1
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Sun J, Durmaz AD, Babu A, Macabenta F, Stathopoulos A. Two sequential gene expression programs bridged by cell division support long-distance collective cell migration. Development 2024; 151:dev202262. [PMID: 38646822 PMCID: PMC11165717 DOI: 10.1242/dev.202262] [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: 08/14/2023] [Accepted: 04/08/2024] [Indexed: 04/23/2024]
Abstract
The precise assembly of tissues and organs relies on spatiotemporal regulation of gene expression to coordinate the collective behavior of cells. In Drosophila embryos, the midgut musculature is formed through collective migration of caudal visceral mesoderm (CVM) cells, but how gene expression changes as cells migrate is not well understood. Here, we have focused on ten genes expressed in the CVM and the cis-regulatory sequences controlling their expression. Although some genes are continuously expressed, others are expressed only early or late during migration. Late expression relates to cell cycle progression, as driving string/Cdc25 causes earlier division of CVM cells and accelerates the transition to late gene expression. In particular, we found that the cell cycle effector transcription factor E2F1 is a required input for the late gene CG5080. Furthermore, whereas late genes are broadly expressed in all CVM cells, early gene transcripts are polarized to the anterior or posterior ends of the migrating collective. We show this polarization requires transcription factors Snail, Zfh1 and Dorsocross. Collectively, these results identify two sequential gene expression programs bridged by cell division that support long-distance directional migration of CVM cells.
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Affiliation(s)
- Jingjing Sun
- California Institute of Technology, Division of Biology and Biological Engineering, 1200 East California Boulevard, Pasadena, CA 91125, USA
| | - Ayse Damla Durmaz
- California Institute of Technology, Division of Biology and Biological Engineering, 1200 East California Boulevard, Pasadena, CA 91125, USA
- Faculty of Biology, Ludwig-Maximilians Universität München, München, 82152 DE, Germany
| | - Aswini Babu
- California Institute of Technology, Division of Biology and Biological Engineering, 1200 East California Boulevard, Pasadena, CA 91125, USA
| | - Frank Macabenta
- California Institute of Technology, Division of Biology and Biological Engineering, 1200 East California Boulevard, Pasadena, CA 91125, USA
- California State University, Monterey Bay, Seaside, CA 93955, USA
| | - Angelike Stathopoulos
- California Institute of Technology, Division of Biology and Biological Engineering, 1200 East California Boulevard, Pasadena, CA 91125, USA
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2
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Hoareau M, Rincheval-Arnold A, Gaumer S, Guénal I. DREAM a little dREAM of DRM: Model organisms and conservation of DREAM-like complexes: Model organisms uncover the mechanisms of DREAM-mediated transcription regulation. Bioessays 2024; 46:e2300125. [PMID: 38059789 DOI: 10.1002/bies.202300125] [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: 07/07/2023] [Revised: 11/23/2023] [Accepted: 11/24/2023] [Indexed: 12/08/2023]
Abstract
DREAM complexes are transcriptional regulators that control the expression of hundreds to thousands of target genes involved in the cell cycle, quiescence, differentiation, and apoptosis. These complexes contain many subunits that can vary according to the considered target genes. Depending on their composition and the nature of the partners they recruit, DREAM complexes control gene expression through diverse mechanisms, including chromatin remodeling, transcription cofactor and factor recruitment at various genomic binding sites. This complexity is particularly high in mammals. Since the discovery of the first dREAM complex (drosophila Rb, E2F, and Myb) in Drosophila melanogaster, model organisms such as Caenorhabditis elegans, and plants allowed a deeper understanding of the processes regulated by DREAM-like complexes. Here, we review the conservation of these complexes. We discuss the contribution of model organisms to the study of DREAM-mediated transcriptional regulatory mechanisms and their relevance in characterizing novel activities of DREAM complexes.
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Affiliation(s)
- Marion Hoareau
- Université Paris-Saclay, UVSQ, LGBC, Versailles, France
- Université PSL, EPHE, Paris, France
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3
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Zappia M, Kwon YJ, Westacott A, Liseth I, Lee H, Islam ABMMK, Kim J, Frolov M. E2F regulation of the Phosphoglycerate kinase gene is functionally important in Drosophila development. Proc Natl Acad Sci U S A 2023; 120:e2220770120. [PMID: 37011211 PMCID: PMC10104548 DOI: 10.1073/pnas.2220770120] [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: 12/06/2022] [Accepted: 03/03/2023] [Indexed: 04/05/2023] Open
Abstract
The canonical role of the transcription factor E2F is to control the expression of cell cycle genes by binding to the E2F sites in their promoters. However, the list of putative E2F target genes is extensive and includes many metabolic genes, yet the significance of E2F in controlling the expression of these genes remains largely unknown. Here, we used the CRISPR/Cas9 technology to introduce point mutations in the E2F sites upstream of five endogenous metabolic genes in Drosophila melanogaster. We found that the impact of these mutations on both the recruitment of E2F and the expression of the target genes varied, with the glycolytic gene, Phosphoglycerate kinase (Pgk), being mostly affected. The loss of E2F regulation on the Pgk gene led to a decrease in glycolytic flux, tricarboxylic acid cycle intermediates levels, adenosine triphosphate (ATP) content, and an abnormal mitochondrial morphology. Remarkably, chromatin accessibility was significantly reduced at multiple genomic regions in PgkΔE2F mutants. These regions contained hundreds of genes, including metabolic genes that were downregulated in PgkΔE2F mutants. Moreover, PgkΔE2F animals had shortened life span and exhibited defects in high-energy consuming organs, such as ovaries and muscles. Collectively, our results illustrate how the pleiotropic effects on metabolism, gene expression, and development in the PgkΔE2F animals underscore the importance of E2F regulation on a single E2F target, Pgk.
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Affiliation(s)
- Maria Paula Zappia
- Department of Biochemistry and Molecular Genetics, University of Illinois at Chicago, Chicago, IL 60607
| | - Yong-Jae Kwon
- Department of Biochemistry and Molecular Genetics, University of Illinois at Chicago, Chicago, IL 60607
| | - Anton Westacott
- Department of Biochemistry and Molecular Genetics, University of Illinois at Chicago, Chicago, IL 60607
| | - Isabel Liseth
- Department of Biochemistry and Molecular Genetics, University of Illinois at Chicago, Chicago, IL 60607
| | - Hyun Min Lee
- Department of Biochemistry and Molecular Genetics, University of Illinois at Chicago, Chicago, IL 60607
| | - Abul B. M. M. K. Islam
- Department of Genetic Engineering and Biotechnology, University of Dhaka, Dhaka1000, Bangladesh
| | - Jiyeon Kim
- Department of Biochemistry and Molecular Genetics, University of Illinois at Chicago, Chicago, IL 60607
| | - Maxim V. Frolov
- Department of Biochemistry and Molecular Genetics, University of Illinois at Chicago, Chicago, IL 60607
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4
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Yamamoto‐Matsuda H, Miyoshi K, Moritoh M, Yoshitane H, Fukada Y, Saito K, Yamanaka S, Siomi MC. Lint‐O
cooperates with L(3)mbt in target gene suppression to maintain homeostasis in fly ovary and brain. EMBO Rep 2022; 23:e53813. [PMID: 35993198 PMCID: PMC9535798 DOI: 10.15252/embr.202153813] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Revised: 08/08/2022] [Accepted: 08/09/2022] [Indexed: 11/23/2022] Open
Abstract
Loss‐of‐function mutations in Drosophila lethal(3)malignant brain tumor [l(3)mbt] cause ectopic expression of germline genes and brain tumors. Loss of L(3)mbt function in ovarian somatic cells (OSCs) aberrantly activates germ‐specific piRNA amplification and leads to infertility. However, the underlying mechanism remains unclear. Here, ChIP‐seq for L(3)mbt in cultured OSCs and RNA‐seq before and after L(3)mbt depletion shows that L(3)mbt genomic binding is not necessarily linked to gene regulation and that L(3)mbt controls piRNA pathway genes in multiple ways. Lack of known L(3)mbt co‐repressors, such as Lint‐1, has little effect on the levels of piRNA amplifiers. Identification of L(3)mbt interactors in OSCs and subsequent analysis reveals CG2662 as a novel co‐regulator of L(3)mbt, termed “L(3)mbt interactor in OSCs” (Lint‐O). Most of the L(3)mbt‐bound piRNA amplifier genes are also bound by Lint‐O in a similar fashion. Loss of Lint‐O impacts the levels of piRNA amplifiers, similar to the lack of L(3)mbt. The lint‐O‐deficient flies exhibit female sterility and tumorous brains. Thus, L(3)mbt and its novel co‐suppressor Lint‐O cooperate in suppressing target genes to maintain homeostasis in the ovary and brain.
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Affiliation(s)
- Hitomi Yamamoto‐Matsuda
- Department of Biological Sciences, Graduate School of Science The University of Tokyo Tokyo Japan
| | - Keita Miyoshi
- Department of Chromosome Science National Institute of Genetics, Research Organization of Information and Systems Shizuoka Japan
- Department of Genetics School of Life Science, SOKENDAI Shizuoka Japan
| | - Mai Moritoh
- Department of Biological Sciences, Graduate School of Science The University of Tokyo Tokyo Japan
| | - Hikari Yoshitane
- Department of Biological Sciences, Graduate School of Science The University of Tokyo Tokyo Japan
| | - Yoshitaka Fukada
- Department of Biological Sciences, Graduate School of Science The University of Tokyo Tokyo Japan
| | - Kuniaki Saito
- Department of Chromosome Science National Institute of Genetics, Research Organization of Information and Systems Shizuoka Japan
- Department of Genetics School of Life Science, SOKENDAI Shizuoka Japan
| | - Soichiro Yamanaka
- Department of Biological Sciences, Graduate School of Science The University of Tokyo Tokyo Japan
| | - Mikiko C Siomi
- Department of Biological Sciences, Graduate School of Science The University of Tokyo Tokyo Japan
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5
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Oxidative Stress Is Associated with Overgrowth in Drosophila l(3)mbt Mutant Imaginal Discs. Cells 2022; 11:cells11162542. [PMID: 36010619 PMCID: PMC9406541 DOI: 10.3390/cells11162542] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Revised: 08/04/2022] [Accepted: 08/13/2022] [Indexed: 11/17/2022] Open
Abstract
The loss-of-function conditions for an l(3)malignant brain tumour (l(3)mbt) in larvae reared at 29 °C results in malignant brain tumours and hyperplastic imaginal discs. Unlike the former that have been extensively characterised, little is known about the latter. Here we report the results of a study of the hyperplastic l(3)mbt mutant wing imaginal discs. We identify the l(3)mbt wing disc tumour transcriptome and find it to include genes involved in reactive oxygen species (ROS) metabolism. Furthermore, we show the presence of oxidative stress in l(3)mbt hyperplastic discs, even in apoptosis-blocked conditions, but not in l(3)mbt brain tumours. We also find that chemically blocking oxidative stress in l(3)mbt wing discs reduces the incidence of wing disc overgrowths. Our results reveal the involvement of oxidative stress in l(3)mbt wing discs hyperplastic growth.
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6
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Payankaulam S, Hickey SL, Arnosti DN. Cell cycle expression of polarity genes features Rb targeting of Vang. Cells Dev 2022; 169:203747. [PMID: 34583062 PMCID: PMC8934252 DOI: 10.1016/j.cdev.2021.203747] [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: 03/28/2021] [Revised: 08/28/2021] [Accepted: 09/17/2021] [Indexed: 11/17/2022]
Abstract
Specification of cellular polarity is vital to normal tissue development and function. Pioneering studies in Drosophila and C. elegans have elucidated the composition and dynamics of protein complexes critical for establishment of cell polarity, which is manifest in processes such as cell migration and asymmetric cell division. Conserved throughout metazoans, planar cell polarity (PCP) genes are implicated in disease, including neural tube closure defects associated with mutations in VANGL1/2. PCP protein regulation is well studied; however, relatively little is known about transcriptional regulation of these genes. Our earlier study revealed an unexpected role for the fly Rbf1 retinoblastoma corepressor protein, a regulator of cell cycle genes, in transcriptional regulation of polarity genes. Here we analyze the physiological relevance of the role of E2F/Rbf proteins in the transcription of the key core polarity gene Vang. Targeted mutations to the E2F site within the Vang promoter disrupts binding of E2F/Rbf proteins in vivo, leading to polarity defects in wing hairs. E2F regulation of Vang is supported by the requirement for this motif in a reporter gene. Interestingly, the promoter is repressed by overexpression of E2F1, a transcription factor generally identified as an activator. Consistent with the regulation of this polarity gene by E2F and Rbf factors, expression of Vang and other polarity genes is found to peak in G2/M phase in cells of the embryo and wing imaginal disc, suggesting that cell cycle signals may play a role in regulation of these genes. These findings suggest that the E2F/Rbf complex mechanistically links cell proliferation and polarity.
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Affiliation(s)
- Sandhya Payankaulam
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI, USA
| | - Stephanie L Hickey
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI, USA; Department of Computational Mathematics, Science, and Engineering, Michigan State University, East Lansing, MI, USA
| | - David N Arnosti
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI, USA.
