1
|
Soukar I, Mitra A, Vo L, Rofoo M, Greenberg ML, Pile LA. The histone modification regulator, SIN3, plays a role in the cellular response to changes in glycolytic flux. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2025:2025.01.15.633193. [PMID: 39868318 PMCID: PMC11761031 DOI: 10.1101/2025.01.15.633193] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/28/2025]
Abstract
Epigenetic regulation and metabolism are connected. Epigenetic regulators, like the SIN3 complex, affect the expression of a wide range of genes, including those encoding metabolic enzymes essential for central carbon metabolism. The idea that epigenetic modifiers can sense and respond to metabolic flux by regulating gene expression has long been proposed. In support of this cross-talk, we provide data linking SIN3 regulatory action on a subset of metabolic genes with the cellular response to changes in metabolic flux. Furthermore, we show that loss of SIN3 is linked to decreases in mitochondrial respiration and the cellular response to mitochondrial and glycolytic stress. Data presented here provide evidence that SIN3 is important for the cellular response to metabolic flux change.
Collapse
Affiliation(s)
- Imad Soukar
- Department of Biological Sciences, Wayne State University, Detroit, MI 48202, USA
| | - Anindita Mitra
- Department of Biological Sciences, Wayne State University, Detroit, MI 48202, USA
| | - Linh Vo
- Department of Biological Sciences, Wayne State University, Detroit, MI 48202, USA
| | - Melanie Rofoo
- Department of Biological Sciences, Wayne State University, Detroit, MI 48202, USA
| | - Miriam L. Greenberg
- Department of Biological Sciences, Wayne State University, Detroit, MI 48202, USA
| | - Lori A. Pile
- Department of Biological Sciences, Wayne State University, Detroit, MI 48202, USA
| |
Collapse
|
2
|
Stokes G, Li Z, Talaba N, Genthe W, Brix MB, Pham B, Wienhold MD, Sandok G, Hernan R, Wynn J, Tang H, Tabima DM, Rodgers A, Hacker TA, Chesler NC, Zhang P, Murad R, Yuan JXJ, Shen Y, Chung WK, McCulley DJ. Rescuing lung development through embryonic inhibition of histone acetylation. Sci Transl Med 2024; 16:eadc8930. [PMID: 38295182 PMCID: PMC12070813 DOI: 10.1126/scitranslmed.adc8930] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2022] [Accepted: 01/10/2024] [Indexed: 02/02/2024]
Abstract
A major barrier to the impact of genomic diagnosis in patients with congenital malformations is the lack of understanding regarding how sequence variants contribute to disease pathogenesis and whether this information could be used to generate patient-specific therapies. Congenital diaphragmatic hernia (CDH) is among the most common and severe of all structural malformations; however, its underlying mechanisms are unclear. We identified loss-of-function sequence variants in the epigenomic regulator gene SIN3A in two patients with complex CDH. Tissue-specific deletion of Sin3a in mice resulted in defects in diaphragm development, lung hypoplasia, and pulmonary hypertension, the cardinal features of CDH and major causes of CDH-associated mortality. Loss of SIN3A in the lung mesenchyme resulted in reduced cellular differentiation, impaired cell proliferation, and increased DNA damage. Treatment of embryonic Sin3a mutant mice with anacardic acid, an inhibitor of histone acetyltransferase, reduced DNA damage, increased cell proliferation and differentiation, improved lung and pulmonary vascular development, and reduced pulmonary hypertension. These findings demonstrate that restoring the balance of histone acetylation can improve lung development in the Sin3a mouse model of CDH.
Collapse
Affiliation(s)
- Giangela Stokes
- Department of Pediatrics, University of California, San Diego, San Diego, CA 92093, USA
| | - Zhuowei Li
- Department of Pediatrics, University of California, San Diego, San Diego, CA 92093, USA
| | - Nicole Talaba
- Department of Pediatrics, University of California, San Diego, San Diego, CA 92093, USA
| | - William Genthe
- Department of Pediatrics, University of Wisconsin-Madison, Madison, WI 53705, USA
| | - Maria B. Brix
- Department of Pediatrics, University of Wisconsin-Madison, Madison, WI 53705, USA
| | - Betty Pham
- Department of Pediatrics, University of California, San Diego, San Diego, CA 92093, USA
| | | | - Gracia Sandok
- Department of Pediatrics, University of Wisconsin-Madison, Madison, WI 53705, USA
| | - Rebecca Hernan
- Department of Pediatrics, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Julia Wynn
- Department of Pediatrics, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Haiyang Tang
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, First Affiliated Hospital of Guangzhou Medical University, Guangzhou 510120, Guangdong, China
| | - Diana M. Tabima
- Department of Biomedical Engineering, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Allison Rodgers
- Department of Medicine, University of Wisconsin-Madison, Madison, WI 53705, USA
| | - Timothy A. Hacker
- Department of Medicine, University of Wisconsin-Madison, Madison, WI 53705, USA
| | - Naomi C. Chesler
- Edwards Lifesciences Foundation Cardiovascular Innovation and Research Center and Department of Biomedical Engineering, University of California, Irvine, Irvine, CA 92697, USA
| | - Pan Zhang
- Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA 92037, USA
| | - Rabi Murad
- Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA 92037, USA
| | - Jason X. -J. Yuan
- Section of Physiology, Division of Pulmonary, Critical Care and Sleep Medicine, Department of Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Yufeng Shen
- Department of Systems Biology, Department of Biomedical Informatics, and JP Sulzberger Columbia Genome Center, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Wendy K. Chung
- Department of Pediatrics, Boston Children’s Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - David J. McCulley
- Department of Pediatrics, University of California, San Diego, San Diego, CA 92093, USA
| |
Collapse
|
3
|
Soukar I, Mitra A, Pile LA. Analysis of the chromatin landscape and RNA polymerase II binding at SIN3-regulated genes. Biol Open 2023; 12:bio060026. [PMID: 37850739 PMCID: PMC10651107 DOI: 10.1242/bio.060026] [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: 06/02/2023] [Accepted: 10/12/2023] [Indexed: 10/19/2023] Open
Abstract
The chromatin environment has a significant impact on gene expression. Chromatin structure is highly regulated by histone modifications and RNA polymerase II binding dynamics. The SIN3 histone modifying complex regulates the chromatin environment leading to changes in gene expression. In Drosophila melanogaster, the Sin3A gene is alternatively spliced to produce different protein isoforms, two of which include SIN3 220 and SIN3 187. Both SIN3 isoforms are scaffolding proteins that interact with several other factors to regulate the chromatin landscape. The mechanism through which the SIN3 isoforms regulate chromatin is not well understood. Here, we analyze publicly available data sets to allow us to ask specific questions on how SIN3 isoforms regulate chromatin and gene activity. We determined that genes repressed by the SIN3 isoforms exhibited enrichment in histone H3K4me2, H3K4me3, H3K14ac and H3K27ac near the transcription start site. We observed an increase in the amount of paused RNA polymerase II on the promoter of genes repressed by the isoforms as compared to genes that require SIN3 for maximum activation. Furthermore, we analyzed a subset of genes regulated by SIN3 187 that suggest a mechanism in which SIN3 187 might exhibit hard regulation as well as soft regulation. Data presented here expand our knowledge of how the SIN3 isoforms regulate the chromatin environment and RNA polymerase II binding dynamics.
Collapse
Affiliation(s)
- Imad Soukar
- Department of Biological Sciences, Wayne State University, Detroit, MI 48202, USA
| | - Anindita Mitra
- Department of Biological Sciences, Wayne State University, Detroit, MI 48202, USA
| | - Lori A. Pile
- Department of Biological Sciences, Wayne State University, Detroit, MI 48202, USA
| |
Collapse
|
4
|
Krasnov AN, Evdokimova AA, Mazina MY, Erokhin M, Chetverina D, Vorobyeva NE. Coregulators Reside within Drosophila Ecdysone-Inducible Loci before and after Ecdysone Treatment. Int J Mol Sci 2023; 24:11844. [PMID: 37511602 PMCID: PMC10380596 DOI: 10.3390/ijms241411844] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2023] [Revised: 07/19/2023] [Accepted: 07/21/2023] [Indexed: 07/30/2023] Open
Abstract
Ecdysone signaling in Drosophila remains a popular model for investigating the mechanisms of steroid action in eukaryotes. The ecdysone receptor EcR can effectively bind ecdysone-response elements with or without the presence of a hormone. For years, EcR enhancers were thought to respond to ecdysone via recruiting coactivator complexes, which replace corepressors and stimulate transcription. However, the exact mechanism of transcription activation by ecdysone remains unclear. Here, we present experimental data on 11 various coregulators at ecdysone-responsive loci of Drosophila S2 cells. We describe the regulatory elements where coregulators reside within these loci and assess changes in their binding levels following 20-hydroxyecdysone treatment. In the current study, we detected the presence of some coregulators at the TSSs (active and inactive) and boundaries marked with CP190 rather than enhancers of the ecdysone-responsive loci where EcR binds. We observed minor changes in the coregulators' binding level. Most were present at inducible loci before and after 20-hydroxyecdysone treatment. Our findings suggest that: (1) coregulators can activate a particular TSS operating from some distal region (which could be an enhancer, boundary regulatory region, or inactive TSS); (2) coregulators are not recruited after 20-hydroxyecdysone treatment to the responsive loci; rather, their functional activity changes (shown as an increase in H3K27 acetylation marks generated by CBP/p300/Nejire acetyltransferase). Taken together, our findings imply that the 20-hydroxyecdysone signal enhances the functional activity of coregulators rather than promoting their binding to regulatory regions during the ecdysone response.
Collapse
Affiliation(s)
- Aleksey N Krasnov
- Institute of Gene Biology, Russian Academy of Sciences, 119334 Moscow, Russia
| | | | - Marina Yu Mazina
- Institute of Gene Biology, Russian Academy of Sciences, 119334 Moscow, Russia
| | - Maksim Erokhin
- Institute of Gene Biology, Russian Academy of Sciences, 119334 Moscow, Russia
| | - Darya Chetverina
- Institute of Gene Biology, Russian Academy of Sciences, 119334 Moscow, Russia
| | - Nadezhda E Vorobyeva
- Institute of Gene Biology, Russian Academy of Sciences, 119334 Moscow, Russia
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Institute of Gene Biology, Russian Academy of Sciences, 119334 Moscow, Russia
| |
Collapse
|
5
|
Mitra A, Vo L, Soukar I, Chaubal A, Greenberg ML, Pile LA. Isoforms of the transcriptional cofactor SIN3 differentially regulate genes necessary for energy metabolism and cell survival. BIOCHIMICA ET BIOPHYSICA ACTA. MOLECULAR CELL RESEARCH 2022; 1869:119322. [PMID: 35820484 PMCID: PMC10557476 DOI: 10.1016/j.bbamcr.2022.119322] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/19/2022] [Revised: 06/28/2022] [Accepted: 06/29/2022] [Indexed: 11/24/2022]
Abstract
The SIN3 scaffolding protein is a conserved transcriptional regulator known to fine-tune gene expression. In Drosophila, there are two major isoforms of SIN3, SIN3 220 and SIN3 187, which each assemble into multi-subunit histone modifying complexes. The isoforms have distinct developmental expression patterns and non-redundant functions. Gene regulatory network analyses indicate that both isoforms affect genes encoding proteins in pathways such as the cell cycle and cell morphogenesis. Interestingly, the SIN3 187 isoform uniquely regulates a subset of pathways including post-embryonic development, phosphate metabolism and apoptosis. Target genes in the phosphate metabolism pathway include nuclear-encoded mitochondrial genes coding for proteins responsible for oxidative phosphorylation. Here, we investigate the physiological effects of SIN3 isoforms on energy metabolism and cell survival. We find that ectopic expression of SIN3 187 represses expression of several nuclear-encoded mitochondrial genes affecting production of ATP and generation of reactive oxygen species (ROS). Forced expression of SIN3 187 also activates several pro-apoptotic and represses a few anti-apoptotic genes. In the SIN3 187 expressing cells, these gene expression patterns are accompanied with an increased sensitivity to paraquat-mediated oxidative stress. These findings indicate that SIN3 187 influences the regulation of mitochondrial function, apoptosis and oxidative stress response in ways that are dissimilar from SIN3 220. The data suggest that the distinct SIN3 histone modifying complexes are deployed in different cellular contexts to maintain cellular homeostasis.
