Faculty Opinions recommendation of Regulation of Polycomb group complexes by the sequence-specific DNA binding proteins Zeste and GAGA.

2003 ◽  
Author(s):  
Steven Henikoff
Keyword(s):  
Dna Binding ◽  
Binding Proteins ◽  
Dna Binding Proteins ◽  
Polycomb Group ◽  
Polycomb Group Complexes

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

Genetics ◽  
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.

scholarly journals Combgap contributes to recruitment of Polycomb group proteins in Drosophila

2016 ◽  
Vol 113 (14) ◽  
pp. 3826-3831 ◽  
Author(s):  
Payal Ray ◽  
Sandip De ◽  
Apratim Mitra ◽  
Karel Bezstarosti ◽  
Jeroen A. A. Demmers ◽  
...  
Keyword(s):  
Dna Binding ◽  
Binding Sites ◽  
Binding Proteins ◽  
Dna Binding Proteins ◽  
Polycomb Group ◽  
Developmentally Regulated ◽  
Polycomb Response Elements ◽  
Protein Recruitment ◽  
Polycomb Repressive Complex 1 ◽  
Transcriptional State

Polycomb group (PcG) proteins are responsible for maintaining the silenced transcriptional state of many developmentally regulated genes. PcG proteins are organized into multiprotein complexes that are recruited to DNA via cis-acting elements known as “Polycomb response elements” (PREs). In Drosophila, PREs consist of binding sites for many different DNA-binding proteins, some known and others unknown. Identification of these DNA-binding proteins is crucial to understanding the mechanism of PcG recruitment to PREs. We report here the identification of Combgap (Cg), a sequence-specific DNA-binding protein that is involved in recruitment of PcG proteins. Cg can bind directly to PREs via GTGT motifs and colocalizes with the PcG proteins Pleiohomeotic (Pho) and Polyhomeotic (Ph) at the majority of PREs in the genome. In addition, Cg colocalizes with Ph at a number of targets independent of Pho. Loss of Cg leads to decreased recruitment of Ph at only a subset of sites; some of these sites are binding sites for other Polycomb repressive complex 1 (PRC1) components, others are not. Our data suggest that Cg can recruit Ph in the absence of PRC1 and illustrate the diversity and redundancy of PcG protein recruitment mechanisms.

scholarly journals Variable Requirements for DNA-Binding Proteins at Polycomb-Dependent Repressive Regions in Human HOX Clusters

2013 ◽  
Vol 33 (16) ◽  
pp. 3274-3285 ◽  
Author(s):  
Caroline J. Woo ◽  
Peter V. Kharchenko ◽  
Laurence Daheron ◽  
Peter J. Park ◽  
Robert E. Kingston
Keyword(s):  
Dna Binding ◽  
Cell Fate ◽  
Binding Proteins ◽  
Regulatory Elements ◽  
Dna Binding Proteins ◽  
Polycomb Group ◽  
Content Type ◽  
Evolutionarily Conserved ◽  
Hoxd Cluster ◽  
Hox Clusters

Polycomb group (PcG)-mediated repression is an evolutionarily conserved process critical for cell fate determination and maintenance of gene expression during embryonic development. However, the mechanisms underlying PcG recruitment in mammals remain unclear since few regulatory sites have been identified. We report two novel prospective PcG-dependent regulatory elements within the human HOXB and HOXC clusters and compare their repressive activities to a previously identified element in the HOXD cluster. These regions recruited the PcG proteins BMI1 and SUZ12 to a reporter construct in mesenchymal stem cells and conferred repression that was dependent upon PcG expression. Furthermore, we examined the potential of two DNA-binding proteins, JARID2 and YY1, to regulate PcG activity at these three elements. JARID2 has differential requirements, whereas YY1 appears to be required for repressive activity at all 3 sites. We conclude that distinct elements of the mammalian HOX clusters can recruit components of the PcG complexes and confer repression, similar to what has been seen inDrosophila. These elements, however, have diverse requirements for binding factors, which, combined with previous data on other loci, speaks to the complexity of PcG targeting in mammals.

scholarly journals A Complex Array of DNA-Binding Proteins Required for Pairing-Sensitive Silencing by a Polycomb Group Response Element From the DrosophilaengrailedGene

Genetics ◽  
2002 ◽  
Vol 160 (4) ◽  
pp. 1561-1571 ◽  
Author(s):  
Jeffrey Americo ◽  
Mary Whiteley ◽  
J Lesley Brown ◽  
Miki Fujioka ◽  
James B Jaynes ◽  
...  
Keyword(s):  
Dna Binding ◽  
Reporter Gene ◽  
Binding Proteins ◽  
Mutational Analysis ◽  
Dna Binding Proteins ◽  
Polycomb Group ◽  
Polycomb Group Protein ◽  
Gaga Factor ◽  
Mobility Shift ◽  
Group Response

