1
|
Nagel AC, Maier D, Scharpf J, Ketelhut M, Preiss A. Limited Availability of General Co-Repressors Uncovered in an Overexpression Context during Wing Venation in Drosophila melanogaster. Genes (Basel) 2020; 11:genes11101141. [PMID: 32998295 PMCID: PMC7601384 DOI: 10.3390/genes11101141] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2020] [Revised: 09/17/2020] [Accepted: 09/25/2020] [Indexed: 12/31/2022] Open
Abstract
Cell fate is determined by the coordinated activity of different pathways, including the conserved Notch pathway. Activation of Notch results in the transcription of Notch targets that are otherwise silenced by repressor complexes. In Drosophila, the repressor complex comprises the transcription factor Suppressor of Hairless (Su(H)) bound to the Notch antagonist Hairless (H) and the general co-repressors Groucho (Gro) and C-terminal binding protein (CtBP). The latter two are shared by different repressors from numerous pathways, raising the possibility that they are rate-limiting. We noted that the overexpression during wing development of H mutants HdNT and HLD compromised in Su(H)-binding induced ectopic veins. On the basis of the role of H as Notch antagonist, overexpression of Su(H)-binding defective H isoforms should be without consequence, implying different mechanisms but repression of Notch signaling activity. Perhaps excess H protein curbs general co-repressor availability. Supporting this model, nearly normal wings developed upon overexpression of H mutant isoforms that bound neither Su(H) nor co-repressor Gro and CtBP. Excessive H protein appeared to sequester general co-repressors, resulting in specific vein defects, indicating their limited availability during wing vein development. In conclusion, interpretation of overexpression phenotypes requires careful consideration of possible dominant negative effects from interception of limiting factors.
Collapse
|
2
|
Chambers M, Turki-Judeh W, Kim MW, Chen K, Gallaher SD, Courey AJ. Mechanisms of Groucho-mediated repression revealed by genome-wide analysis of Groucho binding and activity. BMC Genomics 2017; 18:215. [PMID: 28245789 PMCID: PMC5331681 DOI: 10.1186/s12864-017-3589-6] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2016] [Accepted: 02/13/2017] [Indexed: 12/24/2022] Open
Abstract
Background The transcriptional corepressor Groucho (Gro) is required for the function of many developmentally regulated DNA binding repressors, thus helping to define the gene expression profile of each cell during development. The ability of Gro to repress transcription at a distance together with its ability to oligomerize and bind to histones has led to the suggestion that Gro may spread along chromatin. However, much is unknown about the mechanism of Gro-mediated repression and about the dynamics of Gro targeting. Results Our chromatin immunoprecipitation sequencing analysis of temporally staged Drosophila embryos shows that Gro binds in a highly dynamic manner primarily to clusters of discrete (<1 kb) segments. Consistent with the idea that Gro may facilitate communication between silencers and promoters, Gro binding is enriched at both cis-regulatory modules, as well as within the promotors of potential target genes. While this Gro-recruitment is required for repression, our data show that it is not sufficient for repression. Integration of Gro binding data with transcriptomic analysis suggests that, contrary to what has been observed for another Gro family member, Drosophila Gro is probably a dedicated repressor. This analysis also allows us to define a set of high confidence Gro repression targets. Using publically available data regarding the physical and genetic interactions between these targets, we are able to place them in the regulatory network controlling development. Through analysis of chromatin associated pre-mRNA levels at these targets, we find that genes regulated by Gro in the embryo are enriched for characteristics of promoter proximal paused RNA polymerase II. Conclusions Our findings are inconsistent with a one-dimensional spreading model for long-range repression and suggest that Gro-mediated repression must be regulated at a post-recruitment step. They also show that Gro is likely a dedicated repressor that sits at a prominent highly interconnected regulatory hub in the developmental network. Furthermore, our findings suggest a role for RNA polymerase II pausing in Gro-mediated repression. Electronic supplementary material The online version of this article (doi:10.1186/s12864-017-3589-6) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Michael Chambers
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA, 90095, USA
| | - Wiam Turki-Judeh
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA, 90095, USA.,Molecular Biology Institute, University of California, Los Angeles, CA, 90095, USA
| | - Min Woo Kim
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA, 90095, USA
| | - Kenny Chen
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA, 90095, USA
| | - Sean D Gallaher
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA, 90095, USA.,Department of Energy, Institute of Genomics and Proteomics, University of California, Los Angeles, CA, 90095, USA
| | - Albert J Courey
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA, 90095, USA. .,Molecular Biology Institute, University of California, Los Angeles, CA, 90095, USA.
