scholarly journals A DNA fragment containing the upstream activator sequence determines nucleosome positioning of the transcriptionally repressed PHO5 gene of Saccharomyces cerevisiae.

1986 ◽  
Vol 6 (7) ◽  
pp. 2298-2304 ◽  
Author(s):  
L W Bergman
Keyword(s):  
Transcriptional Regulation ◽  
Nucleosome Positioning ◽  
Vector System ◽  
Growth Media ◽  
Flanking Sequences ◽  
Dna Fragment ◽  
Acid Phosphatase Gene ◽  
Nucleosomal Structure ◽  
Relationship Of ◽  
Pho5 Gene

The functional relationship of nucleosome positioning and gene expression is not known. Using high-copy plasmids, containing the yeast phosphate-repressible acid phosphatase gene (PHO5) and the TRP1/ARS1 vector system, I have determined the nucleosomal structure of the 5' region of the PHO5 gene and demonstrated that the nucleosomal positioning of this region is independent of orientation or position in the various plasmid constructions utilized. However, deletion of a 278-base pair BamHI-ClaI fragment from the 5'-flanking sequences of the PHO5 gene causes the nucleosome positioning to become dependent on orientation or position in the plasmids tested. Use of PHO5-CYC1-lACZ fusions have demonstrated that this DNA fragment contains the sequences responsible for the transcriptional regulation of the PHO5 gene in response to the level of phosphate in the growth media. The nucleosome positioning in the 5' region of PHO5 may be determined by an interaction with the sequences or machinery responsible for transcriptional regulation of the gene.

A DNA fragment containing the upstream activator sequence determines nucleosome positioning of the transcriptionally repressed PHO5 gene of Saccharomyces cerevisiae

1986 ◽  
Vol 6 (7) ◽  
pp. 2298-2304
Author(s):  
L W Bergman
Keyword(s):  
Transcriptional Regulation ◽  
Nucleosome Positioning ◽  
Vector System ◽  
Growth Media ◽  
Flanking Sequences ◽  
Dna Fragment ◽  
Acid Phosphatase Gene ◽  
Nucleosomal Structure ◽  
Relationship Of ◽  
Pho5 Gene

The functional relationship of nucleosome positioning and gene expression is not known. Using high-copy plasmids, containing the yeast phosphate-repressible acid phosphatase gene (PHO5) and the TRP1/ARS1 vector system, I have determined the nucleosomal structure of the 5' region of the PHO5 gene and demonstrated that the nucleosomal positioning of this region is independent of orientation or position in the various plasmid constructions utilized. However, deletion of a 278-base pair BamHI-ClaI fragment from the 5'-flanking sequences of the PHO5 gene causes the nucleosome positioning to become dependent on orientation or position in the plasmids tested. Use of PHO5-CYC1-lACZ fusions have demonstrated that this DNA fragment contains the sequences responsible for the transcriptional regulation of the PHO5 gene in response to the level of phosphate in the growth media. The nucleosome positioning in the 5' region of PHO5 may be determined by an interaction with the sequences or machinery responsible for transcriptional regulation of the gene.

Analysis of transcriptional regulation of the s38 chorion gene of Drosophila by P element-mediated transformation

Development ◽  
1984 ◽  
Vol 83 (Supplement) ◽  
pp. 137-146
Author(s):  
Laura Kalfayan ◽  
Barbara Wakimoto ◽  
Allan Spradling
Keyword(s):  
Transcriptional Regulation ◽  
P Element ◽  
Developmental Expression ◽  
Developmental Profile ◽  
E Coli ◽  
Flanking Sequences ◽  
Dna Fragment ◽  
P Element Transformation ◽  
Lac Z

Transcriptional regulation of the s38 chorion gene was studied using P element-mediated germline transformation. A 5·27 kb DNA fragment containing the s38 gene and 5′- and 3′-flanking sequences, was tested for its ability to be transcribed with correct developmental specificity. Five single-insert transformed lines were generated by microinjection of this DNA fragment cloned into a marked P element transformation vector. In each line, the transformed gene was transcribed according to the precise developmental pattern followed by the native s38 gene. The 1·3 kb at the 5′ end of this tested fragment was fused to the E. coli lac z gene. This fragment was also capable of initiating transcription of E. coli lac z RNA with the developmental profile of the native s38 gene. In vitro deletion studies are underway to determine which sequences in the 1·3 kb fragment are necessary for regulating the developmental expression of the gene.

