A Polycomb and GAGA Dependent Silencer Adjoins the Fab-7 Boundary in the Drosophila Bithorax Complex

The homeotic genes of the Drosophila bithorax complex are controlled by a large cis-regulatory region that ensures their segmentally restricted pattern of expression. A deletion that removes the Frontabdominal-7 cis-regulatory region (Fab-71) dominantly transforms parasegment 11 into parasegment 12. Previous studies suggested that removal of a domain boundary element on the proximal side of Fab-71 is responsible for this gain-of-function phenotype. In this article we demonstrate that the Fab-71 deletion also removes a silencer element, the iab-7 PRE, which maps to a different DNA segment and plays a different role in regulating parasegment-specific expression patterns of the Abd-B gene. The iab-7 PRE mediates pairing-sensitive silencing of mini-white, and can maintain the segmentally restricted expression pattern of a BXD, Ubx/lacZ reporter transgene. Both silencing activities depend upon Polycomb Group proteins. Pairing-sensitive silencing is relieved by removing the transvection protein Zeste, but is enhanced in a novel pairing-independent manner by the zeste1 allele. The iab-7 PRE silencer is contained within a 0.8-kb fragment that spans a nuclease hypersensitive site, and silencing appears to depend on the chromatin remodeling protein, the GAGA factor.

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In situ dissection of the Fab-7 region of the bithorax complex into a chromatin domain boundary and a Polycomb-response element

Development ◽

10.1242/dev.124.9.1809 ◽

1997 ◽

Vol 124 (9) ◽

pp. 1809-1820 ◽

Cited By ~ 5

Author(s):

J. Mihaly ◽

I. Hogga ◽

J. Gausz ◽

H. Gyurkovics ◽

F. Karch

Keyword(s):

Boundary Element ◽

Domain Boundary ◽

P Element ◽

Chromatin Domain ◽

Homeotic Genes ◽

Bithorax Complex ◽

Specific Expression ◽

Response Element ◽

Regulatory Domains ◽

Polycomb Response Element

Parasegmental (PS)-specific expression of the homeotic genes of the bithorax-complex (BX-C) appears to depend upon the subdivision of the complex into a series of functionally independent cis-regulatory domains. Fab-7 is a regulatory element that lies between iab-6 and iab-7 (the PS11- and PS12-specific cis-regulatory domains, respectively). Deletion of Fab-7 causes ectopic expression of iab-7 in PS11 (where normally only iab-6 is active). Two models have been proposed to account for the dominant Fab-7 phenotype. The first considers that Fab-7 functions as a boundary element that insulates iab-6 and iab-7. The second model envisages that Fab-7 contains a silencer element that keeps iab-7 repressed in parasegments anterior to PS12. Using a P-element inserted in the middle of the Fab-7 region (the bit transposon), we have generated an extensive collection of new Fab-7 mutations that allow us to subdivide Fab-7 into a boundary element and a Polycomb-respond element (PRE). The boundary lies within 1 kb of DNA on the proximal side of the bit transposon (towards iab-6). Deletions removing this element alone cause a complex gain- and loss-of-function phenotype in PS11; in some groups of cells, both iab-6 and iab-7 are active, while in others both iab-6 and iab-7 are inactive. Thus, deletion of the boundary allows activating as well as repressing activities to travel between iab-6 and iab-7. We also provide evidences that the boundary region contains an enhancer blocker element. The Polycomb-response element lies within 0.5 kb of DNA immediately distal to the boundary (towards iab-7). Deletions removing the PRE alone do not typically cause any visible phenotype as homozygotes. Interestingly, weak ectopic activation of iab-7 is observed in hemizygous PRE deletions, suggesting that the mechanisms that keep iab-7 repressed in the absence of this element may depend upon chromosome pairing. These results help to reconcile the previously contradictory models on Fab-7 function and to shed light on how a chromatin domain boundary and a nearby PRE concur in the setting up of the appropriate PS-specific expression of the Abd-B gene of the BX-C.