| |
Collapse
|
3
|
Kok K, Ay A, Li LM, Arnosti DN. Genome-wide errant targeting by Hairy. eLife 2015; 4. [PMID: 26305409 PMCID: PMC4547095 DOI: 10.7554/elife.06394] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2015] [Accepted: 07/24/2015] [Indexed: 01/08/2023] Open
Abstract
Metazoan transcriptional repressors regulate chromatin through diverse histone modifications. Contributions of individual factors to the chromatin landscape in development is difficult to establish, as global surveys reflect multiple changes in regulators. Therefore, we studied the conserved Hairy/Enhancer of Split family repressor Hairy, analyzing histone marks and gene expression in Drosophila embryos. This long-range repressor mediates histone acetylation and methylation in large blocks, with highly context-specific effects on target genes. Most strikingly, Hairy exhibits biochemical activity on many loci that are uncoupled to changes in gene expression. Rather than representing inert binding sites, as suggested for many eukaryotic factors, many regions are targeted errantly by Hairy to modify the chromatin landscape. Our findings emphasize that identification of active cis-regulatory elements must extend beyond the survey of prototypical chromatin marks. We speculate that this errant activity may provide a path for creation of new regulatory elements, facilitating the evolution of novel transcriptional circuits.
Collapse
Affiliation(s)
- Kurtulus Kok
- Genetics Program, Michigan State University, East Lansing, United States
| | - Ahmet Ay
- Departments of Biology and Mathematics, Colgate University, Hamilton, United States
| | - Li M Li
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, United States
| | - David N Arnosti
- Genetics Program, Michigan State University, East Lansing, United States
| |
Collapse
|
4
|
Agarwal M, Kumar P, Mathew SJ. The Groucho/Transducin-like enhancer of split protein family in animal development. IUBMB Life 2015; 67:472-81. [PMID: 26172616 DOI: 10.1002/iub.1395] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2015] [Accepted: 06/15/2015] [Indexed: 01/30/2023]
Abstract
Corepressors are proteins that cannot bind DNA directly but repress transcription by interacting with partner proteins. The Groucho/Transducin-Like Enhancer of Split (TLE) are a conserved family of corepressor proteins present in animals ranging from invertebrates such as Drosophila to vertebrates such as mice and humans. Groucho/TLE proteins perform important functions throughout the life span of animals, interacting with several pathways and regulating fundamental processes such as metabolism. However, these proteins have especially crucial functions in animal development, where they are required in multiple tissues in a temporally regulated manner. In this review, we summarize the functions of the Groucho/TLE proteins during animal development, emphasizing on specific tissues where they play essential roles.
