Chromatin Insulators: Regulatory Mechanisms and Epigenetic Inheritance

Bushey, Ashley M.; Dorman, Elizabeth R.; Corcés, Victor G.

doi:10.1016/j.molcel.2008.08.017

Cited by 182 publications

(166 citation statements)

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“…Enhancer-blocking insulators are defined by their ability to prevent enhancer activation of the promoter when placed between the enhancer and the promoter. A large body of evidence is consistent with the idea that insulators work by binding proteins that form DNA loops to other insulators (31)(32)(33)(34)(35). This mechanism of insulator action is rationalized by the loop domain model (36), which proposes that the formation of a DNA loop creates a separate topological domain that inhibits interaction between any site within the loop and any site outside the loop (Fig.…”

mentioning

confidence: 59%

Quantitation of interactions between two DNA loops demonstrates loop domain insulation in E. coli cells

Priest

Kumar²,

Yan³

et al. 2014

Proc. Natl. Acad. Sci. U.S.A.

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Eukaryotic gene regulation involves complex patterns of long-range DNA-looping interactions between enhancers and promoters, but how these specific interactions are achieved is poorly understood. Models that posit other DNA loops-that aid or inhibit enhancerpromoter contact-are difficult to test or quantitate rigorously in eukaryotic cells. Here, we use the well-characterized DNA-looping proteins Lac repressor and phage λ CI to measure interactions between pairs of long DNA loops in E. coli cells in the three possible topological arrangements. We find that side-by-side loops do not affect each other. Nested loops assist each other's formation consistent with their distance-shortening effect. In contrast, alternating loops, where one looping element is placed within the other DNA loop, inhibit each other's formation, thus providing clear support for the loop domain model for insulation. Modeling shows that combining loop assistance and loop interference can provide strong specificity in long-range interactions.Lac repressor | lambda CI | tethered particle motion | statistical mechanical modeling T ranscription of genes is regulated by promoter-proximal DNA elements and distal DNA elements that together determine condition-dependent gene expression. In eukaryotic genomes, enhancers can be many hundreds of kilobases away from the promoter they regulate (1-3), and the intervening DNA can contain other promoters and other enhancers (4-7). How the regulatory influence of distal elements is exerted efficiently and specifically at the correct promoters is poorly understood.Enhancers are clusters of binding sites for transcription factors and chromatin-modifying enzymes, and activate promoters by directly contacting them via DNA looping (8-12). Enhancer trap approaches and mapping of transcription factor binding and chromatin modifications have identified tens of thousands of enhancer elements in metazoan genomes (7,(13)(14)(15)(16). Chromatin capture studies show that enhancers and promoters are connected in highly complex condition-dependent patterns (6,15,17). Although core enhancer and promoter elements can provide some specificity (18), enhancers are often able to activate heterologous promoters if they are placed near to each other. Indeed, this lack of specificity is the basis for standard enhancer assays and screens (7,14,19). Thus, additional mechanisms are clearly needed to target enhancers to the correct promoters over long distances and to prevent their interaction with the wrong promoters. Dedicated DNA-looping elements that can either assist or interfere with enhancer-promoter looping are thought to play a major role.In theory, any DNA loop that brings the enhancer and promoter closer together should assist their interaction (Fig. 1A), because the efficiency of contact increases as the length of the DNA tether between the sites shortens (20-24). Promoter-tethering elements in Drosophila that allow activation by specific enhancers over long distances are proposed to form DNA loops between sequences near the ...

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confidence: 59%

Quantitation of interactions between two DNA loops demonstrates loop domain insulation in E. coli cells

Priest

Kumar²,

Yan³

et al. 2014

Proc. Natl. Acad. Sci. U.S.A.

