scholarly journals Combinatorial analysis of Saccharomyces cerevisiae regulatory elements

2019 ◽  
Author(s):  
N. Dhillon ◽  
R. Shelansky ◽  
B. Townshend ◽  
M. Jain ◽  
H. Boeger ◽  
...  
Keyword(s):  
Gene Expression ◽  
Saccharomyces Cerevisiae ◽  
Specific Interaction ◽  
Principal Component ◽  
Regulatory Elements ◽  
Untranslated Regions ◽  
Core Promoters ◽  
Regulatory Circuits ◽  
Expression Cluster ◽  
Multiple Levels

AbstractGene expression in Saccharomyces cerevisiae is regulated at multiple levels. Genomic and epigenomic mapping of transcription factors and chromatin components has led to the definition and delineation of various regulatory elements. Enhancers, promoters, 5’ untranslated regions (5’UTR) and transcription terminators/3’ untranslated regions (3’UTR) have all been defined. However, the specific contributions of each of these features as part of a regulatory unit and the functional communications between these regulatory elements remains under explored.We built a combinatorial library of 26 different enhancers, core promoters, 5’UTRs and transcription terminators/3’UTRs. This library was analyzed with respect to gene expression in order to better understand the interactions between different regulatory elements. In the process we developed new methods to estimate the contribution of individual regulatory parts from just a few simple measurements. Our data show that different pairs of regulatory parts follow specific interaction rules affecting overall activity either positively or negatively. We find that while enhancers are the initiators of gene activity, core promoters modulate the levels of enhancer mediated expression. Cluster analysis based on expression show that TATA-box containing core promoters appear to increase enhancer-driven transcription to a greater extent than TATA-less promoters. Principal component analysis highlight outliers and suggest differences in mechanisms of regulation. These results provide a system to characterize regulatory elements and use these elements in the design of synthetic regulatory circuits.

scholarly journals Permutational analysis of Saccharomyces cerevisiae regulatory elements

2020 ◽  
Vol 5 (1) ◽  
Author(s):  
Namrita Dhillon ◽  
Robert Shelansky ◽  
Brent Townshend ◽  
Miten Jain ◽  
Hinrich Boeger ◽  
...  
Keyword(s):  
Gene Expression ◽  
Saccharomyces Cerevisiae ◽  
Principal Component ◽  
Regulatory Elements ◽  
Untranslated Regions ◽  
Core Promoters ◽  
Regulatory Circuits ◽  
Multiple Levels ◽  
Functional Components ◽  
Gene Expression Levels

Abstract Gene expression in Saccharomyces cerevisiae is regulated at multiple levels. Genomic and epigenomic mapping of transcription factors and chromatin factors has led to the delineation of various modular regulatory elements—enhancers (upstream activating sequences), core promoters, 5′ untranslated regions (5′ UTRs) and transcription terminators/3′ untranslated regions (3′ UTRs). However, only a few of these elements have been tested in combinations with other elements and the functional interactions between the different modular regulatory elements remain under explored. We describe a simple and rapid approach to build a combinatorial library of regulatory elements and have used this library to study 26 different enhancers, core promoters, 5′ UTRs and transcription terminators/3′ UTRs to estimate the contribution of individual regulatory parts in gene expression. Our combinatorial analysis shows that while enhancers initiate gene expression, core promoters modulate the levels of enhancer-mediated expression and can positively or negatively affect expression from even the strongest enhancers. Principal component analysis (PCA) indicates that enhancer and promoter function can be explained by a single principal component while UTR function involves multiple functional components. The PCA also highlights outliers and suggest differences in mechanisms of regulation by individual elements. Our data also identify numerous regulatory cassettes composed of different individual regulatory elements that exhibit equivalent gene expression levels. These data thus provide a catalog of elements that could in future be used in the design of synthetic regulatory circuits.

scholarly journals Role of Non-Coding Regulatory Elements in the Control of GR-Dependent Gene Expression

2021 ◽  
Vol 22 (8) ◽  
pp. 4258
Author(s):  
Malgorzata Borczyk ◽  
Mateusz Zieba ◽  
Michał Korostyński ◽  
Marcin Piechota
Keyword(s):  
Gene Expression ◽  
Time Course ◽  
Regulatory Elements ◽  
Transcription Activator ◽  
Long Distance ◽  
Core Promoters ◽  
Transcriptional Changes ◽  
Gene Expression Dynamics ◽  
Upregulated Genes

The glucocorticoid receptor (GR, also known as NR3C1) coordinates molecular responses to stress. It is a potent transcription activator and repressor that influences hundreds of genes. Enhancers are non-coding DNA regions outside of the core promoters that increase transcriptional activity via long-distance interactions. Active GR binds to pre-existing enhancer sites and recruits further factors, including EP300, a known transcriptional coactivator. However, it is not known how the timing of GR-binding-induced enhancer remodeling relates to transcriptional changes. Here we analyze data from the ENCODE project that provides ChIP-Seq and RNA-Seq data at distinct time points after dexamethasone exposure of human A549 epithelial-like cell line. This study aimed to investigate the temporal interplay between GR binding, enhancer remodeling, and gene expression. By investigating a single distal GR-binding site for each differentially upregulated gene, we show that transcriptional changes follow GR binding, and that the largest enhancer remodeling coincides in time with the highest gene expression changes. A detailed analysis of the time course showed that for upregulated genes, enhancer activation persists after gene expression changes settle. Moreover, genes with the largest change in EP300 binding showed the highest expression dynamics before the peak of EP300 recruitment. Overall, our results show that enhancer remodeling may not directly be driving gene expression dynamics but rather be a consequence of expression activation.

