Architectural variations of inducible eukaryotic promoters: Preset and remodeling chromatin structures

Abstract

The DNA in a eukaryotic nucleus is packaged into a nucleosome array, punctuated by variations in the regular pattern. The local chromatin structure of inducible genes appears to fall into two categories: preset and remodeling. Preset genes are those in which the binding sites for trans-acting factors are accessible (i.e. in a non-nucleosomal, DNase I hypersensitive configuration) prior to activation. In response to the activation signal, positive factors bind to cis-acting regulatory elements and trigger transcription with no major alterations in the chromatin structure of the promoter region. In contrast, remodeling genes are those in which some of the required cis-acting regulatory elements are packaged into nucleosomes. The nucleosomes must be perturbed in response to an activation signal in order for the trans-acting factors to gain access to cis-acting elements; a chromatin remodeling process which forms DNase I hypersensitive sites must occur. In both cases, precise positioning of nucleosomes along the promoter region of a gene appears to be critical for appropriate regulation of expression.

p53 Targets Chromatin Structure Alteration to Repress α-Fetoprotein Gene Expression

“…Our present study reveals that the functional outcome of p53 DNA binding within the AFP distal repressor region is dictated by chromatin structure organization. Chromatin structure can influence transcription regulation by obstructing transcription factor access to DNA or by facilitating interactions between distal regulatory factors and proximal promoter elements to repress or activate transcription (33)(34)(35)(36)(37)(38). Our in vitro chromatin transcription system recapitulates distal regulation of AFP transcription by p53 bound to DNA 850 base pairs 5Ј of the transcription start site within the AFP developmental repressor domain.…”

Nuclear Factor 1 and Octamer Transcription Factor 1 Binding Preset the Chromatin Structure of the Mouse Mammary Tumor Virus Promoter for Hormone Induction

“…An aliquot was also analyzed by immunoblotting with GR antiserum together with known amounts of GR purified from rat liver (16) to serve as a standard curve for calculation of absolute amounts of Oct1 that followed a linear correlation between injected RNA and translated protein. 2 Based on these calculations done in different oocyte experiments with the same mRNA preparations and a similar time of translation, about 24 h, the intranuclear amounts of GR (after hormone treatment), NF1, and Oct1 were about 0.1, 0.01, and 0.06 pmol, respectively, in a typical injection experiment. Assuming an intranuclear volume of 40 nl, this will result in an intranuclear concentration of 2.5, 0.25, and 1.5 M for GR, NF1, and Oct1, respectively.…”

“…the packaging unit of eukaryotic chromatin) are usually randomly organized on DNA in vivo, but there are particular DNA segments where they are translationally positioned (1,2). Such a nucleosome arrangement is often found within gene regulatory regions during the stepwise differentiation process of tissue-specific genes (3)(4)(5).…”

A comparison of invivo and invitro DNA-binding specificities suggests a new model for homeoprotein DNA binding in Drosophila embryos

“…These two genes are bound most weakly in vivo by Eve, Ftz, Bicoid and Paired, even though these two genes are bound relatively well in vitro ( Figure 7B). The chromatin structure of transcriptionally inactive genes is thought to inhibit DNA binding by certain classes of transcription factor (Wallrath et al, 1994;Beato and Eisfeld, 1997;Kadonaga, 1998). Therefore, closed chromatin structure could explain the reduced binding to Adh and rosy.…”