Chromatin Remodeling Mediated by <i>Drosophila</i> GAGA Factor and ISWI Activates <i>fushi tarazu</i> Gene Transcription In Vitro

Okada, Masahiro; Hirose, Susumu

doi:10.1128/mcb.18.5.2455

Cited by 73 publications

(62 citation statements)

References 51 publications

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“…NURF was first identified by its requirement for making the hsp70 heat shock promoter accessible in the presence of the GAGA transcription factor [83]. This duo was also shown to activate the fushi tarazu gene [84]. The ATPase activity of this complex is specifically stimulated by nucleosomes and not DNA, in contrast to the SWI/SNF complex where DNA and nucleosomes equally stimulate the ATPase activity.…”

Section: Iswi Familymentioning

confidence: 99%

Mechanisms of ATP dependent chromatin remodeling

Gangaraju

Bartholomew

2007

Mutation Research/Fundamental and Molecular Mechanisms of Mutag

126

159

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The inter-relationship between DNA repair and ATP dependent chromatin remodeling has begun to become very apparent with recent discoveries. ATP dependent remodeling complexes mobilize nucleosomes along DNA, promote the exchange of histones, or completely displace nucleosomes from DNA. These remodeling complexes are often categorized based on the domain organization of their catalytic subunit. The biochemical properties and structural information of several of these remodeling complexes are reviewed. The different models for how these complexes are able to mobilize nucleosomes and alter nucleosome structure are presented incorporating several recent findings. Finally the role of histone tails and their respective modifications in ATP-dependent remodeling are discussed.

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Section: Iswi Familymentioning

confidence: 99%

Mechanisms of ATP dependent chromatin remodeling

Gangaraju

Bartholomew

2007

Mutation Research/Fundamental and Molecular Mechanisms of Mutag

126

159

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“…5) demonstrated the uniqueness of TAGteam sites, but revealed non-TAGteam motifs associated with overlapping patterns of binding as well. Of the 30 highest-ranked heptamers associated with overlapping binding, all of the non-TAGteam motifs contained GA or GAG repeats, suggesting a potential association between binding of many factors and GAGA factor, which is encoded by the gene Trithorax-like and implicated in chromatin remodeling (Granok et al 1995;Wall et al 1995;Okada and Hirose 1998). Intriguingly, we observed a 1.5-fold enrichment for GAGA motifs in promoters with high levels of binding when TAGteam motifs were not present (39% of highly bound promoters without TAGteam sites contained GAGA motifs versus 25% with TAGteam sites), suggesting that GAGA factor may help to facilitate binding of transcription factors at some regions not associated with Vielfaltig.…”

Section: Org Downloaded Frommentioning

confidence: 99%

The TAGteam motif facilitates binding of 21 sequence-specific transcription factors in the Drosophila embryo

Satija¹,

Bradley²

2012

Genome Res.

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Highly overlapping patterns of genome-wide binding of many distinct transcription factors have been observed in worms, insects, and mammals, but the origins and consequences of this overlapping binding remain unclear. While analyzing chromatin immunoprecipitation data sets from 21 sequence-specific transcription factors active in the Drosophila embryo, we found that binding of all factors exhibits a dose-dependent relationship with ''TAGteam'' sequence motifs bound by the zinc finger protein Vielfaltig, also known as Zelda, a recently discovered activator of the zygotic genome. TAGteam motifs are present and well conserved in highly bound regions, and are associated with transcription factor binding even in the absence of canonical recognition motifs for these factors. Furthermore, levels of binding in promoters and enhancers of zygotically transcribed genes are correlated with RNA polymerase II occupancy and gene expression levels. Our results suggest that Vielfaltig acts as a master regulator of early development by facilitating the genome-wide establishment of overlapping patterns of binding of diverse transcription factors that drive global gene expression.[Supplemental material is available for this article.]Genome-wide chromatin immunoprecipitation (ChIP) experiments in diverse metazoans have shown that many transcription factors bind thousands of highly overlapping loci in undifferentiated cells (Boyer et al.