Collapse
Affiliation(s)
- Anindita Mitra
- Department of Biological Sciences, Wayne State University, Detroit, MI 48202, United States of America
| | - Linh Vo
- Department of Biological Sciences, Wayne State University, Detroit, MI 48202, United States of America
| | - Imad Soukar
- Department of Biological Sciences, Wayne State University, Detroit, MI 48202, United States of America
| | - Ashlesha Chaubal
- Department of Biological Sciences, Wayne State University, Detroit, MI 48202, United States of America; Integrative Program for Biological and Genome Sciences, University of North Carolina, Chapel Hill, NC 27599, United States of America
| | - Miriam L Greenberg
- Department of Biological Sciences, Wayne State University, Detroit, MI 48202, United States of America
| | - Lori A Pile
- Department of Biological Sciences, Wayne State University, Detroit, MI 48202, United States of America.
| |
Collapse
|
6
|
Stephan OOH. Interactions, structural aspects, and evolutionary perspectives of the yeast 'START'-regulatory network. FEMS Yeast Res 2021; 22:6461095. [PMID: 34905017 DOI: 10.1093/femsyr/foab064] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Accepted: 12/11/2021] [Indexed: 11/12/2022] Open
Abstract
Molecular signal transduction networks which conduct transcription at the G1 to S phase transition of the eukaryotic cell division cycle have been identified in diverse taxa from mammals to baker´s yeast with analogous functional organization. However, regarding some network components, such as the transcriptional regulators STB1 and WHI5, only few orthologs exist which are confined to individual Saccharomycotina species. While Whi5 has been characterized as yeast analog of human Rb protein, in the particular case of Stb1 (Sin three binding protein 1) identification of functional analogs emerges as difficult because to date its exact functionality still remains obscured. By aiming to resolve Stb1´s enigmatic role this Perspectives article especially surveys works covering relations between Cyclin/CDKs, the heteromeric transcription factor complexes SBF (Swi4/Swi6) and MBF (Mbp1/Swi6), as well as additional coregulators (Whi5, Sin3, Rpd3, Nrm1) which are collectively associated with the orderly transcription at 'Start' of the Saccharomyces cerevisiae cell cycle. In this context, interaction capacities of the Sin3-scaffold protein are widely surveyed because its four PAH domains (Paired Amphiphatic Helix) represent a 'recruitment-code' for gene-specific targeting of repressive histone deacetylase activity (Rpd3) via different transcription factors. Here Stb1 plays a role in Sin3´s action on transcription at the G1/S-boundary. Through bioinformatic analyses a potential Sin3-interaction domain (SID) was detected in Stb1, and beyond that, connections within the G1/S-regulatory network are discussed in structural and evolutionary context thereby providing conceptual perspectives.
Collapse
Affiliation(s)
- Octavian O H Stephan
- Department of Biology, Friedrich-Alexander University of Erlangen-Nuremberg, Staudtstr. 5, 91058 Erlangen, Bavaria, Germany
| |
Collapse
|
7
|
He YZ, Aksoy E, Ding Y, Raikhel AS. Hormone-dependent activation and repression of microRNAs by the ecdysone receptor in the dengue vector mosquito Aedes aegypti. Proc Natl Acad Sci U S A 2021; 118:e2102417118. [PMID: 34155112 PMCID: PMC8256052 DOI: 10.1073/pnas.2102417118] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Female mosquitoes transmit numerous devastating human diseases because they require vertebrate blood meal for egg development. MicroRNAs (miRNAs) play critical roles across multiple reproductive processes in female Aedes aegypti mosquitoes. However, how miRNAs are controlled to coordinate their activity with the demands of mosquito reproduction remains largely unknown. We report that the ecdysone receptor (EcR)-mediated 20-hydroxyecdysone (20E) signaling regulates miRNA expression in female mosquitoes. EcR RNA-interference silencing linked to small RNA-sequencing analysis reveals that EcR not only activates but also represses miRNA expression in the female mosquito fat body, a functional analog of the vertebrate liver. EcR directly represses the expression of clustered miR-275 and miR-305 before blood feeding when the 20E titer is low, whereas it activates their expression in response to the increased 20E titer after a blood meal. Furthermore, we find that SMRTER, an insect analog of the vertebrate nuclear receptor corepressors SMRT and N-CoR, interacts with EcR in a 20E-sensitive manner and is required for EcR-mediated repression of miRNA expression in Ae. aegypti mosquitoes. In addition, we demonstrate that miR-275 and miR-305 directly target glutamate semialdehyde dehydrogenase and AAEL009899, respectively, to facilitate egg development. This study reveals a mechanism for how miRNAs are controlled by the 20E signaling pathway to coordinate their activity with the demands of mosquito reproduction.
Collapse
Affiliation(s)
- Ya-Zhou He
- Department of Entomology, University of California, Riverside, CA 92521
- Institute of Integrative Genome Biology, University of California, Riverside, CA 92521
| | - Emre Aksoy
- Department of Entomology, University of California, Riverside, CA 92521
- Graduate Program in Genetics, Genomics, and Bioinformatics, University of California, Riverside, CA 92521
| | - Yike Ding
- Department of Entomology, University of California, Riverside, CA 92521
- Institute of Integrative Genome Biology, University of California, Riverside, CA 92521
| | - Alexander S Raikhel
- Department of Entomology, University of California, Riverside, CA 92521;
- Institute of Integrative Genome Biology, University of California, Riverside, CA 92521
| |
Collapse
|
8
|
Das P, Bhadra MP. Histone deacetylase (Rpd3) regulates Drosophila early brain development via regulation of Tailless. Open Biol 2020; 10:200029. [PMID: 32873153 PMCID: PMC7536075 DOI: 10.1098/rsob.200029] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2020] [Accepted: 07/29/2020] [Indexed: 11/29/2022] Open
Abstract
Tailless is a committed transcriptional repressor and principal regulator of the brain and eye development in Drosophila. Rpd3, the histone deacetylase, is an established repressor that interacts with co-repressors like Sin3a, Prospero, Brakeless and Atrophin. This study aims at deciphering the role of Rpd3 in embryonic segmentation and larval brain development in Drosophila. It delineates the mechanism of Tailless regulation by Rpd3, along with its interacting partners. There was a significant reduction in Tailless in Rpd3 heteroallelic mutant embryos, substantiating that Rpd3 is indispensable for the normal Tailless expression. The expression of the primary readout, Tailless was correlative to the expression of the neural cell adhesion molecule homologue, Fascilin2 (Fas2). Rpd3 also aids in the proper development of the mushroom body. Both Tailless and Fas2 expression are reported to be antagonistic to the epidermal growth factor receptor (EGFR) expression. The decrease in Tailless and Fas2 expression highlights that EGFR is upregulated in the larval mutants, hindering brain development. This study outlines the axis comprising Rpd3, dEGFR, Tailless and Fas2, which interact to fine-tune the early segmentation and larval brain development. Therefore, Rpd3 along with Tailless has immense significance in early embryogenesis and development of the larval brain.
Collapse
Affiliation(s)
- Paromita Das
- Applied Biology Division, CSIR-Indian Institute of Chemical Technology, Uppal Road, Hyderabad 500 007, India
- Academy of Scientific and Innovative Research (AcSIR) Training and Development Complex, CSIR Campus, CSIR Road, Taramani, Chennai 600 113, India
| | - Manika Pal Bhadra
- Applied Biology Division, CSIR-Indian Institute of Chemical Technology, Uppal Road, Hyderabad 500 007, India
- Academy of Scientific and Innovative Research (AcSIR) Training and Development Complex, CSIR Campus, CSIR Road, Taramani, Chennai 600 113, India
| |
Collapse
|
9
|
Liu M, Saha N, Gajan A, Saadat N, Gupta SV, Pile LA. A complex interplay between SAM synthetase and the epigenetic regulator SIN3 controls metabolism and transcription. J Biol Chem 2019; 295:375-389. [PMID: 31776190 DOI: 10.1074/jbc.ra119.010032] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2019] [Revised: 11/25/2019] [Indexed: 12/30/2022] Open
Abstract
The SIN3 histone-modifying complex regulates the expression of multiple methionine catabolic genes, including SAM synthetase (Sam-S), as well as SAM levels. To further dissect the relationship between methionine catabolism and epigenetic regulation by SIN3, we sought to identify genes and metabolic pathways controlled by SIN3 and SAM synthetase (SAM-S) in Drosophila melanogaster Using several approaches, including RNAi-mediated gene silencing, RNA-Seq- and quantitative RT-PCR-based transcriptomics, and ultra-high-performance LC-MS/MS- and GC/MS-based metabolomics, we found that, as a global transcriptional regulator, SIN3 impacted a wide range of genes and pathways. In contrast, SAM-S affected only a narrow range of genes and pathways. The expression and levels of additional genes and metabolites, however, were altered in Sin3A+Sam-S dual knockdown cells. This analysis revealed that SIN3 and SAM-S regulate overlapping pathways, many of which involve one-carbon and central carbon metabolisms. In some cases, the factors acted independently; in some others, redundantly; and for a third set, in opposition. Together, these results, obtained from experiments with the chromatin regulator SIN3 and the metabolic enzyme SAM-S, uncover a complex relationship between metabolism and epigenetic regulation.
