lactobacillus plantarum (LpWJL), constitutes a so far unexpected buffer that masks the contribution of the host's cryptic genetic variation (CGV) to developmental traits while the host is under nutritional stress. During chronic under-nutrition, LpWJL consistently reduces variation in different host phenotypic traits and ensures robust organ patterning during development; LpWJL also decreases genotype-dependent expression variation, particularly for development-associated genes. We further provide evidence that LpWJL buffers via reactive oxygen species (ROS) signaling whose inhibition impairs microbiota-mediated phenotypic robustness. We thus identified a hitherto unappreciated contribution of the gut facultative symbionts to host fitness that, beyond supporting growth rates and maturation timing, confers developmental robustness and phenotypic homogeneity in times of nutritional stress. Upon nutritional stress, fly commensals buffer the effects of cryptic genetic variants Fly gut commensals buffer transcriptional variation in developmental genes Fly commensals buffer phenotypic heterogeneity and mediate developmental canalization Compromising ROS activities impair microbial buffering capacity
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Affiliation(s)
- Dali Ma
- Institut de Génomique Fonctionnelle de Lyon (IGFL), Université de Lyon, Ecole Normale Supérieure de Lyon, Centre National de la Recherche Scientifique, Université Claude Bernard Lyon 1, Unité Mixte de Recherche 5242, 69364 Cedex 07, Lyon, France
| | - Maroun Bou-Sleiman
- Laboratory of Systems Biology and Genetics, Institute of Bioengineering and Swiss Institute of Bioinformatics, School of Life Sciences Ecole Polytechnique Federale de Lausanne (EPFL), 1015, Lausanne, Switzerland
| | - Pauline Joncour
- Institut de Génomique Fonctionnelle de Lyon (IGFL), Université de Lyon, Ecole Normale Supérieure de Lyon, Centre National de la Recherche Scientifique, Université Claude Bernard Lyon 1, Unité Mixte de Recherche 5242, 69364 Cedex 07, Lyon, France
| | - Claire-Emmanuelle Indelicato
- Institut de Génomique Fonctionnelle de Lyon (IGFL), Université de Lyon, Ecole Normale Supérieure de Lyon, Centre National de la Recherche Scientifique, Université Claude Bernard Lyon 1, Unité Mixte de Recherche 5242, 69364 Cedex 07, Lyon, France
| | - Michael Frochaux
- Laboratory of Systems Biology and Genetics, Institute of Bioengineering and Swiss Institute of Bioinformatics, School of Life Sciences Ecole Polytechnique Federale de Lausanne (EPFL), 1015, Lausanne, Switzerland
| | - Virginie Braman
- Laboratory of Systems Biology and Genetics, Institute of Bioengineering and Swiss Institute of Bioinformatics, School of Life Sciences Ecole Polytechnique Federale de Lausanne (EPFL), 1015, Lausanne, Switzerland
| | - Maria Litovchenko
- Laboratory of Systems Biology and Genetics, Institute of Bioengineering and Swiss Institute of Bioinformatics, School of Life Sciences Ecole Polytechnique Federale de Lausanne (EPFL), 1015, Lausanne, Switzerland
| | - Gilles Storelli
- Institut de Génomique Fonctionnelle de Lyon (IGFL), Université de Lyon, Ecole Normale Supérieure de Lyon, Centre National de la Recherche Scientifique, Université Claude Bernard Lyon 1, Unité Mixte de Recherche 5242, 69364 Cedex 07, Lyon, France
| | - Bart Deplancke
- Laboratory of Systems Biology and Genetics, Institute of Bioengineering and Swiss Institute of Bioinformatics, School of Life Sciences Ecole Polytechnique Federale de Lausanne (EPFL), 1015, Lausanne, Switzerland.
| | - François Leulier
- Institut de Génomique Fonctionnelle de Lyon (IGFL), Université de Lyon, Ecole Normale Supérieure de Lyon, Centre National de la Recherche Scientifique, Université Claude Bernard Lyon 1, Unité Mixte de Recherche 5242, 69364 Cedex 07, Lyon, France.
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8
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Hillmer RE, Link BA. The Roles of Hippo Signaling Transducers Yap and Taz in Chromatin Remodeling. Cells 2019; 8:E502. [PMID: 31137701 PMCID: PMC6562424 DOI: 10.3390/cells8050502] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2019] [Revised: 05/15/2019] [Accepted: 05/19/2019] [Indexed: 01/04/2023] Open
Abstract
Hippo signaling controls cellular processes that ultimately impact organogenesis and homeostasis. Consequently, disease states including cancer can emerge when signaling is deregulated. The major pathway transducers Yap and Taz require cofactors to impart transcriptional control over target genes. Research into Yap/Taz-mediated epigenetic modifications has revealed their association with chromatin-remodeling complex proteins as a means of altering chromatin structure, therefore affecting accessibility and activity of target genes. Specifically, Yap/Taz have been found to associate with factors of the GAGA, Ncoa6, Mediator, Switch/sucrose nonfermentable (SWI/SNF), and Nucleosome Remodeling and Deacetylase (NuRD) chromatin-remodeling complexes to alter the accessibility of target genes. This review highlights the different mechanisms by which Yap/Taz collaborate with other factors to modify DNA packing at specific loci to either activate or repress target gene transcription.
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Affiliation(s)
- Ryan E Hillmer
- Department of Cell Biology, Neurobiology and Anatomy, Medical College of Wisconsin, 8701 Watertown Plank Road, Milwaukee, WI 53226, USA.
| | - Brian A Link
- Department of Cell Biology, Neurobiology and Anatomy, Medical College of Wisconsin, 8701 Watertown Plank Road, Milwaukee, WI 53226, USA.
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9
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Fedorova EV, Dorogova NV, Bolobolova EU, Fedorova SA, Karagodin DA, Ogienko AA, Khruscheva AS, Baricheva EM. GAGA protein is required for multiple aspects of Drosophila oogenesis and female fertility. Genesis 2019; 57:e23269. [PMID: 30537428 DOI: 10.1002/dvg.23269] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2018] [Revised: 11/30/2018] [Accepted: 12/03/2018] [Indexed: 08/02/2024]
Abstract
Investigation of Drosophila oogenesis provides the opportunity to understand conservative genetic mechanisms underlying fertile female gamete development. In this study, we showed that the Drosophila DNA-binding protein GAGA factor (GAF) had a multifunctional role in oogenesis and it is involved in the regulation of this process genetic program. We studied the influence on Drosophila oogenesis of a number of mutations in the 5' region of the Trl gene that encodes GAF. We found that our originally generated Trl mutations lead to a decrease in transcriptional gene activity and levels of GAF expression in both germline and follicular cells. Cytological (fluorescence and electron microscopy) analysis showed that GAF loss resulted in multiple oogenesis defects. Mutations affected the actin cytoskeleton, leading to decrease of cytoplasmic filaments in nurse cells and basal actin in follicular cells. GAF depletion also leads to abnormal follicular cells migration, both border and centripetal. In addition, mutant ovaries demonstrated abnormalities in germ cells, including mitochondria, endoplasmic reticulum, karyosome organization, yolk granule formation and selective transport. Loss of GAF also promoted excessive cell death and egg chamber degradation. In sum, these defects caused very high or full female sterility. Since one of the main GAF activities is regulation of transcription, the complex phenotypes of the Trl mutants might be the consequence of its multiple target genes misexpression.
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Affiliation(s)
- Elena V Fedorova
- Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - Natalya V Dorogova
- Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - Elena U Bolobolova
- Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - Svetlana A Fedorova
- Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - Dmitry A Karagodin
- Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - Anna A Ogienko
- Institute of Molecular and Cellular Biology of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - Asja S Khruscheva
- Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - Elina M Baricheva
- Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
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10
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Suggs BZ, Latham AL, Dawes AT, Chamberlin HM. FACT complex gene duplicates exhibit redundant and non-redundant functions in C. elegans. Dev Biol 2018; 444:71-82. [PMID: 30336114 PMCID: PMC6310015 DOI: 10.1016/j.ydbio.2018.10.002] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2018] [Revised: 10/03/2018] [Accepted: 10/04/2018] [Indexed: 01/05/2023]
Abstract
FACT (facilitates chromatin transcription) is a histone chaperone complex important in genomic processes including transcription, DNA replication, and DNA repair. FACT is composed of two proteins, SSRP1 and SPT16, which are highly conserved across eukaryotes. While the mechanisms for FACT in nucleosome reorganization and its relationship to DNA processes is well established, how these roles impact coordination in multicellular animal development are less well understood. Here we characterize the genes encoding FACT complex proteins in the nematode C. elegans. We show that whereas C. elegans includes one SPT16 gene (spt-16), two genes (hmg-3 and hmg-4) encode SSRP1 proteins. Depletion of FACT complex genes interferes with embryonic cell division and cell cycle timing generally, with anterior pharynx development especially sensitive to these defects. hmg-3 and hmg-4 exhibit redundancy for these maternally-provided embryonic functions, but are each uniquely required zygotically for normal germline development. This work provides a framework to study FACT gene function in developmental processes, and identifies that distinct functional requirements for gene duplicates can be manifest within a single tissue.