Transcriptional Regulation Functions of Nucleosome Positioning: a Survey*

2012 ◽  
Vol 39 (9) ◽  
pp. 843-852 ◽  
Author(s):  
Hui LIU ◽  
Zi-Heng Zhuang ◽  
Ji-Hong GUAN ◽  
Shui-Geng ZHOU
Keyword(s):  
Transcriptional Regulation ◽  
Nucleosome Positioning ◽  
Regulation Functions

scholarly journals Topoisomerase activity is linked to altered nucleosome positioning and transcriptional regulation in the fission yeast fbp1 gene

PLoS ONE ◽  
2020 ◽  
Vol 15 (11) ◽  
pp. e0242348
Author(s):  
Ryuta Asada ◽  
Satoshi Senmatsu ◽  
Ben Montpetit ◽  
Kouji Hirota
Keyword(s):  
Transcriptional Regulation ◽  
Fission Yeast ◽  
Chromatin Structure ◽  
Promoter Region ◽  
Nucleosome Positioning ◽  
Dna Topology ◽  
Upstream Region ◽  
Inactive Form ◽  
Topological State ◽  
Transcriptional Output

Chromatin structure, including nucleosome positioning, has a fundamental role in transcriptional regulation through influencing protein-DNA interactions. DNA topology is known to influence chromatin structure, and in doing so, can also alter transcription. However, detailed mechanism(s) linking transcriptional regulation events to chromatin structure that is regulated by changes in DNA topology remain to be well defined. Here we demonstrate that nucleosome positioning and transcriptional output from the fission yeast fbp1 and prp3 genes are altered by excess topoisomerase activity. Given that lncRNAs (long noncoding RNAs) are transcribed from the fbp1 upstream region and are important for fbp1 gene expression, we hypothesized that local changes in DNA topological state caused by topoisomerase activity could alter lncRNA and fbp1 transcription. In support of this, we found that topoisomerase overexpression caused destabilization of positioned nucleosomes within the fbp1 promoter region, which was accompanied by aberrant fbp1 transcription. Similarly, the direct recruitment of topoisomerase, but not a catalytically inactive form, to the promoter region of fbp1 caused local changes in nucleosome positioning that was also accompanied by altered fbp1 transcription. These data indicate that changes in DNA topological state induced by topoisomerase activity could lead to altered fbp1 transcription through modulating nucleosome positioning.

scholarly journals ЦАХИЛДАГНЫ ТӨРЛИЙН УРГАМЛЫН ФИЛОГЕНЕТИК ХОЛБОО

2016 ◽  
pp. 25-31
Author(s):  
Х Алтанзул ◽  
Ю Оюунбилэг
Keyword(s):  
Phylogenetic Tree ◽  
Phylogenetic Relationship ◽  
Dna Sequences ◽  
Fragment Size ◽  
Dna Fragment ◽  
Relationship Of

The phylogenetic relationship of eight Iris species (I.flavisimma, I.ventricosa, I.bungei,I.kaempferi, I.tenuifolia, I.lactea, I.tigrida, I.dichotoma) were studied by PCR using six specificprimers (S-523, Z1204R, trnL, trnF and ITS1, ITS4). All species except I.ventricosa wereidentified when using S-523, Z1204R and trnL, trnF primers and the DNA fragment size rangedbetween 500 to 600 bp and 800 bp, respectively. Primers ITS1 and ITS4 produced double bandsin about 500 and 1500 bp to I.bungei, I.kaempferi, and I.lactea species. On the phylogenetic tree, some iris species have close relations based on chloroplastic DNA sequences. The closest relationships showed between I.sanguinea and I.sibirica, I.rutenica and I.uniflora. Also I.tenuifolia, I.ventricosa and I.halophila located on one branch of phylogenetic tree.

