TheTrithorax-mimicAllele ofEnhancer of zesteRenders Active Domains of Target Genes Accessible toPolycomb-Group-Dependent Silencing inDrosophila melanogaster

AbstractTwo antagonistic groups of genes, the trithorax- and the Polycomb-group, are proposed to maintain the appropriate active or inactive state of homeotic genes set up earlier by transiently expressed segmentation genes. Although some details about the mechanism of maintenance are available, it is still unclear how the initially active or inactive chromatin domains are recognized by either the trithorax-group or the Polycomb-group proteins. We describe an unusual dominant allele of a Polycomb-group gene, Enhancer of zeste, which mimics the phenotype of loss-of-function mutations in trithorax-group genes. This mutation, named E(z)Trithorax mimic [E(z)Trm], contains a single-amino-acid substitution in the conserved SET domain. The strong dominant trithorax-like phenotypes elicited by this E(z) allele suggest that the mutated arginine-741 plays a critical role in distinguishing between active and inactive chromatin domains of the homeotic gene complexes. We have examined the modification of E(z)Trm phenotypes by mutant alleles of PcG and trxG genes and other mutations that alter the phosphorylation of nuclear proteins, covalent modifications of histones, or histone dosage. These data implicate some trxG genes in transcriptional repression as well as activation and provide genetic evidence for involvement of histone modifications in PcG/trxG-dependent transcriptional regulation.

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The domino gene of Drosophila encodes novel members of the SWI2/SNF2 family of DNA-dependent ATPases, which contribute to the silencing of homeotic genes

Development ◽

10.1242/dev.128.8.1429 ◽

2001 ◽

Vol 128 (8) ◽

pp. 1429-1441 ◽

Cited By ~ 6

Author(s):

M.L. Ruhf ◽

A. Braun ◽

O. Papoulas ◽

J.W. Tamkun ◽

N. Randsholt ◽

...

Keyword(s):

Polytene Chromosomes ◽

Gene Mutations ◽

Polycomb Group ◽

Protein Isoforms ◽

Homeotic Genes ◽

Loss Of Function ◽

Trithorax Group ◽

A Subunit ◽

The Common ◽

Hematopoietic Disorders

The Drosophila domino gene has been isolated in a screen for mutations that cause hematopoietic disorders. Generation and analysis of loss-of-function domino alleles show that the phenotypes are typical for proliferation gene mutations. Clonal analysis demonstrates that domino is necessary for cell viability and proliferation, as well as for oogenesis. domino encodes two protein isoforms of 3202 and 2498 amino acids, which contain a common N-terminal region but divergent C termini. The common region includes a 500 amino acid DNA-dependent ATPase domain of the SWI2/SNF2 family of proteins, which function via interaction with chromatin. We show that, although domino alleles do not exhibit homeotic phenotypes by themselves, domino mutations enhance Polycomb group mutations and counteract Trithorax group effects. The Domino proteins are present in large complexes in embryo extracts, and one isoform binds to a number of discrete sites on larval polytene chromosomes. Altogether, the data lead us to propose that domino acts as a repressor by interfering with chromatin structure. This activity is likely to be performed as a subunit of a chromatin-remodeling complex.

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DSP1, an HMG-like Protein, Is Involved in the Regulation of Homeotic Genes

Genetics ◽

10.1093/genetics/157.1.237 ◽

2001 ◽

Vol 157 (1) ◽

pp. 237-244

Author(s):

M Decoville ◽

E Giacomello ◽

M Leng ◽

D Locker

Keyword(s):

Null Allele ◽

Genetic Interaction ◽

Polycomb Group ◽

Homeotic Genes ◽

Loss Of Function ◽

Sex Combs Reduced ◽

Trithorax Group ◽

Sex Combs ◽

Normal Expression ◽

Sex Comb

Abstract The Drosophila dsp1 gene, which encodes an HMG-like protein, was originally identified in a screen for corepressors of Dorsal. Here we report that loss of dsp1 function causes homeotic transformations resembling those associated with loss of function in the homeotic genes Sex combs reduced (Scr), Ultrabithorax (Ubx), and Abdominal-B. The expression pattern of Scr is altered in dsp1 mutant imaginal discs, indicating that dsp1 is required for normal expression of this gene. Genetic interaction studies reveal that a null allele of dsp1 enhances trithorax-group gene (trx-G) mutations and partially suppresses Polycomb-group gene (Pc-G) mutations. On the contrary, overexpression of dsp1 induces an enhancement of the transformation of wings into halteres and of the extra sex comb phenotype of Pc. In addition, dsp1 male mutants exhibit a mild transformation of A4 into A5. Comparison of the chromatin structure at the Mcp locus in wild-type and dsp1 mutant embryos reveals that the 300-bp DNase I hypersensitive region is absent in a dsp1 mutant context. We propose that DSP1 protein is a chromatin remodeling factor, acting as a trx-G or a Pc-G protein depending on the considered function.