Collapse
Affiliation(s)
- Megha Agarwal
- Regional Centre for Biotechnology, NCR Bio-Science Cluster, Faridabad, Haryana, India
| | - Pankaj Kumar
- Regional Centre for Biotechnology, NCR Bio-Science Cluster, Faridabad, Haryana, India
| | - Sam J Mathew
- Regional Centre for Biotechnology, NCR Bio-Science Cluster, Faridabad, Haryana, India
| |
Collapse
|
5
|
Dias JM, Ilkhanizadeh S, Karaca E, Duckworth JK, Lundin V, Rosenfeld MG, Ericson J, Hermanson O, Teixeira AI. CtBPs sense microenvironmental oxygen levels to regulate neural stem cell state. Cell Rep 2014; 8:665-70. [PMID: 25088415 DOI: 10.1016/j.celrep.2014.06.057] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2013] [Revised: 04/30/2014] [Accepted: 06/26/2014] [Indexed: 12/20/2022] Open
Abstract
Bone morphogenetic proteins (BMPs) secreted by the dorsal neural tube and overlying ectoderm are key signals for the specification of the roof plate and dorsal interneuron populations. However, the signals that confer nonneurogenic character to the roof plate region are largely unknown. We report that the roof plate region shows elevated oxygen levels compared to neurogenic regions of the neural tube. These high oxygen levels are required for the expression of the antineuronal transcription factor Hes1 in the roof plate region. The transcriptional corepressor CtBP is a critical mediator of the oxygen-sensing response. High oxygen promotes a decrease in the CtBP occupancy of the promoter of Hes1. Furthermore, under conditions of high oxygen and BMP, CtBP associates with HES1 and represses neurogenesis. We propose that CtBP integrates signals originating from microenvironmental levels of oxygen and BMP to confer nonneurogenic character to the roof plate region.
Collapse
Affiliation(s)
- José M Dias
- Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, 171 77, Sweden
| | - Shirin Ilkhanizadeh
- Department of Neuroscience, Karolinska Institutet, Stockholm, 171 77, Sweden
| | - Esra Karaca
- Department of Neuroscience, Karolinska Institutet, Stockholm, 171 77, Sweden
| | - Joshua K Duckworth
- Department of Neuroscience, Karolinska Institutet, Stockholm, 171 77, Sweden
| | - Vanessa Lundin
- Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, 171 77, Sweden
| | - Michael G Rosenfeld
- Howard Hughes Medical Institute School of Medicine, University of California, San Diego, San Diego, CA 92093, USA
| | - Johan Ericson
- Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, 171 77, Sweden
| | - Ola Hermanson
- Department of Neuroscience, Karolinska Institutet, Stockholm, 171 77, Sweden.
| | - Ana I Teixeira
- Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, 171 77, Sweden.
| |
Collapse
|
6
|
Upadhyai P, Campbell G. Brinker possesses multiple mechanisms for repression because its primary co-repressor, Groucho, may be unavailable in some cell types. Development 2013; 140:4256-65. [PMID: 24086079 DOI: 10.1242/dev.099366] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Transcriptional repressors function primarily by recruiting co-repressors, which are accessory proteins that antagonize transcription by modifying chromatin structure. Although a repressor could function by recruiting just a single co-repressor, many can recruit more than one, with Drosophila Brinker (Brk) recruiting the co-repressors CtBP and Groucho (Gro), in addition to possessing a third repression domain, 3R. Previous studies indicated that Gro is sufficient for Brk to repress targets in the wing, questioning why it should need to recruit CtBP, a short-range co-repressor, when Gro is known to be able to function over longer distances. To resolve this we have used genomic engineering to generate a series of brk mutants that are unable to recruit Gro, CtBP and/or have 3R deleted. These reveal that although the recruitment of Gro is necessary and can be sufficient for Brk to make an almost morphologically wild-type fly, it is insufficient during oogenesis, where Brk must utilize CtBP and 3R to pattern the egg shell appropriately. Gro insufficiency during oogenesis can be explained by its downregulation in Brk-expressing cells through phosphorylation downstream of EGFR signaling.