Collapse
Affiliation(s)
- Mengying Liu
- Department of Nutrition and Food Science, Wayne State University, Detroit, Michigan 48202; Department of Biological Sciences, Wayne State University, Detroit, Michigan 48202
| | - Nirmalya Saha
- Department of Biological Sciences, Wayne State University, Detroit, Michigan 48202; Department of Pathology, Michigan Medicine, University of Michigan, Ann Arbor, Michigan 48109
| | - Ambikai Gajan
- Department of Biological Sciences, Wayne State University, Detroit, Michigan 48202; Department of Oncology, School of Medicine, Wayne State University, Detroit, Michigan 48201; Karmanos Cancer Institute, Detroit, Michigan 48201
| | - Nadia Saadat
- Department of Nutrition and Food Science, Wayne State University, Detroit, Michigan 48202; College of Engineering and Science, University of Detroit Mercy, Detroit, Michigan 48221
| | - Smiti V Gupta
- Department of Nutrition and Food Science, Wayne State University, Detroit, Michigan 48202
| | - Lori A Pile
- Department of Biological Sciences, Wayne State University, Detroit, Michigan 48202.
| |
Collapse
|
10
|
Histone deacetylase 1 suppresses Krüppel homolog 1 gene expression and influences juvenile hormone action in Tribolium castaneum. Proc Natl Acad Sci U S A 2019; 116:17759-17764. [PMID: 31439816 PMCID: PMC6731676 DOI: 10.1073/pnas.1909554116] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Juvenile hormone (JH) regulates many processes in insects, and JH mimics are used to control them. However, not much is known about the epigenetic regulation of JH action. Histone deacetylases (HDACs) are known to modulate hormone action. We identified 12 HDACs and analyzed their function in Tribolium castaneum. RNA interference-mediated knockdown of HDAC genes showed that HDAC1 plays critical roles in the regulation of growth and development by suppressing the expression of many genes, including those involved in JH action. Expression of the HDAC1 gene is suppressed by JH, resulting in an increase in acetylation levels of histones, which promotes expression of JH response genes. SIN3:HDAC1 multiprotein complexes suppress the expression of JH response genes in the absence of JH. Posttranslational modifications, including acetylation and deacetylation of histones and other proteins, modulate hormone action. In Tribolium castaneum TcA cells, Trichostatin A, a histone deacetylase (HDAC) inhibitor, mimics juvenile hormone (JH) in inducing JH response genes (e.g., Kr-h1), suggesting that HDACs may be involved in JH action. To test this hypothesis, we identified genes coding for HDACs in T. castaneum and studied their function. Knockdown of 12 HDAC genes showed variable phenotypes; the most severe phenotype was detected in insects injected with double-stranded RNA targeting HDAC1 (dsHDAC1). The dsHDAC1-injected insects showed arrested growth and development and eventually died. Application of JH analogs hydroprene to T. castaneum larvae and JH III to TcA cells suppressed HDAC1 expression. Sequencing of RNA isolated from control and dsHDAC1-injected larvae identified 1,720 differentially expressed genes, of which 1,664 were up-regulated in dsHDAC1-treated insects. The acetylation levels of core histones were increased in TcA cells exposed to dsHDAC1 or JH III. ChIP assays performed using histone H2BK5ac antibodies showed an increase in acetylation in the Kr-h1 promoter region of cells exposed to JH III or dsHDAC1. Overexpression or knockdown of HDAC1, SIN3, or both resulted in a decrease or increase in Kr-h1 mRNA levels and its promoter activity, respectively. Overexpression of the JH receptor Methoprene tolerant (Met) was unable to induce Kr-h1 in the presence of HDAC1 or SIN3. These data suggest that epigenetic modifications influence JH action by modulating acetylation levels of histones and by affecting the recruitment of proteins involved in the regulation of JH response genes.
Collapse
|
11
|
Systematic Analysis of SIN3 Histone Modifying Complex Components During Development. Sci Rep 2018; 8:17048. [PMID: 30451916 PMCID: PMC6242963 DOI: 10.1038/s41598-018-35093-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2018] [Accepted: 10/17/2018] [Indexed: 12/21/2022] Open
Abstract
Establishment and maintenance of histone acetylation levels are critical for metazoan development and viability. Disruption of the balance between acetylation and deacetylation by treatment with chemical histone deacetylase (HDAC) inhibitors results in loss of cell proliferation, differentiation and/or apoptosis. Histone deacetylation by the SIN3 complex is essential in Drosophila and mice, as loss of the scaffolding factor SIN3 or the associated HDAC results in lethality. The objective of this study is to elucidate contributions of SIN3 complex components to these essential processes. We used the Drosophila model organism to carry out a systematic functional analysis of the SIN3 complex. We find that SIN3 associated proteins are essential for viability and cell proliferation during development. Additionally, tissue specific reduction of SIN3 complex components results in abnormal wing development. Interestingly, while knockdown of each factor resulted in similar phenotypes, their individual effects on recruitment of SIN3 to polytene chromosomes are distinct. Reduction of some factors leads to large changes in the morphology of the chromosome and/or greatly reduced SIN3 binding. These findings suggest that while individual SIN3 complex components work through distinct molecular mechanisms, they each make a substantial contribution to the overall function of this highly conserved histone deacetylase complex.
Collapse
|
12
|
Zheng X, Hou H, Zhang H, Yue M, Hu Y, Li L. Histone acetylation is involved in GA-mediated 45S rDNA decondensation in maize aleurone layers. PLANT CELL REPORTS 2018; 37:115-123. [PMID: 28939922 DOI: 10.1007/s00299-017-2207-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/09/2017] [Accepted: 09/12/2017] [Indexed: 05/04/2023]
Abstract
The aleurone layer is crucial to seed germination. Using dissected aleurone layers, we found that GA increased histone acetylation accompanied by rDNA decondensation in aleurone layers during maize seed germination. Aleurone layers play an important role in cereal seed germination. In this study, we reported that rDNA chromatin was decondensed, accompanied with increased rDNA expression and genomic global hyperacetylation in gibberellin (GA)-treated maize-dissected aleurone layers. The activity analysis of histone acetyltransferase (HAT) and deacetylase (HDAC) showed that GA increased the level of histone acetylation by promoting the ratio of HAT/HDAC activity in aleurone layers. HDAC inhibitors TSA and CUDC-101 elevated the histone acetylation in aleurone layers accompanied by 45S rDNA decondensation. The further chromatin immunoprecipitation experiments showed that GA treatment promoted the level of histone acetylation in the promoter region of the rRNA and HAT/HDAC genes in aleurone layers. Taken together, these data indicated that histone acetylation mediates GA-regulated 45S rDNA chromatin decondensation in aleurone layers during maize seed germination.
Collapse
Affiliation(s)
- Xueke Zheng
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Haoli Hou
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Hao Zhang
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Mengxia Yue
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Yan Hu
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Lijia Li
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, 430072, China.
| |
Collapse
|
13
|
Salas-Armenteros I, Pérez-Calero C, Bayona-Feliu A, Tumini E, Luna R, Aguilera A. Human THO-Sin3A interaction reveals new mechanisms to prevent R-loops that cause genome instability. EMBO J 2017; 36:3532-3547. [PMID: 29074626 DOI: 10.15252/embj.201797208] [Citation(s) in RCA: 102] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2017] [Revised: 09/22/2017] [Accepted: 09/28/2017] [Indexed: 11/09/2022] Open
Abstract
R-loops, formed by co-transcriptional DNA-RNA hybrids and a displaced DNA single strand (ssDNA), fulfill certain positive regulatory roles but are also a source of genomic instability. One key cellular mechanism to prevent R-loop accumulation centers on the conserved THO/TREX complex, an RNA-binding factor involved in transcription elongation and RNA export that contributes to messenger ribonucleoprotein (mRNP) assembly, but whose precise function is still unclear. To understand how THO restrains harmful R-loops, we searched for new THO-interacting factors. We found that human THO interacts with the Sin3A histone deacetylase complex to suppress co-transcriptional R-loops, DNA damage, and replication impairment. Functional analyses show that histone hypo-acetylation prevents accumulation of harmful R-loops and RNA-mediated genomic instability. Diminished histone deacetylase activity in THO- and Sin3A-depleted cell lines correlates with increased R-loop formation, genomic instability, and replication fork stalling. Our study thus uncovers physical and functional crosstalk between RNA-binding factors and chromatin modifiers with a major role in preventing R-loop formation and RNA-mediated genome instability.
Collapse
Affiliation(s)
- Irene Salas-Armenteros
- Centro Andaluz de Biología Molecular y Medicina Regenerativa-CABIMER, Consejo Superior de Investigaciones Científicas-Universidad Pablo de Olavide-Universidad de Sevilla, Seville, Spain
| | - Carmen Pérez-Calero
- Centro Andaluz de Biología Molecular y Medicina Regenerativa-CABIMER, Consejo Superior de Investigaciones Científicas-Universidad Pablo de Olavide-Universidad de Sevilla, Seville, Spain
| | - Aleix Bayona-Feliu
- Centro Andaluz de Biología Molecular y Medicina Regenerativa-CABIMER, Consejo Superior de Investigaciones Científicas-Universidad Pablo de Olavide-Universidad de Sevilla, Seville, Spain
| | - Emanuela Tumini
- Centro Andaluz de Biología Molecular y Medicina Regenerativa-CABIMER, Consejo Superior de Investigaciones Científicas-Universidad Pablo de Olavide-Universidad de Sevilla, Seville, Spain
| | - Rosa Luna
- Centro Andaluz de Biología Molecular y Medicina Regenerativa-CABIMER, Consejo Superior de Investigaciones Científicas-Universidad Pablo de Olavide-Universidad de Sevilla, Seville, Spain
| | - Andrés Aguilera
- Centro Andaluz de Biología Molecular y Medicina Regenerativa-CABIMER, Consejo Superior de Investigaciones Científicas-Universidad Pablo de Olavide-Universidad de Sevilla, Seville, Spain
| |
Collapse
|
14
|
Liu M, Pile LA. The Transcriptional Corepressor SIN3 Directly Regulates Genes Involved in Methionine Catabolism and Affects Histone Methylation, Linking Epigenetics and Metabolism. J Biol Chem 2016; 292:1970-1976. [PMID: 28028175 DOI: 10.1074/jbc.m116.749754] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2016] [Revised: 12/23/2016] [Indexed: 11/06/2022] Open
Abstract
Chromatin modification and cellular metabolism are tightly connected. Chromatin modifiers regulate the expression of genes involved in metabolism and, in turn, the levels of metabolites. The generated metabolites are utilized by chromatin modifiers to affect epigenetic modification. The mechanism for this cross-talk, however, remains incompletely understood. The corepressor SIN3 controls histone acetylation through association with the histone deacetylase RPD3. The SIN3 complex is known to regulate genes involved in a number of metabolic processes. Here, we find that Drosophila SIN3 binds to the promoter region of genes involved in methionine catabolism and that this binding affects histone modification, which in turn influences gene expression. Specifically, we observe that reduced expression of SIN3 leads to an increase in S-adenosylmethionine (SAM), which is the major cellular donor of methyl groups for protein modification. Additionally, Sin3A knockdown results in an increase in global histone H3K4me3 levels. Furthermore, decreased H3K4me3 caused by knockdown of either SAM synthetase (Sam-S) or the histone methyltransferase Set1 is restored to near normal levels when SIN3 is also reduced. Taken together, these results indicate that knockdown of Sin3A directly alters the expression of methionine metabolic genes to increase SAM, which in turn leads to an increase in global H3K4me3. Our study reveals that SIN3 is an important epigenetic regulator directly connecting methionine metabolism and histone modification.
Collapse
Affiliation(s)
- Mengying Liu
- From the Department of Biological Sciences, Wayne State University, Detroit, Michigan 48202
| | - Lori A Pile
- From the Department of Biological Sciences, Wayne State University, Detroit, Michigan 48202.
| |
Collapse
|
15
|
Woods JK, Rogina B. The effects of Rpd3 on fly metabolism, health, and longevity. Exp Gerontol 2016; 86:124-128. [PMID: 26927903 PMCID: PMC5002259 DOI: 10.1016/j.exger.2016.02.015] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2015] [Revised: 02/23/2016] [Accepted: 02/25/2016] [Indexed: 11/29/2022]
Abstract
The epigenetic regulation of DNA structure and function is essential for changes in gene expression involved in development, growth, and maintenance of cellular function. Epigenetic changes include histone modifications such as methylation, acetylation, ubiquitination, and phosphorylation. Histone deacetylase (HDAC) proteins have a major role in epigenetic regulation of chromatin structure. HDACs are enzymes that catalyze the removal of acetyl groups from lysine residues within histones, as well as a range of other proteins including transcriptional factors. HDACs are highly conserved proteins divided into two families and based on sequence similarity in four classes. Here we will discuss the roles of Rpd3 in physiology and longevity with emphasis on its role in flies. Rpd3, the Drosophila HDAC1 homolog, is a class I lysine deacetylase and a member of a large family of HDAC proteins. Rpd3 has multiple functions including control of proliferation, development, metabolism, and aging. Pharmacological and dietary HDAC inhibitors have been used as therapeutics in psychiatry, cancer, and neurology.