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white+ Transgene Insertions Presenting a Dorsal/Ventral Pattern Define a Single Cluster of Homeobox Genes That Is Silenced by the Polycomb-group Proteins in Drosophila melanogaster

Genetics ◽

10.1093/genetics/149.1.257 ◽

1998 ◽

Vol 149 (1) ◽

pp. 257-275 ◽

Cited By ~ 4

Author(s):

Sophie Netter ◽

Marie-Odile Fauvarque ◽

Ruth Diez del Corral ◽

Jean-Maurice Dura ◽

Dario Coen

Keyword(s):

Chromatin Structure ◽

Target Genes ◽

Position Effect ◽

Phenotypic Expression ◽

Positional Information ◽

Genomic Region ◽

Polycomb Group ◽

Position Effect Variegation ◽

Trithorax Group ◽

Clear Cut

AbstractWe used the white gene as an enhancer trap and reporter of chromatin structure. We collected white+ transgene insertions presenting a peculiar pigmentation pattern in the eye: white expression is restricted to the dorsal half of the eye, with a clear-cut dorsal/ventral (D/V) border. This D/V pattern is stable and heritable, indicating that phenotypic expression of the white reporter reflects positional information in the developing eye. Localization of these transgenes led us to identify a unique genomic region encompassing 140 kb in 69D1–3 subject to this D/V effect. This region contains at least three closely related homeobox-containing genes that are constituents of the iroquois complex (IRO-C). IRO-C genes are coordinately regulated and implicated in similar developmental processes. Expression of these genes in the eye is regulated by the products of the Polycomb -group (Pc-G) and trithorax-group (trx-G) genes but is not modified by classical modifiers of position-effect variegation. Our results, together with the report of a Pc -G binding site in 69D, suggest that we have identified a novel cluster of target genes for the Pc-G and trx-G products. We thus propose that ventral silencing of the whole IRO-C in the eye occurs at the level of chromatin structure in a manner similar to that of the homeotic gene complexes, perhaps by local compaction of the region into a heterochromatin-like structure involving the Pc-G products.

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A silencer is required for maintenance of transcriptional repression throughout Drosophila development

Development ◽

10.1242/dev.124.21.4343 ◽

1997 ◽

Vol 124 (21) ◽

pp. 4343-4350 ◽

Cited By ~ 4

Author(s):

A. Busturia ◽

C.D. Wightman ◽

S. Sakonju

Keyword(s):

Protein Interactions ◽

Transcriptional Repression ◽

Transcriptional Silencing ◽

Active Role ◽

Polycomb Group ◽

Homeotic Genes ◽

Protein Protein Interactions ◽

Drosophila Development ◽

Larval Stages ◽

Associated Proteins

Transcriptional silencing by the Polycomb Group of genes maintains the position-specific repression of homeotic genes throughout Drosophila development. The Polycomb Group of genes characterized to date encode chromatin-associated proteins that have been suggested to form heterochromatin-like structures. By studying the expression of reporter genes, we have identified a 725 bp fragment, called MCP725, in the homeotic gene Abdominal-B, that accurately maintains position-specific silencing during proliferation of imaginal cells. Silencing by MCP725 requires the Polycomb and the Polycomblike genes, indicating that it contains a Polycomb response element To investigate the mechanisms of transcriptional silencing by MCP725, we have studied its temporal requirements by removing MCP725 from the transgene at various times during development. We have discovered that excision of MCP725 during larval stages leads to loss of silencing. Our findings indicate that the silencer is required for the maintenance of the repressed state throughout cell proliferation. They also suggest that propagation of the silenced state does not occur merely by templating of a heterochromatin structure by virtue of protein-protein interactions. Rather, they suggest that silencers play an active role in the maintenance of the position-specific repression throughout development.

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Maintenance of the active and inactive states

Epigenetics, Nuclear Organization & Gene Function ◽

10.1093/oso/9780198831204.003.0007 ◽

2019 ◽

pp. 80-92

Author(s):

John C. Lucchesi

Keyword(s):

Transcriptional Repression ◽

Homologous Chromosome ◽

Regulatory Region ◽

Histone H3 ◽

Epigenetic Modifications ◽

Polycomb Group ◽

Histone H2a ◽

Trithorax Group ◽

Non Coding Rnas ◽

Somatic Pairing

The maintenance of a gene in an active or inactive state is carried out by epigenetic modifications of the histones and of the DNA itself. Two major classes of complexes (PRC1 and PRC2), containing Polycomb group (PcG) proteins mediate transcriptional repression. PRC2 trimethylates histone H3 at lysine 27, a modification that attracts PRC1 leading to the ubiquitination of histone H2A. Variant PRC1 complexes can be targeted first, and mono-ubiquitinated histone H2A recruits PRC2 complexes that serve as the target for canonical PRC1 complexes. PRC2 can be targeted to sites of repression by associating with long non-coding RNAs. Trithorax group (TrxG) proteins form complexes that counteract PcG-mediated repression. Some subunits of these complexes maintain and enhance transcription by carrying out different lysine methylations (H3K4me, H3K36me and H3K79me) that are associated with active gene function; other subunits remodel chromatin by displacing and repositioning nucleosomes. Additional effects on transcription are transvections, whereby somatic pairing allows the regulatory region of one allele of a gene to influence the activity of the promoter of the allele on the homologous chromosome

