DNA-binding properties of the yeast SWI/SNF complex

Quinn, Janet; Fyrberg, Amy M.; Ganster, Raymond W.; Schmidt, Martin C.; Peterson, Craig L.

doi:10.1038/379844a0

Cited by 184 publications

(163 citation statements)

References 27 publications

Supporting

Mentioning

148

Contrasting

Unclassified

Order By: Relevance

“…We failed to detect genetic interactions between cfi-1 and either unc-37Groucho (Pflugrad et al 1997), lin-35RB (Fattaey et al 1993;Lu and Horvitz 1998), lin-15A repressor (Clark et al 1994;Huang et al 1994), or psa-1 (swi3) or psa-4 (swi2/snf2; Quinn et al 1996;Sawa et al 2000). These results suggest that repression of CEM fate in the URA and IL2 neurons is either directly mediated by CFI-1, or is mediated by a repression complex unrelated to Groucho, Rb, or SWI/ SNF.…”

Section: Cfi-1 Binds Dna In a Sequence-specific Mannermentioning

confidence: 97%

“…Some, like the yeast SWI1 protein, do so nonspecifically (Quinn et al 1996), whereas eARIDs bind DNA in a sequence-specific fashion (Gregory et al 1996). To examine the DNA-binding capabilities of CFI-1, we assessed the ability of the CFI-1 ARID to bind a short oligonucleotide shown by Gregory et al (1996) to be tightly bound by the Drosophila Dead ringer ARID (the Drosophila Engrailed homeodomain protein binding site, or EBS).…”

Section: Cfi-1 Binds Dna In a Sequence-specific Mannermentioning

confidence: 99%

See 1 more Smart Citation

Control of neuronal subtype identity by the C. elegans ARID protein CFI-1

Shaham¹,

Bargmann²

2002

Genes Dev.

View full text Add to dashboard Cite

The Caenorhabditis elegans hermaphrodite nervous system is composed of 302 neurons that fall into at least 118 diverse classes. Here we describe cfi-1, a gene that contributes to the development of neuronal diversity. cfi-1 promotes appropriate differentiation of the URA sensory neurons and inhibits URA from expressing the male-specific CEM neuronal fate. The UNC-86 POU homeodomain protein is present in CEM and URA neurons, and can promote expression of CEM-specific genes in both CEM and URA, but CFI-1 inhibits expression of these genes in the URA cells. cfi-1 also promotes appropriate differentiation and glutamate receptor expression in the AVD and PVC interneurons. cfi-1 encodes a conserved neuron-and muscle-restricted DNA-binding protein containing an A/T rich interaction domain (ARID). ARID proteins regulate early patterning and muscle fate in Drosophila, but they have not previously been implicated in the control of neuronal subtype identity. In the mammalian nervous system thousands of cell types can be distinguished based on position, gene expression, connectivity, and function. Even in the nematode Caenorhabditis elegans, where the nervous system is composed of only 302 neurons, these can be divided into at least 118 different classes (Sulston and Horvitz 1977;Sulston et al. 1983;White et al. 1986). How is this multitude of neuron types generated? Studies in mammals and in C. elegans suggest that lineage-intrinsic mechanisms are important for the generation of this diversity. Transcriptional regulators that are induced during early development play key roles in determining neuronal subtype identity (Sengupta and Bargmann 1996;Tanabe and Jessell 1996), and are expressed in complex, overlapping patterns.The expression of a particular repertoire of neuronspecific proteins results from the integration of functions of multiple transcription factors. In one well-characterized example, the hermaphrodite-specific neuron (HSN) of C. elegans, which regulates egg-laying, integrates inputs from the position of the cell, the sex of the animal, and its developmental state to achieve its terminally differentiated fate. These cues control HSN differentiation by regulating the expression of an assortment of specific transcriptional regulators. The HSN is born in the tail region of the animal (Sulston et al. 1983), and during embryogenesis its identity is specified, in part, by the tail-restricted homeodomain protein EGL-5 (Desai et al. 1988;Chisholm 1991). Appropriate expression of EGL-5 then allows the HSN to migrate from its early posterior position to its final medial position in the animal. At roughly the same time, the sex-determination pathway, in the form of the zinc-finger transcription factor TRA-1, regulates expression of the programmed cell death gene egl-1 to promote HSN survival in hermaphrodites and death in males (Conradt and Horvitz 1999). In the fourth larval stage (L4), inputs from genes that control developmental timing, such as the period-related gene lin-42, promote HSN terminal differentiation. The...