Collapse
Affiliation(s)
- Jared K Woods
- Department of Genetics & Genome Sciences, School of Medicine, University of Connecticut Health, Farmington, CT, USA
| | - Blanka Rogina
- Department of Genetics & Genome Sciences, School of Medicine, University of Connecticut Health, Farmington, CT, USA; Institute for Systems Genomics, School of Medicine, University of Connecticut Health, Farmington, CT, USA.
| |
Collapse
|
16
|
Chaubal A, Todi SV, Pile LA. Inter-isoform-dependent Regulation of the Drosophila Master Transcriptional Regulator SIN3. J Biol Chem 2016; 291:11566-71. [PMID: 27129248 DOI: 10.1074/jbc.c116.724799] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2016] [Indexed: 11/06/2022] Open
Abstract
SIN3 is a transcriptional corepressor that acts as a scaffold for a histone deacetylase (HDAC) complex. The SIN3 complex regulates various biological processes, including organ development, cell proliferation, and energy metabolism. Little is known, however, about the regulation of SIN3 itself. There are two major isoforms of Drosophila SIN3, 187 and 220, which are differentially expressed. Intrigued by the developmentally timed exchange of SIN3 isoforms, we examined whether SIN3 187 controls the fate of the 220 counterpart. Here, we show that in developing tissue, there is interplay between SIN3 isoforms: when SIN3 187 protein levels increase, SIN3 220 protein decreases concomitantly. SIN3 187 has a dual effect on SIN3 220. Expression of 187 leads to reduced 220 transcript, while also increasing the turnover of SIN3 220 protein by the proteasome. These data support the presence of a novel, inter-isoform-dependent mechanism that regulates the amount of SIN3 protein, and potentially the level of specific SIN3 complexes, during distinct developmental stages.
Collapse
Affiliation(s)
- Ashlesha Chaubal
- From the Department of Biological Sciences, Wayne State University, Detroit, Michigan 48202 and
| | - Sokol V Todi
- the Department of Pharmacology, Wayne State University, Detroit, Michigan 48201
| | - Lori A Pile
- From the Department of Biological Sciences, Wayne State University, Detroit, Michigan 48202 and
| |
Collapse
|
17
|
Wu T, Xiang J, Shan W, Li M, Zhou W, Han X, Chen F. Epigallocatechin-3-Gallate Inhibits Ethanol-Induced Apoptosis Through Neurod1 Regulating CHOP Expression in Pancreatic β-Cells. Anat Rec (Hoboken) 2016; 299:573-82. [DOI: 10.1002/ar.23332] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2015] [Revised: 12/29/2015] [Accepted: 12/31/2015] [Indexed: 01/12/2023]
Affiliation(s)
- Tijun Wu
- Key Laboratory of Human Functional Genomics of Jiangsu Province; Nanjing Medical University; 140 Hanzhong Road Nanjing 210029 China
| | - Jie Xiang
- Department of Endocrinology; Wuxi People's Hospital Affiliated to Nanjing Medical University; Wuxi 214023 China
| | - Wei Shan
- Key Laboratory of Human Functional Genomics of Jiangsu Province; Nanjing Medical University; 140 Hanzhong Road Nanjing 210029 China
| | - Mengxiao Li
- Key Laboratory of Human Functional Genomics of Jiangsu Province; Nanjing Medical University; 140 Hanzhong Road Nanjing 210029 China
| | - Wenbo Zhou
- Key Laboratory of Human Functional Genomics of Jiangsu Province; Nanjing Medical University; 140 Hanzhong Road Nanjing 210029 China
| | - Xiao Han
- Key Laboratory of Human Functional Genomics of Jiangsu Province; Nanjing Medical University; 140 Hanzhong Road Nanjing 210029 China
| | - Fang Chen
- Key Laboratory of Human Functional Genomics of Jiangsu Province; Nanjing Medical University; 140 Hanzhong Road Nanjing 210029 China
| |
Collapse
|
18
|
Ristic G, Tsou WL, Guzi E, Kanack AJ, Scaglione KM, Todi SV. USP5 Is Dispensable for Monoubiquitin Maintenance in Drosophila. J Biol Chem 2016; 291:9161-72. [PMID: 26917723 DOI: 10.1074/jbc.m115.703504] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2015] [Indexed: 11/06/2022] Open
Abstract
Ubiquitination is a post-translational modification that regulates most cellular pathways and processes, including degradation of proteins by the proteasome. Substrate ubiquitination is controlled at various stages, including through its reversal by deubiquitinases (DUBs). A critical outcome of this process is the recycling of monoubiquitin. One DUB whose function has been proposed to include monoubiquitin recycling is USP5. Here, we investigated whether Drosophila USP5 is important for maintaining monoubiquitin in vivo We found that the fruit fly orthologue of USP5 has catalytic preferences similar to its human counterpart and that this DUB is necessary during fly development. Our biochemical and genetic experiments indicate that reduction of USP5 does not lead to monoubiquitin depletion in developing flies. Also, introduction of exogenous ubiquitin does not suppress developmental lethality caused by loss of endogenous USP5. Our work indicates that a primary physiological role of USP5 is not to recycle monoubiquitin for reutilization, but that it may involve disassembly of conjugated ubiquitin to maintain proteasome function.
Collapse
Affiliation(s)
| | | | - Ermal Guzi
- From the Departments of Pharmacology and
| | - Adam J Kanack
- the Department of Biochemistry and the Neuroscience Research Center, Medical College of Wisconsin, Milwaukee Wisconsin 53226
| | - Kenneth Matthew Scaglione
- the Department of Biochemistry and the Neuroscience Research Center, Medical College of Wisconsin, Milwaukee Wisconsin 53226
| | - Sokol V Todi
- From the Departments of Pharmacology and Neurology, Wayne State University School of Medicine, Detroit, Michigan 48201 and
| |
Collapse
|
19
|
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: 2.1] [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.
Collapse
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.
| |
Collapse
|
20
|
Gajan A, Barnes VL, Liu M, Saha N, Pile LA. The histone demethylase dKDM5/LID interacts with the SIN3 histone deacetylase complex and shares functional similarities with SIN3. Epigenetics Chromatin 2016; 9:4. [PMID: 26848313 PMCID: PMC4740996 DOI: 10.1186/s13072-016-0053-9] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2015] [Accepted: 01/14/2016] [Indexed: 01/01/2023] Open
Abstract
Background Regulation of gene expression by histone-modifying enzymes is essential to control cell fate decisions and developmental processes. Two histone-modifying enzymes, RPD3, a deacetylase, and dKDM5/LID, a demethylase, are present in a single complex, coordinated through the SIN3 scaffold protein. While the SIN3 complex has been demonstrated to have functional histone deacetylase activity, the role of the demethylase dKDM5/LID as part of the complex has not been investigated. Results Here, we analyzed the developmental and transcriptional activities of dKDM5/LID in relation to SIN3. Knockdown of either Sin3A or lid resulted in decreased cell proliferation in S2 cells and wing imaginal discs. Conditional knockdown of either Sin3A or lid resulted in flies that displayed wing developmental defects. Interestingly, overexpression of dKDM5/LID rescued the wing developmental defect due to reduced levels of SIN3 in female flies, indicating a major role for dKDM5/LID in cooperation with SIN3 during development. Together, these observed phenotypes strongly suggest that dKDM5/LID as part of the SIN3 complex can impact previously uncharacterized transcriptional networks. Transcriptome analysis revealed that SIN3 and dKDM5/LID regulate many common genes. While several genes implicated in cell cycle and wing developmental pathways were affected upon altering the level of these chromatin factors, a significant affect was also observed on genes required to mount an effective stress response. Further, under conditions of induced oxidative stress, reduction of SIN3 and/or dKDM5/LID altered the expression of a greater number of genes involved in cell cycle-related processes relative to normal conditions. This highlights an important role for SIN3 and dKDM5/LID proteins to maintain proper progression through the cell cycle in environments of cellular stress. Further, we find that target genes are bound by both SIN3 and dKDM5/LID, however, histone acetylation, not methylation, plays a predominant role in gene regulation by the SIN3 complex. Conclusions We have provided genetic evidence to demonstrate functional cooperation between the histone demethylase dKDM5/LID and SIN3. Biochemical and transcriptome data further support functional links between these proteins. Together, the data provide a solid framework for analyzing the gene regulatory pathways through which SIN3 and dKDM5/LID control diverse biological processes in the organism. Electronic supplementary material The online version of this article (doi:10.1186/s13072-016-0053-9) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Ambikai Gajan
- Department of Biological Sciences, Wayne State University, Detroit, MI USA
| | - Valerie L Barnes
- Department of Biological Sciences, Wayne State University, Detroit, MI USA
| | - Mengying Liu
- Department of Biological Sciences, Wayne State University, Detroit, MI USA
| | - Nirmalya Saha
- Department of Biological Sciences, Wayne State University, Detroit, MI USA
| | - Lori A Pile
- Department of Biological Sciences, Wayne State University, Detroit, MI USA
| |
Collapse
|
21
|
Barnes VL, Bhat A, Unnikrishnan A, Heydari AR, Arking R, Pile LA. SIN3 is critical for stress resistance and modulates adult lifespan. Aging (Albany NY) 2015; 6:645-60. [PMID: 25133314 PMCID: PMC4169859 DOI: 10.18632/aging.100684] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
Coordinate control of gene activity is critical for fitness and longevity of an organism. The SIN3 histone deacetylase (HDAC) complex functions as a transcriptional repressor of many genes. SIN3-regulated genes include those that encode proteins affecting multiple aspects of mitochondrial function, such as energy production and stress responsiveness, important for health maintenance. Here we used Drosophila melanogaster as a model organism to examine the role of SIN3 in the regulation of fitness and longevity. Adult flies with RNA interference (RNAi) induced knockdown expression of Sin3A have reduced climbing ability; an activity that likely requires fully functional mitochondria. Additionally, compared to wild type, adult Sin3A knockdown flies were more sensitive to oxidative stress. Interestingly, media supplementation with the antioxidant glutathione largely restored fly tolerance to oxidative stress. Although Sin3A knockdown flies exhibited decreased longevity compared to wild type, no significant changes in expression of many well-categorized aging genes were observed. We found, however, that Sin3A knockdown corresponded to a significant reduction in expression of genes encoding proteins involved in the de novo synthesis of glutathione. Taken together, the data support a model whereby SIN3 regulates a gene expression program required for proper mitochondrial function and effective stress response during adulthood.