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7
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Abstract
Perfectly orchestrated periodic gene expression during cell cycle progression is essential for maintaining genome integrity and ensuring that cell proliferation can be stopped by environmental signals. Genetic and proteomic studies during the past two decades revealed remarkable evolutionary conservation of the key mechanisms that control cell cycle-regulated gene expression, including multisubunit DNA-binding DREAM complexes. DREAM complexes containing a retinoblastoma family member, an E2F transcription factor and its dimerization partner, and five proteins related to products of Caenorhabditis elegans multivulva (Muv) class B genes lin-9, lin-37, lin-52, lin-53, and lin-54 (comprising the MuvB core) have been described in diverse organisms, from worms to humans. This review summarizes the current knowledge of the structure, function, and regulation of DREAM complexes in different organisms, as well as the role of DREAM in human disease. Expected final online publication date for the Annual Review of Genetics, Volume 55 is November 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
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Affiliation(s)
- Hayley Walston
- Department of Human and Molecular Genetics, Virginia Commonwealth University, Richmond, Virginia 23298, USA;
| | - Audra N Iness
- School of Medicine, Virginia Commonwealth University, Richmond, Virginia 23298, USA
| | - Larisa Litovchick
- Department of Human and Molecular Genetics, Virginia Commonwealth University, Richmond, Virginia 23298, USA; .,Division of Hematology, Oncology and Palliative Care, Department of Internal Medicine, Virginia Commonwealth University, Richmond, Virginia 23298, USA.,Massey Cancer Center, Richmond, Virginia 23298, USA
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8
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Nabeel-Shah S, Garg J, Saettone A, Ashraf K, Lee H, Wahab S, Ahmed N, Fine J, Derynck J, Pu S, Ponce M, Marcon E, Zhang Z, Greenblatt JF, Pearlman RE, Lambert JP, Fillingham J. Functional characterization of RebL1 highlights the evolutionary conservation of oncogenic activities of the RBBP4/7 orthologue in Tetrahymena thermophila. Nucleic Acids Res 2021; 49:6196-6212. [PMID: 34086947 PMCID: PMC8216455 DOI: 10.1093/nar/gkab413] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Revised: 04/22/2021] [Accepted: 05/04/2021] [Indexed: 12/18/2022] Open
Abstract
Retinoblastoma-binding proteins 4 and 7 (RBBP4 and RBBP7) are two highly homologous human histone chaperones. They function in epigenetic regulation as subunits of multiple chromatin-related complexes and have been implicated in numerous cancers. Due to their overlapping functions, our understanding of RBBP4 and 7, particularly outside of Opisthokonts, has remained limited. Here, we report that in the ciliate protozoan Tetrahymena thermophila a single orthologue of human RBBP4 and 7 proteins, RebL1, physically interacts with histone H4 and functions in multiple epigenetic regulatory pathways. Functional proteomics identified conserved functional links for Tetrahymena RebL1 protein as well as human RBBP4 and 7. We found that putative subunits of multiple chromatin-related complexes including CAF1, Hat1, Rpd3, and MuvB, co-purified with RebL1 during Tetrahymena growth and conjugation. Iterative proteomics analyses revealed that the cell cycle regulatory MuvB-complex in Tetrahymena is composed of at least five subunits including evolutionarily conserved Lin54, Lin9 and RebL1 proteins. Genome-wide analyses indicated that RebL1 and Lin54 (Anqa1) bind within genic and intergenic regions. Moreover, Anqa1 targets primarily promoter regions suggesting a role for Tetrahymena MuvB in transcription regulation. RebL1 depletion inhibited cellular growth and reduced the expression levels of Anqa1 and Lin9. Consistent with observations in glioblastoma tumors, RebL1 depletion suppressed DNA repair protein Rad51 in Tetrahymena, thus underscoring the evolutionarily conserved functions of RBBP4/7 proteins. Our results suggest the essentiality of RebL1 functions in multiple epigenetic regulatory complexes in which it impacts transcription regulation and cellular viability.
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Affiliation(s)
- Syed Nabeel-Shah
- Department of Chemistry and Biology, Ryerson University, 350 Victoria St., Toronto M5B 2K3, Canada
| | - Jyoti Garg
- Department of Chemistry and Biology, Ryerson University, 350 Victoria St., Toronto M5B 2K3, Canada.,Department of Biology, York University, 4700 Keele St., Toronto M3J 1P3, Canada
| | - Alejandro Saettone
- Department of Chemistry and Biology, Ryerson University, 350 Victoria St., Toronto M5B 2K3, Canada
| | - Kanwal Ashraf
- Department of Biology, York University, 4700 Keele St., Toronto M3J 1P3, Canada
| | - Hyunmin Lee
- Department of Computer Science, University of Toronto, Toronto M5S 1A8, Canada.,Donnelly Centre, University of Toronto, Toronto M5S 3E1, Canada
| | - Suzanne Wahab
- Department of Chemistry and Biology, Ryerson University, 350 Victoria St., Toronto M5B 2K3, Canada
| | - Nujhat Ahmed
- Donnelly Centre, University of Toronto, Toronto M5S 3E1, Canada.,Department of Molecular Genetics, University of Toronto, Toronto M5S 1A8, Canada
| | - Jacob Fine
- Department of Biology, York University, 4700 Keele St., Toronto M3J 1P3, Canada
| | - Joanna Derynck
- Department of Chemistry and Biology, Ryerson University, 350 Victoria St., Toronto M5B 2K3, Canada
| | - Shuye Pu
- Donnelly Centre, University of Toronto, Toronto M5S 3E1, Canada
| | - Marcelo Ponce
- SciNet HPC Consortium, University of Toronto, 661 University Avenue, Suite 1140, Toronto M5G 1M1, Canada
| | - Edyta Marcon
- Donnelly Centre, University of Toronto, Toronto M5S 3E1, Canada
| | - Zhaolei Zhang
- Department of Computer Science, University of Toronto, Toronto M5S 1A8, Canada.,Donnelly Centre, University of Toronto, Toronto M5S 3E1, Canada.,Department of Molecular Genetics, University of Toronto, Toronto M5S 1A8, Canada
| | - Jack F Greenblatt
- Donnelly Centre, University of Toronto, Toronto M5S 3E1, Canada.,Department of Molecular Genetics, University of Toronto, Toronto M5S 1A8, Canada
| | - Ronald E Pearlman
- Department of Biology, York University, 4700 Keele St., Toronto M3J 1P3, Canada
| | - Jean-Philippe Lambert
- Department of Molecular Medicine, Cancer Research Center, Big Data Research Center, Université Laval, Quebec City, Canada; CHU de Québec Research Center, CHUL, 2705 Laurier Boulevard, Quebec City G1V 4G2, Canada
| | - Jeffrey Fillingham
- Department of Chemistry and Biology, Ryerson University, 350 Victoria St., Toronto M5B 2K3, Canada
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9
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The Dm-Myb Oncoprotein Contributes to Insulator Function and Stabilizes Repressive H3K27me3 PcG Domains. Cell Rep 2021; 30:3218-3228.e5. [PMID: 32160531 PMCID: PMC7172335 DOI: 10.1016/j.celrep.2020.02.053] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2019] [Revised: 09/30/2019] [Accepted: 02/12/2020] [Indexed: 12/13/2022] Open
Abstract
Drosophila Myb (Dm-Myb) encodes a protein that plays a key role in regulation of mitotic phase genes. Here, we further refine its role in the context of a developing tissue as a potentiator of gene expression required for proper RNA polymerase II (RNA Pol II) function and efficient H3K4 methylation at promoters. In contrast to its role in gene activation, Myb is also required for repression of many genes, although no specific mechanism for this role has been proposed. We now reveal a critical role for Myb in contributing to insulator function, in part by promoting binding of insulator proteins BEAF-32 and CP190 and stabilizing H3K27me3 Polycomb-group (PcG) domains. In the absence of Myb, H3K27me3 is markedly reduced throughout the genome, leading to H3K4me3 spreading and gene derepression. Finally, Myb is enriched at boundaries that demarcate chromatin environments, including chromatin loop anchors. These results reveal functions of Myb that extend beyond transcriptional regulation. Myb has been considered a transcriptional activator of primarily M phase genes. Here, Santana et al. show that Myb also contributes to insulator function, in part by promoting binding of insulator factors, and is required to stabilize repressive domains in the genome.
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10
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Okumura T, Nomoto Y, Kobayashi K, Suzuki T, Takatsuka H, Ito M. MYB3R-mediated active repression of cell cycle and growth under salt stress in Arabidopsis thaliana. JOURNAL OF PLANT RESEARCH 2021; 134:261-277. [PMID: 33580347 DOI: 10.1007/s10265-020-01250-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/17/2020] [Accepted: 12/23/2020] [Indexed: 06/12/2023]
Abstract
Under environmental stress, plants are believed to actively repress their growth to save resource and alter its allocation to acquire tolerance against the stress. Although a lot of studies have uncovered precise mechanisms for responding to stress and acquiring tolerance, the mechanisms for regulating growth repression under stress are not as well understood. It is especially unclear which particular genes related to cell cycle control are involved in active growth repression. Here, we showed that decreased growth in plants exposed to moderate salt stress is mediated by MYB3R transcription factors that have been known to positively and negatively regulate the transcription of G2/M-specific genes. Our genome-wide gene expression analysis revealed occurrences of general downregulation of G2/M-specific genes in Arabidopsis under salt stress. Importantly, this downregulation is significantly and universally mitigated by the loss of MYB3R repressors by mutations. Accordingly, the growth performance of Arabidopsis plants under salt stress is significantly recovered in mutants lacking MYB3R repressors. This growth recovery involves improved cell proliferation that is possibly due to prolonging and accelerating cell proliferation, which were partly suggested by enlarged root meristem and increased number of cells positive for CYCB1;1-GUS. Our ploidy analysis further suggested that cell cycle progression at the G2 phase was delayed under salt stress, and this delay was recovered by loss of MYB3R repressors. Under salt stress, the changes in expression of MYB3R activators and repressors at both the mRNA and protein levels were not significant. This observation suggests novel mechanisms underlying MYB3R-mediated growth repression under salt stress that are different from the mechanisms operating under other stress conditions such as DNA damage and high temperature.
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Affiliation(s)
- Toru Okumura
- Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, Chikusa, 464-8601, Japan
| | - Yuji Nomoto
- School of Biological Science and Technology, College of Science and Engineering, Kanazawa University, Kakuma-machi, Kanazawa, 920-1192, Japan
| | - Kosuke Kobayashi
- Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, Chikusa, 464-8601, Japan
| | - Takamasa Suzuki
- Department of Biological Chemistry, College of Bioscience and Biotechnology, Chubu University, 1200 Matsumoto-cho, Kasugai, Aichi, 487-8501, Japan
| | - Hirotomo Takatsuka
- School of Biological Science and Technology, College of Science and Engineering, Kanazawa University, Kakuma-machi, Kanazawa, 920-1192, Japan
| | - Masaki Ito
- School of Biological Science and Technology, College of Science and Engineering, Kanazawa University, Kakuma-machi, Kanazawa, 920-1192, Japan.
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11
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Takeuchi T, Lin YT, Fekaris N, Umen J, Sears BB, Benning C. Modulation of CHT7 Complexes during Light/Dark- and Nitrogen-Mediated Life Cycle Transitions of Chlamydomonas. PLANT PHYSIOLOGY 2020; 184:1762-1774. [PMID: 33004613 PMCID: PMC7723089 DOI: 10.1104/pp.20.00864] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Accepted: 09/21/2020] [Indexed: 06/11/2023]
Abstract
The Chlamydomonas reinhardtii Compromised Hydrolysis of Triacylglycerols7 (CHT7) protein has been previously implicated in the regulation of DNA metabolism and cell-cycle-related gene expression during nitrogen (N) deprivation, and its predicted protein interaction domains are necessary for function. Here, we examined impacts of the cht7 mutation during the cell division cycle under nutrient deficiency in light-dark synchronized cultures. We explored the potential mechanisms affecting CHT7 complex activities during the cell cycle and N starvation, with a focus on the possible interaction between CHT7 and the C. reinhardtii retinoblastoma tumor suppressor (RB) protein homolog MAT3. Notably, the absence of CHT7 did not negatively impact the synchrony of cell division and cell cycle progression during diel growth. Although the majority of CHT7 and MAT3/RB proteins were observed in separate complexes by blue native-PAGE, the two proteins coimmunoprecipitated both during synchronized growth and following N deprivation, suggesting the presence of low abundance subcomplexes containing CHT7 and MAT3/RB. Furthermore, we observed several phosphorylated isoforms of CHT7 under these conditions. To test the potential role of phosphorylation on the structure and function of CHT7, we performed site-directed mutagenesis of previously identified phosphorylated amino acids within CHT7. These phosphorylated residues were dispensable for CHT7 function, but phosphorylated variants of CHT7 persisted, indicating that yet-unidentified residues within CHT7 are also likely phosphorylated. Based on the interaction of CHT7 and MAT3/RB, we postulate the presence of a low-abundance or transient regulatory complex in C. reinhardtii that may be similar to DREAM-like complexes in other organisms.
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Affiliation(s)
- Tomomi Takeuchi
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824
- Department of Energy-Plant Research Laboratory, Michigan State University, East Lansing, Michigan 48824
| | - Yang-Tsung Lin
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824
- Department of Energy-Plant Research Laboratory, Michigan State University, East Lansing, Michigan 48824
| | - Nicholas Fekaris
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824
- Department of Energy-Plant Research Laboratory, Michigan State University, East Lansing, Michigan 48824
| | - James Umen
- Donald Danforth Plant Science Center, St. Louis, Missouri 63132
| | - Barbara B Sears
- Department of Energy-Plant Research Laboratory, Michigan State University, East Lansing, Michigan 48824
- Department of Plant Biology, Michigan State University, East Lansing, Michigan 48824
| | - Christoph Benning
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824
- Department of Energy-Plant Research Laboratory, Michigan State University, East Lansing, Michigan 48824
- Department of Plant Biology, Michigan State University, East Lansing, Michigan 48824
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12
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Werwein E, Biyanee A, Klempnauer KH. Intramolecular interaction of B-MYB is regulated through Ser-577 phosphorylation. FEBS Lett 2020; 594:4266-4279. [PMID: 32979888 DOI: 10.1002/1873-3468.13940] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2020] [Revised: 08/11/2020] [Accepted: 09/08/2020] [Indexed: 02/02/2023]
Abstract
The transcription factor B-MYB is an important regulator of cell cycle-related processes that is activated by step-wise phosphorylation of multiple sites by cyclin-dependent kinases (CDKs) and conformational changes induced by the peptidylprolyl cis/trans isomerase Pin1. Here, we show that a conserved amino acid sequence around Ser-577 in the C-terminal part of B-MYB is able to interact with the B-MYB DNA-binding domain. Phosphorylation of Ser-577 disrupts this interaction and is regulated by the interplay of CDKs and the phosphatase CDC14B. Deletion of sequences surrounding Ser-577 hyperactivates the transactivation potential of B-MYB, decreases its proteolytic stability, and causes cell cycle defects. Overall, we show for the first time that B-MYB can undergo an intramolecular interaction that is controlled by the phosphorylation state of Ser-577.
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Affiliation(s)
- Eugen Werwein
- Institute for Biochemistry, Westfälische-Wilhelms-Universität, Münster, Germany
| | - Abhiruchi Biyanee
- Institute for Biochemistry, Westfälische-Wilhelms-Universität, Münster, Germany
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13
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Cibis H, Biyanee A, Dörner W, Mootz HD, Klempnauer KH. Characterization of the zinc finger proteins ZMYM2 and ZMYM4 as novel B-MYB binding proteins. Sci Rep 2020; 10:8390. [PMID: 32439918 PMCID: PMC7242444 DOI: 10.1038/s41598-020-65443-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2020] [Accepted: 04/28/2020] [Indexed: 11/09/2022] Open
Abstract
B-MYB, a highly conserved member of the MYB transcription factor family, is expressed ubiquitously in proliferating cells and plays key roles in important cell cycle-related processes, such as control of G2/M-phase transcription, cytokinesis, G1/S-phase progression and DNA-damage reponse. Deregulation of B-MYB function is characteristic of several types of tumor cells, underlining its oncogenic potential. To gain a better understanding of the functions of B-MYB we have employed affinity purification coupled to mass spectrometry to discover novel B-MYB interacting proteins. Here we have identified the zinc-finger proteins ZMYM2 and ZMYM4 as novel B-MYB binding proteins. ZMYM4 is a poorly studied protein whose initial characterization reported here shows that it is highly SUMOylated and that its interaction with B-MYB is stimulated upon induction of DNA damage. Unlike knockdown of B-MYB, which causes G2/M arrest and defective cytokinesis in HEK293 cells, knockdown of ZMYM2 or ZMYM4 have no obvious effects on the cell cycle of these cells. By contrast, knockdown of ZMYM2 strongly impaired the G1/S-phase progression of HepG2 cells, suggesting that ZMYM2, like B-MYB, is required for entry into S-phase in these cells. Overall, our work identifies two novel B-MYB binding partners with possible functions in the DNA-damage response and the G1/S-transition.