AbstractRegulatory DNA from the Drosophila gene engrailed causes silencing of a linked reporter gene (mini-white) in transgenic Drosophila. This silencing is strengthened in flies homozygous for the transgene and has been called “pairing-sensitive silencing.” The pairing-sensitive silencing activities of a large fragment (2.6 kb) and a small subfragment (181 bp) were explored. Since pairing-sensitive silencing is often associated with Polycomb group response elements (PREs), we tested the activities of each of these engrailed fragments in a construct designed to detect PRE activity in embryos. Both fragments were found to behave as PREs in a bxd-Ubx-lacZ reporter construct, while the larger fragment showed additional silencing capabilities. Using the mini-white reporter gene, a 139-bp minimal pairing-sensitive element (PSE) was defined. DNA mobility-shift assays using Drosophila nuclear extracts suggested that there are eight protein-binding sites within this 139-bp element. Mutational analysis showed that at least five of these sites are important for pairing-sensitive silencing. One of the required sites is for the Polycomb group protein Pleiohomeotic and another is GAGAG, a sequence bound by the proteins GAGA factor and Pipsqueak. The identity of the other proteins is unknown. These data suggest a surprising degree of complexity in the DNA-binding proteins required for PSE function.

scholarly journals Efficient and Specific Targeting of Polycomb Group Proteins Requires Cooperative Interaction between Grainyhead and Pleiohomeotic

2006 ◽  
Vol 26 (4) ◽  
pp. 1434-1444 ◽  
Author(s):  
András Blastyák ◽  
Rakesh K. Mishra ◽  
Francois Karch ◽  
Henrik Gyurkovics
Keyword(s):  
Dna Binding ◽  
Binding Proteins ◽  
Protein Complexes ◽  
Dna Binding Proteins ◽  
Polycomb Group ◽  
Cooperative Interaction ◽  
Protein Protein Interaction ◽  
Specific Targeting

ABSTRACT Specific targeting of the protein complexes formed by the Polycomb group of proteins is critically required to maintain the inactive state of a group of developmentally regulated genes. Although the role of DNA binding proteins in this process has been well established, it is still not understood how these proteins target the Polycomb complexes specifically to their response elements. Here we show that the grainyhead gene, which encodes a DNA binding protein, interacts with one such Polycomb response element of the bithorax complex. Grainyhead binds to this element in vitro. Moreover, grainyhead interacts genetically with pleiohomeotic in a transgene-based, pairing-dependent silencing assay. Grainyhead also interacts with Pleiohomeotic in vitro, which facilitates the binding of both proteins to their respective target DNAs. Such interactions between two DNA binding proteins could provide the basis for the cooperative assembly of a nucleoprotein complex formed in vitro. Based on these results and the available data, we propose that the role of DNA binding proteins in Polycomb group-dependent silencing could be described by a model very similar to that of an enhanceosome, wherein the unique arrangement of protein-protein interaction modules exposed by the cooperatively interacting DNA binding proteins provides targeting specificity.

DBP-PSSM: Combination of evolutionary profiles with the XGBoost algorithm to improve the identification of DNA-binding proteins

2020 ◽  
Vol 23 ◽  
Author(s):  
Yanping Zhang ◽  
Pengcheng Chen ◽  
Ya Gao ◽  
Jianwei Ni ◽  
Xiaosheng Wang
Keyword(s):  
Logistic Regression ◽  
Protein Structure ◽  
Dna Binding ◽  
Molecular Biology ◽  
Binding Proteins ◽  
Protein Sequences ◽  
Low Complexity ◽  
Dna Binding Proteins ◽  
Position Information ◽  
Position Representation

Aim and Objective:: Given the rapidly increasing number of molecular biology data available, computational methods of low complexity are necessary to infer protein structure, function, and evolution. Method:: In the work, we proposed a novel mthod, FermatS, which based on the global position information and local position representation from the curve and normalized moments of inertia, respectively, to extract features information of protein sequences. Furthermore, we use the generated features by FermatS method to analyze the similarity/dissimilarity of nine ND5 proteins and establish the prediction model of DNA-binding proteins based on logistic regression with 5-fold crossvalidation. Results:: In the similarity/dissimilarity analysis of nine ND5 proteins, the results are consistent with evolutionary theory. Moreover, this method can effectively predict the DNA-binding proteins in realistic situations. Conclusion:: The findings demonstrate that the proposed method is effective for comparing, recognizing and predicting protein sequences. The main code and datasets can download from https://github.com/GaoYa1122/FermatS.

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