Collapse
Affiliation(s)
- Valerie L Barnes
- Department of Biological Sciences, Wayne State University, Detroit, Michigan, 48202, USA
| | - Abhineeth Bhat
- Department of Biological Sciences, Wayne State University, Detroit, Michigan, 48202, USA
| | - Archana Unnikrishnan
- Department of Nutrition and Food Science Wayne State University, Detroit, Michigan, 48202,USA
| | - Ahmad R Heydari
- Department of Nutrition and Food Science Wayne State University, Detroit, Michigan, 48202,USA
| | - Robert Arking
- Department of Biological Sciences, Wayne State University, Detroit, Michigan, 48202, USA
| | - Lori A Pile
- Department of Biological Sciences, Wayne State University, Detroit, Michigan, 48202, USA
| |
Collapse
|
22
|
Kadamb R, Mittal S, Bansal N, Batra H, Saluja D. Sin3: insight into its transcription regulatory functions. Eur J Cell Biol 2013; 92:237-46. [PMID: 24189169 DOI: 10.1016/j.ejcb.2013.09.001] [Citation(s) in RCA: 111] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2013] [Revised: 08/27/2013] [Accepted: 09/11/2013] [Indexed: 10/26/2022] Open
Abstract
Sin3, a large acidic protein, shares structural similarity with the helix-loop-helix dimerization domain of proteins of the Myc family of transcription factors. Sin3/HDAC corepressor complex functions in transcriptional regulation of several genes and is therefore implicated in the regulation of key biological processes. Knockdown studies have confirmed the role of Sin3 in cellular proliferation, differentiation, apoptosis and cell cycle regulation, emphasizing Sin3 as an essential regulator of critical cellular events in normal and pathological processes. The present review covers the diverse functions of this master transcriptional regulator as well as illustrates the redundant and distinct functions of its two mammalian isoforms.
Collapse
Affiliation(s)
- Rama Kadamb
- Dr. B.R. Ambedkar Center for Biomedical Research, University of Delhi, Delhi 110007, India.
| | | | | | | | | |
Collapse
|
23
|
Rincon-Arano H, Parkhurst SM, Groudine M. UpSET-ting the balance: modulating open chromatin features in metazoan genomes. Fly (Austin) 2013; 7:153-60. [PMID: 23649046 DOI: 10.4161/fly.24732] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Appropriate gene expression relies on the sophisticated interplay between genetic and epigenetic factors. Histone acetylation and an open chromatin configuration are key features of transcribed regions and are mainly present around active promoters. Our recent identification of the SET-domain containing protein UpSET established a new functional link between the modulation of open chromatin features and active recruitment of well-known co-repressors in metazoans. Structurally, the SET domain of UpSET resembles H3K4 and H3K36 methyltransferases; however, it is does not confer histone methyltransferase activity. Rather than methylating histones to regulate gene expression like other SET domain-containing proteins, UpSET fine-tunes transcription by modulating the chromatin structure around active promoters resulting in suppression of expression of off-target genes or nearby repetitive elements. Chromatin modulation by UpSET occurs in part through its interaction with histone deacetylases. Here, we discuss the different scenarios in which UpSET could play key roles in modulating gene expression.
Collapse
Affiliation(s)
- Hector Rincon-Arano
- Basic Sciences Division; Fred Hutchinson Cancer Research Center; Seattle, WA USA
| | | | | |
Collapse
|
24
|
Rincon-Arano H, Halow J, Delrow JJ, Parkhurst SM, Groudine M. UpSET recruits HDAC complexes and restricts chromatin accessibility and acetylation at promoter regions. Cell 2012. [PMID: 23177352 DOI: 10.1016/j.cell.2012.11.009] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
Developmental gene expression results from the orchestrated interplay between genetic and epigenetic mechanisms. Here, we describe upSET, a transcriptional regulator encoding a SET domain-containing protein recruited to active and inducible genes in Drosophila. However, unlike other Drosophila SET proteins associated with gene transcription, UpSET is part of an Rpd3/Sin3-containing complex that restricts chromatin accessibility and histone acetylation to promoter regions. In the absence of UpSET, active chromatin marks and chromatin accessibility increase and spread to genic and flanking regions due to destabilization of the histone deacetylase complex. Consistent with this, transcriptional noise increases, as manifest by activation of repetitive elements and off-target genes. Interestingly, upSET mutant flies are female sterile due to upregulation of key components of Notch signaling during oogenesis. Thus UpSET defines a class of metazoan transcriptional regulators required to fine tune transcription by preventing the spread of active chromatin.
Collapse
Affiliation(s)
- Hector Rincon-Arano
- Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | | | | | | | | |
Collapse
|
25
|
Swaminathan A, Barnes VL, Fox S, Gammouh S, Pile LA. Identification of genetic suppressors of the Sin3A knockdown wing phenotype. PLoS One 2012; 7:e49563. [PMID: 23166712 PMCID: PMC3499482 DOI: 10.1371/journal.pone.0049563] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2012] [Accepted: 10/11/2012] [Indexed: 11/19/2022] Open
Abstract
The role of the Sin3A transcriptional corepressor in regulating the cell cycle is established in various metazoans. Little is known, however, about the signaling pathways that trigger or are triggered by Sin3A function. To discover genes that work in similar or opposing pathways to Sin3A during development, we have performed an unbiased screen of deficiencies of the Drosophila third chromosome. Additionally, we have performed a targeted loss of function screen to identify cell cycle genes that genetically interact with Sin3A. We have identified genes that encode proteins involved in regulation of gene expression, signaling pathways and cell cycle that can suppress the curved wing phenotype caused by the knockdown of Sin3A. These data indicate that Sin3A function is quite diverse and impacts a wide variety of cellular processes.
Collapse
Affiliation(s)
- Aishwarya Swaminathan
- Department of Microbiology, University of Massachusetts, Amherst, Massachusetts, United States of America
| | - Valerie L. Barnes
- Department of Biological Sciences, Wayne State University, Detroit, Michigan, United States of America
| | - Stephanie Fox
- Department of Biological Sciences, Wayne State University, Detroit, Michigan, United States of America
| | - Sarah Gammouh
- Department of Biological Sciences, Wayne State University, Detroit, Michigan, United States of America
| | - Lori A. Pile
- Department of Biological Sciences, Wayne State University, Detroit, Michigan, United States of America
- * E-mail:
| |
Collapse
|
26
|
Zhimulev IF, Belyaeva ES, Vatolina TY, Demakov SA. Banding patterns in Drosophila melanogaster polytene chromosomes correlate with DNA-binding protein occupancy. Bioessays 2012; 34:498-508. [PMID: 22419120 DOI: 10.1002/bies.201100142] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The most enigmatic feature of polytene chromosomes is their banding pattern, the genetic organization of which has been a very attractive puzzle for many years. Recent genome-wide protein mapping efforts have produced a wealth of data for the chromosome proteins of Drosophila cells. Based on their specific protein composition, the chromosomes comprise two types of bands, as well as interbands. These differ in terms of time of replication and specific types of proteins. The interbands are characterized by their association with "active" chromatin proteins, nucleosome remodeling, and origin recognition complexes, and so they have three functions: acting as binding sites for RNA pol II, initiation of replication and nucleosome remodeling of short fragments of DNA. The borders and organization of the same band and interband regions are largely identical, irrespective of the cell type studied. This demonstrates that the banding pattern is a universal principle of the organization of interphase polytene and non-polytene chromosomes.
Collapse
Affiliation(s)
- Igor F Zhimulev
- Institute of Molecular and Cellular Biology, Siberian Division of Russian Academy of Sciences, Novosibirsk, Russia.
| | | | | | | |
Collapse
|
27
|
Heck BW, Zhang B, Tong X, Pan Z, Deng WM, Tsai CC. The transcriptional corepressor SMRTER influences both Notch and ecdysone signaling during Drosophila development. Biol Open 2011; 1:182-96. [PMID: 23213409 PMCID: PMC3507286 DOI: 10.1242/bio.2012047] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
SMRTER (SMRT-related and ecdysone receptor interacting factor) is the Drosophila homologue of the vertebrate proteins SMRT and N-CoR, and forms with them a well-conserved family of transcriptional corepressors. Molecular characterization of SMRT-family proteins in cultured cells has implicated them in a wide range of transcriptional regulatory pathways. However, little is currently known about how this conserved class of transcriptional corepressors regulates the development of particular tissues via specific pathways. In this study, through our characterization of multiple Smrter (Smr) mutant lines, mosaic analysis of a loss-of-function Smr allele, and studies of two independent Smr RNAi fly lines, we report that SMRTER is required for the development of both ovarian follicle cells and the wing. In these two tissues, SMRTER inhibits not only the ecdysone pathway, but also the Notch pathway. We differentiate SMRTER's influence on these two signaling pathways by showing that SMRTER inhibits the Notch pathway, but not the ecdysone pathway, in a spatiotemporally restricted manner. We further confirm the likely involvement of SMRTER in the Notch pathway by demonstrating a direct interaction between SMRTER and Suppressor of Hairless [Su(H)], a DNA-binding transcription factor pivotal in the Notch pathway, and the colocalization of both proteins at many chromosomal regions in salivary glands. Based on our results, we propose that SMRTER regulates the Notch pathway through its association with Su(H), and that overcoming a SMRTER-mediated transcriptional repression barrier may represent a key mechanism used by the Notch pathway to control the precise timing of events and the formation of sharp boundaries between cells in multiple tissues during development.
Collapse
Affiliation(s)
- Bryan W Heck
- UMDNJ-Robert Wood Johnson Medical School, Department of Physiology and Biophysics , 683 Hoes Lane, Piscataway, NJ 08854 , USA
| | | | | | | | | | | |
Collapse
|
28
|
Yamasaki Y, Lim YM, Niwa N, Hayashi S, Tsuda L. Robust specification of sensory neurons by dual functions of charlatan, a Drosophila NRSF/REST-like repressor of extramacrochaetae and hairy. Genes Cells 2011; 16:896-909. [PMID: 21762412 DOI: 10.1111/j.1365-2443.2011.01537.x] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
Sensory bristle formation in Drosophila is a well-characterized system for studying sensory organ development at the molecular level. The master proneural genes of the achaete-scute (ac-sc) complex, which encode basic-helix-loop-helix (bHLH) transcription factors, are necessary and sufficient for sensory bristle formation. charlatan (chn) was originally identified as a transcriptional activator of ac-sc gene expression through interaction with its enhancer, an activity that promotes sensory bristle development. In contrast, Chn was also identified as a functional homologue of mammalian neuron-restrictive silencing factor or RE1 silencing transcription factor (NRSF/REST), an important transcriptional repressor during vertebrate neurogenesis and stem cell development that acts through epigenetic gene silencing. Here, we report that Chn acts as a repressor of extramacrochaetae (emc) and hairy, molecules that inhibit ac-sc expression. This double-negative mechanism, together with direct activation via the achaete enhancer, increases expression of achaete and ensures robust development of sensory neurons. A mutation in the C-terminal repressor motif of Chn, which causes Chn to lose its repression activity, converted Chn to an activator of emc and hairy, suggesting that Chn is a dual functional regulator of transcription. Because chn-like sequences are found among arthropods, regulation of neuronal development by Chn-like molecules may be widely conserved.
Collapse
Affiliation(s)
- Yasutoyo Yamasaki
- Animal Model of Aging, National Center for Geriatrics and Gerontology, Obu, Aichi 474-8511, Japan
| | | | | | | | | |
Collapse
|
29
|
Burgio G, Cipressa F, Ingrassia AMR, Cenci G, Corona DFV. The histone deacetylase Rpd3 regulates the heterochromatin structure of Drosophila telomeres. J Cell Sci 2011; 124:2041-8. [DOI: 10.1242/jcs.078261] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Telomeres are specialized structures at the end of eukaryotic chromosomes that are required to preserve genome integrity, chromosome stability and nuclear architecture. Telomere maintenance and function are established epigenetically in several eukaryotes. However, the exact chromatin enzymatic modifications regulating telomere homeostasis are poorly understood. In Drosophila melanogaster, telomere length and stability are maintained through the retrotransposition of specialized telomeric sequences and by the specific loading of protecting capping proteins, respectively. Here, we show that the loss of the essential and evolutionarily conserved histone deacetylase Rpd3, the homolog of mammalian HDAC1, causes aberrant telomeric fusions on polytene chromosome ends. Remarkably, these telomere fusion defects are associated with a marked decrease of histone H4 acetylation, as well as an accumulation of heterochromatic epigenetic marks at telomeres, including histone H3K9 trimethylation and the heterochromatic protein HP2. Our work suggests that Drosophila telomere structure is epigenetically regulated by the histone deacetylase Rpd3.