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Affiliation(s)
- Hannah Cibis
- Institute for Biochemistry, Westfälische-Wilhelms-Universität, D-48149, Münster, Germany
| | - Abhiruchi Biyanee
- Institute for Biochemistry, Westfälische-Wilhelms-Universität, D-48149, Münster, Germany
| | - Wolfgang Dörner
- Institute for Biochemistry, Westfälische-Wilhelms-Universität, D-48149, Münster, Germany
| | - Henning D Mootz
- Institute for Biochemistry, Westfälische-Wilhelms-Universität, D-48149, Münster, Germany
| | - Karl-Heinz Klempnauer
- Institute for Biochemistry, Westfälische-Wilhelms-Universität, D-48149, Münster, Germany.
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14
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Vorster PJ, Goetsch P, Wijeratne TU, Guiley KZ, Andrejka L, Tripathi S, Larson BJ, Rubin SM, Strome S, Lipsick JS. A long lost key opens an ancient lock: Drosophila Myb causes a synthetic multivulval phenotype in nematodes. Biol Open 2020; 9:bio051508. [PMID: 32295830 PMCID: PMC7225089 DOI: 10.1242/bio.051508] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2020] [Accepted: 04/05/2020] [Indexed: 01/14/2023] Open
Abstract
The five-protein MuvB core complex is highly conserved in animals. This nuclear complex interacts with RB-family tumor suppressor proteins and E2F-DP transcription factors to form DREAM complexes that repress genes that regulate cell cycle progression and cell fate. The MuvB core complex also interacts with Myb family oncoproteins to form the Myb-MuvB complexes that activate many of the same genes. We show that animal-type Myb genes are present in Bilateria, Cnidaria and Placozoa, the latter including the simplest known animal species. However, bilaterian nematode worms lost their animal-type Myb genes hundreds of millions of years ago. Nevertheless, amino acids in the LIN9 and LIN52 proteins that directly interact with the MuvB-binding domains of human B-Myb and Drosophila Myb are conserved in Caenorhabditiselegans Here, we show that, despite greater than 500 million years since their last common ancestor, the Drosophila melanogaster Myb protein can bind to the nematode LIN9-LIN52 proteins in vitro and can cause a synthetic multivulval (synMuv) phenotype in vivo This phenotype is similar to that caused by loss-of-function mutations in C. elegans synMuvB-class genes including those that encode homologs of the MuvB core, RB, E2F and DP. Furthermore, amino acid substitutions in the MuvB-binding domain of Drosophila Myb that disrupt its functions in vitro and in vivo also disrupt these activities in C. elegans We speculate that nematodes and other animals may contain another protein that can bind to LIN9 and LIN52 in order to activate transcription of genes repressed by DREAM complexes.
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Affiliation(s)
- Paul J Vorster
- Departments of Pathology, Genetics, and Biology, Stanford University, Stanford, CA 94305-5324, USA
| | - Paul Goetsch
- Department of Molecular, Cell, and Developmental Biology, University of California, Santa Cruz, Santa Cruz, CA 95064, USA
| | - Tilini U Wijeratne
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, Santa Cruz, CA 95064, USA
| | - Keelan Z Guiley
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, Santa Cruz, CA 95064, USA
| | - Laura Andrejka
- Departments of Pathology, Genetics, and Biology, Stanford University, Stanford, CA 94305-5324, USA
| | - Sarvind Tripathi
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, Santa Cruz, CA 95064, USA
| | - Braden J Larson
- Department of Molecular, Cell, and Developmental Biology, University of California, Santa Cruz, Santa Cruz, CA 95064, USA
| | - Seth M Rubin
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, Santa Cruz, CA 95064, USA
| | - Susan Strome
- Department of Molecular, Cell, and Developmental Biology, University of California, Santa Cruz, Santa Cruz, CA 95064, USA
| | - Joseph S Lipsick
- Departments of Pathology, Genetics, and Biology, Stanford University, Stanford, CA 94305-5324, USA
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15
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Zappia MP, Rogers A, Islam ABMMK, Frolov MV. Rbf Activates the Myogenic Transcriptional Program to Promote Skeletal Muscle Differentiation. Cell Rep 2020; 26:702-719.e6. [PMID: 30650361 PMCID: PMC6344057 DOI: 10.1016/j.celrep.2018.12.080] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2018] [Revised: 11/18/2018] [Accepted: 12/18/2018] [Indexed: 11/25/2022] Open
Abstract
The importance of the retinoblastoma tumor suppressor protein pRB in cell cycle control is well established. However, less is known about its role in differentiation during animal development. Here, we investigated the role of Rbf, the Drosophila pRB homolog, in adult skeletal muscles. We found that the depletion of Rbf severely reduced muscle growth and altered myofibrillogenesis but only minimally affected myoblast proliferation. We identified an Rbf-dependent transcriptional program in late muscle development that is distinct from the canonical role of Rbf in cell cycle control. Unexpectedly, Rbf acts as a transcriptional activator of the myogenic and metabolic genes in the growing muscles. The genomic regions bound by Rbf contained the binding sites of several factors that genetically interacted with Rbf by modulating Rbf-dependent phenotype. Thus, our results reveal a distinctive role for Rbf as a direct activator of the myogenic transcriptional program that drives late muscle differentiation. Inactivation of the tumor suppressor RB, an obligatory step in most cancers, results in unrestrained cell cycle progression. Zappia et al. show that Rbf, the RB Drosophila ortholog, directly activates the metabolic program that accompanies muscle development. This work expands the understanding of the plethora of Rbf functions.
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Affiliation(s)
- Maria Paula Zappia
- Department of Biochemistry and Molecular Genetics, University of Illinois at Chicago, 900 S. Ashland Avenue, Chicago, IL 60607, USA
| | - Alice Rogers
- Department of Biochemistry and Molecular Genetics, University of Illinois at Chicago, 900 S. Ashland Avenue, Chicago, IL 60607, USA
| | - Abul B M M K Islam
- Department of Genetic Engineering and Biotechnology, University of Dhaka, Dhaka 1000, Bangladesh
| | - Maxim V Frolov
- Department of Biochemistry and Molecular Genetics, University of Illinois at Chicago, 900 S. Ashland Avenue, Chicago, IL 60607, USA.
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16
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Takeuchi T, Sears BB, Lindeboom C, Lin YT, Fekaris N, Zienkiewicz K, Zienkiewicz A, Poliner E, Benning C. Chlamydomonas CHT7 Is Required for an Effective Quiescent State by Regulating Nutrient-Responsive Cell Cycle Gene Expression. THE PLANT CELL 2020; 32:1240-1269. [PMID: 32001503 PMCID: PMC7145468 DOI: 10.1105/tpc.19.00628] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/15/2019] [Revised: 01/07/2020] [Accepted: 01/27/2020] [Indexed: 06/10/2023]
Abstract
COMPROMISED HYDROLYSIS OF TRIACYLGLYCEROLS7 (CHT7) in Chlamydomonas (Chlamydomonas reinhardtii) was previously shown to affect the transcription of a subset of genes during nitrogen (N)-replete growth and following N refeeding. Here, we show that an extensive derepression of genes involved in DNA metabolism and cell cycle-related processes, as well as downregulation of genes encoding oxidoreductases and nutrient transporters, occurs in the cht7 mutant during N deprivation. Cellular mutant phenotypes are consistent with the observed transcriptome misregulation, as cht7 cells fail to properly arrest growth, nuclear replication, and cell division following N deprivation. Reduction in cht7 colony formation following N refeeding is explained by its compromised viability during N deprivation and by the occurrence of abortive divisions during N refeeding. Surprisingly, the largely unstructured C-terminal half of CHT7 with predicted protein binding domains, but not the canonical CXC DNA binding domain, is essential for the ability of CHT7 to form stable complexes and reverse the cellular phenotypes and transcription levels in the cht7 mutant. Hence, although lacking the presumed DNA binding domain, CHT7 modulates the expression of cell cycle genes in response to N availability, which is essential for establishing an effective quiescent state and the coordinated resumption of growth following N refeeding.
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Affiliation(s)
- Tomomi Takeuchi
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824
- Department of Energy-Plant Research Laboratory, Michigan State University, East Lansing, Michigan 48824
| | - Barbara B Sears
- Department of Energy-Plant Research Laboratory, Michigan State University, East Lansing, Michigan 48824
- Department of Plant Biology, Michigan State University, East Lansing, Michigan 48824
| | - Chase Lindeboom
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824
| | - Yang-Tsung Lin
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824
- Department of Energy-Plant Research Laboratory, Michigan State University, East Lansing, Michigan 48824
| | - Nicholas Fekaris
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824
| | - Krzysztof Zienkiewicz
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824
- Department of Energy-Plant Research Laboratory, Michigan State University, East Lansing, Michigan 48824
- Centre of Modern Interdisciplinary Technologies, Nicolaus Copernicus University in Toruń, 87-100 Toruń, Poland
| | - Agnieszka Zienkiewicz
- Department of Energy-Plant Research Laboratory, Michigan State University, East Lansing, Michigan 48824
- Centre of Modern Interdisciplinary Technologies, Nicolaus Copernicus University in Toruń, 87-100 Toruń, Poland
- Great Lakes Bioenergy Research Center, Michigan State University, East Lansing, Michigan 48824
| | - Eric Poliner
- Department of Energy-Plant Research Laboratory, Michigan State University, East Lansing, Michigan 48824
- Department of Plant Biology, Michigan State University, East Lansing, Michigan 48824
| | - Christoph Benning
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824
- Department of Energy-Plant Research Laboratory, Michigan State University, East Lansing, Michigan 48824
- Department of Plant Biology, Michigan State University, East Lansing, Michigan 48824
- Great Lakes Bioenergy Research Center, Michigan State University, East Lansing, Michigan 48824
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17
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Mouawad R, Prasad J, Thorley D, Himadewi P, Kadiyala D, Wilson N, Kapranov P, Arnosti DN. Diversification of Retinoblastoma Protein Function Associated with Cis and Trans Adaptations. Mol Biol Evol 2020; 36:2790-2804. [PMID: 31418797 DOI: 10.1093/molbev/msz187] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Retinoblastoma proteins are eukaryotic transcriptional corepressors that play central roles in cell cycle control, among other functions. Although most metazoan genomes encode a single retinoblastoma protein, gene duplications have occurred at least twice: in the vertebrate lineage, leading to Rb, p107, and p130, and in Drosophila, an ancestral Rbf1 gene and a derived Rbf2 gene. Structurally, Rbf1 resembles p107 and p130, and mutation of the gene is lethal. Rbf2 is more divergent and mutation does not lead to lethality. However, the retention of Rbf2 >60 My in Drosophila points to essential functions, which prior cell-based assays have been unable to elucidate. Here, using genomic approaches, we provide new insights on the function of Rbf2. Strikingly, we show that Rbf2 regulates a set of cell growth-related genes and can antagonize Rbf1 on specific genes. These unique properties have important implications for the fly; Rbf2 mutants show reduced egg laying, and lifespan is reduced in females and males. Structural alterations in conserved regions of Rbf2 gene suggest that it was sub- or neofunctionalized to develop specific regulatory specificity and activity. We define cis-regulatory features of Rbf2 target genes that allow preferential repression by this protein, indicating that it is not a weaker version of Rbf1 as previously thought. The specialization of retinoblastoma function in Drosophila may reflect a parallel evolution found in vertebrates, and raises the possibility that cell growth control is equally important to cell cycle function for this conserved family of transcriptional corepressors.
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Affiliation(s)
- Rima Mouawad
- Graduate Program in Cell and Molecular Biology, Michigan State University, East Lansing, MI
| | - Jaideep Prasad
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI
| | - Dominic Thorley
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI
| | - Pamela Himadewi
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI
| | - Dhruva Kadiyala
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI
| | - Nathan Wilson
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI
| | - Philipp Kapranov
- Institute of Genomics, School of Biomedical Sciences, Huaqiao University, Xiamen, China
| | - David N Arnosti
- Graduate Program in Cell and Molecular Biology, Michigan State University, East Lansing, MI.,Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI
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18
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Rotelli MD, Bolling AM, Killion AW, Weinberg AJ, Dixon MJ, Calvi BR. An RNAi Screen for Genes Required for Growth of Drosophila Wing Tissue. G3 (BETHESDA, MD.) 2019; 9:3087-3100. [PMID: 31387856 PMCID: PMC6778782 DOI: 10.1534/g3.119.400581] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/21/2019] [Accepted: 07/31/2019] [Indexed: 12/23/2022]
Abstract
Cell division and tissue growth must be coordinated with development. Defects in these processes are the basis for a number of diseases, including developmental malformations and cancer. We have conducted an unbiased RNAi screen for genes that are required for growth in the Drosophila wing, using GAL4-inducible short hairpin RNA (shRNA) fly strains made by the Drosophila RNAi Screening Center. shRNA expression down the center of the larval wing disc using dpp-GAL4, and the central region of the adult wing was then scored for tissue growth and wing hair morphology. Out of 4,753 shRNA crosses that survived to adulthood, 18 had impaired wing growth. FlyBase and the new Alliance of Genome Resources knowledgebases were used to determine the known or predicted functions of these genes and the association of their human orthologs with disease. The function of eight of the genes identified has not been previously defined in Drosophila The genes identified included those with known or predicted functions in cell cycle, chromosome segregation, morphogenesis, metabolism, steroid processing, transcription, and translation. All but one of the genes are similar to those in humans, and many are associated with disease. Knockdown of lin-52, a subunit of the Myb-MuvB transcription factor, or βNACtes6, a gene involved in protein folding and trafficking, resulted in a switch from cell proliferation to an endoreplication growth program through which wing tissue grew by an increase in cell size (hypertrophy). It is anticipated that further analysis of the genes that we have identified will reveal new mechanisms that regulate tissue growth during development.