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Key Mechanisms of Early Lung Development

Pediatric and Developmental Pathology ◽

10.2350/07-06-0290.1 ◽

2007 ◽

Vol 10 (5) ◽

pp. 335-347 ◽

Cited By ~ 54

Author(s):

Jun Kimura ◽

Gail H. Deutsch

Keyword(s):

Respiratory Tract ◽

Cell Fate ◽

Target Genes ◽

Critical Role ◽

Hierarchical Classification ◽

Branching Morphogenesis ◽

Loss Of Function ◽

Innovative Strategies ◽

Downstream Target ◽

Molecular Events

Lung morphogenesis requires the integration of multiple regulatory factors, which results in a functional air-blood interface required for gas exchange at birth. The respiratory tract is composed of endodermally derived epithelium surrounded by cells of mesodermal origin. Inductive signaling between these 2 tissue compartments plays a critical role in formation and differentiation of the lung, which is mediated by evolutionarily conserved signaling families used reiteratively during lung formation, including the fibroblast growth factor, hedgehog, retinoic acid, bone morphogenetic protein, and Wnt signaling pathways. Cells coordinate their response to these signaling proteins largely through transcription factors, which determine respiratory cell fate and pattern formation via the activation and repression of downstream target genes. Gain- and loss-of-function studies in null mutant and transgenic mice models have greatly facilitated the identification and hierarchical classification of these molecular programs. In this review, we highlight select molecular events that drive key phases of pulmonary development, including specification of a lung cell fate, primary lung bud formation, tracheoesophageal septation, branching morphogenesis, and proximal-distal epithelial patterning. Understanding the genetic pathways that regulate respiratory tract development is essential to provide insight into the pathogenesis of congenital anomalies and to develop innovative strategies to treat inherited and acquired lung disease.

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YY1 DNA binding and interaction with YAF2 is essential for Polycomb recruitment

Nucleic Acids Research ◽

10.1093/nar/gkt1187 ◽

2013 ◽

Vol 42 (4) ◽

pp. 2208-2223 ◽

Cited By ~ 38

Author(s):

Arindam Basu ◽

Frank H. Wilkinson ◽

Kristen Colavita ◽

Colin Fennelly ◽

Michael L. Atchison

Keyword(s):

Dna Binding ◽

Biochemical Analysis ◽

Target Genes ◽

A Priori ◽

Epigenetic Inheritance ◽

Polycomb Group ◽

Homeotic Genes ◽

Functional Conservation ◽

Body Patterning ◽

Transcription Factor Yy1

Abstract Polycomb Group (PcG) proteins are crucial for epigenetic inheritance of cell identity and are functionally conserved from Drosophila to humans. PcG proteins regulate expression of homeotic genes and are essential for axial body patterning during development. Earlier we showed that transcription factor YY1 functions as a PcG protein. YY1 also physically interacts with YAF2, a homolog of RYBP. Here we characterize the mechanism and physiologic relevance of this interaction. We found phenotypic and biochemical correction of dRYBP mutant flies by mouse YAF2 demonstrating functional conservation across species. Further biochemical analysis revealed that YAF2 bridges interaction between YY1 and the PRC1 complex. ChIP assays in HeLa cells showed that YAF2 is responsible for PcG recruitment to DNA, which is mediated by YY1 DNA binding. Knock-down of YY1 abrogated PcG recruitment, which was not compensated by exogenous YAF2 demonstrating that YY1 DNA binding is a priori necessary for Polycomb assembly on chromatin. Finally, we found that although YAF2 and RYBP regulate a similar number of Polycomb target genes, there are very few genes that are regulated by both implying functional distinction between the two proteins. We present a model of YAF2-dependent and independent PcG DNA recruitment by YY1.

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Histone H2AK119 Mono-Ubiquitination is Essential for Polycomb-Mediated Transcriptional Repression

10.1101/690461 ◽

2019 ◽

Cited By ~ 3

Author(s):

Simone Tamburri ◽

Elisa Lavarone ◽

Daniel Fernández-Pérez ◽

Marika Zanotti ◽

Daria Manganaro ◽

...