Collapse
Affiliation(s)
- Priyanka Upadhyai
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA 15260, USA
| | | |
Collapse
|
7
|
Mannervik M. Control of Drosophila embryo patterning by transcriptional co-regulators. Exp Cell Res 2013; 321:47-57. [PMID: 24157250 DOI: 10.1016/j.yexcr.2013.10.010] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2013] [Revised: 10/10/2013] [Accepted: 10/14/2013] [Indexed: 12/29/2022]
Abstract
A combination of broadly expressed transcriptional activators and spatially restricted repressors are used to pattern embryos into cells of different fate. Transcriptional co-regulators are essential mediators of transcription factor function, and contribute to selective transcriptional responses in embryo development. A two step mechanism of transcriptional regulation is discussed, where remodeling of chromatin is initially required, followed by stimulation of recruitment or release of RNA polymerase from the promoter. Transcriptional co-regulators are essential for both of these steps. In particular, most co-activators are associated with histone acetylation and co-repressors with histone deacetylation. In the early Drosophila embryo, genome-wide studies have shown that the CBP co-activator has a preference for associating with some transcription factors and regulatory regions. The Groucho, CtBP, Ebi, Atrophin and Brakeless co-repressors are selectively used to limit zygotic gene expression. New findings are summarized which show that different co-repressors are often utilized by a single repressor, that the context in which a co-repressor is recruited to DNA can affect its activity, and that co-regulators may switch from co-repressors to co-activators and vice versa. The possibility that co-regulator activity is regulated and plays an instructive role in development is discussed as well. This review highlights how findings in Drosophila embryos have contributed to the understanding of transcriptional regulation in eukaryotes as well as to mechanisms of animal embryo patterning.
Collapse
Affiliation(s)
- Mattias Mannervik
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Arrheniuslaboratories E3, SE-106 91 Stockholm, Sweden.
| |
Collapse
|
8
|
Surkova S, Golubkova E, Manu, Panok L, Mamon L, Reinitz J, Samsonova M. Quantitative dynamics and increased variability of segmentation gene expression in the Drosophila Krüppel and knirps mutants. Dev Biol 2013; 376:99-112. [PMID: 23333947 DOI: 10.1016/j.ydbio.2013.01.008] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2012] [Revised: 12/30/2012] [Accepted: 01/09/2013] [Indexed: 11/28/2022]
Abstract
Here we characterize the response of the Drosophila segmentation system to mutations in two gap genes, Kr and kni, in the form of single or double homozygotes and single heterozygotes. Segmentation gene expression in these genotypes was quantitatively monitored with cellular resolution in space and 6.5 to 13min resolution in time. As is the case with wild type, we found that gene expression domains in the posterior portion of the embryo shift to the anterior over time. In certain cases, such as the gt posterior domain in Kr mutants, the shifts are significantly larger than is seen in wild type embryos. We also investigated the effects of Kr and kni on the variability of gene expression. Mutations often produce variable phenotypes, and it is well known that the cuticular phenotype of Kr mutants is variable. We sought to understand the molecular basis of this effect. We find that throughout cycle 14A the relative levels of eve and ftz expression in stripes 2 and 3 are variable among individual embryos. Moreover, in Kr and kni mutants, unlike wild type, the variability in positioning of the posterior Hb domain and eve stripe 7 is not decreased or filtered with time. The posterior Gt domain in Kr mutants is highly variable at early times, but this variability decreases when this domain shifts in the anterior direction to the position of the neighboring Kni domain. In contrast to these findings, positional variability throughout the embryo does not decrease over time in double Kr;kni mutants. In heterozygotes the early expression patterns of segmentation genes resemble patterns seen in homozygous mutants but by the onset of gastrulation they become similar to the wild type patterns. Finally, we note that gene expression levels are reduced in Kr and kni mutant embryos and have a tendency to decrease over time. This is a surprising result in view of the role that mutual repression is thought to play in the gap gene system.