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Affiliation(s)
- Michael D Rotelli
- Department of Biology, Indiana University, Bloomington, IN 47405 and
| | - Anna M Bolling
- Department of Biology, Indiana University, Bloomington, IN 47405 and
| | - Andrew W Killion
- Department of Biology, Indiana University, Bloomington, IN 47405 and
| | | | - Michael J Dixon
- Department of Biology, Indiana University, Bloomington, IN 47405 and
| | - Brian R Calvi
- Department of Biology, Indiana University, Bloomington, IN 47405 and
- Melvin and Bren Simon Cancer Center, Indiana University, Indianapolis, IN 46202
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19
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Ma Y, McKay DJ, Buttitta L. Changes in chromatin accessibility ensure robust cell cycle exit in terminally differentiated cells. PLoS Biol 2019; 17:e3000378. [PMID: 31479438 PMCID: PMC6743789 DOI: 10.1371/journal.pbio.3000378] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2019] [Revised: 09/13/2019] [Accepted: 08/13/2019] [Indexed: 12/12/2022] Open
Abstract
During terminal differentiation, most cells exit the cell cycle and enter into a prolonged or permanent G0 in which they are refractory to mitogenic signals. Entry into G0 is usually initiated through the repression of cell cycle gene expression by formation of a transcriptional repressor complex called dimerization partner (DP), retinoblastoma (RB)-like, E2F and MuvB (DREAM). However, when DREAM repressive function is compromised during terminal differentiation, additional unknown mechanisms act to stably repress cycling and ensure robust cell cycle exit. Here, we provide evidence that developmentally programmed, temporal changes in chromatin accessibility at a small subset of critical cell cycle genes act to enforce cell cycle exit during terminal differentiation in the Drosophila melanogaster wing. We show that during terminal differentiation, chromatin closes at a set of pupal wing enhancers for the key rate-limiting cell cycle regulators Cyclin E (cycE), E2F transcription factor 1 (e2f1), and string (stg). This closing coincides with wing cells entering a robust postmitotic state that is strongly refractory to cell cycle reactivation, and the regions that close contain known binding sites for effectors of mitogenic signaling pathways such as Yorkie and Notch. When cell cycle exit is genetically disrupted, chromatin accessibility at cell cycle genes remains unaffected, and the closing of distal enhancers at cycE, e2f1, and stg proceeds independent of the cell cycling status. Instead, disruption of cell cycle exit leads to changes in accessibility and expression of a subset of hormone-induced transcription factors involved in the progression of terminal differentiation. Our results uncover a mechanism that acts as a cell cycle–independent timer to limit the response to mitogenic signaling and aberrant cycling in terminally differentiating tissues. In addition, we provide a new molecular description of the cross talk between cell cycle exit and terminal differentiation during metamorphosis. The longer a cell remains in G0, the more refractory it becomes to re-entering the cell cycle. This study shows that in terminally differentiated cells in vivo, regulatory elements at genes encoding just three key cell cycle regulators (cycE, e2f1 and stg) become inaccessible, limiting their aberrant activation and maintaining a prolonged, robust G0.
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Affiliation(s)
- Yiqin Ma
- Department of Molecular Cellular and Developmental Biology, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Daniel J McKay
- Department of Biology, Department of Genetics, Integrative Program for Biological and Genome Sciences, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Laura Buttitta
- Department of Molecular Cellular and Developmental Biology, University of Michigan, Ann Arbor, Michigan, United States of America
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20
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Molnar C, Heinen JP, Reina J, Llamazares S, Palumbo E, Breschi A, Gay M, Villarreal L, Vilaseca M, Pollarolo G, Gonzalez C. The histone code reader PHD finger protein 7 controls sex-linked disparities in gene expression and malignancy in Drosophila. SCIENCE ADVANCES 2019; 5:eaaw7965. [PMID: 31453329 PMCID: PMC6693905 DOI: 10.1126/sciadv.aaw7965] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/25/2019] [Accepted: 07/11/2019] [Indexed: 05/03/2023]
Abstract
The notable male predominance across many human cancer types remains unexplained. Here, we show that Drosophila l(3)mbt brain tumors are more invasive and develop as malignant neoplasms more often in males than in females. By quantitative proteomics, we have identified a signature of proteins that are differentially expressed between male and female tumor samples. Prominent among them is the conserved chromatin reader PHD finger protein 7 (Phf7). We show that Phf7 depletion reduces sex-dependent differences in gene expression and suppresses the enhanced malignant traits of male tumors. Our results identify potential regulators of sex-linked tumor dimorphism and show that these genes may serve as targets to suppress sex-linked malignant traits.
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Affiliation(s)
- Cristina Molnar
- IRB Barcelona, BIST, Carrer de Baldiri Reixac, 10, 08028 Barcelona, Spain
| | - Jan Peter Heinen
- IRB Barcelona, BIST, Carrer de Baldiri Reixac, 10, 08028 Barcelona, Spain
| | - Jose Reina
- IRB Barcelona, BIST, Carrer de Baldiri Reixac, 10, 08028 Barcelona, Spain
| | - Salud Llamazares
- IRB Barcelona, BIST, Carrer de Baldiri Reixac, 10, 08028 Barcelona, Spain
| | - Emilio Palumbo
- CRG, BIST, Carrer del Dr. Aiguader, 88, 08003 Barcelona, Spain
- UPF, Plaça de la Mercè, 10, 08002 Barcelona, Spain
- IMIM, Carrer del Dr. Aiguader, 88, 08003 Barcelona, Spain
| | | | - Marina Gay
- IRB Barcelona, BIST, Carrer de Baldiri Reixac, 10, 08028 Barcelona, Spain
| | - Laura Villarreal
- IRB Barcelona, BIST, Carrer de Baldiri Reixac, 10, 08028 Barcelona, Spain
| | - Marta Vilaseca
- IRB Barcelona, BIST, Carrer de Baldiri Reixac, 10, 08028 Barcelona, Spain
| | - Giulia Pollarolo
- IRB Barcelona, BIST, Carrer de Baldiri Reixac, 10, 08028 Barcelona, Spain
| | - Cayetano Gonzalez
- IRB Barcelona, BIST, Carrer de Baldiri Reixac, 10, 08028 Barcelona, Spain
- ICREA, Passeig Lluís Companys, 08010 Barcelona, Spain
- Corresponding author.
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21
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Rotelli MD, Policastro RA, Bolling AM, Killion AW, Weinberg AJ, Dixon MJ, Zentner GE, Walczak CE, Lilly MA, Calvi BR. A Cyclin A-Myb-MuvB-Aurora B network regulates the choice between mitotic cycles and polyploid endoreplication cycles. PLoS Genet 2019; 15:e1008253. [PMID: 31291240 PMCID: PMC6645565 DOI: 10.1371/journal.pgen.1008253] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2019] [Revised: 07/22/2019] [Accepted: 06/18/2019] [Indexed: 12/30/2022] Open
Abstract
Endoreplication is a cell cycle variant that entails cell growth and periodic genome duplication without cell division, and results in large, polyploid cells. Cells switch from mitotic cycles to endoreplication cycles during development, and also in response to conditional stimuli during wound healing, regeneration, aging, and cancer. In this study, we use integrated approaches in Drosophila to determine how mitotic cycles are remodeled into endoreplication cycles, and how similar this remodeling is between induced and developmental endoreplicating cells (iECs and devECs). Our evidence suggests that Cyclin A / CDK directly activates the Myb-MuvB (MMB) complex to induce transcription of a battery of genes required for mitosis, and that repression of CDK activity dampens this MMB mitotic transcriptome to promote endoreplication in both iECs and devECs. iECs and devECs differed, however, in that devECs had reduced expression of E2F1-dependent genes that function in S phase, whereas repression of the MMB transcriptome in iECs was sufficient to induce endoreplication without a reduction in S phase gene expression. Among the MMB regulated genes, knockdown of AurB protein and other subunits of the chromosomal passenger complex (CPC) induced endoreplication, as did knockdown of CPC-regulated cytokinetic, but not kinetochore, proteins. Together, our results indicate that the status of a CycA-Myb-MuvB-AurB network determines the decision to commit to mitosis or switch to endoreplication in both iECs and devECs, and suggest that regulation of different steps of this network may explain the known diversity of polyploid cycle types in development and disease.
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Affiliation(s)
- Michael D. Rotelli
- Department of Biology. Indiana University, Bloomington, Indiana, United States of America
- Melvin and Bren Simon Cancer Center, Indianapolis, Indiana, United States of America
| | - Robert A. Policastro
- Department of Biology. Indiana University, Bloomington, Indiana, United States of America
- Melvin and Bren Simon Cancer Center, Indianapolis, Indiana, United States of America
| | - Anna M. Bolling
- Department of Biology. Indiana University, Bloomington, Indiana, United States of America
- Melvin and Bren Simon Cancer Center, Indianapolis, Indiana, United States of America
| | - Andrew W. Killion
- Department of Biology. Indiana University, Bloomington, Indiana, United States of America
- Melvin and Bren Simon Cancer Center, Indianapolis, Indiana, United States of America
| | - Abraham J. Weinberg
- Department of Biology. Indiana University, Bloomington, Indiana, United States of America
- Melvin and Bren Simon Cancer Center, Indianapolis, Indiana, United States of America
| | - Michael J. Dixon
- Department of Biology. Indiana University, Bloomington, Indiana, United States of America
- Melvin and Bren Simon Cancer Center, Indianapolis, Indiana, United States of America
| | - Gabriel E. Zentner
- Department of Biology. Indiana University, Bloomington, Indiana, United States of America
- Melvin and Bren Simon Cancer Center, Indianapolis, Indiana, United States of America
| | - Claire E. Walczak
- Melvin and Bren Simon Cancer Center, Indianapolis, Indiana, United States of America
- Indiana University School of Medicine, Bloomington, Indiana, United States of America
| | - Mary A. Lilly
- National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Brian R. Calvi
- Department of Biology. Indiana University, Bloomington, Indiana, United States of America
- Melvin and Bren Simon Cancer Center, Indianapolis, Indiana, United States of America
- Indiana University School of Medicine, Bloomington, Indiana, United States of America
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22
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Takahashi N, Ogita N, Takahashi T, Taniguchi S, Tanaka M, Seki M, Umeda M. A regulatory module controlling stress-induced cell cycle arrest in Arabidopsis. eLife 2019; 8:43944. [PMID: 30944065 PMCID: PMC6449083 DOI: 10.7554/elife.43944] [Citation(s) in RCA: 66] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2018] [Accepted: 03/10/2019] [Indexed: 11/13/2022] Open
Abstract
Cell cycle arrest is an active response to stresses that enables organisms to survive under fluctuating environmental conditions. While signalling pathways that inhibit cell cycle progression have been elucidated, the putative core module orchestrating cell cycle arrest in response to various stresses is still elusive. Here we report that in Arabidopsis, the NAC-type transcription factors ANAC044 and ANAC085 are required for DNA damage-induced G2 arrest. Under genotoxic stress conditions, ANAC044 and ANAC085 enhance protein accumulation of the R1R2R3-type Myb transcription factor (Rep-MYB), which represses G2/M-specific genes. ANAC044/ANAC085-dependent accumulation of Rep-MYB and cell cycle arrest are also observed in the response to heat stress that causes G2 arrest, but not to osmotic stress that retards G1 progression. These results suggest that plants deploy the ANAC044/ANAC085-mediated signalling module as a hub which perceives distinct stress signals and leads to G2 arrest. During environmental stresses, such as high light or a drought, plants do not have the opportunity to up and leave. Instead, they need to buy time and energy by pausing their growth, which means stopping their cells from dividing. In this case, the cell cycle, a series of stages during which a cell prepares itself for division, must be halted. If the genetic information in cells is damaged, often under the influence of the environment, plants stop their cell cycle in the step just before division. However, it is still unclear how this process takes place, and which proteins participate in it. Researchers also do not know whether environmental stresses can directly trigger this mechanism. To investigate, Takahashi et al. conducted a series of genetic experiments on a common plant known as Arabidopsis thaliana, and they identified two proteins, ANAC044 and ANAC085, which could stop the cell cycle when the genetic information is damaged. In particular, ANAC044 and ANAC085 worked by stabilizing other proteins that turn off certain genes that the cell needed to divide. Additional experiments showed that other types of stresses, such as heat, halted the cell cycle using the ANAC044 and ANAC085 pathway. This suggests that this mechanism may be a central ‘hub’ that responds to various stress signals from the environment to prevent cells from dividing. In the field, environmental stresses stop plants from growing, which reduces crop yields; ultimately, manipulating ANAC044 or ANAC085 might help to boost plant productivity even when external conditions fluctuate.
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Affiliation(s)
- Naoki Takahashi
- Graduate School of Science and Technology, Nara Institute of Science and Technology, Nara, Japan
| | - Nobuo Ogita
- Graduate School of Science and Technology, Nara Institute of Science and Technology, Nara, Japan
| | - Tomonobu Takahashi
- Graduate School of Science and Technology, Nara Institute of Science and Technology, Nara, Japan
| | - Shoji Taniguchi
- Graduate School of Science and Technology, Nara Institute of Science and Technology, Nara, Japan
| | - Maho Tanaka
- RIKEN Center for Sustainable Resource Science, Yokohama, Japan.,RIKEN Cluster for Pioneering Research, Wako, Japan
| | - Motoaki Seki
- RIKEN Cluster for Pioneering Research, Wako, Japan
| | - Masaaki Umeda
- Graduate School of Science and Technology, Nara Institute of Science and Technology, Nara, Japan
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23
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Coux RX, Teixeira FK, Lehmann R. L(3)mbt and the LINT complex safeguard cellular identity in the Drosophila ovary. Development 2018; 145:dev.160721. [PMID: 29511022 PMCID: PMC5963868 DOI: 10.1242/dev.160721] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2017] [Accepted: 02/19/2018] [Indexed: 01/10/2023]
Abstract
Maintenance of cellular identity is essential for tissue development and homeostasis. At the molecular level, cell identity is determined by the coordinated activation and repression of defined sets of genes. The tumor suppressor L(3)mbt has been shown to secure cellular identity in Drosophila larval brains by repressing germline-specific genes. Here, we interrogate the temporal and spatial requirements for L(3)mbt in the Drosophila ovary, and show that it safeguards the integrity of both somatic and germline tissues. l(3)mbt mutant ovaries exhibit multiple developmental defects, which we find to be largely caused by the inappropriate expression of a single gene, nanos, a key regulator of germline fate, in the somatic ovarian cells. In the female germline, we find that L(3)mbt represses testis-specific and neuronal genes. At the molecular level, we show that L(3)mbt function in the ovary is mediated through its co-factor Lint-1 but independently of the dREAM complex. Together, our work uncovers a more complex role for L(3)mbt than previously understood and demonstrates that L(3)mbt secures tissue identity by preventing the simultaneous expression of original identity markers and tissue-specific misexpression signatures. Highlighted Article: Characterization of the developmental defects of l(3)mbt mutant ovaries shows that L(3)mbt regulates tissue-specific gene signatures to secure the identity of somatic ovarian and germline tissues.