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Transcription through Intergenic Chromosomal Memory Elements of the Drosophila Bithorax Complex Correlates with an Epigenetic Switch

Molecular and Cellular Biology ◽

10.1128/mcb.22.22.8026-8034.2002 ◽

2002 ◽

Vol 22 (22) ◽

pp. 8026-8034 ◽

Cited By ~ 99

Author(s):

Gerhard Rank ◽

Matthias Prestel ◽

Renato Paro

Keyword(s):

Memory Function ◽

Polycomb Group ◽

Published Data ◽

Homeotic Genes ◽

Bithorax Complex ◽

Memory Element ◽

Cellular Memory ◽

Response Elements ◽

Group Response ◽

Differential Expression Pattern

ABSTRACT The proteins of the trithorax and Polycomb groups maintain the differential expression pattern of homeotic genes established by the early embryonic patterning system during development. These proteins generate stable and heritable chromatin structures by acting via particular chromosomal memory elements. We established a transgenic assay system showing that the Polycomb group response elements bxd and Mcp confer epigenetic inheritance throughout development. With previously published data for the Fab7 cellular memory module, we confirmed the cellular memory function of Polycomb group response elements. In Drosophila melanogaster, several of these memory elements are located in the large intergenic regulatory regions of the homeotic bithorax complex. Using a transgene assay, we showed that transcription through a memory element correlated with the relief of silencing imposed by the Polycomb group proteins and established an epigenetically heritable active chromatin mode. A memory element remodeled by the process of transcription was able to maintain active expression of a reporter gene throughout development. Thus, transcription appears to reset and change epigenetic marks at chromosomal memory elements regulated by the Polycomb and trithorax proteins. Interestingly, in the bithorax complex of D. melanogaster, the segment-specific expression of noncoding intergenic transcripts during embryogenesis seems to fulfill this switching role for memory elements regulating the homeotic genes.

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H3K27 modifications define segmental regulatory domains in the Drosophila bithorax complex

eLife ◽

10.7554/elife.02833 ◽

2014 ◽

Vol 3 ◽

Cited By ~ 69

Author(s):

Sarah K Bowman ◽

Aimee M Deaton ◽

Heber Domingues ◽

Peggy I Wang ◽

Ruslan I Sadreyev ◽

...

Keyword(s):

Drosophila Melanogaster ◽

Binding Protein ◽

Histone H3 ◽

Polycomb Group ◽

Homeotic Genes ◽

Bithorax Complex ◽

Body Segment ◽

Regulatory Domains ◽

Definition Of ◽

Identity Expression

The bithorax complex (BX-C) in Drosophila melanogaster is a cluster of homeotic genes that determine body segment identity. Expression of these genes is governed by cis-regulatory domains, one for each parasegment. Stable repression of these domains depends on Polycomb Group (PcG) functions, which include trimethylation of lysine 27 of histone H3 (H3K27me3). To search for parasegment-specific signatures that reflect PcG function, chromatin from single parasegments was isolated and profiled. The H3K27me3 profiles across the BX-C in successive parasegments showed a ‘stairstep’ pattern that revealed sharp boundaries of the BX-C regulatory domains. Acetylated H3K27 was broadly enriched across active domains, in a pattern complementary to H3K27me3. The CCCTC-binding protein (CTCF) bound the borders between H3K27 modification domains; it was retained even in parasegments where adjacent domains lack H3K27me3. These findings provide a molecular definition of the homeotic domains, and implicate precisely positioned H3K27 modifications as a central determinant of segment identity.

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pipsqueak Encodes a Factor Essential for Sequence-Specific Targeting of a Polycomb Group Protein Complex

Molecular and Cellular Biology ◽

10.1128/mcb.22.17.6261-6271.2002 ◽

2002 ◽

Vol 22 (17) ◽

pp. 6261-6271 ◽

Cited By ~ 50

Author(s):

Der-Hwa Huang ◽

Yuh-Long Chang ◽

Chih-Chao Yang ◽

I-Ching Pan ◽

Balas King

Keyword(s):