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Affiliation(s)
- Brittany Z Suggs
- Department of Molecular Genetics, Ohio State University, United States
| | - Aislinn L Latham
- Department of Molecular Genetics, Ohio State University, United States
| | - Adriana T Dawes
- Department of Molecular Genetics, Ohio State University, United States; Department of Mathematics, Ohio State University, United States
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11
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Shen Z, Formosa T, Tantin D. FACT Inhibition Blocks Induction But Not Maintenance of Pluripotency. Stem Cells Dev 2018; 27:1693-1701. [PMID: 30319048 PMCID: PMC6302925 DOI: 10.1089/scd.2018.0150] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2018] [Accepted: 10/11/2018] [Indexed: 01/23/2023] Open
Abstract
The histone chaperone facilitates chromatin transactions (FACT) is associated with nuclear processes, including DNA transcription, replication, and repair. We previously showed that FACT is transiently recruited to pluripotency-associated target genes by newly bound Oct4. In this study, we tested the effects of FACT depletion by knockout or chemical inhibition on the induction and maintenance of pluripotency. Clustered regularly interspaced short palindromic repeat (CRISPR)-mediated deletion of the FACT subunit Spt16 did not affect the viability or proliferation of fibroblasts but blocked their ability to form induced pluripotent stem cells. Similarly, a small molecule inhibitor of FACT blocked the induction of pluripotency at an early step in reprogramming, without affecting the viability, proliferation, undifferentiated state, or the expression of core pluripotency genes. Notably, trypsinization and passage of pluripotent cells transiently reintroduced a requirement for FACT. Although FACT has been considered to be an essential transcription elongation factor, these results contribute to the emerging view that it instead promotes transitions between stable chromatin states, including during reprogramming to pluripotency.
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Affiliation(s)
- Zuolian Shen
- Department of Pathology, University of Utah School of Medicine, Salt Lake City, Utah
| | - Tim Formosa
- Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, Utah
| | - Dean Tantin
- Department of Pathology, University of Utah School of Medicine, Salt Lake City, Utah
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12
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Haberle V, Stark A. Eukaryotic core promoters and the functional basis of transcription initiation. Nat Rev Mol Cell Biol 2018; 19:621-637. [PMID: 29946135 PMCID: PMC6205604 DOI: 10.1038/s41580-018-0028-8] [Citation(s) in RCA: 373] [Impact Index Per Article: 62.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
RNA polymerase II (Pol II) core promoters are specialized DNA sequences at transcription start sites of protein-coding and non-coding genes that support the assembly of the transcription machinery and transcription initiation. They enable the highly regulated transcription of genes by selectively integrating regulatory cues from distal enhancers and their associated regulatory proteins. In this Review, we discuss the defining properties of gene core promoters, including their sequence features, chromatin architecture and transcription initiation patterns. We provide an overview of molecular mechanisms underlying the function and regulation of core promoters and their emerging functional diversity, which defines distinct transcription programmes. On the basis of the established properties of gene core promoters, we discuss transcription start sites within enhancers and integrate recent results obtained from dedicated functional assays to propose a functional model of transcription initiation. This model can explain the nature and function of transcription initiation at gene starts and at enhancers and can explain the different roles of core promoters, of Pol II and its associated factors and of the activating cues provided by enhancers and the transcription factors and cofactors they recruit.
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Affiliation(s)
- Vanja Haberle
- Research Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC), Vienna, Austria
| | - Alexander Stark
- Research Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC), Vienna, Austria.
- Medical University of Vienna, Vienna Biocenter (VBC), Vienna, Austria.
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13
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Srivastava A, Kumar AS, Mishra RK. Vertebrate GAF/ThPOK: emerging functions in chromatin architecture and transcriptional regulation. Cell Mol Life Sci 2018; 75:623-633. [PMID: 28856379 PMCID: PMC11105447 DOI: 10.1007/s00018-017-2633-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2017] [Revised: 08/09/2017] [Accepted: 08/25/2017] [Indexed: 12/31/2022]
Abstract
GAGA factor of Drosophila melanogaster (DmGAF) is a multifaceted transcription factor with diverse roles in chromatin regulation. Recently, ThPOK/c-Krox was identified as its vertebrate homologue (vGAF), which has a basic domain structure similar to DmGAF and is decorated with a number of post-translationally modified residues. In vertebrate genomes, vGAF associates with purine-rich GAGA sequences and performs diverse chromatin-mediated functions, viz., gene activation, repression and enhancer blocking. Expansion of regulatory chromatin proteins with the acquisition of PTMs appears to be the general trend that facilitated the evolution of complexity in vertebrates. Here, we compare the structural and functional features of vGAF with those of DmGAF and also assess the possible functional redundancy among paralogues of vGAF. We also discuss the underlying mechanisms which aid in the diverse and context-dependent functions of this protein.
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Affiliation(s)
- Avinash Srivastava
- CSIR-Centre for Cellular and Molecular Biology (CCMB), Uppal Road, Hyderabad, 500007, India
| | - Amitha Sampath Kumar
- CSIR-Centre for Cellular and Molecular Biology (CCMB), Uppal Road, Hyderabad, 500007, India
| | - Rakesh K Mishra
- CSIR-Centre for Cellular and Molecular Biology (CCMB), Uppal Road, Hyderabad, 500007, India.
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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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15
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Shi L, Wen H, Shi X. The Histone Variant H3.3 in Transcriptional Regulation and Human Disease. J Mol Biol 2017; 429:1934-1945. [PMID: 27894815 PMCID: PMC5446305 DOI: 10.1016/j.jmb.2016.11.019] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2016] [Revised: 11/17/2016] [Accepted: 11/17/2016] [Indexed: 01/19/2023]
Abstract
Histone proteins wrap around DNA to form nucleosomes, which further compact into the higher-order structure of chromatin. In addition to the canonical histones, there are also variant histones that often have pivotal roles in regulating chromatin dynamics and in the accessibility of the underlying DNA. H3.3 is the most common non-centromeric variant of histone H3 that differs from the canonical H3 by just 4-5 aa. Here, we discuss the current knowledge of H3.3 in transcriptional regulation and the recent discoveries and molecular mechanisms of H3.3 mutations in human cancer.
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Affiliation(s)
- Leilei Shi
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; Center for Cancer Epigenetics, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Hong Wen
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; Center for Cancer Epigenetics, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Xiaobing Shi
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; Center for Cancer Epigenetics, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; The University of Texas Graduate School of Biomedical Sciences, Houston, TX 77030, USA.
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16
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Xu D, Yang Q, Cui M, Zhang Q. The novel transcriptional factor HP1BP3 negatively regulates Hsp70 transcription in Crassostrea hongkongensis. Sci Rep 2017; 7:1401. [PMID: 28469151 PMCID: PMC5431216 DOI: 10.1038/s41598-017-01573-y] [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: 10/18/2016] [Accepted: 03/29/2017] [Indexed: 11/29/2022] Open
Abstract
ChHP1BP3, a chromatin complex-related protein known with dynamic features, was identified as a ChHsp70 promoter-associated factor in Crassostrea hongkongensis by DNA-affinity purification and mass spectrometry analysis. Direct interaction between purified ChHP1BP3 and the ChHsp70 promoter region was demonstrated using EMSA. ChHp1bp3 depletion led to clear enhancements in ChHsp70 mRNA expression in C. hongkongensis hemocytes. However, ChHp1bp3 overexpression in heterologous HEK293T cells correlated with fluctuations in ChHsp70 transcription. Quantitative RT-PCR analysis showed that both ChHsp70 and ChHp1bp3 transcription were responsive to external physical/chemical stresses by heat, CdCl2 and NP. This indicated a plausible correlation between ChHsp70 and ChHp1bp3 in the stress-induced genetic regulatory pathway. While, the distinctive ChHp1bp3 expression patterns upon physical and chemical stresses suggest that the mechanisms that mediate ChHp1bp3 induction might be stress-specific. This study discovered a novel role for HP1BP3 as a negative regulator in controlling Hsp70 transcription in C. hongkongensis, and contributed to better understanding the complex regulatory mechanisms governing Hsp70 transcription.
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Affiliation(s)
- Delin Xu
- Department of Ecology, Institute of Hydrobiology, School of Life Science and Technology, Key Laboratory of Eutrophication and Red Tide Prevention of Guangdong Higher Education Institutes, Engineering Research Center of Tropical and Subtropical Aquatic Ecological Engineering, Ministry of Education, Jinan University, Guangzhou, 510632, P.R. China
| | - Qin Yang
- Department of Ecology, Institute of Hydrobiology, School of Life Science and Technology, Key Laboratory of Eutrophication and Red Tide Prevention of Guangdong Higher Education Institutes, Engineering Research Center of Tropical and Subtropical Aquatic Ecological Engineering, Ministry of Education, Jinan University, Guangzhou, 510632, P.R. China
| | - Miao Cui
- Department of Ecology, Institute of Hydrobiology, School of Life Science and Technology, Key Laboratory of Eutrophication and Red Tide Prevention of Guangdong Higher Education Institutes, Engineering Research Center of Tropical and Subtropical Aquatic Ecological Engineering, Ministry of Education, Jinan University, Guangzhou, 510632, P.R. China.
| | - Qizhong Zhang
- Department of Ecology, Institute of Hydrobiology, School of Life Science and Technology, Key Laboratory of Eutrophication and Red Tide Prevention of Guangdong Higher Education Institutes, Engineering Research Center of Tropical and Subtropical Aquatic Ecological Engineering, Ministry of Education, Jinan University, Guangzhou, 510632, P.R. China.
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17
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Yeung K, Boija A, Karlsson E, Holmqvist PH, Tsatskis Y, Nisoli I, Yap D, Lorzadeh A, Moksa M, Hirst M, Aparicio S, Fanto M, Stenberg P, Mannervik M, McNeill H. Atrophin controls developmental signaling pathways via interactions with Trithorax-like. eLife 2017; 6:e23084. [PMID: 28327288 PMCID: PMC5409829 DOI: 10.7554/elife.23084] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2016] [Accepted: 03/15/2017] [Indexed: 12/30/2022] Open
Abstract
Mutations in human Atrophin1, a transcriptional corepressor, cause dentatorubral-pallidoluysian atrophy, a neurodegenerative disease. Drosophila Atrophin (Atro) mutants display many phenotypes, including neurodegeneration, segmentation, patterning and planar polarity defects. Despite Atro's critical role in development and disease, relatively little is known about Atro's binding partners and downstream targets. We present the first genomic analysis of Atro using ChIP-seq against endogenous Atro. ChIP-seq identified 1300 potential direct targets of Atro including engrailed, and components of the Dpp and Notch signaling pathways. We show that Atro regulates Dpp and Notch signaling in larval imaginal discs, at least partially via regulation of thickveins and fringe. In addition, bioinformatics analyses, sequential ChIP and coimmunoprecipitation experiments reveal that Atro interacts with the Drosophila GAGA Factor, Trithorax-like (Trl), and they bind to the same loci simultaneously. Phenotypic analyses of Trl and Atro clones suggest that Atro is required to modulate the transcription activation by Trl in larval imaginal discs. Taken together, these data indicate that Atro is a major Trl cofactor that functions to moderate developmental gene transcription.