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Affiliation(s)
- Rémi-Xavier Coux
- Howard Hughes Medical Institute (HHMI) and Kimmel Center for Biology and Medicine of the Skirball Institute, Department of Cell Biology, New York University School of Medicine, New York, NY 10016, USA
| | - Felipe Karam Teixeira
- Howard Hughes Medical Institute (HHMI) and Kimmel Center for Biology and Medicine of the Skirball Institute, Department of Cell Biology, New York University School of Medicine, New York, NY 10016, USA.,Department of Genetics, University of Cambridge, Downing Street, Cambridge CB2 3EH, UK
| | - Ruth Lehmann
- Howard Hughes Medical Institute (HHMI) and Kimmel Center for Biology and Medicine of the Skirball Institute, Department of Cell Biology, New York University School of Medicine, New York, NY 10016, USA
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24
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Laktionov PP, Maksimov DA, Romanov SE, Antoshina PA, Posukh OV, White-Cooper H, Koryakov DE, Belyakin SN. Genome-wide analysis of gene regulation mechanisms during Drosophila spermatogenesis. Epigenetics Chromatin 2018; 11:14. [PMID: 29609617 PMCID: PMC5879934 DOI: 10.1186/s13072-018-0183-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2017] [Accepted: 03/22/2018] [Indexed: 01/01/2023] Open
Abstract
BACKGROUND During Drosophila spermatogenesis, testis-specific meiotic arrest complex (tMAC) and testis-specific TBP-associated factors (tTAF) contribute to activation of hundreds of genes required for meiosis and spermiogenesis. Intriguingly, tMAC is paralogous to the broadly expressed complex Myb-MuvB (MMB)/dREAM and Mip40 protein is shared by both complexes. tMAC acts as a gene activator in spermatocytes, while MMB/dREAM was shown to repress gene activity in many cell types. RESULTS Our study addresses the intricate interplay between tMAC, tTAF, and MMB/dREAM during spermatogenesis. We used cell type-specific DamID to build the DNA-binding profiles of Cookie monster (tMAC), Cannonball (tTAF), and Mip40 (MMB/dREAM and tMAC) proteins in male germline cells. Incorporating the whole transcriptome analysis, we characterized the regulatory effects of these proteins and identified their gene targets. This analysis revealed that tTAFs complex is involved in activation of achi, vis, and topi meiosis arrest genes, implying that tTAFs may indirectly contribute to the regulation of Achi, Vis, and Topi targets. To understand the relationship between tMAC and MMB/dREAM, we performed Mip40 DamID in tTAF- and tMAC-deficient mutants demonstrating meiosis arrest phenotype. DamID profiles of Mip40 were highly dynamic across the stages of spermatogenesis and demonstrated a strong dependence on tMAC in spermatocytes. Integrative analysis of our data indicated that MMB/dREAM represses genes that are not expressed in spermatogenesis, whereas tMAC recruits Mip40 for subsequent gene activation in spermatocytes. CONCLUSIONS Discovered interdependencies allow to formulate a renewed model for tMAC and tTAFs action in Drosophila spermatogenesis demonstrating how tissue-specific genes are regulated.
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Affiliation(s)
- Petr P Laktionov
- Institute of Molecular and Cellular Biology SB RAS, 8/2 Lavrentyev Ave, Novosibirsk, Russia, 630090
| | - Daniil A Maksimov
- Institute of Molecular and Cellular Biology SB RAS, 8/2 Lavrentyev Ave, Novosibirsk, Russia, 630090
| | - Stanislav E Romanov
- Institute of Molecular and Cellular Biology SB RAS, 8/2 Lavrentyev Ave, Novosibirsk, Russia, 630090
| | - Polina A Antoshina
- Institute of Molecular and Cellular Biology SB RAS, 8/2 Lavrentyev Ave, Novosibirsk, Russia, 630090
| | - Olga V Posukh
- Institute of Molecular and Cellular Biology SB RAS, 8/2 Lavrentyev Ave, Novosibirsk, Russia, 630090
| | | | - Dmitry E Koryakov
- Institute of Molecular and Cellular Biology SB RAS, 8/2 Lavrentyev Ave, Novosibirsk, Russia, 630090.,Novosibirsk State University, Novosibirsk, Russia, 630090
| | - Stepan N Belyakin
- Institute of Molecular and Cellular Biology SB RAS, 8/2 Lavrentyev Ave, Novosibirsk, Russia, 630090. .,Novosibirsk State University, Novosibirsk, Russia, 630090.
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25
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Dominado N, La Marca JE, Siddall NA, Heaney J, Tran M, Cai Y, Yu F, Wang H, Somers WG, Quinn LM, Hime GR. Rbf Regulates Drosophila Spermatogenesis via Control of Somatic Stem and Progenitor Cell Fate in the Larval Testis. Stem Cell Reports 2017; 7:1152-1163. [PMID: 27974223 PMCID: PMC5161748 DOI: 10.1016/j.stemcr.2016.11.007] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2016] [Revised: 11/17/2016] [Accepted: 11/18/2016] [Indexed: 12/02/2022] Open
Abstract
The Drosophila testis has been fundamental to understanding how stem cells interact with their endogenous microenvironment, or niche, to control organ growth in vivo. Here, we report the identification of two independent alleles for the highly conserved tumor suppressor gene, Retinoblastoma-family protein (Rbf), in a screen for testis phenotypes in X chromosome third-instar lethal alleles. Rbf mutant alleles exhibit overproliferation of spermatogonial cells, which is phenocopied by the molecularly characterized Rbf11 null allele. We demonstrate that Rbf promotes cell-cycle exit and differentiation of the somatic and germline stem cells of the testes. Intriguingly, depletion of Rbf specifically in the germline does not disrupt stem cell differentiation, rather Rbf loss of function in the somatic lineage drives overproliferation and differentiation defects in both lineages. Together our observations suggest that Rbf in the somatic lineage controls germline stem cell renewal and differentiation non-autonomously via essential roles in the microenvironment of the germline lineage. Rbf null testes exhibit failure of germline stem cells to differentiate Rbf expression in somatic cells of L3 testes rescues the GSC differentiation defect Somatic Rbf RNAi disrupts cyst stem cell and germline stem cell differentiation Somatic depletion of E2f1 rescues Rbf germline proliferation and differentiation
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Affiliation(s)
- Nicole Dominado
- Centre for Stem Cell Systems, Department of Anatomy and Neuroscience, The University of Melbourne, Melbourne, VIC 3010, Australia; Department of Anatomy and Neuroscience, The University of Melbourne, Melbourne, VIC 3010, Australia
| | - John E La Marca
- Department of Genetics, La Trobe University, Melbourne, VIC 3086, Australia
| | - Nicole A Siddall
- Centre for Stem Cell Systems, Department of Anatomy and Neuroscience, The University of Melbourne, Melbourne, VIC 3010, Australia; Department of Anatomy and Neuroscience, The University of Melbourne, Melbourne, VIC 3010, Australia
| | - James Heaney
- Centre for Stem Cell Systems, Department of Anatomy and Neuroscience, The University of Melbourne, Melbourne, VIC 3010, Australia; Department of Anatomy and Neuroscience, The University of Melbourne, Melbourne, VIC 3010, Australia
| | - Mai Tran
- Department of Anatomy and Neuroscience, The University of Melbourne, Melbourne, VIC 3010, Australia
| | - Yu Cai
- Temasek Life Sciences Laboratory, National University of Singapore, Singapore 117543, Singapore; Department of Biological Sciences, National University of Singapore, Singapore 117543, Singapore
| | - Fengwei Yu
- Temasek Life Sciences Laboratory, National University of Singapore, Singapore 117543, Singapore
| | - Hongyan Wang
- Neuroscience & Behavioral Disorder Program, Duke-National University of Singapore, Singapore 169857, Singapore; Department of Physiology, National University of Singapore, Singapore 117597, Singapore
| | - W Gregory Somers
- Department of Genetics, La Trobe University, Melbourne, VIC 3086, Australia
| | - Leonie M Quinn
- Department of Anatomy and Neuroscience, The University of Melbourne, Melbourne, VIC 3010, Australia; The John Curtin School of Medical Research, The Australian National University, Acton, ACT 2601, Australia.
| | - Gary R Hime
- Centre for Stem Cell Systems, Department of Anatomy and Neuroscience, The University of Melbourne, Melbourne, VIC 3010, Australia; Department of Anatomy and Neuroscience, The University of Melbourne, Melbourne, VIC 3010, Australia.
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26
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Kang Y, Liow HH, Maier EJ, Brent MR. NetProphet 2.0: mapping transcription factor networks by exploiting scalable data resources. Bioinformatics 2017; 34:249-257. [PMID: 28968736 PMCID: PMC5860202 DOI: 10.1093/bioinformatics/btx563] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2017] [Revised: 03/14/2017] [Accepted: 09/11/2017] [Indexed: 11/15/2022] Open
Abstract
Motivation Cells process information, in part, through transcription factor (TF) networks, which control the rates at which individual genes produce their products. A TF network map is a graph that indicates which TFs bind and directly regulate each gene. Previous work has described network mapping algorithms that rely exclusively on gene expression data and ‘integrative’ algorithms that exploit a wide range of data sources including chromatin immunoprecipitation sequencing (ChIP-seq) of many TFs, genome-wide chromatin marks, and binding specificities for many TFs determined in vitro. However, such resources are available only for a few major model systems and cannot be easily replicated for new organisms or cell types. Results We present NetProphet 2.0, a ‘data light’ algorithm for TF network mapping, and show that it is more accurate at identifying direct targets of TFs than other, similarly data light algorithms. In particular, it improves on the accuracy of NetProphet 1.0, which used only gene expression data, by exploiting three principles. First, combining multiple approaches to network mapping from expression data can improve accuracy relative to the constituent approaches. Second, TFs with similar DNA binding domains bind similar sets of target genes. Third, even a noisy, preliminary network map can be used to infer DNA binding specificities from promoter sequences and these inferred specificities can be used to further improve the accuracy of the network map. Availability and implementation Source code and comprehensive documentation are freely available at https://github.com/yiming-kang/NetProphet_2.0. Supplementary information Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Yiming Kang
- Department of Computer Science and Engineering and Center for Genome Sciences and Systems Biology, Washington University, Saint Louis, MO, USA
| | - Hien-Haw Liow
- Department of Mathematics, Washington University, Saint Louis, MO, USA
| | - Ezekiel J Maier
- Department of Computer Science and Engineering and Center for Genome Sciences and Systems Biology, Washington University, Saint Louis, MO, USA
| | - Michael R Brent
- Department of Computer Science and Engineering and Center for Genome Sciences and Systems Biology, Washington University, Saint Louis, MO, USA
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27
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Wei Y, Gokhale RH, Sonnenschein A, Montgomery KM, Ingersoll A, Arnosti DN. Complex cis-regulatory landscape of the insulin receptor gene underlies the broad expression of a central signaling regulator. Development 2017; 143:3591-3603. [PMID: 27702787 DOI: 10.1242/dev.138073] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2016] [Accepted: 08/10/2016] [Indexed: 12/16/2022]
Abstract
Insulin signaling plays key roles in development, growth and metabolism through dynamic control of glucose uptake, global protein translation and transcriptional regulation. Altered levels of insulin signaling are known to play key roles in development and disease, yet the molecular basis of such differential signaling remains obscure. Expression of the insulin receptor (InR) gene itself appears to play an important role, but the nature of the molecular wiring controlling InR transcription has not been elucidated. We characterized the regulatory elements driving Drosophila InR expression and found that the generally broad expression of this gene is belied by complex individual switch elements, the dynamic regulation of which reflects direct and indirect contributions of FOXO, EcR, Rbf and additional transcription factors through redundant elements dispersed throughout ∼40 kb of non-coding regions. The control of InR transcription in response to nutritional and tissue-specific inputs represents an integration of multiple cis-regulatory elements, the structure and function of which may have been sculpted by evolutionary selection to provide a highly tailored set of signaling responses on developmental and tissue-specific levels.
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Affiliation(s)
- Yiliang Wei
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824, USA
| | - Rewatee H Gokhale
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824, USA
| | - Anne Sonnenschein
- Genetics Program, Michigan State University, East Lansing, MI 48824, USA
| | - Kelly Mone't Montgomery
- Pharmaceutical Sciences, School of Pharmacy, University of Wisconsin-Madison, Madison, WI 53705, USA
| | - Andrew Ingersoll
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824, USA
| | - David N Arnosti
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824, USA Genetics Program, Michigan State University, East Lansing, MI 48824, USA
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28
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Fischer M, Müller GA. Cell cycle transcription control: DREAM/MuvB and RB-E2F complexes. Crit Rev Biochem Mol Biol 2017; 52:638-662. [PMID: 28799433 DOI: 10.1080/10409238.2017.1360836] [Citation(s) in RCA: 150] [Impact Index Per Article: 21.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The precise timing of cell cycle gene expression is critical for the control of cell proliferation; de-regulation of this timing promotes the formation of cancer and leads to defects during differentiation and development. Entry into and progression through S phase requires expression of genes coding for proteins that function in DNA replication. Expression of a distinct set of genes is essential to pass through mitosis and cytokinesis. Expression of these groups of cell cycle-dependent genes is regulated by the RB pocket protein family, the E2F transcription factor family, and MuvB complexes together with B-MYB and FOXM1. Distinct combinations of these transcription factors promote the transcription of the two major groups of cell cycle genes that are maximally expressed either in S phase (G1/S) or in mitosis (G2/M). In this review, we discuss recent work that has started to uncover the molecular mechanisms controlling the precisely timed expression of these genes at specific cell cycle phases, as well as the repression of the genes when a cell exits the cell cycle.
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Affiliation(s)
- Martin Fischer
- a Molecular Oncology, Medical School, University of Leipzig , Leipzig , Germany.,b Department of Medical Oncology , Dana-Farber Cancer Institute , Boston , MA , USA.,c Department of Medicine, Brigham and Women's Hospital , Harvard Medical School , Boston , MA , USA
| | - Gerd A Müller
- a Molecular Oncology, Medical School, University of Leipzig , Leipzig , Germany
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29
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Cheng MH, Andrejka L, Vorster PJ, Hinman A, Lipsick JS. The Drosophila LIN54 homolog Mip120 controls two aspects of oogenesis. Biol Open 2017; 6:967-978. [PMID: 28522430 PMCID: PMC5550918 DOI: 10.1242/bio.025825] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
The conserved multi-protein MuvB core associates with the Myb oncoproteins and with the RB-E2F-DP tumor suppressor proteins in complexes that regulate cell proliferation, differentiation, and apoptosis. Drosophila Mip120, a homolog of LIN54, is a sequence-specific DNA-binding protein within the MuvB core. A mutant of Drosophilamip120 was previously shown to cause female and male sterility. We now show that Mip120 regulates two different aspects of oogenesis. First, in the absence of the Mip120 protein, egg chambers arrest during the transition from stage 7 to 8 with a failure of the normal program of chromosomal dynamics in the ovarian nurse cells. Specifically, the decondensation, disassembly and dispersion of the endoreplicated polytene chromosomes fail to occur without Mip120. The conserved carboxy-terminal DNA-binding and protein-protein interaction domains of Mip120 are necessary but not sufficient for this process. Second, we show that a lack of Mip120 causes a dramatic increase in the expression of benign gonial cell neoplasm (bgcn), a gene that is normally expressed in only a small number of cells within the ovary including the germline stem cells. Summary:Drosophila Mip120/LIN54, regulates ovarian nurse cell chromosome disassembly and germline-specific gene expression. These functions of Mip120 require its less conserved N-terminus in addition to its CXC DNA-binding and HCH protein-interaction domains.