show abstract

Section: Cfi-1 Binds Dna In a Sequence-specific Mannermentioning

confidence: 97%

Section: Cfi-1 Binds Dna In a Sequence-specific Mannermentioning

confidence: 99%

Control of neuronal subtype identity by the C. elegans ARID protein CFI-1

Shaham¹,

Bargmann²

2002

Genes Dev.

View full text Add to dashboard Cite

show abstract

“…However, in principle, proteins that constrain negative superhelicity might be expected to bind preferentially to DNA within a narrow range of superhelical density, as has been shown for the FIS protein, which favors a low negative superhelical density (Schneider et al 1997). There is unfortunately little information available for other proteins, but another possible example would be the eukaryotic HMG domain, which, in addition to being the principal component of the small HMGB proteins (Thomas and Travers 2001), is found in certain subunits of chromatin remodeling complexes (Quinn et al 1996) and of transcription elongation complexes (Orphanides et al 1999;Brewster et al 2001;Formosa et al 2001;Mason and Struhl 2003). The small HMGB proteins themselves may also play an essential role in these processes (Moreira and Holmberg 2000).…”

Section: Gradients Of Superhelicity and Protein Bindingmentioning

confidence: 99%

The regulatory role of DNA supercoiling in nucleoprotein complex assembly and genetic activity

Muskhelishvili

Travers

2016

Biophys Rev

View full text Add to dashboard Cite

We argue that dynamic changes in DNA supercoiling in vivo determine both how DNA is packaged and how it is accessed for transcription and for other manipulations such as recombination. In both bacteria and eukaryotes, the principal generators of DNA superhelicity are DNA translocases, supplemented in bacteria by DNA gyrase. By generating gradients of superhelicity upstream and downstream of their site of activity, translocases enable the differential binding of proteins which preferentially interact with respectively more untwisted or more writhed DNA. Such preferences enable, in principle, the sequential binding of different classes of protein and so constitute an essential driver of chromatin organization.Keywords DNA supercoiling . DNA translocases . Chromatin organization . Superhelicity gradients . DNA untwisting . DNAwrithing Dynamic changes of DNA supercoiling act as a driving force behind the alterations of genetic activity and DNA compaction both in eukaryotes and prokaryotes. Both these processes involve formation of spatially organized nucleoprotein structures by DNA architectural proteins. Whereas in eukaryotes the paradigmal example is the histone octamer, in prokaryotes a similar function is attributed to a small class of highly abundant nucleoid-associated proteins. We argue that, depending on the primary sequence organization, the changes of superhelicity elicit various alterations of local DNA geometry, while these, in turn, facilitate the assembly of distinct nucleoprotein structures pertinent to genetic function. Genome-wide conversion of the superhelical energy into various three-dimensional DNA structures thus acts as an analogue code coordinating the energy supply with the genetic expression of the chromosome.Recent studies make it increasingly clear that the DNA double helix carries at least two types of encoded information and that these include the well-known genetic code and the structural information determining the form and physical properties of the double helix itself. Since both these information types are inscribed in the same DNA sequence, and yet one is discrete whereas the other is continuous, they have been respectively dubbed the digital and analog DNA codes (Marr et al. 2008;Travers et al. 2012;Muskhelishvili and Travers 2013). The potential of the DNA to adopt distinct configurations is strongly modulated by DNA supercoiling, which is increasingly recognized as one of the major forces coordinating the cellular DNA transactions in both prokaryotes (including Archaea) and eukaryotes.DNA supercoiling can be generated by the simple application of torque to the double helix (Strick et al. 1998) but, importantly, because the DNA molecule itself possesses chirality-it is, after all, a right-handed double helix-the local structures stabilized by changes in superhelical density depend on both the sign and strength of the applied torque. For example, both positive and negative torque (respectively overand underwinding of the double helix) can change the intrinsic coiling of ...