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Affiliation(s)
- Kelvin Yeung
- Department of Molecular Genetics, University of Toronto, Toronto, Canada
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Canada
| | - Ann Boija
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Stockholm, Sweden
| | - Edvin Karlsson
- Department of Molecular Biology, Umeå University, Umeå, Sweden
- Division of CBRN Security and Defence, FOI-Swedish Defence Research Agency, Umeå, Sweden
| | - Per-Henrik Holmqvist
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Stockholm, Sweden
| | - Yonit Tsatskis
- Department of Molecular Genetics, University of Toronto, Toronto, Canada
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Canada
| | - Ilaria Nisoli
- Department of Basic and Clinical Neuroscience, Maurice Wohl Clinical Neuroscience Institute, King’s College London, London, United Kingdom
| | - Damian Yap
- Department of Molecular Oncology, British Columbia Cancer Research Centre, Vancouver, Canada
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, Canada
| | - Alireza Lorzadeh
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, Canada
- Michael Smith Laboratories, Vancouver, Canada
- Canada’s Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, Canada
| | - Michelle Moksa
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, Canada
- Michael Smith Laboratories, Vancouver, Canada
- Canada’s Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, Canada
| | - Martin Hirst
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, Canada
- Michael Smith Laboratories, Vancouver, Canada
- Canada’s Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, Canada
| | - Samuel Aparicio
- Department of Molecular Oncology, British Columbia Cancer Research Centre, Vancouver, Canada
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, Canada
| | - Manolis Fanto
- Department of Basic and Clinical Neuroscience, Maurice Wohl Clinical Neuroscience Institute, King’s College London, London, United Kingdom
| | - Per Stenberg
- Department of Molecular Biology, Umeå University, Umeå, Sweden
- Division of CBRN Security and Defence, FOI-Swedish Defence Research Agency, Umeå, Sweden
| | - Mattias Mannervik
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Stockholm, Sweden
| | - Helen McNeill
- Department of Molecular Genetics, University of Toronto, Toronto, Canada
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Canada
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18
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Lomaev D, Mikhailova A, Erokhin M, Shaposhnikov AV, Moresco JJ, Blokhina T, Wolle D, Aoki T, Ryabykh V, Yates JR, Shidlovskii YV, Georgiev P, Schedl P, Chetverina D. The GAGA factor regulatory network: Identification of GAGA factor associated proteins. PLoS One 2017; 12:e0173602. [PMID: 28296955 PMCID: PMC5351981 DOI: 10.1371/journal.pone.0173602] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2016] [Accepted: 02/23/2017] [Indexed: 11/24/2022] Open
Abstract
The Drosophila GAGA factor (GAF) has an extraordinarily diverse set of functions that include the activation and silencing of gene expression, nucleosome organization and remodeling, higher order chromosome architecture and mitosis. One hypothesis that could account for these diverse activities is that GAF is able to interact with partners that have specific and dedicated functions. To test this possibility we used affinity purification coupled with high throughput mass spectrometry to identify GAF associated partners. Consistent with this hypothesis the GAF interacting network includes a large collection of factors and complexes that have been implicated in many different aspects of gene activity, chromosome structure and function. Moreover, we show that GAF interactions with a small subset of partners is direct; however for many others the interactions could be indirect, and depend upon intermediates that serve to diversify the functional capabilities of the GAF protein.
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Affiliation(s)
- Dmitry Lomaev
- Institute of Gene Biology, Russian Academy of Sciences, Moscow, Russia
| | - Anna Mikhailova
- Institute of Gene Biology, Russian Academy of Sciences, Moscow, Russia
| | - Maksim Erokhin
- Institute of Gene Biology, Russian Academy of Sciences, Moscow, Russia
| | | | - James J. Moresco
- Department of Chemical Physiology, SR302B, The Scripps Research Institute, La Jolla, California, United States of America
| | - Tatiana Blokhina
- Institute of Gene Biology, Russian Academy of Sciences, Moscow, Russia
| | - Daniel Wolle
- Department of Molecular Biology Princeton University, Princeton, NJ, United States of America
| | - Tsutomu Aoki
- Department of Molecular Biology Princeton University, Princeton, NJ, United States of America
| | - Vladimir Ryabykh
- Institute of Animal Physiology, Biochemistry and Nutrition, Borovsk, Russia
| | - John R. Yates
- Department of Chemical Physiology, SR302B, The Scripps Research Institute, La Jolla, California, United States of America
| | | | - Pavel Georgiev
- Institute of Gene Biology, Russian Academy of Sciences, Moscow, Russia
- * E-mail: (DC); (PS); (PG)
| | - Paul Schedl
- Institute of Gene Biology, Russian Academy of Sciences, Moscow, Russia
- Department of Molecular Biology Princeton University, Princeton, NJ, United States of America
- * E-mail: (DC); (PS); (PG)
| | - Darya Chetverina
- Institute of Gene Biology, Russian Academy of Sciences, Moscow, Russia
- * E-mail: (DC); (PS); (PG)
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19
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Mazina MY, Derevyanko PK, Kocheryzhkina EV, Nikolenko YV, Krasnov AN, Vorobyeva NE. Coactivator complexes participate in different stages of the Drosophila melanogaster hsp70 gene transcription. RUSS J GENET+ 2017. [DOI: 10.1134/s1022795417010094] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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20
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Emamalizadeh B, Movafagh A, Darvish H, Kazeminasab S, Andarva M, Namdar-Aligoodarzi P, Ohadi M. The human RIT2 core promoter short tandem repeat predominant allele is species-specific in length: a selective advantage for human evolution? Mol Genet Genomics 2017; 292:611-617. [DOI: 10.1007/s00438-017-1294-4] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2016] [Accepted: 01/27/2017] [Indexed: 12/17/2022]
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21
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Chetverina DA, Elizar’ev PV, Lomaev DV, Georgiev PG, Erokhin MM. Control of the gene activity by polycomb and trithorax group proteins in Drosophila. RUSS J GENET+ 2017. [DOI: 10.1134/s1022795417020028] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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22
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Chaharbakhshi E, Jemc JC. Broad-complex, tramtrack, and bric-à-brac (BTB) proteins: Critical regulators of development. Genesis 2016; 54:505-518. [DOI: 10.1002/dvg.22964] [Citation(s) in RCA: 64] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2016] [Revised: 08/08/2016] [Accepted: 08/11/2016] [Indexed: 01/21/2023]
Affiliation(s)
- Edwin Chaharbakhshi
- Department of Biology; Loyola University Chicago; Chicago IL
- Stritch School of Medicine; Loyola University Chicago; Maywood IL
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23
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Tsai SY, Chang YL, Swamy KBS, Chiang RL, Huang DH. GAGA factor, a positive regulator of global gene expression, modulates transcriptional pausing and organization of upstream nucleosomes. Epigenetics Chromatin 2016; 9:32. [PMID: 27468311 PMCID: PMC4962548 DOI: 10.1186/s13072-016-0082-4] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2016] [Accepted: 07/20/2016] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Genome-wide studies in higher eukaryotes have revealed the presence of paused RNA polymerase II (RNA-Pol) at about 30-50 bp downstream of the transcription start site of genes involved in developmental control, cell proliferation and intercellular signaling. Promoter-proximal pausing is believed to represent a critical step in transcriptional regulation. GAGA sequence motifs have frequently been found in the upstream region of paused genes in Drosophila, implicating a prevalent binding factor, GAF, in transcriptional pausing. RESULTS Using newly isolated mutants that retain only ~3 % normal GAF level, we analyzed its impacts on transcriptional regulation in whole animals. We first examined the abundance of three major isoforms of RNA-Pol on Hsp70 during heat shock. By cytogenetic analyses on polytene chromosomes and chromatin immunoprecipitation (ChIP), we show that paused RNA-Pol of Hsp70 is substantially reduced in mutants. Conversely, a global increase in paused RNA-Pol is observed when GAF is over-expressed. Coupled analyses of transcriptome and GAF genomic distribution show that 269 genes enriched for upstream GAF binding are down-regulated in mutants. Interestingly, ~15 % of them encode transcriptional factors, which might control ~2000 additional genes down-regulated in mutants. Further examination of RNA-Pol distribution in GAF targets reveals that a positive correlation exists between promoter-proximal RNA-Pol density and GAF occupancy in WT, but not in mutants. Comparison of nucleosome profiles indicates that nucleosome occupancy is preferentially attenuated by GAF in the upstream region that strongly favors nucleosome assembly. Using a dominant eye phenotype caused by GAF over-expression, we detect significant genetic interactions between GAF and the nucleosome remodeler NURF, the pausing factor NELF, and BAB1 whose binding sites are enriched specifically in genes displaying GAF-dependent pausing. CONCLUSION Our results provide direct evidence to support a critical role of GAF in global gene expression, transcriptional pausing and upstream nucleosome organization of a group of genes. By cooperating with factors acting at different levels, GAF orchestrates a series of events from local nucleosome displacement to paused transcription. The use of whole animals containing broad tissue types attests the physiological relevance of this regulatory network.