Collapse
Affiliation(s)
- Giosalba Burgio
- Istituto Telethon Dulbecco, c/o STEMBIO, Viale delle Scienze, Edificio 16, 90128 Palermo, Italy
- Università degli Studi di Palermo–Dipartimento di Scienze e Tecnologie Molecolari e Biomolecolari – Sezione di Biologia Cellulare, Viale delle Scienze, Edificio 16, 90128 Palermo, Italy
| | - Francesca Cipressa
- Dipartimento di Biologia di Base ed Applicata, Università dell'Aquila, 67100 Coppito, L'Aquila, Italy
| | - Antonia Maria Rita Ingrassia
- Istituto Telethon Dulbecco, c/o STEMBIO, Viale delle Scienze, Edificio 16, 90128 Palermo, Italy
- Università degli Studi di Palermo–Dipartimento di Scienze e Tecnologie Molecolari e Biomolecolari – Sezione di Biologia Cellulare, Viale delle Scienze, Edificio 16, 90128 Palermo, Italy
| | - Giovanni Cenci
- Dipartimento di Biologia di Base ed Applicata, Università dell'Aquila, 67100 Coppito, L'Aquila, Italy
| | - Davide F. V. Corona
- Istituto Telethon Dulbecco, c/o STEMBIO, Viale delle Scienze, Edificio 16, 90128 Palermo, Italy
- Università degli Studi di Palermo–Dipartimento di Scienze e Tecnologie Molecolari e Biomolecolari – Sezione di Biologia Cellulare, Viale delle Scienze, Edificio 16, 90128 Palermo, Italy
| |
Collapse
|
30
|
Barnes VL, Strunk BS, Lee I, Hüttemann M, Pile LA. Loss of the SIN3 transcriptional corepressor results in aberrant mitochondrial function. BMC BIOCHEMISTRY 2010; 11:26. [PMID: 20618965 PMCID: PMC2909972 DOI: 10.1186/1471-2091-11-26] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/05/2010] [Accepted: 07/09/2010] [Indexed: 11/17/2022]
Abstract
BACKGROUND SIN3 is a transcriptional repressor protein known to regulate many genes, including a number of those that encode mitochondrial components. RESULTS By monitoring RNA levels, we find that loss of SIN3 in Drosophila cultured cells results in up-regulation of not only nuclear encoded mitochondrial genes, but also those encoded by the mitochondrial genome. The up-regulation of gene expression is accompanied by a perturbation in ATP levels in SIN3-deficient cells, suggesting that the changes in mitochondrial gene expression result in altered mitochondrial activity. In support of the hypothesis that SIN3 is necessary for normal mitochondrial function, yeast sin3 null mutants exhibit very poor growth on non-fermentable carbon sources and show lower levels of ATP and reduced respiration rates. CONCLUSIONS The findings that both yeast and Drosophila SIN3 affect mitochondrial activity suggest an evolutionarily conserved role for SIN3 in the control of cellular energy production.
Collapse
Affiliation(s)
- Valerie L Barnes
- Department of Biological Sciences, Wayne State University, 5047 Gullen Mall, Detroit, Michigan 48202, USA
| | - Bethany S Strunk
- Department of Biological Sciences, Wayne State University, 5047 Gullen Mall, Detroit, Michigan 48202, USA
- Chemical Biology, University of Michigan, 930 N. University Ave. Rm. 4250, Ann Arbor, Michigan 48109, USA
| | - Icksoo Lee
- Center for Molecular Medicine and Genetics, Wayne State University School of Medicine, 540 E. Canfield, Detroit, Michigan 48201, USA
| | - Maik Hüttemann
- Center for Molecular Medicine and Genetics, Wayne State University School of Medicine, 540 E. Canfield, Detroit, Michigan 48201, USA
| | - Lori A Pile
- Department of Biological Sciences, Wayne State University, 5047 Gullen Mall, Detroit, Michigan 48202, USA
| |
Collapse
|
31
|
Spain MM, Caruso JA, Swaminathan A, Pile LA. Drosophila SIN3 isoforms interact with distinct proteins and have unique biological functions. J Biol Chem 2010; 285:27457-27467. [PMID: 20566628 DOI: 10.1074/jbc.m110.130245] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
The SIN3 corepressor serves as a scaffold for the assembly of histone deacetylase (HDAC) complexes. SIN3 and its associated HDAC have been shown to have critical roles in both development and the regulation of cell cycle progression. Although multiple SIN3 isoforms have been reported in simple to complex eukaryotic organisms, the mechanisms by which such isoforms regulate specific biological processes are still largely uncharacterized. To gain insight into how SIN3 isoform-specific function contributes to the growth and development of a metazoan organism, we have affinity-purified two SIN3 isoform-specific complexes, SIN3 187 and 220, from Drosophila S2 cells and embryos. We have identified a number of proteins common to the complexes, including the HDAC RPD3, as well as orthologs of several proteins known to have roles in regulating cell proliferation in other organisms. We additionally identified factors, including the histone demethylase little imaginal discs and histone-interacting protein p55, that exhibited a preferential interaction with the largest SIN3 isoform. Our experiments indicate that the isoforms are associated with distinct HDAC activity and are recruited to unique and shared sites along polytene chromosome arms. Furthermore, although expression of SIN3 220 can substitute for genetic loss of other isoforms, expression of SIN3 187 does not support Drosophila viability. Together our findings suggest that SIN3 isoforms serve distinct roles in transcriptional regulation by partnering with different histone-modifying enzymes.
Collapse
Affiliation(s)
- Marla M Spain
- Department of Biological Sciences, Wayne State University, Detroit, Michigan 48202
| | - Joseph A Caruso
- Institute of Environmental Health Sciences, Wayne State University, Detroit, Michigan 48202
| | | | - Lori A Pile
- Department of Biological Sciences, Wayne State University, Detroit, Michigan 48202.
| |
Collapse
|
32
|
Regulation of cell proliferation and wing development by Drosophila SIN3 and String. Mech Dev 2010; 127:96-106. [DOI: 10.1016/j.mod.2009.10.003] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2009] [Revised: 09/23/2009] [Accepted: 10/06/2009] [Indexed: 11/23/2022]
|
33
|
van Steensel B, Braunschweig U, Filion GJ, Chen M, van Bemmel JG, Ideker T. Bayesian network analysis of targeting interactions in chromatin. Genome Res 2009; 20:190-200. [PMID: 20007327 DOI: 10.1101/gr.098822.109] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
In eukaryotes, many chromatin proteins together regulate gene expression. Chromatin proteins often direct the genomic binding pattern of other chromatin proteins, for example, by recruitment or competition mechanisms. The network of such targeting interactions in chromatin is complex and still poorly understood. Based on genome-wide binding maps, we constructed a Bayesian network model of the targeting interactions among a broad set of 43 chromatin components in Drosophila cells. This model predicts many novel functional relationships. For example, we found that the homologous proteins HP1 and HP1C each target the heterochromatin protein HP3 to distinct sets of genes in a competitive manner. We also discovered a central role for the remodeling factor Brahma in the targeting of several DNA-binding factors, including GAGA factor, JRA, and SU(VAR)3-7. Our network model provides a global view of the targeting interplay among dozens of chromatin components.
Collapse
Affiliation(s)
- Bas van Steensel
- Division of Gene Regulation, Netherlands Cancer Institute, 1066 CX Amsterdam, the Netherlands.
| | | | | | | | | | | |
Collapse
|
34
|
Cai Y, Laughon A. The Drosophila Smad cofactor Schnurri engages in redundant and synergistic interactions with multiple corepressors. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2009; 1789:232-45. [PMID: 19437622 DOI: 10.1016/j.bbagrm.2009.01.001] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
In Drosophila a large zinc finger protein, Schnurri, functions as a Smad cofactor required for repression of brinker and other negative targets in response to signaling by the transforming growth factor beta ligand, Decapentaplegic. Schnurri binds to the silencer-bound Smads through a cluster of zinc fingers located near its carboxy-terminus and silences via a separate repression domain adjacent to this zinc-finger cluster. Here we show that this repression domain functions through interaction with two corepressors, dCtBP and dSin3A, and that either interaction is sufficient for repression. We also report that Schnurri contains additional repression domains that function through interaction with dCtBP, Groucho, dSin3A and SMRTER. By testing for the ability to rescue a shn RNAi phenotype we provide evidence that these diverse repression domains are both cooperative and partially redundant. In addition we find that Shn harbors a region capable of transcriptional activation, consistent with evidence that Schnurri can function as an activator as well as a repressor.
Collapse
Affiliation(s)
- Yi Cai
- Laboratory of Genetics, University of Wisconsin, 425G Henry Mall, Madison, WI 53706, USA
| | | |
Collapse
|
35
|
The H3K4 demethylase lid associates with and inhibits histone deacetylase Rpd3. Mol Cell Biol 2008; 29:1401-10. [PMID: 19114561 DOI: 10.1128/mcb.01643-08] [Citation(s) in RCA: 62] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
JmjC domain-containing proteins have been shown to possess histone demethylase activity. One of these proteins is the Drosophila histone H3 lysine 4 demethylase Little imaginal discs (Lid), which has been genetically classified as a Trithorax group protein. However, contrary to the supposed function of Lid in gene activation, the biochemical activity of this protein entails the removal of a histone mark that is correlated with active transcription. To understand the molecular mechanism behind the function of Lid, we have purified a Lid-containing protein complex from Drosophila embryo nuclear extracts. In addition to Lid, the complex contains Rpd3, CG3815/Drosophila Pf1, CG13367, and Mrg15. Rpd3 is a histone deacetylase, and along with Polycomb group proteins, which antagonize the function of Trithorax group proteins, it negatively regulates transcription. By reconstituting the Lid complex, we demonstrated that the demethylase activity of Lid is not affected by its association with other proteins. However, the deacetylase activity of Rpd3 is greatly diminished upon incorporation into the Lid complex. Thus, our finding that Lid antagonizes Rpd3 function provides an explanation for the genetic classification of Lid as a positive transcription regulator.
Collapse
|
36
|
Plata MP, Kang HJ, Zhang S, Kuruganti S, Hsu SJ, Labrador M. Changes in chromatin structure correlate with transcriptional activity of nucleolar rDNA in polytene chromosomes. Chromosoma 2008; 118:303-22. [PMID: 19066928 DOI: 10.1007/s00412-008-0198-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2008] [Revised: 11/14/2008] [Accepted: 11/19/2008] [Indexed: 12/30/2022]
Abstract
Ribosomal DNA genes (rDNA) are found in tandem arrays of hundreds of repeated genes, but only a fraction of these genes are actively transcribed. The regulatory mechanism controlling the transition between active and inactive rDNA in higher eukaryotes is vital for cell survival. Here, we show that the nucleolus from Drosophila salivary gland cells contains two levels of chromatin organization reflecting differences in transcriptional activity: Decondensed chromatin is highly occupied with TATA-box-binding protein (TBP), phosphorylated H3S10, and acetylated H3K14, suggesting that rDNA in decondensed nucleolar areas is actively transcribed. Condensed chromatin lacks TBP, phosphorylated H3S10, or acetylated H3K14 and is enriched in the rDNA retrotransposons R1 and R2. The data show that R1 and R2 retrotransposons are not actively transcribed in salivary glands and may lead to the epigenetic silencing of flanking rDNA genes and that the silencing mechanisms of these sequences might be partially independent of heterochromatin formation by methylation of histone H3 at lysine 9 and binding of heterochromatin protein 1.