show abstract

“…We do not believe that the high molecular mass ADA complexes arise as the result of the interaction of the 200-kDa complex with DNA. This possibility was suggested by the finding that the Swi⅐Snf complex interacts with DNA (39). First, the yeast whole cell extract used for the chromatography experiments was treated with protamine sulfate to remove DNA.…”

Section: Stability Of Ngg1p and Ada2pmentioning

confidence: 99%

Identification of Native Complexes Containing the Yeast Coactivator/Repressor Proteins NGG1/ADA3 and ADA2

Saleh

Lang

Cook

et al. 1997

Journal of Biological Chemistry

109

119

View full text Add to dashboard Cite

NGG1p/ADA3p and ADA2p are dual function regulators that stimulate or inhibit a set of yeast transcriptional activator proteins. In vitro, NGG1p and ADA2p associate in a complex that also contains GCN5p (Horiuchi, J., Silverman, N., Marcus, G. A., and Guarente, L. (1995) Mol. Cell. Biol. 15, 1203-1209). We have found that NGG1p and ADA2p are coimmunoprecipitated from yeast whole cell extracts. In fact, <2% of cellular ADA2p was not associated with NGG1p. Also in agreement with their association in vivo, the stability of ADA2p and NGG1p depended on the presence of each other. In addition, three NGG1p-and ADA2p-containing peak fractions were resolved by Q-Sepharose Fast Flow ion-exchange chromatography of whole cell extract. The presence of another high molecular mass complex was supported by the separation of one of the NGG1p-and ADA2p-containing peak fractions by gel-filtration chromatography. Together, the combination of ion-exchange and gel-filtration chromatography suggests a total of four complexes, two with sizes of >2 MDa and single complexes of ϳ900 and 200 kDa. At least one of these complexes was found to associate with the TATA-binding protein (TBP) since TBP was present in immunoprecipitates with NGG1p. The association of TBP with the ADA proteins required amino acids 274 -307 of NGG1p, a region of NGG1p required for activity. This supports a role for NGG1p in the interaction with TBP and suggests that the interaction with TBP is functionally relevant.Activated transcription by RNA polymerase II requires the action of the basal transcriptional machinery, sequence-specific activator proteins, and coactivator or mediator proteins (1). Coactivators positively influence activator function either by providing a regulatory interface between the basal machinery and the activator protein or by enabling these components to contend with a DNA template in the form of chromatin. Coactivators have generally been found as components of regulatory complexes. The TBP 1 ⅐TBP-associated factor complex, the RNA polymerase II holoenzyme complex, and the Swi⅐Snf complex represent principal examples (reviewed in Refs. 2-4). The mechanisms and component structure of these complexes may overlap as suggested by the finding of Swi/Snf components (5) within the RNA polymerase II holoenzyme (6), the TBP-associated factor complex, and transcription factor IIF (7).Probably through related mechanisms, coactivator complexes can also be involved in repression. We initially discovered NGG1 based on its requirement for full inhibition of the GAL4 activator protein in glucose media (8). NGG1p likely acts as a more general repressor because transcriptional activation by the carboxyl-terminal activation domain of PDR1p is enhanced in a ngg1 background (9). Guarente and co-workers (10) independently isolated NGG1/ADA3 based on suppression of the toxicity of overexpression of VP16 in yeast. Mutations within four ADA genes, ADA2, NGG1/ADA3, GCN5/ADA4, and ADA5, suppress the toxicity of VP16 by inhibiting its ability to activate transcription (...

show abstract

DNA-binding properties of the yeast SWI/SNF complex

Cited by 184 publications

References 27 publications

Control of neuronal subtype identity by the C. elegans ARID protein CFI-1

Control of neuronal subtype identity by the C. elegans ARID protein CFI-1

The regulatory role of DNA supercoiling in nucleoprotein complex assembly and genetic activity

Identification of Native Complexes Containing the Yeast Coactivator/Repressor Proteins NGG1/ADA3 and ADA2

Contact Info

Product

Resources

About