Collapse
Affiliation(s)
- Svetlana Surkova
- Department of Computational Biology, Center for Advanced Studies, St. Petersburg State Polytechnical University, 29 Polytehnicheskaya Street, St. Petersburg 195251, Russia
| | | | | | | | | | | | | |
Collapse
|
9
|
The Tbx20 homolog Midline represses wingless in conjunction with Groucho during the maintenance of segment polarity. Dev Biol 2012; 369:319-29. [PMID: 22814213 DOI: 10.1016/j.ydbio.2012.07.004] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2011] [Revised: 07/07/2012] [Accepted: 07/09/2012] [Indexed: 11/20/2022]
Abstract
The regulation of the segment polarity gene wingless is essential for the correct patterning of the Drosophila ectoderm. We have previously shown that the asymmetric activation of wingless downstream of Hedghog-signaling depends on the T-box transcription factors, midline and H15. Hedgehog activates wingless anterior to the Hedgehog domain. midline/H15 are responsible in part for repressing wingless in cells posterior to the Hedgehog expressing cells. Here, we show that Midline binds the Groucho co-repressor directly via the engrailed homology-1 domain and requires an intact engrailed-homology-1 domain to repress wingless. In contrast, the regulation of Serrate, a second target of midline repression, is not dependent on the engrailed-homology-1 domain. Furthermore, we identify a midline responsive region of the wingless cis-regulatory region and show that Midline binds to sequences within this region. Mutating these sequences in transgenic reporter constructs results in ectopic reporter expression in the midline-expression domain, consistent with wingless being a direct target of Midline repression.
Collapse
|
10
|
Turki-Judeh W, Courey AJ. The unconserved groucho central region is essential for viability and modulates target gene specificity. PLoS One 2012; 7:e30610. [PMID: 22319573 PMCID: PMC3272004 DOI: 10.1371/journal.pone.0030610] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2011] [Accepted: 12/26/2011] [Indexed: 12/31/2022] Open
Abstract
Groucho (Gro) is a Drosophila corepressor required by numerous DNA-binding repressors, many of which are distributed in gradients and provide positional information during development. Gro contains well-conserved domains at its N- and C-termini, and a poorly conserved central region that includes the GP, CcN, and SP domains. All lethal point mutations in gro map to the conserved regions, leading to speculation that the unconserved central domains are dispensable. However, our sequence analysis suggests that the central domains are disordered leading us to suspect that the lack of lethal mutations in this region reflects a lack of order rather than an absence of essential functions. In support of this conclusion, genomic rescue experiments with Gro deletion variants demonstrate that the GP and CcN domains are required for viability. Misexpression assays using these same deletion variants show that the SP domain prevents unrestrained and promiscuous repression by Gro, while the GP and CcN domains are indispensable for repression. Deletion of the GP domain leads to loss of nuclear import, while deletion of the CcN domain leads to complete loss of repression. Changes in Gro activity levels reset the threshold concentrations at which graded repressors silence target gene expression. We conclude that co-regulators such as Gro are not simply permissive components of the repression machinery, but cooperate with graded DNA-binding factors in setting borders of gene expression. We suspect that disorder in the Gro central domains may provide the flexibility that allows this region to mediate multiple interactions required for repression.
Collapse
Affiliation(s)
- Wiam Turki-Judeh
- Department of Chemistry and Biochemistry and Molecular Biology Institute, University of California Los Angeles, Los Angeles, California, United States of America
| | - Albert J. Courey
- Department of Chemistry and Biochemistry and Molecular Biology Institute, University of California Los Angeles, Los Angeles, California, United States of America
- * E-mail:
| |
Collapse
|
11
|
Abstract
Drosophila Groucho (Gro) is the founding member of a family of metazoan corepressors. Gro mediates repression through interactions with a myriad of DNA-binding repressor proteins to direct the silencing of genes involved in many developmental processes, including neurogenesis and patterning of the main body axis, as well as receptor tyrosine kinase/Ras/MAPK, Notch, Wingless (Wg)/Wnt, and Decapentaplegic (Dpp) signaling. Gro mediates repression by multiple molecular mechanisms, depending on the regulatory context. Because Gro is a broadly expressed nuclear factor, whereas its repressor partners display restricted temporal and spatial distribution, it was presumed that this corepressor played permissive rather than instructive roles in development. However, a wide range of studies demonstrates that this is not the case. Gro can sense and integrate many cellular inputs to modulate the expression of variety of genes, making it a versatile corepressor with crucial instructive roles in development and signaling.
