scholarly journals Characterization of the Polycomb Group Response Elements of the Drosophila melanogaster invected Locus

2009 ◽  
Vol 30 (3) ◽  
pp. 820-828 ◽  
Author(s):  
Melissa D. Cunningham ◽  
J. Lesley Brown ◽  
Judith A. Kassis
Keyword(s):  
Drosophila Melanogaster ◽  
Binding Sites ◽  
Expression Patterns ◽  
Vital Role ◽  
Polycomb Group ◽  
Response Elements ◽  
Dna Binding Sites ◽  
Group Response ◽  
Dna Elements ◽  
Regulatory Dna

ABSTRACT The Polycomb group proteins (PcGs) play a vital role throughout development by maintaining precise gene expression patterns. In Drosophila melanogaster, PcG-mediated gene silencing is achieved through DNA elements called Polycomb response elements (PREs); however, the mechanism for establishing silencing and the requirements and composition of a working PRE are not fully understood. We have used the computer program jPREdictor to uncover PREs located within the invected (inv) locus. The functionalities of these predicted PREs were tested in two different assays: one analyzing their abilities to maintain expression of a β-galactosidase reporter gene and the other evaluating their abilities to establish pairing-sensitive silencing of the mini-white reporter in the vector pCaSpeR. We have identified two previously uncharacterized PREs at the inv gene and demonstrate that they produce similar results in the two assays. Our results indicate that clusters of protein binding sites do not accurately predict PREs and provide new insight into the DNA sequence requirements for the binding of the PcG protein Pho. Finally, our data show that PREs and regulatory DNA from different genes can function together to establish PcG-mediated silencing, highlighting the versatility of PREs despite discrepancies in the number and location of DNA binding sites.

scholarly journals DNA sequence models of genome-wide Drosophila melanogaster Polycomb binding sites improve generalization to independent Polycomb Response Elements

2019 ◽  
Vol 47 (15) ◽  
pp. 7781-7797 ◽  
Author(s):  
Bjørn André Bredesen ◽  
Marc Rehmsmeier
Keyword(s):  
Drosophila Melanogaster ◽  
Sequence Similarity ◽  
Sequence Motifs ◽  
Chromatin Binding ◽  
Training Set ◽  
Response Elements ◽  
Genome Wide ◽  
Dna Elements ◽  
Polycomb Response Elements ◽  
Regulatory Dna

Abstract Polycomb Response Elements (PREs) are cis-regulatory DNA elements that maintain gene transcription states through DNA replication and mitosis. PREs have little sequence similarity, but are enriched in a number of sequence motifs. Previous methods for modelling Drosophila melanogaster PRE sequences (PREdictor and EpiPredictor) have used a set of 7 motifs and a training set of 12 PREs and 16-23 non-PREs. Advances in experimental methods for mapping chromatin binding factors and modifications has led to the publication of several genome-wide sets of Polycomb targets. In addition to the seven motifs previously used, PREs are enriched in the GTGT motif, recently associated with the sequence-specific DNA binding protein Combgap. We investigated whether models trained on genome-wide Polycomb sites generalize to independent PREs when trained with control sequences generated by naive PRE models and including the GTGT motif. We also developed a new PRE predictor: SVM-MOCCA. Training PRE predictors with genome-wide experimental data improves generalization to independent data, and SVM-MOCCA predicts the majority of PREs in three independent experimental sets. We present 2908 candidate PREs enriched in sequence and chromatin signatures. 2412 of these are also enriched in H3K4me1, a mark of Trithorax activated chromatin, suggesting that PREs/TREs have a common sequence code.

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

1999 ◽  
Vol 19 (7) ◽  
pp. 5189-5202 ◽  
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.

scholarly journals P-Element Homing Is Facilitated by engrailed Polycomb-Group Response Elements in Drosophila melanogaster

PLoS ONE ◽  
2012 ◽  
Vol 7 (1) ◽  
pp. e30437 ◽  
Author(s):  
Yuzhong Cheng ◽  
Deborah Y. Kwon ◽  
Allison L. Arai ◽  
Diane Mucci ◽  
Judith A. Kassis
Keyword(s):  
Drosophila Melanogaster ◽  
Polycomb Group ◽  
P Element ◽  
Response Elements ◽  
Group Response

scholarly journals The role of Polycomb-group response elements in regulation of engrailed transcription in Drosophila

Development ◽  
2008 ◽  
Vol 135 (4) ◽  
pp. 669-676 ◽  
Author(s):  
S. K. DeVido ◽  
D. Kwon ◽  
J. L. Brown ◽  
J. A. Kassis
Keyword(s):  
Polycomb Group ◽  
Response Elements ◽  
Group Response

scholarly journals Structure and function of an ectopic Polycomb chromatin domain

2019 ◽  
Vol 5 (1) ◽  
pp. eaau9739 ◽  
Author(s):  
Sandip De ◽  
Yuzhong Cheng ◽  
Ming-an Sun ◽  
Natalie D. Gehred ◽  
Judith A. Kassis
Keyword(s):  
Domain Structure ◽  
Regulatory Elements ◽  
Structure And Function ◽  
Polycomb Group ◽  
Chromatin Domain ◽  
Repressive Mark ◽  
Group Response ◽  
Dna Elements ◽  
And Function