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Affiliation(s)
- Shih-Ying Tsai
- Institute of Molecular Biology, Academia Sinica, Nankang, Taipei Taiwan, ROC ; Molecular Cell Biology, Taiwan International Graduate Program, Institute of Molecular Biology, Academia Sinica, Graduate Institute of Life Sciences, National Defense Medical Center, Taipei, Taiwan, ROC
| | - Yuh-Long Chang
- Institute of Molecular Biology, Academia Sinica, Nankang, Taipei Taiwan, ROC
| | - Krishna B S Swamy
- Institute of Molecular Biology, Academia Sinica, Nankang, Taipei Taiwan, ROC
| | - Ruei-Lin Chiang
- Institute of Molecular Biology, Academia Sinica, Nankang, Taipei Taiwan, ROC
| | - Der-Hwa Huang
- Institute of Molecular Biology, Academia Sinica, Nankang, Taipei Taiwan, ROC
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True JD, Muldoon JJ, Carver MN, Poorey K, Shetty SJ, Bekiranov S, Auble DT. The Modifier of Transcription 1 (Mot1) ATPase and Spt16 Histone Chaperone Co-regulate Transcription through Preinitiation Complex Assembly and Nucleosome Organization. J Biol Chem 2016; 291:15307-19. [PMID: 27226635 DOI: 10.1074/jbc.m116.735134] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2016] [Indexed: 11/06/2022] Open
Abstract
Modifier of transcription 1 (Mot1) is a conserved and essential Swi2/Snf2 ATPase that can remove TATA-binding protein (TBP) from DNA using ATP hydrolysis and in so doing exerts global effects on transcription. Spt16 is also essential and functions globally in transcriptional regulation as a component of the facilitates chromatin transcription (FACT) histone chaperone complex. Here we demonstrate that Mot1 and Spt16 regulate a largely overlapping set of genes in Saccharomyces cerevisiae. As expected, Mot1 was found to control TBP levels at co-regulated promoters. In contrast, Spt16 did not affect TBP recruitment. On a global scale, Spt16 was required for Mot1 promoter localization, and Mot1 also affected Spt16 localization to genes. Interestingly, we found that Mot1 has an unanticipated role in establishing or maintaining the occupancy and positioning of nucleosomes at the 5' ends of genes. Spt16 has a broad role in regulating chromatin organization in gene bodies, including those nucleosomes affected by Mot1. These results suggest that the large scale overlap in Mot1 and Spt16 function arises from a combination of both their unique and shared functions in transcription complex assembly and chromatin structure regulation.
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Affiliation(s)
- Jason D True
- From the Department of Biochemistry and Molecular Genetics, University of Virginia Health System, Charlottesville, Virginia 22908
| | - Joseph J Muldoon
- From the Department of Biochemistry and Molecular Genetics, University of Virginia Health System, Charlottesville, Virginia 22908
| | - Melissa N Carver
- From the Department of Biochemistry and Molecular Genetics, University of Virginia Health System, Charlottesville, Virginia 22908
| | - Kunal Poorey
- From the Department of Biochemistry and Molecular Genetics, University of Virginia Health System, Charlottesville, Virginia 22908
| | - Savera J Shetty
- From the Department of Biochemistry and Molecular Genetics, University of Virginia Health System, Charlottesville, Virginia 22908
| | - Stefan Bekiranov
- From the Department of Biochemistry and Molecular Genetics, University of Virginia Health System, Charlottesville, Virginia 22908
| | - David T Auble
- From the Department of Biochemistry and Molecular Genetics, University of Virginia Health System, Charlottesville, Virginia 22908
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25
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Shirk PD, Perera OP, Shelby KS, Furlong RB, LoVullo ED, Popham HJR. Unique synteny and alternate splicing of the chitin synthases in closely related heliothine moths. Gene 2015; 574:121-39. [PMID: 26253161 DOI: 10.1016/j.gene.2015.08.001] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2014] [Revised: 07/20/2015] [Accepted: 08/01/2015] [Indexed: 12/20/2022]
Abstract
Chitin is an extracellular biopolymer that contributes to the cuticular structural matrix in arthropods. As a consequence of its rigid structure, the chitinous cuticle must be shed and replaced to accommodate growth. Two chitin synthase genes that encode for chitin synthase A (ChSA), which produces cuticular exoskeleton, and chitin synthase B (ChSB), which produces peritrophic membrane, were characterized in the genomes of two heliothine moths: the corn earworm/cotton bollworm, Helicoverpa zea (Boddie) (Lepidoptera: Noctuidae) and the cotton bollworm, Helicoverpa armigera (Hübner) (Lepidoptera: Noctuidae). In both moths, the two genes were arranged in tandem with the same orientation on the same strand with ChSB located 5' of ChSA. Sequence comparisons showed that the coding sequences were highly conserved with homologues from other species but that the tandem juxtaposed genomic arrangement of the two genes was unique in these insects. The mechanism that has led to this arrangement is unclear but is most likely a recent recombinational event. Transcript mapping of HzChSB and HzChSA in H. zea demonstrated that both transcripts were differentially spliced in various tissues and larval stages. The identification of the HzChSB-E12b alternate spliced transcript is the first report of alternate splicing for the ChSB group. The importance of this splice form is not clear because the protein produced would lack any enzymatic activity but retain the membrane insertion motifs. As for other insects, these genes provide an important target for potential control through RNAi but also provide a subject for broad scale genomic recombinational events.
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Affiliation(s)
- Paul D Shirk
- USDA ARS CMAVE, 1700 SW 23rd Drive, Gainesville, FL 32608 USA.
| | | | - Kent S Shelby
- USDA ARS BCIRL, 1503 S. Providence, Columbia, MO 65203 USA.
| | | | - Eric D LoVullo
- USDA ARS CMAVE, 1700 SW 23rd Drive, Gainesville, FL 32608 USA.
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26
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A large-scale in vivo RNAi screen to identify genes involved in Notch-mediated follicle cell differentiation and cell cycle switches. Sci Rep 2015. [PMID: 26205122 PMCID: PMC4513280 DOI: 10.1038/srep12328] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
During Drosophila oogenesis, follicle cells sequentially undergo three distinct cell-cycle programs: the mitotic cycle, endocycle, and gene amplification. Notch signaling plays a central role in regulating follicle-cell differentiation and cell-cycle switches; its activation is essential for the mitotic cycle/endocycle (M/E) switch. Cut, a linker between Notch signaling and cell-cycle regulators, is specifically downregulated by Notch during the endocycle stage. To determine how signaling pathways coordinate during the M/E switch and to identify novel genes involved in follicle cell differentiation, we performed an in vivo RNAi screen through induced knockdown of gene expression and examination of Cut expression in follicle cells. We screened 2205 RNAi lines and found 33 genes regulating Cut expression during the M/E switch. These genes were confirmed with the staining of two other Notch signaling downstream factors, Hindsight and Broad, and validated with multiple independent RNAi lines. We applied gene ontology software to find enriched biological meaning and compared our results with other publications to find conserved genes across tissues. Specifically, we found earlier endocycle entry in anterior follicle cells than those in the posterior, identified that the insulin-PI3K pathway participates in the precise M/E switch, and suggested Nejire as a cofactor of Notch signaling during oogenesis.
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27
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Chen CC, Bowers S, Lipinszki Z, Palladino J, Trusiak S, Bettini E, Rosin L, Przewloka MR, Glover DM, O'Neill RJ, Mellone BG. Establishment of Centromeric Chromatin by the CENP-A Assembly Factor CAL1 Requires FACT-Mediated Transcription. Dev Cell 2015; 34:73-84. [PMID: 26151904 PMCID: PMC4495351 DOI: 10.1016/j.devcel.2015.05.012] [Citation(s) in RCA: 98] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2014] [Revised: 04/09/2015] [Accepted: 05/18/2015] [Indexed: 01/09/2023]
Abstract
Centromeres are essential chromosomal structures that mediate accurate chromosome segregation during cell division. Centromeres are specified epigenetically by the heritable incorporation of the centromeric histone H3 variant CENP-A. While many of the primary factors that mediate centromeric deposition of CENP-A are known, the chromatin and DNA requirements of this process have remained elusive. Here, we uncover a role for transcription in Drosophila CENP-A deposition. Using an inducible ectopic centromere system that uncouples CENP-A deposition from endogenous centromere function and cell-cycle progression, we demonstrate that CENP-A assembly by its loading factor, CAL1, requires RNAPII-mediated transcription of the underlying DNA. This transcription depends on the CAL1 binding partner FACT, but not on CENP-A incorporation. Our work establishes RNAPII passage as a key step in chaperone-mediated CENP-A chromatin establishment and propagation.
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Affiliation(s)
- Chin-Chi Chen
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT 06269, USA
| | - Sarion Bowers
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT 06269, USA
| | - Zoltan Lipinszki
- Department of Genetics, University of Cambridge, Cambridge CB2 3EH, UK; Biological Research Centre of the Hungarian Academy of Sciences, Institute of Biochemistry, P.O. Box 521, 6701 Szeged, Hungary
| | - Jason Palladino
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT 06269, USA
| | - Sarah Trusiak
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT 06269, USA
| | - Emily Bettini
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT 06269, USA
| | - Leah Rosin
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT 06269, USA
| | | | - David M Glover
- Department of Genetics, University of Cambridge, Cambridge CB2 3EH, UK
| | - Rachel J O'Neill
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT 06269, USA; Institute for Systems Genomics, University of Connecticut, Storrs, CT 06269, USA
| | - Barbara G Mellone
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT 06269, USA; Institute for Systems Genomics, University of Connecticut, Storrs, CT 06269, USA.
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Blanch M, Piñeyro D, Bernués J. New insights for Drosophila GAGA factor in larvae. ROYAL SOCIETY OPEN SCIENCE 2015; 2:150011. [PMID: 26064623 PMCID: PMC4448821 DOI: 10.1098/rsos.150011] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/22/2015] [Accepted: 02/17/2015] [Indexed: 06/04/2023]
Abstract
GAGA factor plays important roles during Drosophila embryogenesis and its maternal contribution is essential for early development. Here, the role of GAGA factor was studied in 3rd instar larvae using depletion and overexpression conditions in wing disc and transcriptome analysis. We found that genes changing expression were different to those previously described using GAGA mutants in embryos. No apparent phenotypes on GAGA depletion could usually be observed at larval stages in imaginal discs but a strong effect on salivary gland polytene chromosomes was observed. In the adult, GAGA depletion produced many defects like abnormal cell proliferation in the wing, impaired dorsal closure and resulted in homeotic transformation of abdominal segment A5. Unexpectedly, no effects on Ultrabithorax expression were observed. Short overexpression of GAGA factor in 3rd instar larvae also resulted in activation of a set of genes not previously described to be under GAGA regulation, and in lethality at pupa. Our results suggest a little contribution of GAGA factor on gene transcription in wing discs and a change of the genes regulated in comparison with embryo. GAGA factor activity thus correlates with the global changes in gene expression that take place at the embryo-to-larva and, later, at the larva-to-pupa transitions.