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Affiliation(s)
- Mei-Hsin Cheng
- Departments of Pathology, Genetics, and Biology, Stanford University, Stanford, CA 94305-5324, USA
| | - Laura Andrejka
- Departments of Pathology, Genetics, and Biology, Stanford University, Stanford, CA 94305-5324, USA
| | - Paul J Vorster
- Departments of Pathology, Genetics, and Biology, Stanford University, Stanford, CA 94305-5324, USA
| | - Albert Hinman
- Departments of Pathology, Genetics, and Biology, Stanford University, Stanford, CA 94305-5324, USA
| | - Joseph S Lipsick
- Departments of Pathology, Genetics, and Biology, Stanford University, Stanford, CA 94305-5324, USA
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30
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Henrich SM, Usadel C, Werwein E, Burdova K, Janscak P, Ferrari S, Hess D, Klempnauer KH. Interplay with the Mre11-Rad50-Nbs1 complex and phosphorylation by GSK3β implicate human B-Myb in DNA-damage signaling. Sci Rep 2017; 7:41663. [PMID: 28128338 PMCID: PMC5269693 DOI: 10.1038/srep41663] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2016] [Accepted: 12/21/2016] [Indexed: 12/30/2022] Open
Abstract
B-Myb, a highly conserved member of the Myb transcription factor family, is expressed ubiquitously in proliferating cells and controls the cell cycle dependent transcription of G2/M-phase genes. Deregulation of B-Myb has been implicated in oncogenesis and loss of genomic stability. We have identified B-Myb as a novel interaction partner of the Mre11-Rad50-Nbs1 (MRN) complex, a key player in the repair of DNA double strand breaks. We show that B-Myb directly interacts with the Nbs1 subunit of the MRN complex and is recruited transiently to DNA-damage sites. In response to DNA-damage B-Myb is phosphorylated by protein kinase GSK3β and released from the MRN complex. A B-Myb mutant that cannot be phosphorylated by GSK3β disturbs the regulation of pro-mitotic B-Myb target genes and leads to inappropriate mitotic entry in response to DNA-damage. Overall, our work suggests a novel function of B-Myb in the cellular DNA-damage signalling.
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Affiliation(s)
- Sarah Marie Henrich
- Institut for Biochemistry, Westfälische-Wilhelms-Universität, D-48149 Münster, Germany
- Graduate School of Chemistry (GSC-MS), Westfälische-Wilhelms-Universität, D-48149 Münster, Germany
| | - Clemens Usadel
- Institut for Biochemistry, Westfälische-Wilhelms-Universität, D-48149 Münster, Germany
| | - Eugen Werwein
- Institut for Biochemistry, Westfälische-Wilhelms-Universität, D-48149 Münster, Germany
| | - Kamila Burdova
- Institute of Molecular Genetics, Academy of Sciences of the Czech Republic, 143 00 Prague, Czech Republic
| | - Pavel Janscak
- Institute of Molecular Genetics, Academy of Sciences of the Czech Republic, 143 00 Prague, Czech Republic
- Institute of Molecular Cancer Research, University of Zurich, Winterthurerstr.190, CH-8057 Zürich, Switzerland
| | - Stefano Ferrari
- Institute of Molecular Cancer Research, University of Zurich, Winterthurerstr.190, CH-8057 Zürich, Switzerland
| | - Daniel Hess
- Friedrich Miescher Institute for Biomedical Research, Maulbeerstr. 66, CH-4058 Basel, Switzerland
| | - Karl-Heinz Klempnauer
- Institut for Biochemistry, Westfälische-Wilhelms-Universität, D-48149 Münster, Germany
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31
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Abstract
The E2F family of transcription factors is a key determinant of cell proliferation in response to extra- and intra-cellular signals. Within this family, E2F4 is a transcriptional repressor whose activity is critical to engage and maintain cell cycle arrest in G0/G1 in conjunction with members of the retinoblastoma (RB) family. However, recent observations challenge this paradigm and indicate that E2F4 has a multitude of functions in cells besides this cell cycle regulatory role, including in embryonic and adult stem cells, during regenerative processes, and in cancer. Some of these new functions are independent of the RB family and involve direct activation of target genes. Here we review the canonical functions of E2F4 and discuss recent evidence expanding the role of this transcription factor, with a focus on cell fate decisions in tissue homeostasis and regeneration.
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Affiliation(s)
- Jenny Hsu
- a Departments of Pediatrics and Genetics , Stanford University , Stanford , CA , USA
| | - Julien Sage
- a Departments of Pediatrics and Genetics , Stanford University , Stanford , CA , USA
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32
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Kobayashi K, Suzuki T, Iwata E, Magyar Z, Bögre L, Ito M. MYB3Rs, plant homologs of Myb oncoproteins, control cell cycle-regulated transcription and form DREAM-like complexes. Transcription 2016; 6:106-11. [PMID: 26556011 DOI: 10.1080/21541264.2015.1109746] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
Plant MYB3R transcription factors, homologous to Myb oncoproteins, regulate the genes expressed at G2 and M phases in the cell cycle. Recent studies showed that MYB3Rs constitute multiprotein complexes that may correspond to animal complexes known as DREAM or dREAM. Discovery of the putative homologous complex in plants uncovered their significant varieties in structure, function, dynamics, and heterogeneity, providing insight into conserved and diversified aspects of cell cycle-regulated gene transcription.
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Affiliation(s)
- Kosuke Kobayashi
- a Graduate School of Bioagricultural Sciences; Nagoya University ; Chikusa , Nagoya , Japan
| | - Toshiya Suzuki
- a Graduate School of Bioagricultural Sciences; Nagoya University ; Chikusa , Nagoya , Japan.,b JST; CREST ; Chikusa , Nagoya , Japan
| | - Eriko Iwata
- a Graduate School of Bioagricultural Sciences; Nagoya University ; Chikusa , Nagoya , Japan
| | - Zoltán Magyar
- c Institute of Plant Biology; Biological Research Centre ; Szeged , Hungary.,d Royal Holloway; University of London; School of Biological Sciences ; Egham , Surrey , UK
| | - László Bögre
- d Royal Holloway; University of London; School of Biological Sciences ; Egham , Surrey , UK
| | - Masaki Ito
- a Graduate School of Bioagricultural Sciences; Nagoya University ; Chikusa , Nagoya , Japan.,b JST; CREST ; Chikusa , Nagoya , Japan
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33
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Roles for the Histone Modifying and Exchange Complex NuA4 in Cell Cycle Progression in Drosophila melanogaster. Genetics 2016; 203:1265-81. [PMID: 27184390 DOI: 10.1534/genetics.116.188581] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2016] [Accepted: 05/04/2016] [Indexed: 11/18/2022] Open
Abstract
Robust and synchronous repression of E2F-dependent gene expression is critical to the proper timing of cell cycle exit when cells transition to a postmitotic state. Previously NuA4 was suggested to act as a barrier to proliferation in Drosophila by repressing E2F-dependent gene expression. Here we show that NuA4 activity is required for proper cell cycle exit and the repression of cell cycle genes during the transition to a postmitotic state in vivo However, the delay of cell cycle exit caused by compromising NuA4 is not due to additional proliferation or effects on E2F activity. Instead NuA4 inhibition results in slowed cell cycle progression through late S and G2 phases due to aberrant activation of an intrinsic p53-independent DNA damage response. A reduction in NuA4 function ultimately produces a paradoxical cell cycle gene expression program, where certain cell cycle genes become derepressed in cells that are delayed during the G2 phase of the final cell cycle. Bypassing the G2 delay when NuA4 is inhibited leads to abnormal mitoses and results in severe tissue defects. NuA4 physically and genetically interacts with components of the E2F complex termed D: rosophila, R: bf, E: 2F A: nd M: yb/ M: ulti-vulva class B: (DREAM/MMB), and modulates a DREAM/MMB-dependent ectopic neuron phenotype in the posterior wing margin. However, this effect is also likely due to the cell cycle delay, as simply reducing Cdk1 is sufficient to generate a similar phenotype. Our work reveals that the major requirement for NuA4 in the cell cycle in vivo is to suppress an endogenous DNA damage response, which is required to coordinate proper S and G2 cell cycle progression with differentiation and cell cycle gene expression.
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Regulation of cell polarity determinants by the Retinoblastoma tumor suppressor protein. Sci Rep 2016; 6:22879. [PMID: 26971715 PMCID: PMC4789731 DOI: 10.1038/srep22879] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2015] [Accepted: 02/23/2016] [Indexed: 01/24/2023] Open
Abstract
In addition to their canonical roles in the cell cycle, RB family proteins regulate numerous developmental pathways, although the mechanisms remain obscure. We found that Drosophila Rbf1 associates with genes encoding components of the highly conserved apical-basal and planar cell polarity pathways, suggesting a possible regulatory role. Here, we show that depletion of Rbf1 in Drosophila tissues is indeed associated with polarity defects in the wing and eye. Key polarity genes aPKC, par6, vang, pk, and fmi are upregulated, and an aPKC mutation suppresses the Rbf1-induced phenotypes. RB control of cell polarity may be an evolutionarily conserved function, with important implications in cancer metastasis.
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Billmann M, Horn T, Fischer B, Sandmann T, Huber W, Boutros M. A genetic interaction map of cell cycle regulators. Mol Biol Cell 2016; 27:1397-407. [PMID: 26912791 PMCID: PMC4831891 DOI: 10.1091/mbc.e15-07-0467] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2015] [Accepted: 02/10/2016] [Indexed: 12/20/2022] Open
Abstract
A combination of genome-scale RNA interference screening and genetic interaction analysis using process-directed phenotypes is used to assign components to specific pathways and complexes for modulators of mitosis and cytokinesis in Drosophila S2 cells. Cell-based RNA interference (RNAi) is a powerful approach to screen for modulators of many cellular processes. However, resulting candidate gene lists from cell-based assays comprise diverse effectors, both direct and indirect, and further dissecting their functions can be challenging. Here we screened a genome-wide RNAi library for modulators of mitosis and cytokinesis in Drosophila S2 cells. The screen identified many previously known genes as well as modulators that have previously not been connected to cell cycle control. We then characterized ∼300 candidate modifiers further by genetic interaction analysis using double RNAi and a multiparametric, imaging-based assay. We found that analyzing cell cycle–relevant phenotypes increased the sensitivity for associating novel gene function. Genetic interaction maps based on mitotic index and nuclear size grouped candidates into known regulatory complexes of mitosis or cytokinesis, respectively, and predicted previously uncharacterized components of known processes. For example, we confirmed a role for the Drosophila CCR4 mRNA processing complex component l(2)NC136 during the mitotic exit. Our results show that the combination of genome-scale RNAi screening and genetic interaction analysis using process-directed phenotypes provides a powerful two-step approach to assigning components to specific pathways and complexes.
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Affiliation(s)
- Maximilian Billmann
- Division of Signaling and Functional Genomics, German Cancer Research Center, and Department of Cell and Molecular Biology, Heidelberg University, 69120 Heidelberg, Germany
| | - Thomas Horn
- Division of Signaling and Functional Genomics, German Cancer Research Center, and Department of Cell and Molecular Biology, Heidelberg University, 69120 Heidelberg, Germany
| | - Bernd Fischer
- Genome Biology Unit, EMBL, 69118 Heidelberg, Germany Computational Genome Biology, German Cancer Research Center, 69120 Heidelberg, Germany
| | - Thomas Sandmann
- Division of Signaling and Functional Genomics, German Cancer Research Center, and Department of Cell and Molecular Biology, Heidelberg University, 69120 Heidelberg, Germany
| | | | - Michael Boutros
- Division of Signaling and Functional Genomics, German Cancer Research Center, and Department of Cell and Molecular Biology, Heidelberg University, 69120 Heidelberg, Germany
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Saha N, Liu M, Gajan A, Pile LA. Genome-wide studies reveal novel and distinct biological pathways regulated by SIN3 isoforms. BMC Genomics 2016; 17:111. [PMID: 26872827 PMCID: PMC4752761 DOI: 10.1186/s12864-016-2428-5] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2015] [Accepted: 02/01/2016] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND The multisubunit SIN3 complex is a global transcriptional regulator. In Drosophila, a single Sin3A gene encodes different isoforms of SIN3, of which SIN3 187 and SIN3 220 are the major isoforms. Previous studies have demonstrated functional non-redundancy of SIN3 isoforms. The role of SIN3 isoforms in regulating distinct biological processes, however, is not well characterized. RESULTS We established a Drosophila S2 cell culture model system in which cells predominantly express either SIN3 187 or SIN3 220. To identify genomic targets of SIN3 isoforms, we performed chromatin immunoprecipitation followed by deep sequencing. Our data demonstrate that upon overexpression of SIN3 187, the level of SIN3 220 decreased and the large majority of genomic sites bound by SIN3 220 were instead bound by SIN3 187. We used RNA-seq to identify genes regulated by the expression of one isoform or the other. In S2 cells, which predominantly express SIN3 220, we found that SIN3 220 directly regulates genes involved in metabolism and cell proliferation. We also determined that SIN3 187 regulates a unique set of genes and likely modulates expression of many genes also regulated by SIN3 220. Interestingly, biological pathways enriched for genes specifically regulated by SIN3 187 strongly suggest that this isoform plays an important role during the transition from the embryonic to the larval stage of development. CONCLUSION These data establish the role of SIN3 isoforms in regulating distinct biological processes. This study substantially contributes to our understanding of the complexity of gene regulation by SIN3.
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Affiliation(s)
- Nirmalya Saha
- Department of Biological Sciences, Wayne State University, Detroit, MI, USA.
| | - Mengying Liu
- Department of Biological Sciences, Wayne State University, Detroit, MI, USA.
| | - Ambikai Gajan
- Department of Biological Sciences, Wayne State University, Detroit, MI, USA.
| | - Lori A Pile
- Department of Biological Sciences, Wayne State University, Detroit, MI, USA.
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Harashima H, Sugimoto K. Integration of developmental and environmental signals into cell proliferation and differentiation through RETINOBLASTOMA-RELATED 1. CURRENT OPINION IN PLANT BIOLOGY 2016; 29:95-103. [PMID: 26799131 DOI: 10.1016/j.pbi.2015.12.003] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2015] [Revised: 12/03/2015] [Accepted: 12/06/2015] [Indexed: 05/23/2023]
Abstract
Plants continuously form new organs during post-embryonic development, thus progression of the proliferative cell cycle and subsequent transition into differentiation must be tightly controlled by developmental and environmental cues. Recent studies have begun to uncover how cell proliferation and cell differentiation are coordinated at the molecular level through tight transcriptional regulation of cell cycle and/or developmental regulators. Accumulating evidence suggests that RETINOBLASTOMA-RELATED 1 (RBR1), the Arabidopsis homolog of the human tumor suppressor Retinoblastoma (Rb), functions as a molecular hub linking cell proliferation, differentiation, and environmental response. In this review we will discuss recent findings on cell cycle regulation, highlighting the emerging roles of RBR1 as a key integrator of internal differentiation cues and external stimuli into the cell cycle machinery.