Collapse
Affiliation(s)
- Wiam Turki-Judeh
- Department of Chemistry & Biochemistry and Molecular Biology Institute, University of California, Los Angeles, California, USA
| | | |
Collapse
|
12
|
Bothma JP, Magliocco J, Levine M. The snail repressor inhibits release, not elongation, of paused Pol II in the Drosophila embryo. Curr Biol 2011; 21:1571-7. [PMID: 21920753 DOI: 10.1016/j.cub.2011.08.019] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2011] [Revised: 07/11/2011] [Accepted: 08/08/2011] [Indexed: 12/25/2022]
Abstract
The development of the precellular Drosophila embryo is characterized by exceptionally rapid transitions in gene activity, with broadly distributed maternal regulatory gradients giving way to precise on/off patterns of gene expression within a one-hour window, between two and three hours after fertilization [1]. Transcriptional repression plays a pivotal role in this process, delineating sharp expression patterns (e.g., pair-rule stripes) within broad domains of gene activation. As many as 20 different sequence-specific repressors have been implicated in this process, yet the mechanisms by which they silence gene expression have remained elusive [2]. Here we report the development of a method for the quantitative visualization of transcriptional repression. We focus on the Snail repressor, which establishes the boundary between the presumptive mesoderm and neurogenic ectoderm [3]. We find that elongating Pol II complexes complete transcription after the onset of Snail repression. As a result, moderately sized genes (e.g., the 22 kb sog locus) are fully silenced only after tens of minutes of repression. We propose that this "repression lag" imposes a severe constraint on the regulatory dynamics of embryonic patterning and further suggest that posttranscriptional regulators, like microRNAs, are required to inhibit unwanted transcripts produced during protracted periods of gene silencing.
Collapse
Affiliation(s)
- Jacques P Bothma
- Biophysics Graduate Group, Center for Integrative Genomics, Division of Genetics, Genomics and Development, University of California, Berkeley, Berkeley, CA 94720, USA.
| | | | | |
Collapse
|
13
|
Li LM, Arnosti DN. Long- and short-range transcriptional repressors induce distinct chromatin states on repressed genes. Curr Biol 2011; 21:406-12. [PMID: 21353562 DOI: 10.1016/j.cub.2011.01.054] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2010] [Revised: 12/19/2010] [Accepted: 01/20/2011] [Indexed: 12/25/2022]
Abstract
Transcriptional repression is essential for establishing precise patterns of gene expression during development. Repressors governing early Drosophila segmentation can be classified as short- or long-range factors based on their ranges of action, acting either locally to quench adjacent activators or broadly to silence an entire locus. Paradoxically, these repressors recruit common corepressors, Groucho and CtBP, despite their different ranges of repression. To reveal the mechanisms underlying these two distinct modes of repression, we performed chromatin analysis using the prototypical long-range repressor Hairy and the short-range repressor Knirps. Chromatin immunoprecipitation and micrococcal nuclease mapping studies reveal that Knirps causes local changes of histone density and acetylation, and the inhibition of activator recruitment, without affecting the recruitment of basal transcriptional machinery. In contrast, Hairy induces widespread histone deacetylation and inhibits the recruitment of basal machinery without inducing chromatin compaction. Our study provides detailed mechanistic insight into short- and long-range repression on selected endogenous target genes and suggests that the transcriptional corepressors can be differentially deployed to mediate chromatin changes in a context-dependent manner.
