DNA STRUCTURAL FEATURES AND ARCHITECTURE OF PROMOTER REGIONS PLAY A ROLE IN GENE RESPONSIVENESS OF S. cerevisiae

2013 ◽  
Vol 11 (06) ◽  
pp. 1343001 ◽  
Author(s):  
VENKATA RAJESH YELLA ◽  
MANJU BANSAL
Keyword(s):  
Gene Expression ◽  
Structural Properties ◽  
Transcription Initiation ◽  
Nucleosome Occupancy ◽  
Regulation Of Gene Expression ◽  
Structural Features ◽  
Tata Box ◽  
Promoter Regions ◽  
Expression Variability ◽  
Promoter Architecture

Gene expression is the most fundamental biological process, which is essential for phenotypic variation. It is regulated by various external (environment and evolution) and internal (genetic) factors. The level of gene expression depends on promoter architecture, along with other external factors. Presence of sequence motifs, such as transcription factor binding sites (TFBSs) and TATA-box, or DNA methylation in vertebrates has been implicated in the regulation of expression of some genes in eukaryotes, but a large number of genes lack these sequences. On the other hand, several experimental and computational studies have shown that promoter sequences possess some special structural properties, such as low stability, less bendability, low nucleosome occupancy, and more curvature, which are prevalent across all organisms. These structural features may play role in transcription initiation and regulation of gene expression. We have studied the relationship between the structural features of promoter DNA, promoter directionality and gene expression variability in S. cerevisiae. This relationship has been analyzed for seven different measures of gene expression variability, along with two different regulatory effect measures. We find that a few of the variability measures of gene expression are linked to DNA structural properties, nucleosome occupancy, TATA-box presence, and bidirectionality of promoter regions. Interestingly, gene responsiveness is most intimately correlated with DNA structural features and promoter architecture.

scholarly journals Arginine Methyltransferases as Regulators of RNA-Binding Protein Activities in Pathogenic Kinetoplastids

2021 ◽  
Vol 8 ◽  
Author(s):  
Gustavo D. Campagnaro ◽  
Edward Nay ◽  
Michael J. Plevin ◽  
Angela K. Cruz ◽  
Pegine B. Walrad
Keyword(s):  
Gene Expression ◽  
Transcriptional Control ◽  
Rna Binding ◽  
Methylation Status ◽  
Regulation Of Gene Expression ◽  
Structural Features ◽  
Arginine Methylation ◽  
Diverse Range ◽  
Host Interaction ◽  
Intronless Genes

A large number of eukaryotic proteins are processed by single or combinatorial post-translational covalent modifications that may alter their activity, interactions and fate. The set of modifications of each protein may be considered a “regulatory code”. Among the PTMs, arginine methylation, catalyzed by protein arginine methyltransferases (PRMTs), can affect how a protein interacts with other macromolecules such as nucleic acids or other proteins. In fact, many RNA-binding (RBPs) proteins are targets of PRMTs. The methylation status of RBPs may affect the expression of their bound RNAs and impact a diverse range of physiological and pathological cellular processes. Unlike most eukaryotes, Kinetoplastids have overwhelmingly intronless genes that are arranged within polycistronic units from which mature mRNAs are generated by trans-splicing. Gene expression in these organisms is thus highly dependent on post-transcriptional control, and therefore on the action of RBPs. These genetic features make trypanosomatids excellent models for the study of post-transcriptional regulation of gene expression. The roles of PRMTs in controlling the activity of RBPs in pathogenic kinetoplastids have now been studied for close to 2 decades with important advances achieved in recent years. These include the finding that about 10% of the Trypanosoma brucei proteome carries arginine methylation and that arginine methylation controls Leishmania:host interaction. Herein, we review how trypanosomatid PRMTs regulate the activity of RBPs, including by modulating interactions with RNA and/or protein complex formation, and discuss how this impacts cellular and biological processes. We further highlight unique structural features of trypanosomatid PRMTs and how it contributes to their singular functionality.