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Affiliation(s)
- Marta Blanch
- Departament de Genòmica Molecular, Institut de Biologia Molecular de Barcelona-CSIC, Parc Científic de Barcelona, Barcelona 08028, Spain
- Cell and Developmental Biology Programme, Institute for Research in Biomedicine, Barcelona, Spain
| | - David Piñeyro
- Departament de Genòmica Molecular, Institut de Biologia Molecular de Barcelona-CSIC, Parc Científic de Barcelona, Barcelona 08028, Spain
- Cell and Developmental Biology Programme, Institute for Research in Biomedicine, Barcelona, Spain
| | - Jordi Bernués
- Departament de Genòmica Molecular, Institut de Biologia Molecular de Barcelona-CSIC, Parc Científic de Barcelona, Barcelona 08028, Spain
- Cell and Developmental Biology Programme, Institute for Research in Biomedicine, Barcelona, Spain
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Slattery M, Ma L, Spokony RF, Arthur RK, Kheradpour P, Kundaje A, Nègre N, Crofts A, Ptashkin R, Zieba J, Ostapenko A, Suchy S, Victorsen A, Jameel N, Grundstad AJ, Gao W, Moran JR, Rehm EJ, Grossman RL, Kellis M, White KP. Diverse patterns of genomic targeting by transcriptional regulators in Drosophila melanogaster. Genome Res 2015; 24:1224-35. [PMID: 24985916 PMCID: PMC4079976 DOI: 10.1101/gr.168807.113] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Annotation of regulatory elements and identification of the transcription-related factors (TRFs) targeting these elements are key steps in understanding how cells interpret their genetic blueprint and their environment during development, and how that process goes awry in the case of disease. One goal of the modENCODE (model organism ENCyclopedia of DNA Elements) Project is to survey a diverse sampling of TRFs, both DNA-binding and non-DNA-binding factors, to provide a framework for the subsequent study of the mechanisms by which transcriptional regulators target the genome. Here we provide an updated map of the Drosophila melanogaster regulatory genome based on the location of 84 TRFs at various stages of development. This regulatory map reveals a variety of genomic targeting patterns, including factors with strong preferences toward proximal promoter binding, factors that target intergenic and intronic DNA, and factors with distinct chromatin state preferences. The data also highlight the stringency of the Polycomb regulatory network, and show association of the Trithorax-like (Trl) protein with hotspots of DNA binding throughout development. Furthermore, the data identify more than 5800 instances in which TRFs target DNA regions with demonstrated enhancer activity. Regions of high TRF co-occupancy are more likely to be associated with open enhancers used across cell types, while lower TRF occupancy regions are associated with complex enhancers that are also regulated at the epigenetic level. Together these data serve as a resource for the research community in the continued effort to dissect transcriptional regulatory mechanisms directing Drosophila development.
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Affiliation(s)
- Matthew Slattery
- Institute for Genomics & Systems Biology, Department of Human Genetics, The University of Chicago, Chicago, Illinois 60637, USA
| | - Lijia Ma
- Institute for Genomics & Systems Biology, Department of Human Genetics, The University of Chicago, Chicago, Illinois 60637, USA
| | - Rebecca F Spokony
- Institute for Genomics & Systems Biology, Department of Human Genetics, The University of Chicago, Chicago, Illinois 60637, USA
| | - Robert K Arthur
- Institute for Genomics & Systems Biology, Department of Human Genetics, The University of Chicago, Chicago, Illinois 60637, USA
| | - Pouya Kheradpour
- Computer Science and Artificial Intelligence Laboratory (CSAIL), Massachusetts Institute of Technology (MIT), Cambridge, Massachusetts 02139, USA
| | - Anshul Kundaje
- Computer Science and Artificial Intelligence Laboratory (CSAIL), Massachusetts Institute of Technology (MIT), Cambridge, Massachusetts 02139, USA
| | - Nicolas Nègre
- Institute for Genomics & Systems Biology, Department of Human Genetics, The University of Chicago, Chicago, Illinois 60637, USA; Université de Montpellier II and INRA, UMR1333 DGIMI, F-34095 Montpellier, France
| | - Alex Crofts
- Institute for Genomics & Systems Biology, Department of Human Genetics, The University of Chicago, Chicago, Illinois 60637, USA
| | - Ryan Ptashkin
- Institute for Genomics & Systems Biology, Department of Human Genetics, The University of Chicago, Chicago, Illinois 60637, USA
| | - Jennifer Zieba
- Institute for Genomics & Systems Biology, Department of Human Genetics, The University of Chicago, Chicago, Illinois 60637, USA
| | - Alexander Ostapenko
- Institute for Genomics & Systems Biology, Department of Human Genetics, The University of Chicago, Chicago, Illinois 60637, USA
| | - Sarah Suchy
- Institute for Genomics & Systems Biology, Department of Human Genetics, The University of Chicago, Chicago, Illinois 60637, USA
| | - Alec Victorsen
- Institute for Genomics & Systems Biology, Department of Human Genetics, The University of Chicago, Chicago, Illinois 60637, USA
| | - Nader Jameel
- Institute for Genomics & Systems Biology, Department of Human Genetics, The University of Chicago, Chicago, Illinois 60637, USA
| | - A Jason Grundstad
- Institute for Genomics & Systems Biology, Department of Human Genetics, The University of Chicago, Chicago, Illinois 60637, USA
| | - Wenxuan Gao
- Institute for Genomics & Systems Biology, Department of Human Genetics, The University of Chicago, Chicago, Illinois 60637, USA
| | - Jennifer R Moran
- Institute for Genomics & Systems Biology, Department of Human Genetics, The University of Chicago, Chicago, Illinois 60637, USA
| | - E Jay Rehm
- Institute for Genomics & Systems Biology, Department of Human Genetics, The University of Chicago, Chicago, Illinois 60637, USA
| | - Robert L Grossman
- Institute for Genomics & Systems Biology, Department of Human Genetics, The University of Chicago, Chicago, Illinois 60637, USA
| | - Manolis Kellis
- Computer Science and Artificial Intelligence Laboratory (CSAIL), Massachusetts Institute of Technology (MIT), Cambridge, Massachusetts 02139, USA; Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA
| | - Kevin P White
- Institute for Genomics & Systems Biology, Department of Human Genetics, The University of Chicago, Chicago, Illinois 60637, USA
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30
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Pluripotency transcription factor Oct4 mediates stepwise nucleosome demethylation and depletion. Mol Cell Biol 2015; 35:1014-25. [PMID: 25582194 DOI: 10.1128/mcb.01105-14] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
The mechanisms whereby the crucial pluripotency transcription factor Oct4 regulates target gene expression are incompletely understood. Using an assay system based on partially differentiated embryonic stem cells, we show that Oct4 opposes the accumulation of local H3K9me2 and subsequent Dnmt3a-mediated DNA methylation. Upon binding DNA, Oct4 recruits the histone lysine demethylase Jmjd1c. Chromatin immunoprecipitation (ChIP) time course experiments identify a stepwise Oct4 mechanism involving Jmjd1c recruitment and H3K9me2 demethylation, transient FACT (facilitates chromatin transactions) complex recruitment, and nucleosome depletion. Genome-wide and targeted ChIP confirms binding of newly synthesized Oct4, together with Jmjd1c and FACT, to the Pou5f1 enhancer and a small number of other Oct4 targets, including the Nanog promoter. Histone demethylation is required for both FACT recruitment and H3 depletion. Jmjd1c is required to induce endogenous Oct4 expression and fully reprogram fibroblasts to pluripotency, indicating that the assay system identifies functional Oct4 cofactors. These findings indicate that Oct4 sequentially recruits activities that catalyze histone demethylation and depletion.
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31
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Ando T, Uchihashi T, Scheuring S. Filming biomolecular processes by high-speed atomic force microscopy. Chem Rev 2014; 114:3120-88. [PMID: 24476364 PMCID: PMC4076042 DOI: 10.1021/cr4003837] [Citation(s) in RCA: 234] [Impact Index Per Article: 23.4] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2013] [Indexed: 12/21/2022]
Affiliation(s)
- Toshio Ando
- Department of Physics, and Bio-AFM Frontier
Research Center, Kanazawa University, Kakuma-machi, Kanazawa 920-1192, Japan
- CREST,
Japan Science and Technology Agency, 4-1-8 Honcho, Kawaguchi 332-0012, Japan
| | - Takayuki Uchihashi
- Department of Physics, and Bio-AFM Frontier
Research Center, Kanazawa University, Kakuma-machi, Kanazawa 920-1192, Japan
- CREST,
Japan Science and Technology Agency, 4-1-8 Honcho, Kawaguchi 332-0012, Japan
| | - Simon Scheuring
- U1006
INSERM/Aix-Marseille Université, Parc Scientifique et Technologique
de Luminy Bâtiment Inserm TPR2 bloc 5, 163 avenue de Luminy, 13288 Marseille Cedex 9, France
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McElroy KA, Kang H, Kuroda MI. Are we there yet? Initial targeting of the Male-Specific Lethal and Polycomb group chromatin complexes in Drosophila. Open Biol 2014; 4:140006. [PMID: 24671948 PMCID: PMC3971409 DOI: 10.1098/rsob.140006] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Chromatin-binding proteins must navigate the complex nuclear milieu to find their sites of action, and a constellation of protein factors and other properties are likely to influence targeting specificity. Despite considerable progress, the precise rules by which binding specificity is achieved have remained elusive. Here, we consider early targeting events for two groups of chromatin-binding complexes in Drosophila: the Male-Specific Lethal (MSL) and the Polycomb group (PcG) complexes. These two serve as models for understanding targeting, because they have been extensively studied and play vital roles in Drosophila, and their targets have been documented at high resolution. Furthermore, the proteins and biochemical properties of both complexes are largely conserved in multicellular organisms, including humans. While the MSL complex increases gene expression and PcG members repress genes, the two groups share many similarities such as the ability to modify their chromatin environment to create active or repressive domains, respectively. With legacies of in-depth genetic, biochemical and now genomic approaches, the MSL and PcG complexes will continue to provide tractable systems for understanding the recruitment of multiprotein chromatin complexes to their target loci.