Collapse
Affiliation(s)
- Li M Li
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI 48824-1319, USA
| | | |
Collapse
|
14
|
Payankaulam S, Li LM, Arnosti DN. Transcriptional repression: conserved and evolved features. Curr Biol 2011; 20:R764-71. [PMID: 20833321 DOI: 10.1016/j.cub.2010.06.037] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
The regulation of gene expression by transcriptional repression is an ancient and conserved mechanism that manifests itself in diverse ways. Here we summarize conserved pathways for transcriptional repression prevalent throughout all forms of life, as well as indirect mechanisms that appear to have originated in eukaryotes, consistent with the unique chromatin environment of eukaryotic genes. The direct interactions between transcriptional repressors and the core transcriptional machinery in bacteria and archaea are sufficient to generate a sophisticated suite of mechanisms that provide flexible control. These direct interactions contrast with the activity of corepressors, which provide an additional regulatory control in eukaryotes. Their modulation of chromatin structure represents an indirect pathway to downregulate transcription, and their diversity and modulation provide additional complexity suited to the requirements of elaborate eukaryotic repression patterns. New findings indicate that corepressors are not necessarily restricted to generating a single stereotypic output, but can rather exhibit diverse functional responses depending on the context in which they are recruited, providing a hitherto unsuspected additional source of diversity in transcriptional control. Mechanisms within eukaryotes appear to be highly conserved, with novel aspects chiefly represented by addition of lineage-specific corepressor scaffolds that provide additional opportunities for recruiting the same core machinery.
Collapse
Affiliation(s)
- Sandhya Payankaulam
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48910, USA
| | | | | |
Collapse
|
15
|
Winkler CJ, Ponce A, Courey AJ. Groucho-mediated repression may result from a histone deacetylase-dependent increase in nucleosome density. PLoS One 2010; 5:e10166. [PMID: 20405012 PMCID: PMC2854148 DOI: 10.1371/journal.pone.0010166] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2010] [Accepted: 03/21/2010] [Indexed: 01/19/2023] Open
Abstract
Groucho (Gro) is a Drosophila melanogaster transcriptional corepressor that directly interacts with the histone deacetylase Rpd3. Although previous studies suggest that this interaction is required for repression of Gro-responsive reporters in cultured cells, the in vivo significance of this interaction and the mechanism by which it leads to repression remain largely unexplored. In this study, we show that Gro is partially dependent on Rpd3 for repression, supporting the idea that Rpd3-mediated repression is one mode of Gro-mediated repression. We demonstrate that Gro colocalizes with Rpd3 to the chromatin of a target gene and that this is accompanied by the deacetylation of specific lysines within the N-terminal tails of histones H3 and H4. Gro overexpression leads to wing patterning defects and ectopic repression in the wing disc of transcription directed by the vestigial quadrant enhancer. These effects are reversed by the histone deacetylase inhibitors TSA and HC-Toxin and by the reduction of Rpd3 gene dosage. Furthermore, repression of the vestigial quadrant enhancer is accompanied by a Gro-mediated increase in nucleosome density, an effect that is reversed by histone deacetylase inhibitors. We propose a model in which Gro-mediated histone deacetylation results in increased nucleosome density leading to transcriptional repression.
Collapse
Affiliation(s)
- Clint J. Winkler
- Department of Chemistry and Biochemistry, University of California Los Angeles, Los Angeles, California, United States of America
| | - Alberto Ponce
- Department of Chemistry and Biochemistry, University of California Los Angeles, Los Angeles, California, United States of America
| | - Albert J. Courey
- Department of Chemistry and Biochemistry, University of California Los Angeles, Los Angeles, California, United States of America
- * E-mail:
| |
Collapse
|
16
|
Abstract
One of the most important decisions in development is whether to be male or female. In Drosophila melanogaster, most cells make this choice independent of their neighbors such that diploid cells with one X chromosome (XY) are male and those with two X chromosomes (XX) are female. X-chromosome number is relayed through regulatory proteins that act together to activate Sex-lethal (Sxl) in XX animals. The resulting SXL female specific RNA binding protein modulates the expression of a set of downstream genes, ultimately leading to sexually dimorphic structures and behaviors. Despite the apparent simplicity of this mechanism, Sxl activity is controlled by a host of transcriptional and posttranscriptional mechanisms that tailor its function to specific developmental scenarios. This review describes recent advances in our understanding of Sxl regulation and function, highlighting work that challenges some of the textbook views about this classical (often cited, yet poorly understood) binary switch gene.
Collapse
Affiliation(s)
- Helen K Salz
- Department of Genetics, Case Western Reserve University, Cleveland, OH, USA.
| | | |
Collapse
|