scholarly journals Modeling thecis-regulatory modules of genes expressed in developmental stages ofDrosophila melanogaster

PeerJ ◽  
2017 ◽  
Vol 5 ◽  
pp. e3389 ◽  
Author(s):  
Yosvany López ◽  
Alexis Vandenbon ◽  
Akinao Nose ◽  
Kenta Nakai
Keyword(s):  
Gene Expression ◽  
Developmental Stages ◽  
Expression Profiles ◽  
Regulation Of Gene Expression ◽  
Structural Features ◽  
Extensive Study ◽  
Pairwise Distance ◽  
Sequencing Data ◽  
Binding Motifs ◽  
Promoter Sequences

Because transcription is the first step in the regulation of gene expression, understanding how transcription factors bind to their DNA binding motifs has become absolutely necessary. It has been shown that the promoters of genes with similar expression profiles share common structural patterns. This paper presents an extensive study of the regulatory regions of genes expressed in 24 developmental stages ofDrosophila melanogaster. It proposes the use of a combination of structural features, such as positioning of individual motifs relative to the transcription start site, orientation, pairwise distance between motifs, and presence of motifs anywhere in the promoter for predicting gene expression from structural features of promoter sequences. RNA-sequencing data was utilized to create and validate the 24 models. When genes with high-scoring promoters were compared to those identified by RNA-seq samples, 19 (79.2%) statistically significant models, a number that exceeds previous studies, were obtained. Each model yielded a set of highly informative features, which were used to search for genes with similar biological functions.

scholarly journals Arabidopsis FORGETTER1 mediates stress-induced chromatin memory through nucleosome remodeling

eLife ◽  
2016 ◽  
Vol 5 ◽  
Author(s):  
Krzysztof Brzezinka ◽  
Simone Altmann ◽  
Hjördis Czesnick ◽  
Philippe Nicolas ◽  
Michal Gorka ◽  
...  
Keyword(s):  
Gene Expression ◽  
Heat Stress ◽  
Nucleosome Occupancy ◽  
Promoter Regions ◽  
Nucleosome Remodeling ◽  
Chromatin Remodelers ◽  
Stress Memory ◽  
Active Memory ◽  
Nucleosome Dynamics ◽  
Sessile Organisms

Plants as sessile organisms can adapt to environmental stress to mitigate its adverse effects. As part of such adaptation they maintain an active memory of heat stress for several days that promotes a more efficient response to recurring stress. We show that this heat stress memory requires the activity of the FORGETTER1 (FGT1) locus, with fgt1 mutants displaying reduced maintenance of heat-induced gene expression. FGT1 encodes the Arabidopsis thaliana orthologue of Strawberry notch (Sno), and the protein globally associates with the promoter regions of actively expressed genes in a heat-dependent fashion. FGT1 interacts with chromatin remodelers of the SWI/SNF and ISWI families, which also display reduced heat stress memory. Genomic targets of the BRM remodeler overlap significantly with FGT1 targets. Accordingly, nucleosome dynamics at loci with altered maintenance of heat-induced expression are affected in fgt1. Together, our results suggest that by modulating nucleosome occupancy, FGT1 mediates stress-induced chromatin memory.

scholarly journals An Lrp-Like Protein of the Hyperthermophilic Archaeon Sulfolobus solfataricus Which Binds to Its Own Promoter

1999 ◽  
Vol 181 (5) ◽  
pp. 1474-1480 ◽  
Author(s):  
Alessandra Napoli ◽  
John van der Oost ◽  
Christoph W. Sensen ◽  
Robert L. Charlebois ◽  
Mosé Rossi ◽  
...  
Keyword(s):  
Gene Expression ◽  
Sulfolobus Solfataricus ◽  
Regulation Of Gene Expression ◽  
Open Reading Frames ◽  
Tata Box ◽  
Growth Stages ◽  
Hyperthermophilic Archaeon ◽  
Gene Coding ◽  
Multiple Sequences ◽  
Transcriptional Elements

