New Properties of Drosophila Fab-7 Insulator

Rodin, Sergey; Kyrchanova, Olga; Pomerantseva, Ekaterina; Parshikov, Alexander; Georgiev, Pavel

doi:10.1534/genetics.107.075887

Cited by 27 publications

(35 citation statements)

References 69 publications

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“…As the test genes, we chose yellow and white, which have been extensively used in insulator studies (13,14,22,24,25,33,37,38,39,42,43,44,45,46). Note, however, that we initially removed the Wari-containing sequence 3Ј adjacent to miniwhite in the standard plasmids (13).…”

Section: Resultsmentioning

confidence: 99%

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Enhancer-Promoter Communication Is Regulated by Insulator Pairing in a Drosophila Model Bigenic Locus

Maksimenko

Golovnin

Georgiev

2008

Molecular and Cellular Biology

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The complexity of regulatory systems in higher eukaryotes, featuring many distantly located enhancers that nonetheless properly activate the target promoters, has prompted the hypothesis that the action of enhancers should be restricted by insulators. Continuing our research on the functional role of insulators and the consequences of their interaction in Drosophila, we studied the interplay of different Su(Hw)-dependent Drosophila insulators. The set of transgenic constructs comprised two consecutive genes (yellow and white) with their enhancers and insulator elements differently arranged in between and/or around the gene(s). All insulators were found to interact in twin or mixed tandems, demonstrating the bypass phenomenon. However, insulator pairing around a gene did not always improve its isolation from an outside enhancer. On the other hand, merely two insulator elements (identical or different) in appropriate positions can permit the expression of one gene but not the gene next to it or, conversely, largely block the transcription of the first gene, while allowing full enhancement of the second, or make them behave similarly. Thus, the results of this study support the model that loop formation by insulators is an essential component of insulator action on a positive and negative regulation of an enhancer-promoter communication.

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Section: Resultsmentioning

confidence: 99%

“…prevented if a single insulator is interposed in the DNA sequence between the enhancer and the gene promoter, whereas in any other place the insulator is ineffective (the definitive property known as position dependence) (8,17,20,25,26,30,31,44,47,(57)(58)(59). Insulators may vary in apparent blocking strength (10,47,26,46,57).…”

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Enhancer-Promoter Communication Is Regulated by Insulator Pairing in a Drosophila Model Bigenic Locus

Maksimenko

Golovnin

Georgiev

2008

Molecular and Cellular Biology

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“…Furthermore, the presence of RNA and RNA-binding proteins may also contribute to the formation or maintenance of insulator bodies required to create chromatin loops (Lei and Corces 2006). Finally, insulator bypass that results in the inactivation of insulator activity through pairing of nearby insulator elements, and specialized sequences such as the promoter targeting sequences (PTS), can allow an enhancer to bypass an insulator (Schweinsberg et al 2004;Gruzdeva et al 2005;Kyrchanova et al 2007Kyrchanova et al , 2008Rodin et al 2007). These forms of regulation may alter the ability of insulator proteins to interact with one another to regulate insulator loop formation.…”

Section: Discussionmentioning

confidence: 99%

Three subclasses of a Drosophila insulator show distinct and cell type-specific genomic distributions

Bushey

Ramos²,

Corcés³

2009

Genes Dev.

180

311

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Insulators are protein-bound DNA elements that are thought to play a role in chromatin organization and the regulation of gene expression by mediating intra-and interchromosomal interactions. Suppressor of Hair-wing [Su(Hw)] and Drosophila CTCF (dCTCF) insulators are found at distinct loci throughout the Drosophila melanogaster genome and function by recruiting an additional protein, Centrosomal Protein 190 (CP190). We performed chromatin immunoprecipitation (ChIP) and microarray analysis (ChIP-chip) experiments with wholegenome tiling arrays to compare Su(Hw), dCTCF, boundary element-associated factor (BEAF), and CP190 localization on DNA in two different cell lines and found evidence that BEAF is a third subclass of CP190-containing insulators. The DNA-binding proteins Su(Hw), dCTCF, and BEAF show unique distribution patterns with respect to the location and expression level of genes, suggesting diverse roles for these three subclasses of insulators in genome organization. Notably, cell line-specific localization sites for all three DNA-binding proteins as well as CP190 indicate multiple levels at which insulators can be regulated to affect gene expression. These findings suggest a model in which insulator subclasses may have distinct functions that together organize the genome in a cell type-specific manner, resulting in differential regulation of gene expression.[Keywords: Insulators; chromatin organization; BEAF; CTCF; gypsy] Supplemental material is available at http://www.genesdev.org.

