Tissue-Specific Regulation of Chromatin Insulator Function

Matzat, Leah H.; Dale, Ryan K.; Moshkovich, Nellie; Lei, Elissa P.

doi:10.1371/journal.pgen.1003069

Cited by 51 publications

(111 citation statements)

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“…They can, however, mediate homotypic and heterotypic protein-protein interactions via their BTB/POZ (Broad complex, Tramtrack, Bric-a-brac)/(Poxvirus and Zinc finger) domains. The third group includes biochemically diverse proteins: Elba1, Elba2, Elba3, and Shep (Aoki et al 2012;Matzat et al 2012). Though not required for enhancer blocking, these proteins appear to modulate the enhancer-blocking ability of insulator elements in a tissue-or stage-specific manner.…”

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confidence: 99%

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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confidence: 99%

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

et al. 2015

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“…For example, collected embryos from population cages have been used very successfully in immunoprecipitation assays [6][7][8] , mass collection of larval tissues from dissociated larvae has demonstrated to be a very good source for 3C experiments 4 and RNA preparations 15 , and heads from adult flies have been utilized for ChIP experiments 16 . In addition, adults are often needed to make fly extracts for tissue culture 17 .…”

Section: Discussionmentioning

confidence: 99%

“…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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“…However, it has also been suggested that insulator bodies represent storage sites of insulator proteins (Golovnin et al, 2008) or form as a result of certain stress conditions (Schoborg et al, 2013). Although the presence of insulator bodies is not sufficient for insulator activity (Gerasimova et al, 2007;Golovnin et al, 2008), all mutations that are known to alter the integrity of insulator bodies also affect insulator function (Capelson and Corces, 2005;Capelson and Corces, 2006;Gerasimova and Corces, 1998;Ghosh et al, 2001;Golovnin et al, 2012;Lei and Corces, 2006;Matzat et al, 2013;Matzat et al, 2012;Pai et al, 2004). These results suggest that monitoring these structures serves as a useful phenotypic indicator.…”

Section: Introductionmentioning

confidence: 99%

“…In both Drosophila and mammals, genome-wide binding profiles of insulator proteins are largely invariant across cell types (Bushey et al, 2009;Kim et al, 2007), suggesting that the particular higher-order chromatin configurations mediated by insulator proteins might be regulated in different cell types. Recent work has shown that RNA and RNA-binding proteins can modulate the activities of the gypsy insulator (Lei and Corces, 2006;Matzat et al, 2013;Matzat et al, 2012), the Drosophila CTCF insulator complex (Lim et al, 2013;Moshkovich et al, 2011), and mammalian CTCF and its partner cohesin (Sun et al, 2013;Yao et al, 2010). In the case of the RNA-binding protein Alan Shepard (Shep), gypsy insulator activity and insulator body localization is antagonized in a tissue-specific manner (Matzat et al, 2012).…”

Section: Introductionmentioning

confidence: 99%

The RNA-binding protein Rumpelstiltskin antagonizes gypsy chromatin insulator function in a tissue-specific manner

King

Matzat

Dale

et al. 2014

Journal of Cell Science

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Chromatin insulators are DNA-protein complexes that are situated throughout the genome that are proposed to contribute to higherorder organization and demarcation into distinct transcriptional domains. Mounting evidence in different species implicates RNA and RNA-binding proteins as regulators of chromatin insulator activities. Here, we identify the Drosophila hnRNP M homolog Rumpelstiltskin (Rump) as an antagonist of gypsy chromatin insulator enhancer-blocking and barrier activities. Despite ubiquitous expression of Rump, decreasing Rump levels leads to improvement of barrier activity only in tissues outside of the central nervous system (CNS). Furthermore, rump mutants restore insulator body localization in an insulator mutant background only in non-CNS tissues. Rump associates physically with core gypsy insulator proteins, and chromatin immunoprecipitation and sequencing analysis of Rump demonstrates extensive colocalization with a subset of insulator sites across the genome. The genome-wide binding profile and tissue specificity of Rump contrast with that of Shep, a recently identified RNA-binding protein that antagonizes gypsy insulator activity primarily in the CNS. Our findings indicate parallel roles for RNA-binding proteins in mediating tissue-specific regulation of chromatin insulator activity.

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Tissue-Specific Regulation of Chromatin Insulator Function

Cited by 51 publications

References 58 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

The RNA-binding protein Rumpelstiltskin antagonizes gypsy chromatin insulator function in a tissue-specific manner

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