Keyword(s):

Cross Talk ◽

Transcriptional Repression ◽

Target Genes ◽

Human Tumors ◽

Polycomb Group ◽

Polycomb Group Proteins ◽

Major Function ◽

Cellular Identity

ABSTRACTThe major function of Polycomb group proteins (PcG) is to maintain transcriptional repression to preserve cellular identity. This is exerted by two distinct repressive complexes, PRC1 and PRC2, that modify histones by depositing H2AK119ub1 and H3K27me3, respectively. Both complexes are essential for development and are deregulated in several types of human tumors. PRC1 and PRC2 exist in different variants and show a complex regulatory cross-talk. However, the contribution that H2AK119ub1 plays in mediating PcG repressive functions remains largely controversial. Coupling an inducible system with the expression of a fully catalytic inactive RING1B mutant, we demonstrated that H2AK119ub1 deposition is essential to maintain PcG-target genes repressed in ESC. Loss of H2AK119ub1 induced a rapid displacement of PRC2 activity and a loss of H3K27me3 deposition. This affected both PRC2.1 and PRC2.2 variants and further correlated with a strong displacement and destabilization of canonical PRC1. Finally, we find that variant PRC1 forms can sense H2AK119ub1 deposition, which contributes to their stabilization specifically at sites where this modification is highly enriched. Overall our data place H2AK119ub1 deposition as central hub that mount PcG repressive machineries to preserve cell transcriptional identity.

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Polycomb-group recruitment to a Drosophila target gene is the default state that is inhibited by a transcriptional activator

Science Advances ◽

10.1126/sciadv.abg1556 ◽

2021 ◽

Vol 7 (29) ◽

pp. eabg1556

Author(s):

Elnaz Ghotbi ◽

Piao Ye ◽

Taylor Ervin ◽

Anni Kum ◽

Judith Benes ◽

...

Keyword(s):

Transcriptional Repression ◽

Target Gene ◽

Target Genes ◽

De Novo ◽

Polycomb Group ◽

Polycomb Repressive Complex 2 ◽

Repressive Chromatin ◽

Group Recruitment ◽

Default State ◽

Present Experimental Evidence

Polycomb-group (PcG) proteins are epigenetic regulators that maintain the transcriptional repression of target genes following their initial repression by transcription factors. PcG target genes are repressed in some cells, but active in others. Therefore, a mechanism must exist by which PcG proteins distinguish between the repressed and active states and only assemble repressive chromatin environments at target genes that are repressed. Here, we present experimental evidence that the repressed state of a Drosophila PcG target gene, giant (gt), is not identified by the presence of a repressor. Rather, de novo establishment of PcG-mediated silencing at gt is the default state that is prevented by the presence of an activator or coactivator, which may inhibit the catalytic activity of Polycomb-repressive complex 2 (PRC2).

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Differential Contributions of DNA-Binding Proteins to Polycomb Response Element Activity at the Drosophila giant Gene

Genetics ◽

10.1534/genetics.119.302981 ◽

2020 ◽

Vol 214 (3) ◽

pp. 623-634

Author(s):

Elnaz Ghotbi ◽

Kristina Lackey ◽

Vicki Wong ◽

Katie T. Thompson ◽

Evan G. Caston ◽

...

Keyword(s):

Dna Binding ◽

Dna Sequences ◽

Transcriptional Repression ◽

Binding Proteins ◽

Target Genes ◽

Dna Binding Proteins ◽

Polycomb Group ◽

Link Type ◽

Element Activity

Polycomb-group (PcG) proteins are evolutionarily conserved epigenetic regulators whose primary function is to maintain the transcriptional repression of target genes. Recruitment of Drosophila melanogaster PcG proteins to target genes requires the presence of one or more Polycomb Response Elements (PREs). The functions or necessity for more than one PRE at a gene are not clear and individual PREs at some loci may have distinct regulatory roles. Various combinations of sequence-specific DNA-binding proteins are present at a given PRE, but only Pleiohomeotic (Pho) is present at all strong PREs. The giant (gt) locus has two PREs, a proximal PRE1 and a distal PRE2. During early embryonic development, Pho binds to PRE1 ∼30-min prior to stable binding to PRE2. This observation indicated a possible dependence of PRE2 on PRE1 for PcG recruitment; however, we find here that PRE2 recruits PcG proteins and maintains transcriptional repression independently of Pho binding to PRE1. Pho-like (Phol) is partially redundant with Pho during larval development and binds to the same DNA sequences in vitro. Although binding of Pho to PRE1 is dependent on the presence of consensus Pho-Phol-binding sites, Phol binding is less so and appears to play a minimal role in recruiting other PcG proteins to gt. Another PRE-binding protein, Sp1/Kruppel-like factor, is dependent on the presence of Pho for PRE1 binding. Further, we show that, in addition to silencing gene expression, PcG proteins dampen transcription of an active gene.

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