Two new insulator proteins, Pita and ZIPIC, target CP190 to chromatin

Maksimenko, Oksana; Bartkuhn, Marek; Stakhov, Viacheslav; Herold, Martin; Zolotarev, Nikolay; Jox, Theresa; Buxa, Melanie K.; Kirsch, Ramona; Bonchuk, Artem; Fedotova, Anna; Kyrchanova, Olga; Renkawitz, Rainer; Georgiev, Pavel

doi:10.1101/gr.174169.114

Cited by 112 publications

(191 citation statements)

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“…This argues that the cobinding of Su(Hw), CTCF, Cp190, and Mod(mdg4) or other recently identified Cp190-interacting proteins (Pita, Ibf1, Ibf2, and ZIPIC) (Cuartero et al 2014;Maksimenko et al 2015) does not automatically predict a strong enhancer-blocking ability. It appears that Fub has additional features that make it an exceptionally strong insulator element.…”

Section: Fub Is the Unusual Class 12 Insulator Elementmentioning

confidence: 99%

“…In addition, genomic mapping shows that insulator proteins bind chromatin in distinct combinations (Negre et al 2010;Schwartz et al 2012;Cuartero et al 2014;Maksimenko et al 2015). Importantly, only certain combinations of insulator proteins make these elements capable of blocking enhancerpromoter communications, suggesting that these proteins have additional unrelated functions.…”

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confidence: 99%

“…Of all Drosophila insulator proteins, only CTCF has a clear ortholog in mammals (Baniahmad et al 1990;Lobanenkov et al 1990). Multiple lines of evidence indicate that insulator proteins act as multisubunit complexes (Matzat and Lei 2014).In addition, genomic mapping shows that insulator proteins bind chromatin in distinct combinations (Negre et al 2010;Schwartz et al 2012;Cuartero et al 2014;Maksimenko et al 2015). Importantly, only certain combinations of insulator proteins make these elements capable of blocking enhancerpromoter communications, suggesting that these proteins have additional unrelated functions.…”

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confidence: 99%

“…Based on their biochemical and functional properties, the known Drosophila insulator proteins can be divided in three groups. The first group consists of nine sequence-specific DNA binding proteins: Su(Hw), CTCF, BEAF-32, Ibf1, Ibf2, Pita, ZIPIC (also known as CG7928), Dwg (also known as Zw5), and GAF (the product of Trithorax-like gene) (Geyer and Corces 1992;Zhao et al 1995;Gaszner et al 1999;Schweinsberg et al 2004; Copyright © 2016 Moon Cuartero et al 2014;Maksimenko et al 2015;Wolle et al 2015). The second group includes Cp190 and multiple protein isoforms encoded by the mod(mdg4) gene (Dorn et al 2001;Pai et al 2004;.…”

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confidence: 99%

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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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Section: Fub Is the Unusual Class 12 Insulator Elementmentioning

confidence: 99%

mentioning

confidence: 99%

mentioning

confidence: 99%

mentioning

confidence: 99%

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

et al. 2015

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“…These studies often require large amounts of biological material, not only from adult flies, but also from larvae 4 , pupae 5 and embryos [6][7][8] .…”

Section: Introductionmentioning

confidence: 99%

Maintenance of a <em>Drosophila melanogaster</em> Population Cage

Caravaca

Lei

2016

JoVE

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Large quantities of DNA, RNA, proteins and other cellular components are often required for biochemistry and molecular biology experiments. The short life cycle of Drosophila enables collection of large quantities of material from embryos, larvae, pupae and adult flies, in a synchronized way, at a low economic cost. A major strategy for propagating large numbers of flies is the use of a fly population cage. This useful and common tool in the Drososphila community is an efficient way to regularly produce milligrams to tens of grams of embryos, depending on uniformity of developmental stage desired. While a population cage can be time consuming to set up, maintaining a cage over months takes much less time and enables rapid collection of biological material in a short period. This paper describes a detailed and flexible protocol for the maintenance of a Drosophila melanogaster population cage, starting with 1.5 g of harvested material from the previous cycle.

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Interactions between BTB domain of CP190 and two adjacent regions in Su(Hw) are required for the insulator complex formation

et al. 2017

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The best-studied Drosophila insulator complex consists of two BTB-containing proteins, the Mod(mdg4)-67.2 isoform and CP190, which are recruited cooperatively to chromatin through interactions with the DNA-binding architectural protein Su(Hw). While Mod(mdg4)-67.2 interacts only with Su(Hw), CP190 interacts with many other architectural proteins. In spite of the fact that CP190 is critical for the activity of Su(Hw) insulators, interaction between these proteins has not been studied yet. Therefore, we have performed a detailed analysis of domains involved in the interaction between the Su(Hw) and CP190. The results show that the BTB domain of CP190 interacts with two adjacent regions at the N-terminus of Su(Hw). Deletion of either region in Su(Hw) only weakly affected recruiting of CP190 to the Su(Hw) sites in the presence of Mod(mdg4)-67.2. Deletion of both regions in Su(Hw) prevents its interaction with CP190. Using mutations in vivo, we found that interactions with Su(Hw) and Mod(mdg4)-67.2 are essential for recruiting of CP190 to the Su(Hw) genomic sites.

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Two new insulator proteins, Pita and ZIPIC, target CP190 to chromatin

Cited by 112 publications

References 59 publications

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

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

Maintenance of a <em>Drosophila melanogaster</em> Population Cage

Interactions between BTB domain of CP190 and two adjacent regions in Su(Hw) are required for the insulator complex formation

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