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Affiliation(s)
- Hirofumi Harashima
- RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro, Tsurumi, Yokohama, Kanagawa 230-0045, Japan
| | - Keiko Sugimoto
- RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro, Tsurumi, Yokohama, Kanagawa 230-0045, Japan.
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Zappia MP, Frolov MV. E2F function in muscle growth is necessary and sufficient for viability in Drosophila. Nat Commun 2016; 7:10509. [PMID: 26823289 PMCID: PMC4740182 DOI: 10.1038/ncomms10509] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2015] [Accepted: 12/22/2015] [Indexed: 01/08/2023] Open
Abstract
The E2F transcription factor is a key cell cycle regulator. However, the inactivation of the entire E2F family in Drosophila is permissive throughout most of animal development until pupation when lethality occurs. Here we show that E2F function in the adult skeletal muscle is essential for animal viability since providing E2F function in muscles rescues the lethality of the whole-body E2F-deficient animals. Muscle-specific loss of E2F results in a significant reduction in muscle mass and thinner myofibrils. We demonstrate that E2F is dispensable for proliferation of muscle progenitor cells, but is required during late myogenesis to directly control the expression of a set of muscle-specific genes. Interestingly, E2f1 provides a major contribution to the regulation of myogenic function, while E2f2 appears to be less important. These findings identify a key function of E2F in skeletal muscle required for animal viability, and illustrate how the cell cycle regulator is repurposed in post-mitotic cells.
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Affiliation(s)
- Maria Paula Zappia
- Department of Biochemistry and Molecular Genetics, University of Illinois at Chicago, 900 S Ashland Avenue, Chicago, Illinois 60607, USA
| | - Maxim V. Frolov
- Department of Biochemistry and Molecular Genetics, University of Illinois at Chicago, 900 S Ashland Avenue, Chicago, Illinois 60607, USA
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Absence of canonical marks of active chromatin in developmentally regulated genes. Nat Genet 2015; 47:1158-1167. [PMID: 26280901 PMCID: PMC4625605 DOI: 10.1038/ng.3381] [Citation(s) in RCA: 66] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2015] [Accepted: 07/22/2015] [Indexed: 12/13/2022]
Abstract
The interplay of active and repressive histone modifications is assumed to have a key role in the regulation of gene expression. In contrast to this generally accepted view, we show that the transcription of genes temporally regulated during fly and worm development occurs in the absence of canonically active histone modifications. Conversely, strong chromatin marking is related to transcriptional and post-transcriptional stability, an association that we also observe in mammals. Our results support a model in which chromatin marking is associated with the stable production of RNA, whereas unmarked chromatin would permit rapid gene activation and deactivation during development. In the latter case, regulation by transcription factors would have a comparatively more important regulatory role than chromatin marks.
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A Forward Genetic Screen for Suppressors of Somatic P Granules in Caenorhabditis elegans. G3-GENES GENOMES GENETICS 2015; 5:2209-15. [PMID: 26100681 PMCID: PMC4593002 DOI: 10.1534/g3.115.019257] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
In Caenorhabditis elegans, germline expression programs are actively repressed in somatic tissue by components of the synMuv (synthetic multi-vulva) B chromatin remodeling complex, which include homologs of tumor suppressors Retinoblastoma (Rb/LIN-35) and Malignant Brain Tumor (MBT/LIN-61). However, the full scope of pathways that suppress germline expression in the soma is unknown. To address this, we performed a mutagenesis and screened for somatic expression of GFP-tagged PGL-1, a core P-granule nucleating protein. Eight alleles were isolated from 4000 haploid genomes. Five of these alleles exhibit a synMuv phenotype, whereas the remaining three were identified as hypomorphic alleles of known synMuv B genes, lin-13 and dpl-1. These findings suggest that most suppressors of germline programs in the soma of C. elegans are either required for viability or function through synMuv B chromatin regulation.
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Kobayashi K, Suzuki T, Iwata E, Nakamichi N, Suzuki T, Chen P, Ohtani M, Ishida T, Hosoya H, Müller S, Leviczky T, Pettkó-Szandtner A, Darula Z, Iwamoto A, Nomoto M, Tada Y, Higashiyama T, Demura T, Doonan JH, Hauser MT, Sugimoto K, Umeda M, Magyar Z, Bögre L, Ito M. Transcriptional repression by MYB3R proteins regulates plant organ growth. EMBO J 2015; 34:1992-2007. [PMID: 26069325 DOI: 10.15252/embj.201490899] [Citation(s) in RCA: 98] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2014] [Accepted: 05/12/2015] [Indexed: 11/09/2022] Open
Abstract
In multicellular organisms, temporal and spatial regulation of cell proliferation is central for generating organs with defined sizes and morphologies. For establishing and maintaining the post-mitotic quiescent state during cell differentiation, it is important to repress genes with mitotic functions. We found that three of the Arabidopsis MYB3R transcription factors synergistically maintain G2/M-specific genes repressed in post-mitotic cells and restrict the time window of mitotic gene expression in proliferating cells. The combined mutants of the three repressor-type MYB3R genes displayed long roots, enlarged leaves, embryos, and seeds. Genome-wide chromatin immunoprecipitation revealed that MYB3R3 binds to the promoters of G2/M-specific genes and to E2F target genes. MYB3R3 associates with the repressor-type E2F, E2FC, and the RETINOBLASTOMA RELATED proteins. In contrast, the activator MYB3R4 was in complex with E2FB in proliferating cells. With mass spectrometry and pairwise interaction assays, we identified some of the other conserved components of the multiprotein complexes, known as DREAM/dREAM in human and flies. In plants, these repressor complexes are important for periodic expression during cell cycle and to establish a post-mitotic quiescent state determining organ size.
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Affiliation(s)
- Kosuke Kobayashi
- Graduate School of Bioagricultural Sciences, Nagoya University, Chikusa, Nagoya, Japan
| | - Toshiya Suzuki
- Graduate School of Bioagricultural Sciences, Nagoya University, Chikusa, Nagoya, Japan JST, CREST, Chikusa, Nagoya, Japan
| | - Eriko Iwata
- Graduate School of Bioagricultural Sciences, Nagoya University, Chikusa, Nagoya, Japan
| | - Norihito Nakamichi
- WPI Institute of Transformative Bio-Molecules, Nagoya University, Chikusa, Nagoya, Japan Graduate School of Sciences, Nagoya University, Chikusa, Nagoya, Japan
| | - Takamasa Suzuki
- Graduate School of Sciences, Nagoya University, Chikusa, Nagoya, Japan JST ERATO Higashiyama Live-Holonics Project, Nagoya University, Chikusa, Nagoya, Japan
| | - Poyu Chen
- Graduate School of Biological Sciences, Nara Institute of Science and Technology, Ikoma, Nara, Japan
| | - Misato Ohtani
- Graduate School of Biological Sciences, Nara Institute of Science and Technology, Ikoma, Nara, Japan RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa, Japan
| | - Takashi Ishida
- Graduate School of Science and Technology, Kumamoto University, Kumamoto, Japan
| | - Hanako Hosoya
- Department of Biology, Tokyo Gakugei University, Koganei, Tokyo, Japan
| | - Sabine Müller
- Center for Plant Molecular Biology, University of Tübingen, Tübingen, Germany
| | - Tünde Leviczky
- Institute of Plant Biology, Biological Research Centre, Szeged, Hungary
| | | | - Zsuzsanna Darula
- Laboratory of Proteomic Research, Biological Research Centre, Szeged, Hungary
| | - Akitoshi Iwamoto
- Department of Biology, Tokyo Gakugei University, Koganei, Tokyo, Japan
| | - Mika Nomoto
- Graduate School of Sciences, Nagoya University, Chikusa, Nagoya, Japan
| | - Yasuomi Tada
- Center for Gene Research, Division of Biological Science, Nagoya University, Chikusa, Nagoya, Japan
| | - Tetsuya Higashiyama
- WPI Institute of Transformative Bio-Molecules, Nagoya University, Chikusa, Nagoya, Japan Graduate School of Sciences, Nagoya University, Chikusa, Nagoya, Japan JST ERATO Higashiyama Live-Holonics Project, Nagoya University, Chikusa, Nagoya, Japan
| | - Taku Demura
- Graduate School of Biological Sciences, Nara Institute of Science and Technology, Ikoma, Nara, Japan RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa, Japan
| | - John H Doonan
- The National Plant Phenomics Centre, Aberystwyth University, Aberystwyth, UK
| | - Marie-Theres Hauser
- Department of Applied Genetics and Cell Biology, University of Natural Resources and Life Sciences, Vienna, Austria
| | - Keiko Sugimoto
- RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa, Japan
| | - Masaaki Umeda
- Graduate School of Biological Sciences, Nara Institute of Science and Technology, Ikoma, Nara, Japan JST, CREST, Ikoma, Nara, Japan
| | - Zoltán Magyar
- Institute of Plant Biology, Biological Research Centre, Szeged, Hungary Royal Holloway, School of Biological Sciences, University of London, Egham, Surrey, UK
| | - László Bögre
- Royal Holloway, School of Biological Sciences, University of London, Egham, Surrey, UK
| | - Masaki Ito
- Graduate School of Bioagricultural Sciences, Nagoya University, Chikusa, Nagoya, Japan JST, CREST, Chikusa, Nagoya, Japan
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Genome-Wide Analysis of Drosophila RBf2 Protein Highlights the Diversity of RB Family Targets and Possible Role in Regulation of Ribosome Biosynthesis. G3-GENES GENOMES GENETICS 2015; 5:1503-15. [PMID: 25999584 PMCID: PMC4502384 DOI: 10.1534/g3.115.019166] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
RBf2 is a recently evolved retinoblastoma family member in Drosophila that differs from RBf1, especially in the C-terminus. To investigate whether the unique features of RBf2 contribute to diverse roles in gene regulation, we performed chromatin immunoprecipitation sequencing for both RBf2 and RBf1 in embryos. A previous model for RB−E2F interactions suggested that RBf1 binds dE2F1 or dE2F2, whereas RBf2 is restricted to binding to dE2F2; however, we found that RBf2 targets approximately twice as many genes as RBf1. Highly enriched among the RBf2 targets were ribosomal protein genes. We tested the functional significance of this finding by assessing RBf activity on ribosomal protein promoters and the endogenous genes. RBf1 and RBf2 significantly repressed expression of some ribosomal protein genes, although not all bound genes showed transcriptional effects. Interestingly, many ribosomal protein genes are similarly targeted in human cells, indicating that these interactions may be relevant for control of ribosome biosynthesis and growth. We carried out bioinformatic analysis to investigate the basis for differential targeting by these two proteins and found that RBf2-specific promoters have distinct sequence motifs, suggesting unique targeting mechanisms. Association of RBf2 with these promoters appears to be independent of dE2F2/dDP, although promoters bound by both RBf1 and RBf2 require dE2F2/dDP. The presence of unique RBf2 targets suggest that evolutionary appearance of this corepressor represents the acquisition of potentially novel roles in gene regulation for the RB family.
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43
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Guiley KZ, Liban TJ, Felthousen JG, Ramanan P, Litovchick L, Rubin SM. Structural mechanisms of DREAM complex assembly and regulation. Genes Dev 2015; 29:961-74. [PMID: 25917549 PMCID: PMC4421984 DOI: 10.1101/gad.257568.114] [Citation(s) in RCA: 78] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2014] [Indexed: 01/01/2023]
Abstract
To understand the biochemical mechanisms underpinning DREAM function and regulation, Guiley et al. investigated the structural basis for DREAM assembly. Together, the data inform a novel target interface for studying MuvB and p130 function and the design of inhibitors that prevent tumor escape in quiescence. The DREAM complex represses cell cycle genes during quiescence through scaffolding MuvB proteins with E2F4/5 and the Rb tumor suppressor paralog p107 or p130. Upon cell cycle entry, MuvB dissociates from p107/p130 and recruits B-Myb and FoxM1 for up-regulating mitotic gene expression. To understand the biochemical mechanisms underpinning DREAM function and regulation, we investigated the structural basis for DREAM assembly. We identified a sequence in the MuvB component LIN52 that binds directly to the pocket domains of p107 and p130 when phosphorylated on the DYRK1A kinase site S28. A crystal structure of the LIN52–p107 complex reveals that LIN52 uses a suboptimal LxSxExL sequence together with the phosphate at nearby S28 to bind the LxCxE cleft of the pocket domain with high affinity. The structure explains the specificity for p107/p130 over Rb in the DREAM complex and how the complex is disrupted by viral oncoproteins. Based on insights from the structure, we addressed how DREAM is disassembled upon cell cycle entry. We found that p130 and B-Myb can both bind the core MuvB complex simultaneously but that cyclin-dependent kinase phosphorylation of p130 weakens its association. Together, our data inform a novel target interface for studying MuvB and p130 function and the design of inhibitors that prevent tumor escape in quiescence.