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Affiliation(s)
- Kyle A McElroy
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138, USA
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33
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Rogers WA, Grover S, Stringer SJ, Parks J, Rebeiz M, Williams TM. A survey of the trans-regulatory landscape for Drosophila melanogaster abdominal pigmentation. Dev Biol 2014; 385:417-32. [DOI: 10.1016/j.ydbio.2013.11.013] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2013] [Revised: 10/07/2013] [Accepted: 11/05/2013] [Indexed: 10/26/2022]
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Hashimoto M, Kodera N, Tsunaka Y, Oda M, Tanimoto M, Ando T, Morikawa K, Tate SI. Phosphorylation-coupled intramolecular dynamics of unstructured regions in chromatin remodeler FACT. Biophys J 2013; 104:2222-34. [PMID: 23708362 DOI: 10.1016/j.bpj.2013.04.007] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2012] [Revised: 03/30/2013] [Accepted: 04/04/2013] [Indexed: 10/26/2022] Open
Abstract
The intrinsically disordered region (IDR) of a protein is an important topic in molecular biology. The functional significance of IDRs typically involves gene-regulation processes and is closely related to posttranslational modifications such as phosphorylation. We previously reported that the Drosophila facilitates chromatin transcription (FACT) protein involved in chromatin remodeling contains an acidic ID fragment (AID) whose phosphorylation modulates FACT binding to nucleosomes. Here, we performed dynamic atomic force microscopy and NMR analyses to clarify how the densely phosphorylated AID masks the DNA binding interface of the high-mobility-group domain (HMG). Dynamic atomic force microscopy of the nearly intact FACT revealed that a small globule temporally appears but quickly vanishes within each mobile tail-like image, corresponding to the HMG-containing IDR. The lifespan of the globule increases upon phosphorylation. NMR analysis indicated that phosphorylation induces no ordered structure but increases the number of binding sites in AID to HMG with an adjacent basic segment, thereby retaining the robust electrostatic intramolecular interaction within FACT even in the presence of DNA. These data lead to the conclusion that the inhibitory effect of nucleosome binding is ascribed to the increase in the probability of encounter between HMG and the phosphorylated IDR.
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Affiliation(s)
- Manami Hashimoto
- Department of Mathematical and Life Sciences, Hiroshima University, Hiroshima, Japan
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35
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Valipour E, Kowsari A, Bayat H, Banan M, Kazeminasab S, Mohammadparast S, Ohadi M. Polymorphic core promoter GA-repeats alter gene expression of the early embryonic developmental genes. Gene 2013; 531:175-9. [PMID: 24055488 DOI: 10.1016/j.gene.2013.09.032] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2013] [Revised: 09/05/2013] [Accepted: 09/06/2013] [Indexed: 12/20/2022]
Abstract
Protein complexes that bind to 'GAGA' DNA elements are necessary to replace nucleosomes to create a local chromatin environment that facilitates a variety of site-specific regulatory responses. Three to four elements are required for the disruption of a preassembled nucleosome. We have previously identified human protein-coding gene core promoters that are composed of exceptionally long GA-repeats. The functional implication of those GA-repeats is beginning to emerge in the core promoter of the human SOX5 gene, which is involved in multiple developmental processes. In the current study, we analyze the functional implication of GA-repeats in the core promoter of two additional genes, MECOM and GABRA3, whose expression is largely limited to embryogenesis. We report a significant difference in gene expression as a result of different alleles across those core promoters in the HEK-293 cell line. Across-species homology check for the GABRA3 GA-repeats revealed that those repeats are evolutionary conserved in mouse and primates (p<1 × 10(-8)). The MECOM core promoter GA-repeats are also conserved in numerous species, of which human has the longest repeat and complexity. We propose a novel role for GA-repeat core promoters to regulate gene expression in the genes involved in development and evolution.
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Affiliation(s)
- E Valipour
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
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36
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Li J, Liu Y, Rhee HS, Ghosh SKB, Bai L, Pugh BF, Gilmour DS. Kinetic competition between elongation rate and binding of NELF controls promoter-proximal pausing. Mol Cell 2013; 50:711-22. [PMID: 23746353 DOI: 10.1016/j.molcel.2013.05.016] [Citation(s) in RCA: 88] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2012] [Revised: 04/03/2013] [Accepted: 05/10/2013] [Indexed: 11/29/2022]
Abstract
Pausing of RNA polymerase II (Pol II) 20-60 bp downstream of transcription start sites is a major checkpoint during transcription in animal cells. Mechanisms that control pausing are largely unknown. We developed permanganate-ChIP-seq to evaluate the state of Pol II at promoters throughout the Drosophila genome, and a biochemical system that reconstitutes promoter-proximal pausing to define pausing mechanisms. Stable open complexes of Pol II are largely absent from the transcription start sites of most mRNA genes but are present at snRNA genes and the highly transcribed heat shock genes following their induction. The location of the pause is influenced by the timing between when NELF loads onto Pol II and how fast Pol II escapes the promoter region. Our biochemical analysis reveals that the sequence-specific transcription factor, GAF, orchestrates efficient pausing by recruiting NELF to promoters before transcription initiation and by assisting in loading NELF onto Pol II after initiation.
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Affiliation(s)
- Jian Li
- Center for Eukaryotic Gene Regulation, Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16802, USA
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Tariq M, Wegrzyn R, Anwar S, Bukau B, Paro R. Drosophila GAGA factor polyglutamine domains exhibit prion-like behavior. BMC Genomics 2013; 14:374. [PMID: 23731888 PMCID: PMC3701498 DOI: 10.1186/1471-2164-14-374] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2012] [Accepted: 05/30/2013] [Indexed: 11/30/2022] Open
Abstract
BACKGROUND The Drosophila GAGA factor (GAF) participates in nucleosome remodeling to activate genes, acts as an antirepressor and is associated with heterochromatin, contributing to gene repression. GAF functions are intimately associated to chromatin-based epigenetic control, linking basic transcriptional regulation to heritable long-term maintenance of gene expression. These diverse functions require GAF to interact with different partners in different multiprotein complexes. The two isoforms of GAF depict highly conserved glutamine-rich C-terminal domains (Q domain), which have been implicated in complex formation. RESULTS Here we show that the Q domains exhibit prion-like properties. In an established yeast test system the two GAF Q domains convey prion activities comparable to well known yeast prions. The Q domains stably maintain two distinct conformational states imposing functional constraints on the fused yeast reporter protein. The prion-like phenotype can be reversibly cured in the presence of guanidine HCl or by over-expression of the Hsp104 chaperone protein. Additionally, when fused to GFP, the Q domains form aggregates in yeast cells. CONCLUSION We conclude that prion-like behavior of the GAF Q domain suggests that this C-terminal structure may perform stable conformational switches. Such a self-perpetuating change in the conformation could assist GAF executing its diverse epigenetic functions of gene control in Drosophila.
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Affiliation(s)
- Muhammad Tariq
- Department of Biology, SBA School of Science and Engineering, Lahore University of Management Sciences, Lahore 54792, Pakistan
| | - Renee Wegrzyn
- Zentrum für Molekulare Biologie Heidelberg, Im Neuenheimer Feld 282, Heidelberg 69120, Germany
| | - Saima Anwar
- Department of Biology, SBA School of Science and Engineering, Lahore University of Management Sciences, Lahore 54792, Pakistan
| | - Bernd Bukau
- Zentrum für Molekulare Biologie Heidelberg, Im Neuenheimer Feld 282, Heidelberg 69120, Germany
| | - Renato Paro
- Department of Biosystems Science and Engineering, ETH Zurich, Mattenstrasse 26, Basel 4058, Switzerland
- Faculty of Science, University of Basel, Basel 4056, Switzerland
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Distinct mechanisms of transcriptional pausing orchestrated by GAGA factor and M1BP, a novel transcription factor. EMBO J 2013; 32:1829-41. [PMID: 23708796 DOI: 10.1038/emboj.2013.111] [Citation(s) in RCA: 94] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2012] [Accepted: 04/24/2013] [Indexed: 01/14/2023] Open
Abstract
Thousands of genes in Drosophila have Pol II paused in the promoter proximal region. Almost half of these genes are associated with either GAGA factor (GAF) or a newly discovered factor we call M1BP. Although both factors dictate the association of Pol II at their target promoters, they are nearly mutually exclusive on the genome and mediate different mechanisms of regulation. High-resolution mapping of Pol II using permanganate-ChIP-seq indicates that pausing on M1BP genes is transient and could involve the +1 nucleosome. In contrast, pausing on GAF genes is much stronger and largely independent of nucleosomes. Distinct regulatory mechanisms are reflected by transcriptional plasticity: M1BP genes are constitutively expressed throughout development while GAF genes exhibit much greater developmental specificity. M1BP binds a core promoter element called Motif 1. Motif 1 potentially directs a distinct transcriptional mechanism from the canonical TATA box, which does not correlate with paused Pol II on the genomic scale. In contrast to M1BP and GAF genes, a significant portion of TATA box genes appear to be controlled at preinitiation complex formation.