ABSTRACT Regulation of gene expression in the domain Archaea, and specifically hyperthermophiles, has been poorly investigated so far. Biochemical experiments and genome sequencing have shown that, despite the prokaryotic cell and genome organization, basal transcriptional elements of members of the domain Archaea(i.e., TATA box-like sequences, RNA polymerase, and transcription factors TBP, TFIIB, and TFIIS) are of the eukaryotic type. However, open reading frames potentially coding for bacterium-type transcription regulation factors have been recognized in different archaeal strains. This finding raises the question of how bacterial and eukaryotic elements interact in regulating gene expression in Archaea. We have identified a gene coding for a bacterium-type transcription factor in the hyperthermophilic archaeon Sulfolobus solfataricus. The protein, named Lrs14, contains a potential helix-turn-helix motif and is related to the Lrp-AsnC family of regulators of gene expression in the class Bacteria. We show that Lrs14, expressed in Escherichia coli, is a highly thermostable DNA-binding protein. Bandshift and DNase I footprint analyses show that Lrs14 specifically binds to multiple sequences in its own promoter and that the region of binding overlaps the TATA box, suggesting that, like the E. coli Lrp, Lrs14 is autoregulated. We also show that the lrs14 transcript is accumulated in the late growth stages of S. solfataricus.

scholarly journals Identifying chromatin features that regulate gene expression distribution

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Thanutra Zhang ◽  
Robert Foreman ◽  
Roy Wollman
Keyword(s):  
Gene Expression ◽  
Regulation Of Gene Expression ◽  
Systematic Investigation ◽  
Reporter Expression ◽  
Regulate Gene Expression ◽  
Expression Variability ◽  
Integration Sites ◽  
Average Gene ◽  
Cellular Phenotypes

AbstractGene expression variability, differences in the number of mRNA per cell across a population of cells, is ubiquitous across diverse organisms with broad impacts on cellular phenotypes. The role of chromatin in regulating average gene expression has been extensively studied. However, what aspects of the chromatin contribute to gene expression variability is still underexplored. Here we addressed this problem by leveraging chromatin diversity and using a systematic investigation of randomly integrated expression reporters to identify what aspects of chromatin microenvironment contribute to gene expression variability. Using DNA barcoding and split-pool decoding, we created a large library of isogenic reporter clones and identified reporter integration sites in a massive and parallel manner. By mapping our measurements of reporter expression at different genomic loci with multiple epigenetic profiles including the enrichment of transcription factors and the distance to different chromatin states, we identified new factors that impact the regulation of gene expression distributions.

Insights of potential G-quadruplex sequences in telomeres and proto-oncogenes

2013 ◽  
Vol 21 (3-4) ◽  
pp. 118-124 ◽  
Author(s):  
Rajendra Bhadane ◽  
Rupali Bhadane ◽  
Dhananjay Meshram
Keyword(s):  
Gene Expression ◽  
Transcription Initiation ◽  
Binding Proteins ◽  
Promoter Regions ◽  
Protein Coding ◽  
Protein Coding Genes ◽  
G Quadruplex ◽  
Anticancer Target ◽  
Stable Structures

Guanine rich sequences have the ability to fold into stable 4 stranded structures called G-quadruplex under physiological concentrations of Na+ or K+. G-quadruplexes are found in telomeres, being stable structures under the control of telomerase binding proteins. They are also identified throughout the genome and are enriched in promoter regions of protein coding genes, upstream and downstream of the transcription initiation sites. A number of these promoter quadruplexes have been investigated for several proto-oncogenes. The formation of these quadruplexes can lead to chemical intervention of gene expression using a G-quadruplex binding ligand. We review location, configuration, and stabilization of these quadruplexes in some of the important promoters with regards to their potential as anticancer target.

