DNA bending is a determinant of binding specificity for a Drosophila zinc finger protein.

Spana, Carl; Corcés, Victor G.

doi:10.1101/gad.4.9.1505

Cited by 104 publications

(68 citation statements)

References 40 publications

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“…As a result it was hypothesized that formation of a DNA triplex such as H-DNA or other singlestranded-DNA structures in the silencer region may serve to bring the repressor into correct orientation with downstream positive regulatory elements [90]. It is well known that TFs often bind to bent DNA or generate DNA bending upon binding [91][92][93], and this example provides a detailed mechanism as to how DNA bending may occur.…”

Section: Classical Silencers (Silencer Elements)mentioning

confidence: 99%

Transcriptional control and the role of silencers in transcriptional regulation in eukaryotes

Ogbourne

Antalis

1998

Biochemical Journal

227

171

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Mechanisms controlling transcription and its regulation are fundamental to our understanding of molecular biology and, ultimately, cellular biology. Our knowledge of transcription initiation and integral factors such as RNA polymerase is considerable, and more recently our understanding of the involvement of enhancers and complexes such as holoenzyme and mediator has increased dramatically. However, an understanding of transcriptional repression is also essential for a complete understanding of promoter structure and the regulation of gene expression. Transcriptional repression in eukaryotes is achieved through ‘silencers ’, of which there are two types, namely ‘silencer elements ’ and ‘negative regulatory elements ’ (NREs). Silencer elements are classical, position-independent elements that direct an active repression mechanism, and NREs are position-dependent elements that direct a passive repression mechanism. In addition, ‘repressors ’ are DNA-binding trasncription factors that interact directly with silencers. A review of the recent literature reveals that it is the silencer itself and its context within a given promoter, rather than the interacting repressor, that determines the mechanism of repression. Silencers form an intrinsic part of many eukaryotic promoters and, consequently, knowledge of their interactive role with enchancers and other transcriptional elements is essential for our understanding of gene regulation in eukaryotes.

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Section: Classical Silencers (Silencer Elements)mentioning

confidence: 99%

Transcriptional control and the role of silencers in transcriptional regulation in eukaryotes

Ogbourne

Antalis

1998

Biochemical Journal

227

171

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“…A fourth protein component of the gypsy insulator dTopors may play a role in regulating its activity (Capelson and Corces 2005). The Su(Hw) protein binds to insulator DNA through a domain containing 12 zinc fingers (Dorsett 1990;Spana and Corces 1990). Results from biochemical experiments suggest that the binding site for the Su(Hw) protein consists of the sequence YRTTGCA TACCY with a 6-bp invariant core motif TGCATA (Y ¼ C or T, R ¼ A or G) (Spana and Corces 1990).…”

mentioning

confidence: 99%

“…In total, there are 12 Su(Hw)-binding sites in the 340-bp gypsy insulator element, which are sufficient for the full insulator activity attributed to the gypsy retrotransposon (Geyer and Corces 1992;Scott et al 1999). The Su(Hw) binding sites in gypsy are flanked by A/T tracts, and these sequences are also required for proper insulator function (Spana and Corces 1990). These A/T-rich sequences function as matrix attachment regions (MARs) (Nabirochkin et al 1998) and may represent binding sites for DNA topoisomerase II or some other MARs-binding protein.…”

mentioning

confidence: 99%

“…The Su(Hw) protein binds to insulator DNA through a domain containing 12 zinc fingers (Dorsett 1990;Spana and Corces 1990). Results from biochemical experiments suggest that the binding site for the Su(Hw) protein consists of the sequence YRTTGCA TACCY with a 6-bp invariant core motif TGCATA (Y ¼ C or T, R ¼ A or G) (Spana and Corces 1990). In total, there are 12 Su(Hw)-binding sites in the 340-bp gypsy insulator element, which are sufficient for the full insulator activity attributed to the gypsy retrotransposon (Geyer and Corces 1992;Scott et al 1999).…”

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confidence: 99%

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Genomic Organization of gypsy Chromatin Insulators in Drosophila melanogaster