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Karagodin DA, Omelina ES, Fedorova EV, Baricheva EM. Identification of functionally significant elements in the second intron of the Drosophila melanogaster Trithorax-like gene. Gene 2013; 520:178-84. [PMID: 23481306 DOI: 10.1016/j.gene.2013.02.012] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2012] [Revised: 01/14/2013] [Accepted: 02/07/2013] [Indexed: 10/27/2022]
Abstract
It is known that a lot of genes having a distinct expression pattern require the complex system of transcription regulation. The regulatory regions of such genes can include not only the 5'-flanking regions, but also other regions, particularly their intron sequences. The Drosophila melanogaster Trithorax-like (Trl) gene, encoding the GAGA protein, is one of the genes with complex expression pattern. GAGA is one of a few transcription factors that can regulate gene expression at multiple levels. The GAGA-mediated modulation of expression seems to be linked with modifications of the chromatin structure. Nowadays, the regulatory potential of the Trl 5'-flanking region that contains multiple GAGA binding sites has been analyzed, but the presence of the functionally significant elements in other Trl regions has not been examined. We found DNase I hypersensitive sites, evolutionary-conserved sequences and numerous GAGA binding sites in the second intron of the Trl gene. Interestingly, these sequences localize in two main regions of the intron in immediate proximity to preferred regions of transposon insertions. Additionally, we revealed that deletion of the intron fragment in the Trl(1-72) mutants caused an alteration of the Trl expression pattern. These results allow us to conclude that the second intron of the Trl gene contains functionally significant elements.
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Affiliation(s)
- D A Karagodin
- Institute of Cytology and Genetics, Siberian Branch, Russian Academy of Sciences, 10 Lavrentieva Street, Novosibirsk 630090, Russian Federation
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Darbo E, Herrmann C, Lecuit T, Thieffry D, van Helden J. Transcriptional and epigenetic signatures of zygotic genome activation during early Drosophila embryogenesis. BMC Genomics 2013; 14:226. [PMID: 23560912 PMCID: PMC3706223 DOI: 10.1186/1471-2164-14-226] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2012] [Accepted: 02/28/2013] [Indexed: 01/25/2023] Open
Abstract
Background In all Metazoa, transcription is inactive during the first mitotic cycles after fertilisation. In Drosophila melanogaster, Zygotic Genome Activation (ZGA) occurs in two waves, starting respectively at mitotic cycles 8 (approximately 60 genes) and 14 (over a thousand genes). The regulatory mechanisms underlying these drastic transcriptional changes remain largely unknown. Results We developed an original gene clustering method based on discretized transition profiles, and applied it to datasets from three landmark early embryonic transcriptome studies. We identified 417 genes significantly up-regulated during ZGA. De novo motif discovery returned nine motifs over-represented in their non-coding sequences (upstream, introns, UTR), three of which correspond to previously known transcription factors: Zelda, Tramtrack and Trithorax-like (Trl). The nine discovered motifs were combined to scan ZGA-associated regions and predict about 1300 putative cis-regulatory modules. The fact that Trl is known to act as chromatin remodelling factor suggests that epigenetic regulation might play an important role in zygotic genome activation. We thus systematically compared the locations of predicted CRMs with ChIP-seq profiles for various transcription factors, 38 epigenetic marks from ModENCODE, and DNAse1 accessibility profiles. This analysis highlighted a strong and specific enrichment of predicted ZGA-associated CRMs for Zelda, CBP, Trl binding sites, as well as for histone marks associated with active enhancers (H3K4me1) and for open chromatin regions. Conclusion Based on the results of our computational analyses, we suggest a temporal model explaining the onset of zygotic genome activation by the combined action of transcription factors and epigenetic signals. Although this study is mainly based on the analysis of publicly available transcriptome and ChiP-seq datasets, the resulting model suggests novel mechanisms that underly the coordinated activation of several hundreds genes at a precise time point during embryonic development.
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Affiliation(s)
- Elodie Darbo
- Technological Advances for Genomics and Clinics (TAGC), INSERM U1090, Université de la Méditerranée, Campus de Luminy, 13288 Marseille Cedex 9, France.
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Koltowska K, Apitz H, Stamataki D, Hirst EMA, Verkade H, Salecker I, Ober EA. Ssrp1a controls organogenesis by promoting cell cycle progression and RNA synthesis. Development 2013; 140:1912-8. [PMID: 23515471 DOI: 10.1242/dev.093583] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Tightly controlled DNA replication and RNA transcription are essential for differentiation and tissue growth in multicellular organisms. Histone chaperones, including the FACT (facilitates chromatin transcription) complex, are central for these processes and act by mediating DNA access through nucleosome reorganisation. However, their roles in vertebrate organogenesis are poorly understood. Here, we report the identification of zebrafish mutants for the gene encoding Structure specific recognition protein 1a (Ssrp1a), which, together with Spt16, forms the FACT heterodimer. Focussing on the liver and eye, we show that zygotic Ssrp1a is essential for proliferation and differentiation during organogenesis. Specifically, gene expression indicative of progressive organ differentiation is disrupted and RNA transcription is globally reduced. Ssrp1a-deficient embryos exhibit DNA synthesis defects and prolonged S phase, uncovering a role distinct from that of Spt16, which promotes G1 phase progression. Gene deletion/replacement experiments in Drosophila show that Ssrp1b, Ssrp1a and N-terminal Ssrp1a, equivalent to the yeast homologue Pob3, can substitute Drosophila Ssrp function. These data suggest that (1) Ssrp1b does not compensate for Ssrp1a loss in the zebrafish embryo, probably owing to insufficient expression levels, and (2) despite fundamental structural differences, the mechanisms mediating DNA accessibility by FACT are conserved between yeast and metazoans. We propose that the essential functions of Ssrp1a in DNA replication and gene transcription, together with its dynamic spatiotemporal expression, ensure organ-specific differentiation and proportional growth, which are crucial for the forming embryo.
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Affiliation(s)
- Katarzyna Koltowska
- Developmental Biology, MRC National Institute for Medical Research, London, UK
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42
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Oh H, Slattery M, Ma L, Crofts A, White KP, Mann RS, Irvine KD. Genome-wide association of Yorkie with chromatin and chromatin-remodeling complexes. Cell Rep 2013; 3:309-18. [PMID: 23395637 DOI: 10.1016/j.celrep.2013.01.008] [Citation(s) in RCA: 114] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2012] [Revised: 10/29/2012] [Accepted: 01/11/2013] [Indexed: 12/19/2022] Open
Abstract
The Hippo pathway regulates growth through the transcriptional coactivator Yorkie, but how Yorkie promotes transcription remains poorly understood. We address this by characterizing Yorkie's association with chromatin and by identifying nuclear partners that effect transcriptional activation. Coimmunoprecipitation and mass spectrometry identify GAGA factor (GAF), the Brahma complex, and the Mediator complex as Yorkie-associated nuclear protein complexes. All three are required for Yorkie's transcriptional activation of downstream genes, and GAF and the Brahma complex subunit Moira interact directly with Yorkie. Genome-wide chromatin-binding experiments identify thousands of Yorkie sites, most of which are associated with elevated transcription, based on genome-wide analysis of messenger RNA and histone H3K4Me3 modification. Chromatin binding also supports extensive functional overlap between Yorkie and GAF. Our studies suggest a widespread role for Yorkie as a regulator of transcription and identify recruitment of the chromatin-modifying GAF protein and BRM complex as a molecular mechanism for transcriptional activation by Yorkie.
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Affiliation(s)
- Hyangyee Oh
- Howard Hughes Medical Institute, Waksman Institute, and Department of Molecular Biology and Biochemistry, Rutgers University, Piscataway, NJ 08854, USA
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43
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Ou Q, King-Jones K. What goes up must come down: transcription factors have their say in making ecdysone pulses. Curr Top Dev Biol 2013; 103:35-71. [PMID: 23347515 DOI: 10.1016/b978-0-12-385979-2.00002-2] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Insect metamorphosis is one of the most fascinating biological processes in the animal kingdom. The dramatic transition from an immature juvenile to a reproductive adult is under the control of the steroid hormone ecdysone, also known as the insect molting hormone. During Drosophila development, periodic pulses of ecdysone are released from the prothoracic glands, upon which the hormone is rapidly converted in peripheral tissues to its biologically active form, 20-hydroxyecdysone. Each hormone pulse has a unique profile and causes different developmental events, but we only have a rudimentary understanding of how the timing, amplitude, and duration of a given pulse are controlled. A key component involved in the timing of ecdysone pulses is PTTH, a brain-derived neuropeptide. PTTH stimulates ecdysone production through a Ras/Raf/ERK signaling cascade; however, comparatively little is known about the downstream targets of this pathway. In recent years, it has become apparent that transcriptional regulation plays a critical role in regulating the synthesis of ecdysone, but only one transcription factor has a well-defined link to PTTH. Interestingly, many of the ecdysteroidogenic transcription factors were originally characterized as primary response genes in the ecdysone signaling cascade that elicits the biological responses to the hormone in target tissues. To review these developments, we will first provide an overview of the transcription factors that act in the Drosophila ecdysone regulatory hierarchy. We will then discuss the roles of these transcriptional regulators in controlling ecdysone synthesis. In the last section, we will briefly outline transcription factors that likely have roles in regulating ecdysone synthesis but have not been formally identified as downstream effectors of ecdysone.
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Affiliation(s)
- Qiuxiang Ou
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta, Canada
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44
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Zhang H, Zhu JK. Active DNA demethylation in plants and animals. COLD SPRING HARBOR SYMPOSIA ON QUANTITATIVE BIOLOGY 2012. [PMID: 23197304 DOI: 10.1101/sqb.2012.77.014936] [Citation(s) in RCA: 98] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Active DNA demethylation regulates many vital biological processes, including early development and locus-specific gene expression in plants and animals. In Arabidopsis, bifunctional DNA glycosylases directly excise the 5-methylcytosine base and then cleave the DNA backbone at the abasic site. Recent evidence suggests that mammals utilize DNA glycosylases after 5-methylcytosine is oxidized and/or deaminated. In both cases, the resultant single-nucleotide gap is subsequently filled with an unmodified cytosine through the DNA base excision repair pathway. The enzymatic removal of 5-methylcytosine is tightly integrated with histone modifications and possibly noncoding RNAs. Future research will increase our understanding of the mechanisms and critical roles of active DNA demethylation in various cellular processes as well as inspire novel genetic and chemical therapies for epigenetic disorders.
