Effects of
            <i>cis</i>
            Arrangement of Chromatin Insulators on Enhancer-Blocking Activity

Cai, Houjian; Shen, Ping

doi:10.1126/science.291.5503.493

Cited by 183 publications

(185 citation statements)

References 28 publications

Supporting

Mentioning

172

Contrasting

Unclassified

Order By: Relevance

“…The UAS-npf construct was made by inserting a full-length npf cDNA. The H1-lacZ transgene was cloned into a pCaSpeR-based vector that also contains a miniwhite gene (16).…”

Section: Methodsmentioning

confidence: 99%

Drosophila neuropeptide F and its receptor, NPFR1, define a signaling pathway that acutely modulates alcohol sensitivity

Wen

Parrish²,

Xu³

et al. 2005

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

Self Cite

170

191

View full text Add to dashboard Cite

Alcohol is likely to affect neurons nonselectively, and the understanding of its action in the CNS requires elucidation of underlying neuronal circuits and associated cellular processes. We have identified a Drosophila signaling system, comprising neurons expressing neuropeptide F (NPF, a homolog of mammalian neuropeptide Y) and its receptor, NPFR1, that acutely mediates sensitivity to ethanol sedation. Flies deficient in NPF͞NPFR1 signaling showed decreased alcohol sensitivity, whereas those overexpressing NPF exhibited the opposite phenotype. Furthermore, controlled functional disruption of NPF or NPFR1 neurons in adults rapidly confers resistance to ethanol sedation. Finally, the NPF͞NPFR1 system selectively mediates sedation by ethanol vapor but not diethyl ether, indicating that the observed NPF͞NPFR1 activity reflects a specialized response to alcohol sedation rather than a general response to intoxication by sedative agents. Together, our results provide the molecular and neural basis for the strikingly similar alcohol-responsive behaviors between flies and mammals.acute ethanol response ͉ neuropeptide Y ͉ neuropeptide F receptor A lcohol, a widely abused drug, impacts the functioning of the CNS in diverse animals. The behavioral responses to acute alcohol exposure are remarkably similar among humans, rodents, and even fruit flies. Alcohol induces an excitatory state at lower concentrations but exerts a sedative effect at higher doses (1, 2). The current knowledge about how this drug impacts the functioning of the CNS is rather limited. Ethanol is highly soluble in both water and lipids, and is likely to act on neurons in a nonselective manner. However, the sensitivity of neurons in different neural circuits to this drug may vary greatly (3). Thus, elucidation of neuronal circuits and underlying molecular mechanisms essential for alcohol sensitivity is a prerequisite for understanding how alcohol interferes with the functioning of the CNS.Neuropeptides are a group of chemically diverse signal molecules implicated in modulating a broad spectrum of physiological processes and behaviors (4). Mammalian neuropeptide Y (NPY) is a 36 aa neuromodulator present abundantly in many regions of the CNS, and acts thorough a number of Y receptor subtypes (5). Mice lacking NPY or Y1 displayed increased ethanol consumption and resistance to alcohol sedation, whereas animals overexpressing NPY showed opposite behavioral phenotypes (6, 7). These results provide genetic evidence of a critical role of the NPY signaling system in acute ethanol response. However, the elucidation of the physiological role of the NPY system and the action sites has been difficult largely because of the complexity of mammalian models.NPY family molecules have been found in diverse organisms (8-10). Neuropeptide F (NPF) is the sole member of the NPY family in the Drosophila genome, and its action is mediated by G protein-coupled seven-transmembrane receptors related to mammalian NPY receptors (11). Both NPY and NPF are present prominently, although...

show abstract

“…The UAS-npf construct was made by inserting a full-length npf cDNA. The H1-lacZ transgene was cloned into a pCaSpeR-based vector that also contains a miniwhite gene (16).…”

Section: Methodsmentioning

confidence: 99%

Drosophila neuropeptide F and its receptor, NPFR1, define a signaling pathway that acutely modulates alcohol sensitivity

Wen

Parrish²,

Xu³

et al. 2005

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

Self Cite

170

191

View full text Add to dashboard Cite

show abstract

“…This loss of insulator activity has been proposed to result from intrachromosomal pairing between the two gypsy insulators, causing chromatin to fold and allowing the distal enhancer to contact the promoter. By extension, a single intervening gypsy insulator would block enhancer-promoter communication by interacting either with other insulators located at distant loci or at specific nuclear sites (Cai and Shen, 2001;Muravyova et al, 2001). Evidence that the gypsy insulator establishes chromatin domains is strengthened by the fact that Su(Hw) and Mod(mdg)4 associate with 500 sites in the Drosophila genome, but coalesce into only 25 large structures.…”

Section: Insulators and Higher-order Chromatin Structuresmentioning

confidence: 99%

“…They have also helped to define the general properties of insulators such as their enhancer-blocker and/or barrier functions. However, we are at present unable to understand the molecular mechanisms underlying these functions or to integrate into a general scheme additional observations such as: (i) the enhancer-blocker and barrier activities are separable ; (ii) insulator effectiveness is influenced by its structure, and by the nature of the enhancer, promoter and genomic context (Scott et al, 1999;Walters et al, 1999); and (iii) insulators are not permanent and impassable elements (Cai and Shen, 2001;Muravyova et al, 2001). Two nonexclusive models are currently proposed: one of them is established according to a series of data reporting links between insulators and the higher-order chromatin structures, and the other integrate data reporting connections between the insulator properties and gene transcription.…”

Section: What Are the Mechanisms Of Action Of Insulators?mentioning

confidence: 99%

Insulators are fundamental components of the eukaryotic genomes

Brasset

Vaury

2005

Heredity

View full text Add to dashboard Cite

The properties of cis-regulatory elements able to influence gene transcription over large distances have led to the hypothesis that elements called insulators should exist to limit the action of enhancers and silencers. During the last decades, insulators have been identified in many eukaryotes from yeast to human. Insulators possess two main properties: (i) they can block enhancer-promoter communication ('enhancer blocker activity'), and (ii) they can prevent the spread of repressive chromatin ('barrier activity'). This review focuses on recent studies designed to elucidate the molecular mechanisms of the insulator function, and gives an overview of the critical role of insulators in nuclear organization and functional identity of chromatin. Heredity (2005) 94, 571-576.

show abstract

“…1A). This model is the only one that can currently explain the requirement that an insulator must be between the enhancer and promoter to block activation, as well as observations that two insulators between the enhancer and promoter sometimes do not block activation (37,38). The loop domain model is also a potential explanation (35) of the topologically associated domains (TADs) revealed by genome-wide mapping of DNA contacts by chromatin capture methods in genomes from mice to bacteria (39)(40)(41)(42)(43)(44)(45).…”

mentioning

confidence: 99%

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.

View full text Add to dashboard Cite

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 ...

show abstract

Effects of cis Arrangement of Chromatin Insulators on Enhancer-Blocking Activity

Cited by 183 publications

References 28 publications

Drosophila neuropeptide F and its receptor, NPFR1, define a signaling pathway that acutely modulates alcohol sensitivity

Drosophila neuropeptide F and its receptor, NPFR1, define a signaling pathway that acutely modulates alcohol sensitivity

Insulators are fundamental components of the eukaryotic genomes

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

Contact Info

Product

Resources

About