Protein Complex ◽

Specific Binding ◽

Binding Activity ◽

Polycomb Group ◽

Homeotic Genes ◽

Polycomb Group Protein ◽

Gaga Factor ◽

Dna Binding Activity ◽

Group Protein ◽

Functional Relevance

ABSTRACT The Polycomb (Pc) group (Pc-G) of repressors is essential for transcriptional silencing of homeotic genes that determine the axial development of metazoan animals. It is generally believed that the multimeric complexes formed by these proteins nucleate certain chromatin structures to silence promoter activity upon binding to Pc-G response elements (PRE). Little is known, however, about the molecular mechanism involved in sequence-specific binding of these complexes. Here, we show that an immunoaffinity-purified Pc protein complex contains a DNA binding activity specific to the (GA) n motif in a PRE from the bithoraxoid region. We found that this activity can be attributed primarily to the large protein isoform encoded by pipsqueak (psq) instead of to the well-characterized GAGA factor. The functional relevance of psq to the silencing mechanism is strongly supported by its synergistic interactions with a subset of Pc-G that cause misexpression of homeotic genes.

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Overlapping genes in Nalp6/PYPAF5 locus encode two V2-type vasopressin isoreceptors: angiotensin-vasopressin receptor (AVR) and non-AVR

Physiological Genomics ◽

10.1152/physiolgenomics.00199.2007 ◽

2008 ◽

Vol 34 (1) ◽

pp. 65-77 ◽

Cited By ~ 8

Author(s):

Victoria L. M. Herrera ◽

Pia Bagamasbad ◽

Tamara Didishvili ◽

Julius L. Decano ◽

Nelson Ruiz-Opazo

Keyword(s):

Core Promoter ◽

Expression Patterns ◽

Regulatory Region ◽

Gene Arrangement ◽

Vasopressin Receptor ◽

Ang Ii ◽

Binding Studies ◽

Specific Expression ◽

Vasopressin Receptors ◽

Stimulation Of

The angiotensin-vasopressin receptor (AVR) responds with equivalent affinities to angiotensin II (ANG II) and vasopressin and is coupled to adenylate cyclase and hence a V2-type vasopressin receptor. AVR maps to the Nalp6 locus and overlaps with the larger Nalp6/PYPAF5 reported to be a T cell/granulocyte-specific, cytoplasmic-specific proapoptotic protein, thus questioning the existence of AVR. Here we confirm, through different experimental modalities, that AVR is distinct from Nalp6/PYPAF5 based on different mRNA and protein sizes, subcellular localization, and tissue-specific expression patterns. Binding studies of PYPAF5-specific Cos1 transfectants detect high-affinity binding to vasopressin but not ANG II, thus assigning PYPAF5 as a non-AVR (NAVR). Signaling array analysis reveals that AVP stimulation of AVR- and NAVR-specific Cos1 transfectants results in diametrical activation as well as coactivation of signaling pathways known to mediate renal sodium and water balance. Likewise, ANG II stimulation of Cos1-AVR transfectants reveals a signaling profile distinct from that of AVP-stimulated Cos1-AVR transfectants. Analysis of genomic organization of the AVR/NAVR locus shows an overlapping gene arrangement with alternative promoter usage resulting in different NH2 termini for NAVR and AVR. In addition to core promoter elements, androgen and estrogen response elements are detected. Promoter analysis of NAVR/AVR 5′-regulatory region detects transcriptional upregulation by testosterone and synergistic upregulation by testosterone and estrogen, thus suggesting that AVR and/or NAVR contribute to sex-specific V2-type vasopressin-mediated effects. Altogether, confirmation of AVR and identification of NAVR as vasopressin receptors are concordant with emerging vasopressin functions not attributable to V1a, V1b, or V2 receptors and add molecular bases for the multifunctional complexity of vasopressin-mediated functions and regulation.

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Genome-wide Identification and Abiotic Stress Response Pattern Analysis of NF-Y Gene Family in Peanut (Arachis Hypogaea L.)

Tropical Plant Biology ◽

10.1007/s12042-021-09295-2 ◽

2021 ◽

Author(s):

Qian Wan ◽

Lu Luo ◽

Xiurong Zhang ◽

Yuying Lv ◽

Suqing Zhu ◽

...