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“…The three-dimensional organization of the chromatin fiber in the nucleus is important for the spatial and temporal regulation of transcription during development. Our laboratory studies the role of insulators in chromatin organization and gene expression (Geyer et al 1988;Bushey et al 2008). Previous studies have shown that Drosophila insulator proteins are present at hundreds of sites throughout the genome that colocalize to distinct foci predominantly around the nuclear periphery in diploid cells (Ramos et al 2006;Gerasimova et al 2007).…”

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confidence: 99%

Opening Pathways for Underrepresented High School Students to Biomedical Research Careers: The Emory University RISE Program

Rohrbaugh

Corcés

2011

Genetics

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Increasing the college graduation rates of underrepresented minority students in science disciplines is essential to attain a diverse workforce for the 21st century. The Research Internship and Science Education (RISE) program attempts to motivate and prepare students from the Atlanta Public School system, where underrepresented minority (URM) students comprise a majority of the population, for biomedical science careers by offering the opportunity to participate in an original research project. Students work in a research laboratory from the summer of their sophomore year until graduation, mentored by undergraduate and graduate students and postdoctoral fellows (postdocs). In addition, they receive instruction in college-level biology, scholastic assessment test (SAT) preparation classes, and help with the college application process. During the last 4 yr, RISE students have succeeded in the identification and characterization of a series of proteins involved in the regulation of nuclear organization and transcription. All but 1 of 39 RISE students have continued on to 4-year college undergraduate studies and 61% of those students are currently enrolled in sciencerelated majors. These results suggest that the use of research-based experiences at the high school level may contribute to the increased recruitment of underrepresented students into science-related careers.

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“…The transcriptional model and the structural model are two of the most discussed models (Kuhn and Geyer 2003;Gaszner and Felsenfeld 2006;Bushey et al 2008). The former emphasized the competition between insulators and enhancers/repressors, and the latter stressed the formation of a chromatin loop with the help of insulators.…”

Section: Discussionmentioning

confidence: 99%

“…Studies have revealed that it contains a cluster of binding sites for the Suppressor of Hairy-wing [Su(Hw)] protein, a zinc-finger DNA-binding protein (Harrison et al 1993;Gaszner and Felsenfeld 2006). The gypsy insulator is believed to regulate gene expression by establishing higher-order domains of chromatin structure and blocking the interference of nearby enhancers or repressors (Gaszner and Felsenfeld 2006;Bushey et al 2008).…”

Section: G Enetic Engineering Has Become a Routinementioning

confidence: 99%

The gypsy Insulator of Drosophila melanogaster, Together With Its Binding Protein Suppressor of Hairy-Wing, Facilitate High and Precise Expression of Transgenes in Arabidopsis thaliana

et al. 2010

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The variation of expression pattern exhibited by a transgene as a result of random integration, known as position effect, is, among other mechanisms, a particular challenge to reverse genetics. We present a strategy to counteract position effect in Arabidopsis thaliana by flanking the transgenes with the gypsy insulator from Drosophila melanogaster. In addition, Suppressor of Hairy-wing [Su(Hw)], the binding protein of the gypsy insulator, was coexpressed. Results indicated that the gypsy insulators could efficiently improve the expression levels of reporter genes driven by various kinds of promoters by 8-to 13-fold. Coexpression of the Su(Hw) protein led to a more uniform expression level of transgenes, as the coefficient of variation of expression levels was reduced further. The gypsy-Su(Hw) system enhanced expression levels, but did not alter the specificity of promoter activities, as experimentally evidenced by the promoters of the PIN and the AFB gene families. Interestingly, the gypsy insulator was also able to improve the expression of a selectable marker gene outside the insulated region, which facilitated the screen of transformants. Our system will likely decrease the number of lines that experimenters need to create and examine for a given transgene by contributing to relatively high and precise expression of transgenes in plants. Certain features of the gypsy insulator in Arabidopsis also provide new perspectives on the insulator field.

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Chromatin Insulators: Regulatory Mechanisms and Epigenetic Inheritance

Cited by 182 publications

References 65 publications

Quantitation of interactions between two DNA loops demonstrates loop domain insulation in E. coli cells

Quantitation of interactions between two DNA loops demonstrates loop domain insulation in E. coli cells

Opening Pathways for Underrepresented High School Students to Biomedical Research Careers: The Emory University RISE Program

The gypsy Insulator of Drosophila melanogaster, Together With Its Binding Protein Suppressor of Hairy-Wing, Facilitate High and Precise Expression of Transgenes in Arabidopsis thaliana

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