Stability of transcription complexes on class II genes

1989 ◽  
Vol 9 (1) ◽  
pp. 342-344
Author(s):  
M W Van Dyke ◽  
M Sawadogo ◽  
R G Roeder
Keyword(s):  
Gene Expression ◽  
Transcription Factor ◽  
Rna Polymerase ◽  
Rna Polymerase Ii ◽  
Reaction Pathway ◽  
Regulation Of Gene Expression ◽  
Class Ii ◽  
Tata Box ◽  
Promoter Complex ◽  
Transcription Complexes

Commitment of a TATA box-driven class II gene to transcription requires binding of only one transcription factor, TFIID. Additional factors (TFIIB, TFIIE, and RNA polymerase II) do not remain associated with the TFIID-promoter complex during the course of transcription. This indicates that there are two intermediates along the transcription reaction pathway which may be potential targets for the regulation of gene expression.

scholarly journals Regulation by the Modulation of Gene Expression Variability

2015 ◽  
Vol 197 (12) ◽  
pp. 1974-1975 ◽  
Author(s):  
David Dubnau
Keyword(s):  
Gene Expression ◽  
Regulation Of Gene Expression ◽  
Content Type ◽  
Expression Variability ◽  
Link Type ◽  
Article Type ◽  
Modulation Of Gene Expression ◽  
The Mean ◽  
Cell Changes ◽  
Expression Variance

Classically, transcription is regulated so that the average expression per cell changes, often with a distribution that extends across the population. Roggiani and Goulian (M. Roggiani and M. Goulian, J. Bacteriol. 197:1976–1987, 2015, doi:http://dx.doi.org/10.1128/JB.00074-15) have shown that this is what happens when thetorCADoperon ofEscherichia coliis induced anaerobically by the addition of trimethylamine-N-oxide (TMAO). However, when the same inducer is added to aerobically growing cells, only a subset of the cells respond, although the mean expression per cell is similar to that obtained anaerobically. Thus, in the presence of oxygen, the variance but not the expression mean is altered. The regulation of gene expression variance appears to be due to noise in the phosphorelay that governstorCADtranscription.

scholarly journals Identification of the Main Promoter Directing Cereulide Biosynthesis in Emetic Bacillus cereus and Its Application for Real-Time Monitoring of ces Gene Expression in Foods

2009 ◽  
Vol 76 (4) ◽  
pp. 1232-1240 ◽  
Author(s):  
Monica K. Dommel ◽  
Elrike Frenzel ◽  
Bernd Strasser ◽  
Claudia Blöchinger ◽  
Siegfried Scherer ◽  
...  
Keyword(s):  
Gene Expression ◽  
Bacillus Cereus ◽  
Transcription Initiation ◽  
Promoter Activity ◽  
Biochemical Characterization ◽  
Phosphopantetheinyl Transferase ◽  
Reporter System ◽  
Promoter Regions ◽  
Rapid Amplification ◽  
Translational Start

ABSTRACT Cereulide, the emetic Bacillus cereus toxin, is synthesized by cereulide synthetase via a nonribosomal peptide synthetase (NRPS) mechanism. Previous studies focused on the identification, structural organization, and biochemical characterization of the ces gene locus encoding cereulide synthetase; however, detailed information about the transcriptional organization of the ces genes was lacking. The present study shows that the cesPTABCD genes are transcribed as a 23-kb polycistronic transcript, while cesH, encoding a putative hydrolase, is transcribed from its own promoter. Transcription initiation was mapped by primer extension and rapid amplification of cDNA ends (RACE). Deletion analysis of promoter elements revealed a main promoter located upstream of the cesP coding sequence, encoding a 4′-phosphopantetheinyl transferase. This promoter drives transcription of cesPTABCD. In addition, intracistronic promoter regions in proximity to the translational start sites of cesB and cesT were identified but were only weakly active under the chosen assay conditions. The identified main promoter was amplified from the emetic reference strain B. cereus F4810/72 and fused to luciferase genes in order to study promoter activity in complex environments and to establish a biomonitoring system to assess cereulide production in different types of foods. ces promoter activity was strongly influenced by the food matrix and varied by 5 orders of magnitude. The amount of cereulide toxin extracted from spiked foods correlated well with the bioluminescence data, thus illustrating the potential of the established reporter system for monitoring of ces gene expression in complex matrices.

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