Polycomb group proteins (PcGs) drive target gene repression and form large chromatin domains. InDrosophila, DNA elements known as Polycomb group response elements (PREs) recruit PcGs to the DNA. We have shown that, within theinvected-engrailed(inv-en) Polycomb domain, strong, constitutive PREs are dispensable for Polycomb domain structure and function. We suggest that the endogenous chromosomal location imparts stability to this Polycomb domain. To test this possibility, a 79-kbentransgene was inserted into other chromosomal locations. This transgene is functional and forms a Polycomb domain. The spreading of the H3K27me3 repressive mark, characteristic of PcG domains, varies depending on the chromatin context of the transgene. Unlike at the endogenous locus, deletion of the strong, constitutive PREs from the transgene leads to both loss- and gain-of function phenotypes, demonstrating the important role of these regulatory elements. Our data show that chromatin context plays an important role in Polycomb domain structure and function.

The nuclear organization of Polycomb/Trithorax group response elements in larval tissues of Drosophila melanogaster

2008 ◽  
Vol 16 (4) ◽  
pp. 649-673 ◽  
Author(s):  
Elena Fedorova ◽  
Nicolas Sadoni ◽  
Ina K. Dahlsveen ◽  
Jeannette Koch ◽  
Elisabeth Kremmer ◽  
...  
Keyword(s):  
Drosophila Melanogaster ◽  
Nuclear Organization ◽  
Trithorax Group ◽  
Response Elements ◽  
Group Response

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

2002 ◽  
Vol 22 (22) ◽  
pp. 8026-8034 ◽  
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.

scholarly journals Recruitment of components of Polycomb Group chromatin complexes in Drosophila

Development ◽  
2001 ◽  
Vol 128 (1) ◽  
pp. 75-85 ◽  
Author(s):  
S. Poux ◽  
D. McCabe ◽  
V. Pirrotta
Keyword(s):  
Binding Sites ◽  
Imaginal Discs ◽  
Polycomb Group ◽  
Dna Binding Domain ◽  
Response Elements ◽  
Nuclear Extracts ◽  
Polycomb Response Elements ◽  
Polycomb Group Complexes ◽  
State Of Activity

Polycomb Group complexes assemble at polycomb response elements (PREs) in vivo and silence genes in the surrounding chromatin. To study the recruitment of silencing complexes, we have targeted various Polycomb Group (PcG) proteins by fusing them to the LexA DNA binding domain. When LexA-PC, -PSC, -PH or -SU(Z)2 are targeted to a reporter gene, they recruit functional PcG-silencing complexes that recapitulate the silencing behavior of a PRE: silencing is sensitive to the state of activity of the target chromatin. When the target is transcriptionally active, silencing is not established but when the target is not active at syncytial blastoderm, it becomes silenced. The repressed state persists through embryonic development but cannot be maintained in larval imaginal discs even when the LexA-PcG fusion is constitutively expressed, suggesting a discontinuity in the mechanism of repression. These proteins also interact with other PC-containing complexes in embryonic nuclear extracts. In contrast LexA-PHO is neither able to silence nor to interact with PC-containing complexes. Analysis of pho mutant embryos and of PRE constructs whose PHO-binding sites are mutated suggests that, while PHO is important for silencing in imaginal discs, it is not necessary for embryonic PcG silencing.

Ten different Polycomb group genes are required for spatial control of the abdA and AbdB homeotic products

Development ◽  
1992 ◽  
Vol 114 (2) ◽  
pp. 493-505 ◽  
Author(s):  
J. Simon ◽  
A. Chiang ◽  
W. Bender
Keyword(s):  
Expression Patterns ◽  
Ectopic Expression ◽  
Specific Pattern ◽  
Polycomb Group ◽  
Polycomb Group Genes ◽  
Sex Combs ◽  
Normal Expression ◽  
Sex Comb ◽  
Regulatory Dna ◽  
Pair Rule

Mutations in genes of the Polycomb (Pc) group cause abnormal segmental development due to ectopic expression of the homeotic products of the Antennapedia and bithorax complexes. Here the requirements for Pc group genes in controlling the abdA and AbdB products of the bithorax complex are described. Embryos containing mutations in the genes Polycomb (Pc), extra sex combs (esc), Enhancer of zeste [E(z)], polyhomeotic (ph), Sex comb on midleg (Scm), Polycomb-like (Pcl), Sex comb extra (Sce), Additional sex combs (Asx), Posterior sex combs (Psc) and pleiohomeotic (pho) were examined. In every case, both abdA and AbdB are expressed outside of their normal domains along the anterior-posterior (A-P) axis, consistent with these Pc group products acting in a single pathway or molecular complex. The earliest detectable ectopic expression is highest in the parasegments immediately adjacent to the normal expression boundary. Surprisingly, in the most severe Pc group mutants, the earliest ectopic AbdB is distributed in a pair-rule pattern. At all stages, ectopic abdA in the epidermis is highest along the anterior edges of the parasegments, in a pattern that mimics the normal abdA cell-specific pattern. These examples of highly patterned mis-expression show that Pc group mutations do not cause indiscriminate activation of homeotic products. We suggest that the ectopic expression patterns result from factors that normally activate abdA and AbdB only in certain parasegments, but that in Pc group mutants these factors gain access to regulatory DNA in all parasegments.

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