Keyword(s):

Abiotic Stress ◽

Stress Response ◽

Gene Family ◽

Developmental Stages ◽

Expression Patterns ◽

Regulatory Region ◽

Amino Acid Sequences ◽

Start Codon ◽

Abiotic Stress Response ◽

Specific Expression

AbstractThe nuclear factor Y (NF-Y) transcription factor (TF) family consists of three subfamilies NF-YA, NF-YB and NF-YC. Many studies have proven that NF-Y complex plays multiple essential roles in stress response in Arabidopsis and other plant species. However, little attention has been given to these genes in peanut. In this study, thirty-three AhNF-Y genes were identified in cultivated peanut and they were distributed on 16 chromosomes. A phylogenetic analysis of the NF-Y amino acid sequences indicated that the peanut NF-Y proteins were clustered in pairs at the end of the branches and showed high conservation with previous reported plant NF-Ys. Evolutionary history analysis showed that only segmental duplication contributed to expansion of this gene family. Analysis of the 1500-bp regulatory regions upstream the start codon showed that, except for AhNF-YB6, peanut NF-Ys contained at least one abiotic stress response element in their regulatory region. Expression patterns of peanut NF-Ys in 22 tissues and developmental stages were analyzed. A few NF-Ys showed universal expression patterns, while most NF-Ys showed specific expression patterns. Through RNA-seq and qRT-PCR analyses, expression of six AhNF-Y genes was induced under salt stress in leaves or roots. In addition, AhNF-YA4/8/11, NF-YB4 and NF-YC2/8 also responded to osmotic stress, ABA (abscisic acid) and salicylic acid (SA) treatment.

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TheDrosophilaTrithorax protein is a coactivator required to prevent re-establishment of Polycomb silencing

Development ◽

10.1242/dev.129.10.2483 ◽

2002 ◽

Vol 129 (10) ◽

pp. 2483-2493 ◽

Cited By ~ 1

Author(s):

Sylvain Poux ◽

Béatrice Horard ◽

Christian J. A. Sigrist ◽

Vincenzo Pirrotta

Keyword(s):

Imaginal Discs ◽

Polycomb Group ◽

Active State ◽

Homeotic Genes ◽

Epigenetic Memory ◽

Gaga Factor ◽

Response Elements ◽

Active Gene ◽

Polycomb Response Elements

Polycomb group (PcG) and Trithorax (TRX) complexes assemble at Polycomb response elements (PREs) and maintain respectively the repressed and active state of homeotic genes. Although PcG and TRX complexes are distinct, their binding to some PRE fragments in vitro depends on GAGA motifs. GAGA factor immunoprecipitates with both complexes. In presence of a PRE, TRX stimulates expression and prevents the return of repression at later stages. When TRX levels are reduced, repression is re-established in inappropriate regions of imaginal discs, suggesting that TRX insufficiency impairs the epigenetic memory of the active state. Targeting a GAL-TRX fusion shows that TRX is a coactivator that stimulates expression of an active gene but cannot initiate expression by itself. Targeting a histone acetylase to a PRE does not affect embryonic silencing but causes a loss of memory in imaginal discs, suggesting that deacetylation is required to establish the memory of the repressed state.

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Trithorax- and Polycomb-Group Response Elements within an Ultrabithorax Transcription Maintenance Unit Consist of Closely Situated but Separable Sequences

Molecular and Cellular Biology ◽

10.1128/mcb.19.7.5189 ◽

1999 ◽

Vol 19 (7) ◽

pp. 5189-5202 ◽

Cited By ~ 70

Author(s):

Sergei Tillib ◽

Svetlana Petruk ◽

Yurii Sedkov ◽

Alexander Kuzin ◽

Miki Fujioka ◽

...

Keyword(s):