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“…As far as we know, Fub and 62D are the strongest insulator elements naturally present in the Drosophila genome (Figure 8) (Golovnin et al 2003;Parnell et al 2003;Gruzdeva et al 2005;Parnell et al 2006;Ramos et al 2006;Rodin et al 2007;Schwartz et al 2012). The strength of the gypsy insulator is explained by its unusual composition of an array of 12 binding sites for the Su(Hw) protein (Spana et al 1988 2R: 19488971-19489908; R4, X: 17613897-17614889; R5, 3R: 2737495-2738551; d2, 2R: 18984278-18985246; d3, 3R: 5925961-5926884; d4, 3R: 12934220-12935236; and d6, X: 2763148-2764144 (all coordinates are in Dm3 2006 genome release) were PCR amplified from genomic DNA and cloned into the FRT cassette of yellow-attB-mobile vector (Schwartz et al 2012) using XbaI, NotI, NheI, or Aor51HI sites.…”

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Distinct Roles of Chromatin Insulator Proteins in Control of the Drosophila Bithorax Complex

et al. 2015

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Chromatin insulators are remarkable regulatory elements that can bring distant genomic sites together and block unscheduled enhancer-promoter communications. Insulators act via associated insulator proteins of two classes: sequence-specific DNA binding factors and "bridging" proteins. The latter are required to mediate interactions between distant insulator elements. Chromatin insulators are critical for correct expression of complex loci; however, their mode of action is poorly understood. Here, we use the Drosophila bithorax complex as a model to investigate the roles of the bridging proteins Cp190 and Mod(mdg4). The bithorax complex consists of three evolutionarily conserved homeotic genes Ubx, abd-A, and Abd-B, which specify anterior-posterior identity of the last thoracic and all abdominal segments of the fly. Looking at effects of CTCF, mod(mdg4), and Cp190 mutations on expression of the bithorax complex genes, we provide the first functional evidence that Mod(mdg4) acts in concert with the DNA binding insulator protein CTCF. We find that Mod(mdg4) and Cp190 are not redundant and may have distinct functional properties. We, for the first time, demonstrate that Cp190 is critical for correct regulation of the bithorax complex and show that Cp190 is required at an exceptionally strong Fub insulator to partition the bithorax complex into two topological domains.KEYWORDS HOX genes; chromatin; chromatin insulators; Drosophila; gene regulation T HE eukaryotic genome is folded extensively to fit inside the cell nucleus. The folding patterns vary between individual cells but certain conformations occur more frequently. In some cases, the likelihood of acquiring a particular conformation is linked to activation or repression of specific genes. Such links are especially important for complex loci in which multiple regulatory elements are positioned tens of thousands of base pairs (kb) away from their target promoters. The Drosophila bithorax complex is one of the best studied complex loci. The bithorax complex consists of three evolutionarily conserved homeotic genes Ubx, abd-A, and Abd-B that encode transcription factors and specify anterior-posterior identity of the last thoracic and all abdominal segments of the fly . Segment-specific expression of the bithorax complex genes is controlled by distal transcriptional enhancers and polycomb/trithorax response elements (PRE/TREs). The correct function of enhancers and PREs/ TREs is further orchestrated by chromatin insulator elements that modulate the topology of the bithorax complex by mechanisms that are not well understood.Chromatin insulator elements were first discovered in Drosophila and later found in vertebrates and plants. They are short (1 kb) DNA elements that can block ("insulate") transcriptional activation of a promoter by a remote enhancer when interposed between the two. In contrast to transcriptional repression, insulation leaves the promoter transcriptionally competent so it is free to engage with other enhancers as long as those are not sepa...

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New Properties of Drosophila Fab-7 Insulator

Cited by 27 publications

References 69 publications

Enhancer-Promoter Communication Is Regulated by Insulator Pairing in a Drosophila Model Bigenic Locus

Enhancer-Promoter Communication Is Regulated by Insulator Pairing in a Drosophila Model Bigenic Locus

Three subclasses of a Drosophila insulator show distinct and cell type-specific genomic distributions

Distinct Roles of Chromatin Insulator Proteins in Control of the Drosophila Bithorax Complex

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