Ramos

Ghosh²,

Baxter

et al. 2006

Genetics

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Chromatin insulators have been implicated in the regulation of higher-order chromatin structure and may function to compartmentalize the eukaryotic genome into independent domains of gene expression. To test this possibility, we used biochemical and computational approaches to identify gypsy-like genomicbinding sites for the Suppressor of Hairy-wing [Su(Hw)] protein, a component of the gypsy insulator. EMSA and FISH analyses suggest that these are genuine Su(Hw)-binding sites. In addition, functional tests indicate that genomic Su(Hw)-binding sites can inhibit enhancer-promoter interactions and thus function as bona fide insulators. The insulator strength is dependent on the genomic location of the transgene and the number of Su(Hw)-binding sites, with clusters of two to three sites showing a stronger effect than individual sites. These clusters of Su(Hw)-binding sites are located mostly in intergenic regions or in introns of large genes, an arrangement that fits well with their proposed role in the formation of chromatin domains. Taken together, these data suggest that genomic gypsy-like insulators may provide a means for the compartmentalization of the genome within the nucleus.

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“…SHWBS recruits the Su(Hw) (Suppressor of Hairy-wing) (27,28) and additional proteins to form insulator bodies that are not influenced by either positive or negative position effects (29). The su(Hw) v /su(Hw) f allele combination eliminates insulator activity (30) and can reduce the amplification level of transposons buffered by SHWBS, if they are inserted at sites subject to negative position effects (9).…”

Section: The Two Rounds Of Origin Firing At Dafc-62d Are Interspersed Bymentioning

confidence: 99%

Isolation of aDrosophilaamplification origin developmentally activated by transcription

Xie

Orr‐Weaver

2008

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

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We exploited the Drosophila Amplicon in Follicle Cells, DAFC-62D, to identify a new metazoan amplification origin, ori62. In addition to the origin, DAFC-62D contains two other developmental stagespecific binding regions for the Origin Recognition Complex (ORC) and the replicative helicase MCM2-7. All three of these regions are required for proper amplification. There are two rounds of amplification initiation at ori62, and the second round is preceded by transcription across ori62. We show by ␣-amanitin inhibition that RNA polymerase II (RNAPII) transcription is required to localize MCM2-7 (but not ORC) to permit the second round of origin firing. This role for transcription appears unique to DAFC-62D, because neither other DAFCs nor ectopic transposons with the DAFC-62D replication elements bounded by functional chromatin insulators are affected by ␣-amanitin. By sequential chromatin immunoprecipitation, we show that the MCM complex and RNAPII are bound to the same 100 -500 bp pieces of chromatin during late origin firing. These results raise the possibility that RNAPII may recruit MCM2-7 at some metazoan replication origins.DNA replication ͉ gene amplification ͉ MCM ͉ ORC ͉ RNA polymerase II P roper regulation of the initiation of DNA replication is crucial for cell division in eukaryotes. The first step of initiation is the selection of origins by the prereplicative complex (pre-RC), composed of the six-subunit origin recognition complex (ORC), Cdc6, Cdt1, and MCM2-7 (1). Although these protein factors are highly conserved, the DNA sequences that define origin activity in different organisms are not (2). With recent advances in DNA microarray technology, genome-wide mapping of replication origins has begun to establish the spatial and temporal program of replication initiation (3). However, the mechanisms of origin selection, especially in response to developmental cues in metazoans, remain poorly understood. Only a handful of model metazoan replicons have been studied in detail (2, 4). Furthermore, few observations of cell-type specific or developmental regulation of replication origins have been reported (5, 6).Developmental gene amplification in the ovarian follicle cells of Drosophila provides a powerful system for the analysis of metazoan DNA replication and developmental regulation of origin firing (7,8). Amplification occurs by repeated rounds of origin firing and bidirectional movement of replication forks from these origins to produce 100 kb gradients of amplified DNA (7). This process depends on the same replication initiation and elongation proteins necessary for genomic replication (7, 8). P-element mediated transformation experiments, facilitated by the use of insulators to buffer transposons from chromosomal position effects (9), have allowed dissection of cis regulatory elements required for amplification. In the well characterized third chromosome chorion amplicon, DAFC-66D, both an origin of replication (ori␤) and a replication enhancer (ACE3) have been defined [for review see (8)]. ACE3 sti...

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DNA bending is a determinant of binding specificity for a Drosophila zinc finger protein.

Cited by 104 publications

References 40 publications

Transcriptional control and the role of silencers in transcriptional regulation in eukaryotes

Transcriptional control and the role of silencers in transcriptional regulation in eukaryotes

Genomic Organization of gypsy Chromatin Insulators in Drosophila melanogaster

Isolation of aDrosophilaamplification origin developmentally activated by transcription

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