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Affiliation(s)
- H Zhang
- Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette, Indiana 47907, USA
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45
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Nakayama T, Shimojima T, Hirose S. The PBAP remodeling complex is required for histone H3.3 replacement at chromatin boundaries and for boundary functions. Development 2012; 139:4582-90. [PMID: 23136390 DOI: 10.1242/dev.083246] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Establishment and maintenance of epigenetic memories are essential for development. Replacement of canonical histone H3 by its variant H3.3 has been implicated in cellular memory. Drosophila sequence-specific DNA-binding protein GAGA factor and a chromatin factor FACT direct H3.3 replacement in conjunction with H3.3-specific chaperone HIRA at chromatin boundaries to counteract the spreading of silent chromatin. However, little is known about which ATP-driven chromatin remodeling factor is responsible for the H3.3 replacement at chromatin boundaries. Here, we report that GAGA factor associates with the Polybromo-associated Brm (PBAP) remodeling complex, which consists of many Trithorax group proteins, and recruits this complex to chromatin boundaries d1 (which is downstream of w), the Fab-7 DNase-hypersensitive site (HS) 1 of Abd-B and the bxd region of Ubx. Trl-encoding GAGA factor, brm and polybromo/bap180 mutations compromise the H3.3 replacement and boundary functions in a synergistic manner. Furthermore, Polybromo is necessary for generation of the DNase HS at d1, and HIRA functions to restore the alteration. Taken together, we propose that FACT and PBAP complexes are recruited to chromatin boundaries in a GAGA factor-dependent manner, and are needed for H3.3 replacement to execute boundary functions. Our results provide new insight into the function of the trithorax group during development.
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Affiliation(s)
- Takahiro Nakayama
- Department of Developmental Genetics, National Institute of Genetics, Mishima, Shizuoka-ken 411-8540, Japan
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46
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Bayarmagnai B, Nicolay BN, Islam ABMMK, Lopez-Bigas N, Frolov MV. Drosophila GAGA factor is required for full activation of the dE2f1-Yki/Sd transcriptional program. Cell Cycle 2012; 11:4191-202. [PMID: 23070566 DOI: 10.4161/cc.22486] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
The Hippo signaling pathway regulates organ size by controlling the activity of the transcriptional co-activator Yorkie (Yki). Yki is recruited to its target genes by DNA-binding proteins such as Scalloped (Sd). In addition, transcription factor dE2f1, of the Retinoblastoma (Rb) pathway, cooperates with Yki/Sd to synergistically activate a set of common cell cycle target genes. However, little is known about other factors that ensure the proper transcriptional output of Hippo signaling. In this report we identified the chromatin protein GAGA factor (GAF), which is encoded by the Trithorax-like (Trl) gene, as a novel and critical partner in transcriptional regulation by Yki/Sd and dE2f1. We show that GAF is required for the full activation of target genes by dE2f1 and Yki/Sd; while ablation of GAF compromises both normal and inappropriate cell proliferation driven by Yki and dE2f1 in multiple tissues. The importance of GAF is further supported by strong genetic interactions between GAF and the Rb and Hippo pathways. Additionally, we show that GAF directly interacts with RBF, a Drosophila pRB homolog, and partially co-localizes with RBF on polytene chromosomes. Collectively, our data provide a novel connection between a chromatin-binding protein and a transcriptional program governed by the Hippo and Rb pathways.
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Affiliation(s)
- Battuya Bayarmagnai
- Department of Biochemistry and Molecular Genetics, University of Illinois at Chicago, Chicago, IL, USA
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47
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Simonini S, Roig-Villanova I, Gregis V, Colombo B, Colombo L, Kater MM. Basic pentacysteine proteins mediate MADS domain complex binding to the DNA for tissue-specific expression of target genes in Arabidopsis. THE PLANT CELL 2012; 24:4163-72. [PMID: 23054472 PMCID: PMC3517243 DOI: 10.1105/tpc.112.103952] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
Basic pentacysteine (BPC) transcription factors have been identified in a large variety of plant species. In Arabidopsis thaliana there are seven BPC genes, which, except for BPC5, are expressed ubiquitously. BPC genes are functionally redundant in a wide range of developmental processes. Recently, we reported that BPC1 binds to guanine and adenine (GA)-rich consensus sequences in the seedstick (STK) promoter in vitro and induces conformational changes. Here we show by chromatin immunoprecipitation experiments that in vivo BPCs also bind to the consensus boxes, and when these were mutated, expression from the STK promoter was derepressed, resulting in ectopic expression in the inflorescence. We also reveal that short vegetative phase (SVP) is a direct regulator of STK. SVP is a floral meristem identity gene belonging to the MADS box gene family. The SVP-APETALA1 (AP1) dimer recruits the SEUSS (SEU)-LEUNIG (LUG) transcriptional cosuppressor to repress floral homeotic gene expression in the floral meristem. Interestingly, we found that GA consensus sequences in the STK promoter to which BPCs bind are essential for recruitment of the corepressor complex to this promoter. Our data suggest that we have identified a new regulatory mechanism controlling plant gene expression that is probably generally used, when considering BPCs' wide expression profile and the frequent presence of consensus binding sites in plant promoters.
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Affiliation(s)
- Sara Simonini
- Dipartimento di Bioscienze, Università degli Studi di Milano, 20133 Milano, Italy
| | - Irma Roig-Villanova
- Dipartimento di Bioscienze, Università degli Studi di Milano, 20133 Milano, Italy
| | - Veronica Gregis
- Dipartimento di Bioscienze, Università degli Studi di Milano, 20133 Milano, Italy
| | - Bilitis Colombo
- Dipartimento di Bioscienze, Università degli Studi di Milano, 20133 Milano, Italy
| | - Lucia Colombo
- Dipartimento di Bioscienze, Università degli Studi di Milano, 20133 Milano, Italy
- Consiglio Nazionale delle Richerche, Istituto di Biofisica, Università degli Studi di Milano, 20133 Milano, Italy
| | - Martin M. Kater
- Dipartimento di Bioscienze, Università degli Studi di Milano, 20133 Milano, Italy
- Address correspondence to
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48
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Berger N, Dubreucq B. Evolution goes GAGA: GAGA binding proteins across kingdoms. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2012; 1819:863-8. [PMID: 22425673 DOI: 10.1016/j.bbagrm.2012.02.022] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/17/2011] [Revised: 02/17/2012] [Accepted: 02/22/2012] [Indexed: 01/21/2023]
Abstract
Chromatin-associated proteins (CAP) play a crucial role in the regulation of gene expression and development in higher organisms. They are involved in the control of chromatin structure and dynamics. CAP have been extensively studied over the past years and are classified into two major groups: enzymes that modify histone stability and organization by post-translational modification of histone N-Terminal tails; and proteins that use ATP hydrolysis to modify chromatin structure. All of these proteins show a relatively high degree of sequence conservation across the animal and plant kingdoms. The essential Drosophila melanogaster GAGA factor (dGAF) interacts with these two types of CAP to regulate homeobox genes and thus contributes to a wide range of developmental events. Surprisingly, however, it is not conserved in plants. In this review, following an overview of fly GAF functions, we discuss the role of plant BBR/BPC proteins. These appear to functionally converge with dGAF despite a completely divergent amino acid sequence. Some suggestions are given for further investigation into the function of BPC proteins in plants.
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Abstract
High-speed atomic force microscopy (HS-AFM) is now materialized. It allows direct visualization of dynamic structural changes and dynamic processes of functioning biological molecules in physiological solutions, at high spatiotemporal resolution. Dynamic molecular events unselectively appear in detail in an AFM movie, facilitating our understanding of how biological molecules operate to function. This review describes a historical overview of technical development towards HS-AFM, summarizes elementary devices and techniques used in the current HS-AFM, and then highlights recent imaging studies. Finally, future challenges of HS-AFM studies are briefly discussed.
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Affiliation(s)
- Toshio Ando
- Department of Physics and Bio-AFM Frontier Research Center, Kanazawa University, Kakuma-machi, Kanazawa, Japan
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50
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Rohn JL, Sims D, Liu T, Fedorova M, Schöck F, Dopie J, Vartiainen MK, Kiger AA, Perrimon N, Baum B. Comparative RNAi screening identifies a conserved core metazoan actinome by phenotype. ACTA ACUST UNITED AC 2012; 194:789-805. [PMID: 21893601 PMCID: PMC3171124 DOI: 10.1083/jcb.201103168] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
RNAi screens in Drosophila and human cells for novel actin
regulators revealed conserved roles for proteins involved in nuclear actin
export, RNA splicing, and ubiquitination. Although a large number of actin-binding proteins and their regulators have been
identified through classical approaches, gaps in our knowledge remain. Here, we
used genome-wide RNA interference as a systematic method to define metazoan
actin regulators based on visual phenotype. Using comparative screens in
cultured Drosophila and human cells, we generated phenotypic
profiles for annotated actin regulators together with proteins bearing predicted
actin-binding domains. These phenotypic clusters for the known metazoan
“actinome” were used to identify putative new core actin
regulators, together with a number of genes with conserved but poorly studied
roles in the regulation of the actin cytoskeleton, several of which we studied
in detail. This work suggests that although our search for new components of the
core actin machinery is nearing saturation, regulation at the level of nuclear
actin export, RNA splicing, ubiquitination, and other upstream processes remains
an important but unexplored frontier of actin biology.
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Affiliation(s)
- Jennifer L Rohn
- MRC Laboratory for Molecular Cell Biology, University College London, London WC1E 6BT, England, UK.
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