Dna Sequences ◽

Protein Complexes ◽

Expression Patterns ◽

Regulatory Region ◽

Protein Product ◽

Polycomb Group ◽

Response Elements ◽

Complex Element ◽

Group Response

ABSTRACT In Drosophila, two classes of genes, thetrithorax group and the Polycomb group, are required in concert to maintain gene expression by regulating chromatin structure. We have identified Trithorax protein (TRX) binding elements within the bithorax complex and have found that within thebxd/pbx regulatory region these elements are functionally relevant for normal expression patterns in embryos and confer TRX binding in vivo. TRX was localized to three closely situated sites within a 3-kb chromatin maintenance unit with a modular structure. Results of an in vivo analysis showed that these DNA fragments (each ∼400 bp) contain both TRX- and Polycomb-group response elements (TREs and PREs) and that in the context of the endogenousUltrabithorax gene, all of these elements are essential for proper maintenance of expression in embryos. Dissection of one of these maintenance modules showed that TRX- and Polycomb-group responsiveness is conferred by neighboring but separable DNA sequences, suggesting that independent protein complexes are formed at their respective response elements. Furthermore, we have found that the activity of this TRE requires a sequence (∼90 bp) which maps to within several tens of base pairs from the closest neighboring PRE and that the PRE activity in one of the elements may require a binding site for PHO, the protein product of the Polycomb-group genepleiohomeotic. Our results show that long-range maintenance of Ultrabithorax expression requires a complex element composed of cooperating modules, each capable of interacting with both positive and negative chromatin regulators.

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Transcription through the iab-7 cis-regulatory domain of the bithorax complex interferes with maintenance of Polycomb-mediated silencing

Development ◽

10.1242/dev.129.21.4915 ◽

2002 ◽

Vol 129 (21) ◽

pp. 4915-4922 ◽

Cited By ~ 1

Author(s):

Ilham Hogga ◽

François Karch

Keyword(s):

Domain Boundary ◽

Regulatory Region ◽

Chromatin Domain ◽

Dependent Manner ◽

Regulatory Domain ◽

Bithorax Complex ◽

Regulatory Domains ◽

Repression Complex ◽

Ectopic Activation ◽

Functional Autonomy

The Fab-7 chromatin domain boundary insures functional autonomy of the iab-6 and iab-7 cis-regulatory domains in the bithorax complex (BX-C). We have previously shown that chromatin insulators such asgypsy or scsmin are potent insulators that cannot substitute for Fab-7 function within the BX-C. During the early stages of these swapping experiments, we initially used a fragment of scs that was slightly larger than a minimal scs element (scsmin). We report that this scs fragment, unlike scsmin, interferes in an orientation-dependent manner with the output of a regulatory region covering 80 kb of DNA (from iab-4 to iab-8). At the core of this orientation-dependent phenotype is a promoter located immediately adjacent to the scs insulator. In one orientation, the promoter traps the activity of theiab-3 through iab-5 cis-regulatory domains, diverting them from the abd-A gene. In the opposite orientation, the promoter is transcribing the iab-7 cis-regulatory domain, resulting in ectopic activation of the latter. Our data suggest that transcription through aPolycomb-Response Element (PRE) interferes with the maintenance of aPolycomb repression complex.

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The rat elastase I regulatory element is an enhancer that directs correct cell specificity and developmental onset of expression in transgenic mice

Molecular and Cellular Biology ◽

10.1128/mcb.7.8.2956-2967.1987 ◽

1987 ◽

Vol 7 (8) ◽

pp. 2956-2967

Author(s):

R E Hammer ◽

G H Swift ◽

D M Ornitz ◽

C J Quaife ◽

R D Palmiter ◽

...

Keyword(s):

Fusion Gene ◽

Regulatory Element ◽

Regulatory Region ◽

Human Growth ◽

Transgenic Animals ◽

Growth Hormone Gene ◽

Flanking Sequence ◽

Transcriptional Enhancer ◽

Independent Manner ◽

Specific Expression

A total of 134 base pairs of the 5' flanking sequence of the elastase I gene is sufficient and necessary to direct expression of the passive human growth hormone gene (hGH) to the exocrine pancreas. We demonstrate that this elastase I regulatory region contains a transcriptional enhancer which directs acinar cell-specific expression in transgenic animals. The elastase I enhancer specifies correct expression of the linked hGH gene in an orientation- and position-independent manner and can activate a heterologous promoter. The enhancer also directs the appropriate temporal activation of the hGH gene in the developing pancreas. Transcription is initiated correctly for the elastase I or hGH promoter, and the transcripts are correctly processed regardless of the enhancer position within or outside the fusion gene. The elastase I enhancer generates coincident DNase I-hypersensitive sites in pancreatic chromatin when moved 3 kilobases upstream or within the first intron of the hGH gene and when associated with the hGH promoter.

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