Collapse
Affiliation(s)
- Maria Piedad Plata
- Department of Biochemistry, Cellular and Molecular Biology, M407 Walters Life Sciences, The University of Tennessee, 1414 Cumberland Avenue, Knoxville, TN 37996, USA
| | | | | | | | | | | |
Collapse
|
37
|
Sharma V, Swaminathan A, Bao R, Pile LA. Drosophila SIN3 is required at multiple stages of development. Dev Dyn 2008; 237:3040-50. [PMID: 18816856 DOI: 10.1002/dvdy.21706] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
SIN3 is a component of a histone deacetylase complex known to be important for transcription repression. While multiple isoforms of SIN3 have been reported, little is known about their relative expression or role in development. Using a combination of techniques, we have determined that SIN3 is expressed throughout the Drosophila life cycle. The pattern of expression for each individual isoform, however, is distinct. Knock down of all SIN3 expression reveals a requirement for this protein in embryonic and larval periods. Taken together, the data suggest that SIN3 is required for multiple developmental events during the Drosophila life cycle.
Collapse
Affiliation(s)
- Vishal Sharma
- Department of Biological Sciences, Wayne State University, Detroit, Michigan 48202, USA
| | | | | | | |
Collapse
|
38
|
The Lawc protein is required for proper transcription by RNA polymerase II in Drosophila. Mol Genet Genomics 2008; 280:385-96. [PMID: 18716797 DOI: 10.1007/s00438-008-0372-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2008] [Accepted: 08/07/2008] [Indexed: 01/28/2023]
Abstract
Genetic analysis of the Drosophila leg-arista-wing complex (lawc) gene suggests a role for the Lawc protein in chromatin-related processes based on its classification as a trxG gene but the molecular mechanisms of its function remain elusive. We have found that Lawc is a small, cysteine-rich protein that is present in most of the interbands of polytene chromosomes. In agreement with this observation, Lawc co-localizes with RNA polymerase IIo (Pol IIo) and it is recruited to transcribed loci after elongation by Pol IIo has begun. Lawc interacts with the nuclear proteasome regulator dREGgamma in a yeast two-hybrid assay and both proteins co-localize on polytene chromosomes. In addition, a mutation in lawc interacts genetically with a mutation in a component of the proteasome. lawc mutants show decreased expression of some genes, while the levels of Pol IIoSer2 increase. We conclude that Lawc is required for proper transcription by RNA polymerase II in a process that involves the nuclear proteasome.
Collapse
|
39
|
Burgio G, La Rocca G, Sala A, Arancio W, Di Gesù D, Collesano M, Sperling AS, Armstrong JA, van Heeringen SJ, Logie C, Tamkun JW, Corona DFV. Genetic identification of a network of factors that functionally interact with the nucleosome remodeling ATPase ISWI. PLoS Genet 2008; 4:e1000089. [PMID: 18535655 PMCID: PMC2390755 DOI: 10.1371/journal.pgen.1000089] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2008] [Accepted: 05/02/2008] [Indexed: 02/03/2023] Open
Abstract
Nucleosome remodeling and covalent modifications of histones play fundamental roles in chromatin structure and function. However, much remains to be learned about how the action of ATP-dependent chromatin remodeling factors and histone-modifying enzymes is coordinated to modulate chromatin organization and transcription. The evolutionarily conserved ATP-dependent chromatin-remodeling factor ISWI plays essential roles in chromosome organization, DNA replication, and transcription regulation. To gain insight into regulation and mechanism of action of ISWI, we conducted an unbiased genetic screen to identify factors with which it interacts in vivo. We found that ISWI interacts with a network of factors that escaped detection in previous biochemical analyses, including the Sin3A gene. The Sin3A protein and the histone deacetylase Rpd3 are part of a conserved histone deacetylase complex involved in transcriptional repression. ISWI and the Sin3A/Rpd3 complex co-localize at specific chromosome domains. Loss of ISWI activity causes a reduction in the binding of the Sin3A/Rpd3 complex to chromatin. Biochemical analysis showed that the ISWI physically interacts with the histone deacetylase activity of the Sin3A/Rpd3 complex. Consistent with these findings, the acetylation of histone H4 is altered when ISWI activity is perturbed in vivo. These findings suggest that ISWI associates with the Sin3A/Rpd3 complex to support its function in vivo.
Collapse
Affiliation(s)
- Giosalba Burgio
- Dipartimento di Scienze Biochimiche, Universita' degli Studi di Palermo, Palermo, Italy
| | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
40
|
Rimkus SA, Katzenberger RJ, Trinh AT, Dodson GE, Tibbetts RS, Wassarman DA. Mutations in String/CDC25 inhibit cell cycle re-entry and neurodegeneration in a Drosophila model of Ataxia telangiectasia. Genes Dev 2008; 22:1205-20. [PMID: 18408079 DOI: 10.1101/gad.1639608] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Mutations in ATM (Ataxia telangiectasia mutated) result in Ataxia telangiectasia (A-T), a disorder characterized by progressive neurodegeneration. Despite advances in understanding how ATM signals cell cycle arrest, DNA repair, and apoptosis in response to DNA damage, it remains unclear why loss of ATM causes degeneration of post-mitotic neurons and why the neurological phenotype of ATM-null individuals varies in severity. To address these issues, we generated a Drosophila model of A-T. RNAi knockdown of ATM in the eye caused progressive degeneration of adult neurons in the absence of exogenously induced DNA damage. Heterozygous mutations in select genes modified the neurodegeneration phenotype, suggesting that genetic background underlies variable neurodegeneration in A-T. The neuroprotective activity of ATM may be negatively regulated by deacetylation since mutations in a protein deacetylase gene, RPD3, suppressed neurodegeneration, and a human homolog of RPD3, histone deacetylase 2, bound ATM and abrogated ATM activation in cell culture. Moreover, knockdown of ATM in post-mitotic neurons caused cell cycle re-entry, and heterozygous mutations in the cell cycle activator gene String/CDC25 inhibited cell cycle re-entry and neurodegeneration. Thus, we hypothesize that ATM performs a cell cycle checkpoint function to protect post-mitotic neurons from degeneration and that cell cycle re-entry causes neurodegeneration in A-T.
Collapse
Affiliation(s)
- Stacey A Rimkus
- Department of Biomolecular Chemistry, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin 53706, USA
| | | | | | | | | | | |
Collapse
|
41
|
Sasai N, Kato Y, Kimura G, Takeuchi T, Yamaguchi M. The Drosophila jumonji gene encodes a JmjC-containing nuclear protein that is required for metamorphosis. FEBS J 2007; 274:6139-51. [PMID: 17970746 DOI: 10.1111/j.1742-4658.2007.06135.x] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Jumonji (Jmj) is a transcriptional repressor that plays important roles in the suppression of cell proliferation and development of various tissues in the mouse. To further clarify the roles of Jmj during development and gain insight into mechanisms of Jmj-mediated transcriptional regulation, we have taken advantage of Drosophila as a model organism. Drosophila Jmj (dJmj) shares high homology with mammalian Jmj in the JmjN, JmjC and AT-rich interaction domains, as well as in the N-terminal repression domain. dJmj localizes to hundreds of euchromatic sites but not to chromocenter heterochromatin on salivary gland polytene chromosomes. In addition, dJmj is excluded from regions stained with an antibody against Ser5-phosphorylated RNA polymerase II, suggesting a function of dJmj in transcriptionally inactive chromatin. Loss of djmj results in larval and pupal lethality with phenotypes similar to those observed in mutants of ecdysone-regulated genes, implying the involvement of dJmj in the repression of gene expression in the ecdysone pathway. Transgenic mouse Jmj mostly colocalizes with dJmj and partially rescues the phenotypes of djmj mutants, indicating that dJmj is a functional homolog of mammalian Jmj. Furthermore, mutation in djmj suppresses position effect variegation of the T(2;3)Sb(V) rearrangement. These findings suggest that dJmj controls expression of developmentally important genes through modification of chromatin into a transcriptionally silenced state.
Collapse
Affiliation(s)
- Nobuhiro Sasai
- Venture Laboratory, Kyoto Institute of Technology, Japan
| | | | | | | | | |
Collapse
|
42
|
Dekker J. GC- and AT-rich chromatin domains differ in conformation and histone modification status and are differentially modulated by Rpd3p. Genome Biol 2007; 8:R116. [PMID: 17577398 PMCID: PMC2394764 DOI: 10.1186/gb-2007-8-6-r116] [Citation(s) in RCA: 52] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2007] [Accepted: 06/18/2007] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Base-composition varies throughout the genome and is related to organization of chromosomes in distinct domains (isochores). Isochore domains differ in gene expression levels, replication timing, levels of meiotic recombination and chromatin structure. The molecular basis for these differences is poorly understood. RESULTS We have compared GC- and AT-rich isochores of yeast with respect to chromatin conformation, histone modification status and transcription. Using 3C analysis we show that, along chromosome III, GC-rich isochores have a chromatin structure that is characterized by lower chromatin interaction frequencies compared to AT-rich isochores, which may point to a more extended chromatin conformation. In addition, we find that throughout the genome, GC-rich and AT-rich genes display distinct levels of histone modifications. Interestingly, elimination of the histone deacetylase Rpd3p differentially affects conformation of GC- and AT-rich domains. Further, deletion of RPD3 activates expression of GC-rich genes more strongly than AT-rich genes. Analyses of effects of the histone deacetylase inhibitor trichostatin A, global patterns of Rpd3p binding and effects of deletion of RPD3 on histone H4 acetylation confirmed that conformation and activity of GC-rich chromatin are more sensitive to Rpd3p-mediated deacetylation than AT-rich chromatin. CONCLUSION We find that GC-rich and AT-rich chromatin domains display distinct chromatin conformations and are marked by distinct patterns of histone modifications. We identified the histone deacetylase Rpd3p as an attenuator of these base composition-dependent differences in chromatin status. We propose that GC-rich chromatin domains tend to occur in a more active conformation and that Rpd3p activity represses this propensity throughout the genome.
Collapse
Affiliation(s)
- Job Dekker
- Program in Gene Function and Expression and Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Plantation Street, Worcester, MA 01605-4321, USA.
| |
Collapse
|
43
|
Orian A. Chromatin profiling, DamID and the emerging landscape of gene expression. Curr Opin Genet Dev 2006; 16:157-64. [PMID: 16503134 DOI: 10.1016/j.gde.2006.02.008] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2006] [Accepted: 02/13/2006] [Indexed: 11/16/2022]
Abstract
Determining how genes are normally expressed throughout development and how they are mis-regulated in cancer is challenging. The availability of complete genome sequences, the advances in microarray technologies, and the development of novel functional genomic techniques such as 'chromatin profiling' facilitate dissection of the interplay among transcriptional networks and reveals chromosome organization in vivo. Recently, a novel methylation-based tagging technique, termed DamID (DNA adenine methyltransferase identification), has emerged as a powerful tool to decipher transcriptional networks, to study chromatin-associated proteins, and to monitor higher-order chromatin organization on a genome-wide scale. The molecular picture that emerges from DamID and similar studies is that genomes integrate inputs from both genetic and epigenetic machineries to dynamically regulate gene expression.