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“…Brief treatment of chromatin with MNase followed by gel analysis of purified DNA reveals a pattern of DNA fragments increasing in size by approximately 200-base pair increments derived from digestion within linker DNA at mono-, di-, tri-nucleosomal, etc., intervals. MNase analysis of the hsp70 (10), hsp26 (11), and ftz (12) promoters reconstituted into chromatin in vitro showed that addition of GAGA factor, in the presence of both embryonic nuclear extract and ATP, led to a localized disruption of the nucleosomal array at the GAGA sequences. Because both cofactors were essential, it was suggested that the observed remodeling depended critically on the presence of NURF in the extract.…”

Section: Strategy For Investigating the Role Of Gaga Factor In Genementioning

confidence: 99%

“…18). Carefully controlled in vitro experiments showed that GAGA factor had no overt transcription activating ability on naked DNA templates (13,14) but could relieve the repression of basal transcription at a linked promoter assembled into chromatin when the remodeling factor NURF was present (12). The observed stimulation of transcription by GAGA factor in crude extracts or transient assays (35,36,42) might then reflect its ability to partake in the suppression or destabilization of the many nonspecific DNA-protein interactions that are likely to occur on DNA templates in such assays.…”

Section: Role Of Gaga Factor In Trans-activation Versus Chromatinmentioning

confidence: 99%

“…Other in vitro studies have revealed that although GAGA factor stimulates transcription of repressed promoters, it does not activate transcription above basal (i.e. nonrepressed) levels (12)(13)(14). Null mutations of the Trithorax-like (Trl) gene, which encodes GAGA factor, result in larval lethality (15), whereas less severe alleles show enhancement of position effect variegation as well as deficiencies in chromosome condensation, segregation, and nuclear cleavage (15,16).…”

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confidence: 99%

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GAGA Factor-dependent Transcription and Establishment of DNase Hypersensitivity Are Independent and Unrelated Events in Vivo

Pile¹,

Cartwright

2000

Journal of Biological Chemistry

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Using a Drosophila transgenic system we investigated the ability of GAGA factor, a putative anti-repressor, to modulate transcription-related events in the absence or presence of a bona fide activator, the Adf-1 transcription factor. In contrast to previous in vitro and in vivo data linking the binding of GAGA factor to the acquisition of DNase hypersensitivity at heat shock promoters, we observed that inserting multiple GAGA binding motifs adjacent to a minimal alcohol dehydrogenase (Adh) promoter led to strongly elevated embryonic transcription without creation of a promoter-associated DNase-hypersensitive (DH) site. Establishment of DNase hypersensitivity required the presence of both GAGA and Adf-1 binding sites and was accompanied by a further, synergistic increase in transcription. Because Adf-1 is capable neither of establishing a DH site nor of promoting efficient transcription by itself in embryos, it is likely that DH site formation depends on a GAGA factor-mediated binding of Adf-1 to chromatin, perhaps facilitated by a locally remodeled downstream promoter region. More generally we suggest that GAGA factor-binding sequences may operate in a promoter-specific context, with transcriptional activation, polymerase pausing, and/or DH site formation critically dependent on the nature of the sequences (and their binding partners) linked in cis.Control of eukaryotic transcription is a complex, tightly regulated process requiring the action of many distinct proteins, including chromatin-interacting/modifying proteins, transcriptional activators, and general transcription factors (GTFs) 1 (for review see Refs. 1-3). In addition to recent progress in determining the role of chromatin-interacting proteins, unraveling the mechanisms by which sequence-specific, DNA-binding activators promote transcription has traditionally occupied a good deal of effort in the field. The consensus emerging from studies on many activators is that a significant activity of these proteins is to recruit components of the general transcription machinery and/or chromatin-interacting factors to promoters through direct protein-protein interactions (4).The Drosophila GAGA factor is unusual in that its activity in transcription appears to be neither that of a purely sequencespecific transactivator nor that of an ATP-dependent chromatin-interacting factor. GAGA protein was first identified as a transcription factor that bound a repetitive GA element upstream of the engrailed (5) and Ultrabithorax (6) promoters. So-called GAGA elements have subsequently been identified in numerous promoters, including those controlling housekeeping, developmentally regulated, and inducible genes (7). GA repeats appear to be important in the acquisition of constitutive DNase I-hypersensitive (DH) sites found at the transcriptionally inactive but inducible hsp26 (8) and hsp70 (9) promoters in vivo. Moreover, in concert with the ATP-dependent nucleosome remodeling factor (NURF), GAGA factor aids in the local remodeling of GAGA element-containing chromatin templ...

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Chromatin Remodeling Mediated by Drosophila GAGA Factor and ISWI Activates fushi tarazu Gene Transcription In Vitro

Cited by 73 publications

References 51 publications

Mechanisms of ATP dependent chromatin remodeling

Mechanisms of ATP dependent chromatin remodeling

The TAGteam motif facilitates binding of 21 sequence-specific transcription factors in the Drosophila embryo

GAGA Factor-dependent Transcription and Establishment of DNase Hypersensitivity Are Independent and Unrelated Events in Vivo

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