scholarly journals The histone variant H2A.Z and chromatin remodeler BRAHMA act coordinately and antagonistically to regulate transcription and nucleosome dynamics in Arabidopsis

2018 ◽  
Author(s):  
E. Shannon Torres ◽  
Roger B. Deal
Keyword(s):  
Transcriptional Regulation ◽  
Transcription Factors ◽  
Binding Sites ◽  
Transcriptional Repression ◽  
Nucleosome Positioning ◽  
Chromatin Organization ◽  
Histone H2a ◽  
Nucleosome Dynamics ◽  
Environmentally Responsive ◽  
Context Specific

ABSTRACTPlants adapt to changes in their environment by regulating transcription and chromatin organization. The histone H2A variant H2A.Z and the SWI2/SNF2 ATPase BRAHMA have overlapping roles in positively and negatively regulating environmentally responsive genes in Arabidopsis, but the extent of this overlap was uncharacterized. Both have been associated with various changes in nucleosome positioning and stability in different contexts, but their specific roles in transcriptional regulation and chromatin organization need further characterization. We show that H2A.Z and BRM act both cooperatively and antagonistically to contribute directly to transcriptional repression and activation of genes involved in development and response to environmental stimuli. We identified 8 classes of genes that show distinct relationships between H2A.Z and BRM and their roles in transcription. We found that H2A.Z contributes to a range of different nucleosome properties, while BRM stabilizes nucleosomes where it binds and destabilizes and/or repositions flanking nucleosomes. H2A.Z and BRM contribute to +1 nucleosome destabilization, especially where they coordinately regulate transcription. We also found that at genes regulated by both BRM and H2A.Z, both factors overlap with the binding sites of light-regulated transcription factors PIF4, PIF5, and FRS9, and that some of the FRS9 binding sites are dependent on H2A.Z and BRM for accessibility. Collectively, we comprehensively characterized the antagonistic and cooperative contributions of H2A.Z and BRM to transcriptional regulation, and illuminated their interrelated roles in chromatin organization. The variability observed in their individual functions implies that both BRM and H2A.Z have more context-specific roles within diverse chromatin environments than previously assumed.

Tissue-specific and efficient expression of the human simple epithelial keratin 8 gene in transgenic mice

1995 ◽  
Vol 108 (2) ◽  
pp. 811-820 ◽  
Author(s):  
L. Casanova ◽  
A. Bravo ◽  
F. Were ◽  
A. Ramirez ◽  
J.J. Jorcano ◽  
...  
Keyword(s):  
Transgenic Mice ◽  
The Body ◽  
Gene Copy ◽  
Intermediate Filament Protein ◽  
Lacz Gene ◽  
Tissue Specific ◽  
Endogenous Gene ◽  
Flanking Sequences ◽  
Dna Fragment ◽  
Keratin 8

Keratin 8 is a type II intermediate filament protein found in simple epithelia. We have introduced a 12 kb DNA fragment of the human K8 locus into the germ line of mice. The transgene, containing 1.1 kb of 5′ flanking sequences, 7.7 kb corresponding to the body of the gene and 3.2 kb of 3′ flanking sequences, was expressed in all six lines obtained. Immunolocalization and RNA analysis of adult tissues showed that the tissue-specific expression pattern of the transgene was almost indistinguishable from that of the endogenous gene. This pattern was found in organs containing single epithelial cell types, such as trachea, lung, stomach, intestine, liver, kidney, thymus and glands. The highest expressing line, however, also produced human K8 in tissues such as stratified epithelia, where it formed part of the pre-existing keratin cytoskeleton of basal cells. Steady state levels of human K8 RNA were proportional to the copy number of the transgene, but transgene expression was less efficient, per gene copy, than that of the endogenous gene. When in the 12 kb DNA fragment the exons and introns of the gene were replaced by the Escherichia coli lacZ gene, the resulting construct showed no expression in transgenic mice. This suggests that 5′ and 3′ flanking sequences, in the absence of intragenic sequences, are not sufficient for K8 expression and that important control elements are located in the body of the K8 gene.

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