Collapse
Affiliation(s)
- Amir Orian
- Vascular and Tumor Biology Research Center, The Rappaport Research Institute and Faculty of Medicine, Technion-Israel Institute of Technology, 4 Efron Street, Bat Galim, Haifa 31096, Israel.
| |
Collapse
|
44
|
Gonzales E, Chen H, Munuve R, Mehrani T, Britten-Webb J, Nadel A, Alam HB, Wherry D, Burris D, Koustova E. VALPROIC ACID PREVENTS HEMORRHAGE-ASSOCIATED LETHALITY AND AFFECTS THE ACETYLATION PATTERN OF CARDIAC HISTONES. Shock 2006; 25:395-401. [PMID: 16670643 DOI: 10.1097/01.shk.0000209522.28120.c8] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
Pharmacological inhibitors of histone deacetylases (HDAC) demonstrate cytoprotective effects both in vitro and in vivo. In this study, we investigated whether valproic acid (VPA), a known mood stabilizer and anticonvulsant with HDAC-inhibiting activity, improves survival following otherwise lethal hemorrhage in rats. We found that preinsult injection of VPA (300 mg/kg, twice) prolonged the survival of severely hypotensive animals up to 5 times. VPA treatment increased the acetylation of nonhistone and histone proteins in the rat heart. The pattern of modifications of individual histones revealed hyperacetylation of histones H2A, H3, and H4, indicating the presence of active genes. Expression of HSP70 and superoxide dismutase, implicated in the modulation of vitality, was increased by VPA. Our results reveal that VPA offers considerable protection in the hemorrhagic shock model and suggest a role for HDAC inhibition in mediating VPA actions.
Collapse
Affiliation(s)
- Earl Gonzales
- Department of Surgery, Trauma Research and Readiness Institute for Surgery, Uniformed Services University of the Health Sciences, Bethesda, , MD 20814, USA
| | | | | | | | | | | | | | | | | | | |
Collapse
|
45
|
Struffi P, Arnosti DN. Functional interaction between the Drosophila knirps short range transcriptional repressor and RPD3 histone deacetylase. J Biol Chem 2005; 280:40757-65. [PMID: 16186109 PMCID: PMC1802102 DOI: 10.1074/jbc.m506819200] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Knirps and other short range transcriptional repressors play critical roles in patterning the early Drosophila embryo. These repressors are known to bind the C-terminal binding protein corepressor, but their mechanism of action is poorly understood. We purified functional recombinant Knirps protein from transgenic embryos to identify possible cofactors that contribute to the activity of this protein. The protein migrates in a complex of approximately 450 kDa and was found to copurify with the Rpd3 histone deacetylase protein during a double affinity purification procedure. Association of Rpd3 with Knirps was dependent on the presence of the C-terminal binding protein-dependent repression domain of Knirps. Previous studies of an rpd3 mutant had not shown defects in the pattern of expression of even-skipped, a target of the Knirps repressor. However, in embryos doubly heterozygous for knirps and rpd3, a marked increase in the frequency of defects in the Knirps-regulated posterior domain of even-skipped expression was found, indicating that Rpd3 contributes to Knirps repression activity in vivo. This finding implicates deacetylation in the mechanism of short range repression in Drosophila.
Collapse
Affiliation(s)
- Paolo Struffi
- Department of Biochemistry and Molecular Biology and Program in Genetics, Michigan State University, East Lansing, Michigan 48824, USA
| | | |
Collapse
|
46
|
Canudas S, Pérez S, Fanti L, Pimpinelli S, Singh N, Hanes SD, Azorín F, Espinás ML. dSAP18 and dHDAC1 contribute to the functional regulation of the Drosophila Fab-7 element. Nucleic Acids Res 2005; 33:4857-64. [PMID: 16135462 PMCID: PMC1196206 DOI: 10.1093/nar/gki776] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022] Open
Abstract
It was described earlier that the Drosophila GAGA factor [Trithorax-like (Trl)] interacts with dSAP18, which, in mammals, was reported to be a component of the Sin3–HDAC co-repressor complex. GAGA–dSAP18 interaction was proposed to contribute to the functional regulation of the bithorax complex (BX-C). Here, we show that mutant alleles of Trl, dsap18 and drpd3/hdac1 enhance A6-to-A5 transformation indicating a contribution to the regulation of Abd-B expression at A6. In A6, expression of Abd-B is driven by the iab-6 enhancer, which is insulated from iab-7 by the Fab-7 element. Here, we report that GAGA, dSAP18 and dRPD3/HDAC1 co-localize to ectopic Fab-7 sites in polytene chromosomes and that mutant Trl, dsap18 and drpd3/hdac1 alleles affect Fab-7-dependent silencing. Consistent with these findings, chromatin immunoprecipitation analysis shows that, in Drosophila embryos, the endogenous Fab-7 element is hypoacetylated at histones H3 and H4. These results indicate a contribution of GAGA, dSAP18 and dRPD3/HDAC1 to the regulation of Fab-7 function.
Collapse
Affiliation(s)
| | | | - Laura Fanti
- Dipartimento di Genetica e Biologia Molecolare, Università ‘La Sapienza’00185 Rome, Italy
| | - Sergio Pimpinelli
- Dipartimento di Genetica e Biologia Molecolare, Università ‘La Sapienza’00185 Rome, Italy
| | - Navjot Singh
- New York State Department of Health, Wadsworth Center, State University of New YorkAlbany, NY 12208, USA
| | - Steven D. Hanes
- New York State Department of Health, Wadsworth Center, State University of New YorkAlbany, NY 12208, USA
| | - Fernando Azorín
- To whom correspondence should be addressed. Tel: +34 93 4034958; Fax: +34 93 4034979;
| | | |
Collapse
|
47
|
Fu D, Ma J. Interplay between positive and negative activities that influence the role of Bicoid in transcription. Nucleic Acids Res 2005; 33:3985-93. [PMID: 16030350 PMCID: PMC1178001 DOI: 10.1093/nar/gki691] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2005] [Revised: 05/20/2005] [Accepted: 06/16/2005] [Indexed: 11/13/2022] Open
Abstract
The Drosophila mophogenetic protein Bicoid (Bcd) can activate transcription in a concentration-dependent manner in embryos. It contains a self-inhibitory domain that can interact with the co-repressor Sin3A. In this report, we study a Bcd mutant, Bcd(A57-61), which has a strengthened self-inhibitory function and is unable to activate the hb-CAT reporter in Drosophila cells, to analyze the role of co-factors in regulating Bcd function. We show that increased concentrations of the co-activator dCBP in cells can switch this protein from its inactive state to an active state on the hb-CAT reporter. The C-terminal portion of Bcd(A57-61) is required to mediate such activity-rescuing function of dCBP. Although capable of binding to DNA in vitro, Bcd(A57-61) is unable to access the hb enhancer element in cells, suggesting that its DNA binding defect is only manifested in a cellular context. Increased concentrations of dCBP restore not only the ability of Bcd(A57-61) to access the hb enhancer element in cells but also the occupancy of the general transcription factors TBP and TFIIB at the reporter promoter. These and other results suggest that an activator can undergo switches between its active and inactive states through sensing the opposing actions of positive and negative co-factors.
Collapse
Affiliation(s)
- Dechen Fu
- Division of Developmental Biology, Cincinnati Children's Hospital Research Foundation, Graduate Program in Molecular and Developmental Biology, University of Cincinnati College of Medicine3333 Burnet Avenue Cincinnati, OH 45229, USA
| | - Jun Ma
- Division of Developmental Biology, Cincinnati Children's Hospital Research Foundation, Graduate Program in Molecular and Developmental Biology, University of Cincinnati College of Medicine3333 Burnet Avenue Cincinnati, OH 45229, USA
| |
Collapse
|
48
|
Fujita N, Wade PA. Use of bifunctional cross-linking reagents in mapping genomic distribution of chromatin remodeling complexes. Methods 2005; 33:81-5. [PMID: 15039090 DOI: 10.1016/j.ymeth.2003.10.022] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/30/2003] [Indexed: 11/26/2022] Open
Abstract
Chromatin remodeling complexes consist of multiple subunits, some of which are in intimate contact with DNA while others are not. The ability to effectively cross-link proteins to DNA with formaldehyde is impacted by the average distance between the two species. Productive cross-linking of proteins not in direct contact with DNA is greatly facilitated by the inclusion of an initial cross-linking reaction using bifunctional imidoester cross-linking reagents.
Collapse
Affiliation(s)
- Naoyuki Fujita
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Whitehead Building, Room 142, 615 Michael Street, Atlanta, GA 30322, USA
| | | |
Collapse
|
49
|
Abstract
To gain insight into the essential functions of E2F, we have examined the phenotypes caused by complete inactivation of E2F and DP family members in Drosophila. Our results show that dDP requires dE2F1 and dE2F2 for DNA-binding activity in vitro and in vivo. In tissue culture cells and in mutant animals, the levels of dE2F and dDP proteins are strongly interdependent. In the absence of dDP, the levels of dE2F1 and dE2F2 decline dramatically, and vice versa. Accordingly, the cell cycle and transcriptional phenotypes caused by targeting dDP mimic the effects of targeting both dE2F1 and dE2F2 and are indistinguishable from the effects of inactivating all three proteins. Although trans-heterozygous dDP mutant animals develop to late pupal stages, the analysis of somatic mutant clones shows that dDP mutant cells are at a severe proliferative disadvantage when compared directly with wild-type neighbors. Strikingly, the timing of S-phase entry or exit is not delayed in dDP mutant clones, nor is the accumulation of cyclin A or cyclin B. However, the maximal level of bromodeoxyuridine incorporation is reduced in dDP mutant clones, and RNA interference experiments show that dDP-depleted cells are prone to stall in S phase. In addition, dDP mutant clones contain reduced numbers of mitotic cells, indicating that dDP mutant cells have a defect in G2/M-phase progression. Thus, dDP is not essential for developmental control of the G1-to-S transition, but it is required for normal cell proliferation, for optimal DNA synthesis, and for efficient G2/M progression.
Collapse
Affiliation(s)
- Maxim V Frolov
- Massachusetts General Hospital Cancer Center, Bldg. 149, 13th St., Charlestown, MA 02129, USA
| | | | | |
Collapse
|
50
|
Abstract
Two highly conserved histone deacetylases, Sir2 and Rpd3, have been linked to caloric restriction and the extension of longevity. Because the Drosophila forms of each protein can silence genes in either euchromatin or heterochromatin, we determined whether longevity extension is mediated by silencing in the latter domain. When silencing was increased and decreased using mutations that affect heterochromatin protein 1 (HP1), but have no direct effect upon Sir2 or Rpd3, lifespan was unaffected. Heterochromatin-mediated gene silencing was then modulated without directly influencing HP1 as well as the deacetylases, again yielding no effect on lifespan. Mortality rates were unchanged by all manipulations, indicating that euchromatic targets are likely to be the effectors of deacetylase-mediated longevity extension in Drosophila [corrected]
Collapse
Affiliation(s)
- Stewart Frankel
- Department of Pediatrics and Boyer Center for Molecular Medicine, Yale University School of Medicine, 295 Congress Avenue, New Haven, CT 06536, USA
| | | |
Collapse
|