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Affiliation(s)
- Keelan Z Guiley
- Department of Chemistry and Biochemistry, University of California at Santa Cruz, Santa Cruz, California 95064, USA
| | - Tyler J Liban
- Department of Chemistry and Biochemistry, University of California at Santa Cruz, Santa Cruz, California 95064, USA
| | - Jessica G Felthousen
- Division of Hematology, Oncology, and Palliative Care, Richmond, Virginia 23298, USA; Massey Cancer Center, Virginia Commonwealth University, Richmond, Virginia 23298, USA
| | - Parameshwaran Ramanan
- Department of Chemistry and Biochemistry, University of California at Santa Cruz, Santa Cruz, California 95064, USA
| | - Larisa Litovchick
- Division of Hematology, Oncology, and Palliative Care, Richmond, Virginia 23298, USA; Massey Cancer Center, Virginia Commonwealth University, Richmond, Virginia 23298, USA
| | - Seth M Rubin
- Department of Chemistry and Biochemistry, University of California at Santa Cruz, Santa Cruz, California 95064, USA;
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Fischer B, Sandmann T, Horn T, Billmann M, Chaudhary V, Huber W, Boutros M. A map of directional genetic interactions in a metazoan cell. eLife 2015; 4. [PMID: 25748138 PMCID: PMC4384530 DOI: 10.7554/elife.05464] [Citation(s) in RCA: 69] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2014] [Accepted: 02/28/2015] [Indexed: 12/12/2022] Open
Abstract
Gene–gene interactions shape complex phenotypes and modify the effects of mutations during development and disease. The effects of statistical gene–gene interactions on phenotypes have been used to assign genes to functional modules. However, directional, epistatic interactions, which reflect regulatory relationships between genes, have been challenging to map at large-scale. Here, we used combinatorial RNA interference and automated single-cell phenotyping to generate a large genetic interaction map for 21 phenotypic features of Drosophila cells. We devised a method that combines genetic interactions on multiple phenotypes to reveal directional relationships. This network reconstructed the sequence of protein activities in mitosis. Moreover, it revealed that the Ras pathway interacts with the SWI/SNF chromatin-remodelling complex, an interaction that we show is conserved in human cancer cells. Our study presents a powerful approach for reconstructing directional regulatory networks and provides a resource for the interpretation of functional consequences of genetic alterations. DOI:http://dx.doi.org/10.7554/eLife.05464.001 Genes encode instructions that control our physical characteristics, known as traits. Although some traits are controlled by the activity of a single gene, most traits are influenced by the activities of multiple genes. The genes that influence a particular trait may work independently of each other. However, it is also possible for the genes to interact so that one gene may mask or amplify the effect of another gene. Although gene interactions were first described almost 100 years ago, it has been difficult to identify them and work out the direction of these interactions (i.e., does gene A affect gene B, or vice versa?). Fischer, Sandmann et al. have now studied the interactions between the genes involved in 21 different traits of fruit fly cells. A technique called RNA interference was used to lower the expression of the genes in different combinations, which made it possible to analyze any changes in the traits that occurred when particular genes were not working properly. Fischer, Sandmann et al. took hundreds of thousands images of the cells and analyzed the changes in cell shape, cell size, cell division and other traits. Next, they developed a method to infer the directions of the interactions between individual pairs of genes from the data and then made a map of the genetic interactions for the traits. This map was able to reconstruct the known order of activity of genes during cell division and other cell processes. Furthermore, it revealed previously unknown interactions between genes. For example, genes involved in the Ras signaling pathway—which promotes cell growth and is frequently mutated in human tumors—interacted with genes that encode a group of proteins called the SWI/SNF complex. This complex alters how DNA is packaged in cells to control the expression of genes, and these gene interactions may play an important role in the control of cell growth by Ras signaling. The approach developed by Fischer, Sandmann et al. can shed light on the interactions between genes that produce complex traits of cells. In future, this approach might be helpful to find out which genetic differences between individuals alter the effectiveness of drug treatments, and the impact of using combinations of drugs to treat diseases. DOI:http://dx.doi.org/10.7554/eLife.05464.002
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Affiliation(s)
- Bernd Fischer
- Genome Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Thomas Sandmann
- Division of Signaling and Functional Genomics, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Thomas Horn
- Division of Signaling and Functional Genomics, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Maximilian Billmann
- Division of Signaling and Functional Genomics, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Varun Chaudhary
- Division of Signaling and Functional Genomics, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Wolfgang Huber
- Genome Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Michael Boutros
- Division of Signaling and Functional Genomics, German Cancer Research Center (DKFZ), Heidelberg, Germany
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Miles WO, Korenjak M, Griffiths LM, Dyer MA, Provero P, Dyson NJ. Post-transcriptional gene expression control by NANOS is up-regulated and functionally important in pRb-deficient cells. EMBO J 2014; 33:2201-15. [PMID: 25100735 PMCID: PMC4282507 DOI: 10.15252/embj.201488057] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2014] [Revised: 07/11/2014] [Accepted: 07/15/2014] [Indexed: 11/09/2022] Open
Abstract
Inactivation of the retinoblastoma tumor suppressor (pRb) is a common oncogenic event that alters the expression of genes important for cell cycle progression, senescence, and apoptosis. However, in many contexts, the properties of pRb-deficient cells are similar to wild-type cells suggesting there may be processes that counterbalance the transcriptional changes associated with pRb inactivation. Therefore, we have looked for sets of evolutionary conserved, functionally related genes that are direct targets of pRb/E2F proteins. We show that the expression of NANOS, a key facilitator of the Pumilio (PUM) post-transcriptional repressor complex, is directly repressed by pRb/E2F in flies and humans. In both species, NANOS expression increases following inactivation of pRb/RBF1 and becomes important for tissue homeostasis. By analyzing datasets from normal retinal tissue and pRb-null retinoblastomas, we find a strong enrichment for putative PUM substrates among genes de-regulated in tumors. These include pro-apoptotic genes that are transcriptionally down-regulated upon pRb loss, and we characterize two such candidates, MAP2K3 and MAP3K1, as direct PUM substrates. Our data suggest that NANOS increases in importance in pRb-deficient cells and helps to maintain homeostasis by repressing the translation of transcripts containing PUM Regulatory Elements (PRE).
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Affiliation(s)
- Wayne O Miles
- Massachusetts General Hospital Cancer Center and Harvard Medical School Laboratory of Molecular Oncology, Charlestown, MA, USA
| | - Michael Korenjak
- Massachusetts General Hospital Cancer Center and Harvard Medical School Laboratory of Molecular Oncology, Charlestown, MA, USA
| | - Lyra M Griffiths
- Department of Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Michael A Dyer
- Department of Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Paolo Provero
- Department of Molecular Biotechnology and Health Sciences, University of Turin, Turin, Italy Center for Translational Genomics and Bioinformatics, San Raffaele Scientific Institute, Milan, Italy
| | - Nicholas J Dyson
- Massachusetts General Hospital Cancer Center and Harvard Medical School Laboratory of Molecular Oncology, Charlestown, MA, USA
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Chromatin reader L(3)mbt requires the Myb-MuvB/DREAM transcriptional regulatory complex for chromosomal recruitment. Proc Natl Acad Sci U S A 2014; 111:E4234-43. [PMID: 25249635 DOI: 10.1073/pnas.1416321111] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Lethal malignant brain tumors (lmbt) result from the loss of the conserved transcriptional repressor l(3)mbt, in Drosophila melanogaster. Similar mutations in the human homolog L3MBTL1 correlate with some cancers. The protein's C-terminal MBT repeats bind mono and dimethylated histones in vitro, which could influence recruitment of L3MBTL1 to its target sites. The L(3)mbt chromatin targeting mechanism, however, is controversial and several studies suggest insufficiency or a minor role for histone methylation in determining the site specificity for recruitment. We report that L(3)mbt colocalizes with core members of the Myb-MuvB/DREAM (MMB/DREAM) transcriptional regulatory complex genome-wide, and that L(3)mbt-mediated repression requires this complex in salivary glands and larval brains. Loss of l(3)mbt or of MMB components through mutation cause similar spurious expression of genes, including the transposon regulatory gene piwi, in terminally differentiated cells. The DNA-binding MMB core component Mip120 (Lin54) is required for L(3)mbt recruitment to chromosomes, whereas Mip130 (Lin9) (an MMB core protein) and E2f2 (an MMB transcriptional repressor) are not, but are essential for repression. Cytolocalization experiments suggest the presence of site-specific differential composition of MMB in polytene chromosomes where some loci were bound by a Myb-containing or alternatively, an E2f2 and L(3)mbt form of the complex.
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A functional insulator screen identifies NURF and dREAM components to be required for enhancer-blocking. PLoS One 2014; 9:e107765. [PMID: 25247414 PMCID: PMC4172637 DOI: 10.1371/journal.pone.0107765] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2014] [Accepted: 08/08/2014] [Indexed: 12/27/2022] Open
Abstract
Chromatin insulators of higher eukaryotes functionally divide the genome into active and inactive domains. Furthermore, insulators regulate enhancer/promoter communication, which is evident from the Drosophila bithorax locus in which a multitude of regulatory elements control segment specific gene activity. Centrosomal protein 190 (CP190) is targeted to insulators by CTCF or other insulator DNA-binding factors. Chromatin analyses revealed that insulators are characterized by open and nucleosome depleted regions. Here, we wanted to identify chromatin modification and remodelling factors required for an enhancer blocking function. We used the well-studied Fab-8 insulator of the bithorax locus to apply a genome-wide RNAi screen for factors that contribute to the enhancer blocking function of CTCF and CP190. Among 78 genes required for optimal Fab-8 mediated enhancer blocking, all four components of the NURF complex as well as several subunits of the dREAM complex were most evident. Mass spectrometric analyses of CTCF or CP190 bound proteins as well as immune precipitation confirmed NURF and dREAM binding. Both co-localise with most CP190 binding sites in the genome and chromatin immune precipitation showed that CP190 recruits NURF and dREAM. Nucleosome occupancy and histone H3 binding analyses revealed that CP190 mediated NURF binding results in nucleosomal depletion at CP190 binding sites. Thus, we conclude that CP190 binding to CTCF or to other DNA binding insulator factors mediates recruitment of NURF and dREAM. Furthermore, the enhancer blocking function of insulators is associated with nucleosomal depletion and requires NURF and dREAM.
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Rhee DY, Cho DY, Zhai B, Slattery M, Ma L, Mintseris J, Wong CY, White KP, Celniker SE, Przytycka TM, Gygi SP, Obar RA, Artavanis-Tsakonas S. Transcription factor networks in Drosophila melanogaster. Cell Rep 2014; 8:2031-2043. [PMID: 25242320 DOI: 10.1016/j.celrep.2014.08.038] [Citation(s) in RCA: 72] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2014] [Revised: 06/09/2014] [Accepted: 08/16/2014] [Indexed: 11/15/2022] Open
Abstract
Specific cellular fates and functions depend on differential gene expression, which occurs primarily at the transcriptional level and is controlled by complex regulatory networks of transcription factors (TFs). TFs act through combinatorial interactions with other TFs, cofactors, and chromatin-remodeling proteins. Here, we define protein-protein interactions using a coaffinity purification/mass spectrometry method and study 459 Drosophila melanogaster transcription-related factors, representing approximately half of the established catalog of TFs. We probe this network in vivo, demonstrating functional interactions for many interacting proteins, and test the predictive value of our data set. Building on these analyses, we combine regulatory network inference models with physical interactions to define an integrated network that connects combinatorial TF protein interactions to the transcriptional regulatory network of the cell. We use this integrated network as a tool to connect the functional network of genetic modifiers related to mastermind, a transcriptional cofactor of the Notch pathway.
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Affiliation(s)
- David Y Rhee
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Dong-Yeon Cho
- Computational Biology Branch, National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
| | - Bo Zhai
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Matthew Slattery
- Institute for Genomics and Systems Biology, University of Chicago, Chicago, IL 60637, USA
| | - Lijia Ma
- Institute for Genomics and Systems Biology, University of Chicago, Chicago, IL 60637, USA
| | - Julian Mintseris
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Christina Y Wong
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Kevin P White
- Institute for Genomics and Systems Biology, University of Chicago, Chicago, IL 60637, USA
| | - Susan E Celniker
- Berkeley Drosophila Genome Project, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Teresa M Przytycka
- Computational Biology Branch, National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
| | - Steven P Gygi
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Robert A Obar
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Spyros Artavanis-Tsakonas
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA; Biogen Idec, Inc., Cambridge, MA 02142, USA.
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The pro-apoptotic activity of Drosophila Rbf1 involves dE2F2-dependent downregulation of diap1 and buffy mRNA. Cell Death Dis 2014; 5:e1405. [PMID: 25188515 PMCID: PMC4540203 DOI: 10.1038/cddis.2014.372] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2014] [Revised: 07/23/2014] [Accepted: 07/28/2014] [Indexed: 11/16/2022]
Abstract
The retinoblastoma gene, rb, ensures at least its tumor suppressor function by inhibiting cell proliferation. Its role in apoptosis is more complex and less described than its role in cell cycle regulation. Rbf1, the Drosophila homolog of Rb, has been found to be pro-apoptotic in proliferative tissue. However, the way it induces apoptosis at the molecular level is still unknown. To decipher this mechanism, we induced rbf1 expression in wing proliferative tissue. We found that Rbf1-induced apoptosis depends on dE2F2/dDP heterodimer, whereas dE2F1 transcriptional activity is not required. Furthermore, we highlight that Rbf1 and dE2F2 downregulate two major anti-apoptotic genes in Drosophila: buffy, an anti-apoptotic member of Bcl-2 family and diap1, a gene encoding a caspase inhibitor. On the one hand, Rbf1/dE2F2 repress buffy at the transcriptional level, which contributes to cell death. On the other hand, Rbf1 and dE2F2 upregulate how expression. How is a RNA binding protein involved in diap1 mRNA degradation. By this way, Rbf1 downregulates diap1 at a post-transcriptional level. Moreover, we show that the dREAM complex has a part in these transcriptional regulations. Taken together, these data show that Rbf1, in cooperation with dE2F2 and some members of the dREAM complex, can downregulate the anti-apoptotic genes buffy and diap1, and thus promote cell death in a proliferative tissue.
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Müller GA, Wintsche A, Stangner K, Prohaska SJ, Stadler PF, Engeland K. The CHR site: definition and genome-wide identification of a cell cycle transcriptional element. Nucleic Acids Res 2014; 42:10331-50. [PMID: 25106871 PMCID: PMC4176359 DOI: 10.1093/nar/gku696] [Citation(s) in RCA: 73] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
The cell cycle genes homology region (CHR) has been identified as a DNA element with an important role in transcriptional regulation of late cell cycle genes. It has been shown that such genes are controlled by DREAM, MMB and FOXM1-MuvB and that these protein complexes can contact DNA via CHR sites. However, it has not been elucidated which sequence variations of the canonical CHR are functional and how frequent CHR-based regulation is utilized in mammalian genomes. Here, we define the spectrum of functional CHR elements. As the basis for a computational meta-analysis, we identify new CHR sequences and compile phylogenetic motif conservation as well as genome-wide protein-DNA binding and gene expression data. We identify CHR elements in most late cell cycle genes binding DREAM, MMB, or FOXM1-MuvB. In contrast, Myb- and forkhead-binding sites are underrepresented in both early and late cell cycle genes. Our findings support a general mechanism: sequential binding of DREAM, MMB and FOXM1-MuvB complexes to late cell cycle genes requires CHR elements. Taken together, we define the group of CHR-regulated genes in mammalian genomes and provide evidence that the CHR is the central promoter element in transcriptional regulation of late cell cycle genes by DREAM, MMB and FOXM1-MuvB.
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Affiliation(s)
- Gerd A Müller
- Molecular Oncology, Medical School, University of Leipzig, Semmelweisstr. 14, 04103 Leipzig, Germany
| | - Axel Wintsche
- Computational EvoDevo Group, Department of Computer Science and Interdisciplinary Center for Bioinformatics, University of Leipzig, Härtelstraße 16-18, 04107 Leipzig, Germany
| | - Konstanze Stangner
- Molecular Oncology, Medical School, University of Leipzig, Semmelweisstr. 14, 04103 Leipzig, Germany
| | - Sonja J Prohaska
- Computational EvoDevo Group, Department of Computer Science and Interdisciplinary Center for Bioinformatics, University of Leipzig, Härtelstraße 16-18, 04107 Leipzig, Germany
| | - Peter F Stadler
- Bioinformatics Group, Department of Computer Science and Interdisciplinary Center for Bioinformatics, University of Leipzig, Härtelstrasse 16-18, 04107 Leipzig, Germany Max Planck Institute for Mathematics in the Sciences, Inselstraße 22, 04103 Leipzig, Germany Center for Non-coding RNA in Technology and Health, Department of Basic Veterinary and Animal Sciences, Faculty of Life Sciences University of Copenhagen, Grønnegårdsvej 3, 1870 Frederiksberg C Denmark Santa Fe Institute, 1399 Hyde Park Rd, Santa Fe, NM 87501, USA
| | - Kurt Engeland
- Molecular Oncology, Medical School, University of Leipzig, Semmelweisstr. 14, 04103 Leipzig, Germany
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