scholarly journals Pervasive and Dynamic Transcription Initiation in Saccharomyces cerevisiae

2018 ◽  
Author(s):  
Zhaolian Lu ◽  
Zhenguo Lin
Keyword(s):  
Gene Expression ◽  
Saccharomyces Cerevisiae ◽  
Transcription Initiation ◽  
Core Promoter ◽  
Model Organism ◽  
Start Codon ◽  
Yeast Genome ◽  
Core Promoters ◽  
Nucleotide Resolution ◽  
Yeast Genes

AbstractTranscription initiation is finely regulated to ensure the proper expression and function of these genes. The regulated transcription initiation in response to various environmental cues in the model organism Saccharomyces cerevisiae has not been systematically investigated. In this study, we generated quantitative maps of transcription start site (TSS) at a single-nucleotide resolution for S. cerevisiae grown in nine different conditions using no-amplification non-tagging Cap analysis of gene expression (nAnT-iCAGE) sequencing. Based on 337 million uniquely mapped CAGE tags, we mapped ~1 million well-supported TSSs, suggesting highly pervasive transcription initiation in the compact genome of yeast. The comprehensive TSS maps allowed us to identify core promoters for ~96% verified protein-coding genes and to revise the predicted translation start codon for 183 genes. We found that 56% of yeast genes have at least two core promoters and alternative usage of different core promoters in a gene is widespread in response to changing environments. More importantly, most core promoter shifts are coupled with differential gene expression, indicating that core promoter shift might play an important role in controlling transcriptional activity of yeast genes. Based on their dynamic activities, we divided yeast core promoters as constitutive core promoters (55%) and inducible core promoters (45%). The two classes of core promoters exhibit distinctive patterns in transcriptional abundance, chromatin structure, promoter shape, and sequence context. In summary, the quantitative TSS maps generated by this study improved the annotation of yeast genome, and revealed a highly pervasive and dynamic nature of transcription initiation in yeast.

scholarly journals No Need to Stick Together to Be Connected: Multiple Types of Enhancers’ Networking

Cancers ◽  
2021 ◽  
Vol 13 (20) ◽  
pp. 5201
Author(s):  
Emanuele Vitale ◽  
Mila Gugnoni ◽  
Alessia Ciarrocchi
Keyword(s):  
Gene Expression ◽  
Gene Expression Regulation ◽  
Building Blocks ◽  
Regulatory Elements ◽  
Transcriptional Level ◽  
Independent Manner ◽  
Control Of Gene Expression ◽  
Cis Acting ◽  
Regulatory Circuits ◽  
Dna Elements

The control of gene expression at a transcriptional level requires a widespread landscape of regulatory elements. Central to these regulatory circuits are enhancers (ENHs), which are defined as cis-acting DNA elements able to increase the transcription of a target gene in a distance- and orientation-independent manner. ENHs are not independent functional elements but work in a complex and dynamic cooperative network, constituting the building blocks of multimodular domains of gene expression regulation. The information from each of these elements converges on the target promoter, contributing to improving the precision and sharpness of gene modulation. ENHs’ interplay varies in its nature and extent, ranging from an additive to redundant effect depending on contexts. Moving from super-enhancers that drive the high expression levels of identity genes, to shadow-enhancers, whose redundant functions contribute to buffering the variation in gene expression, this review aims to describe the different modalities of ENHs’ interaction and their role in the regulation of complex biological processes like cancer development.

scholarly journals 3’ untranslated regions of Marburg and Ebola virus mRNAs possess negative regulators of translation that are modulated by ADAR1 editing

2021 ◽  
Author(s):  
Sudip Khadka ◽  
Caroline G. Williams ◽  
Joyce Sweeney-Gibbons ◽  
Christopher F. Basler
Keyword(s):  
Gene Expression ◽  
Ebola Virus ◽  
Regulatory Elements ◽  
Marburg Virus ◽  
Untranslated Regions ◽  
Type I ◽  
Negative Effects ◽  
Negative Regulators ◽  
Rna Sequences ◽  
Viral Mrnas

The filovirus family includes deadly pathogens such as Ebola virus (EBOV) and Marburg virus (MARV). A substantial portion of filovirus genomes encode 5’ and 3’ untranslated regions (UTRs) of viral mRNAs. Select viral genomic RNA sequences corresponding to 3’UTRs are prone to editing by ADAR1. A reporter mRNA approach, in which different 5’ or 3’UTRs were inserted into luciferase encoding mRNAs, demonstrates that MARV 3’UTRs yield different levels of reporter gene expression suggesting modulation of translation. The modulation occurs in cells unable to produce miRNAs and can be recapitulated in a MARV minigenome assay. Deletion mutants identified negative regulatory regions at end of the MARV NP and L 3’UTRs. Apparent ADAR1 editing mutants were previously identified within the MARV NP 3’UTR. Introduction of these changes into the MARV nucleoprotein (NP) 3’UTR or deletion of the region targeted for editing enhances translation, as indicated by reporter assays and polysome analysis. In addition, the parental NP 3’UTR, but not the edited or deletion mutant NP 3’UTRs, induce a type I interferon (IFN) response upon transfection into cells. Because some EBOV isolates from the West Africa outbreak exhibited ADAR1 editing of the VP40 3’UTR, VP40 3’UTRs with parental and edited sequences were similarly assayed. The EBOV VP40 3’UTR edits also enhanced translation but neither the wildtype nor the edited 3’UTRs induced IFN. These findings implicate filoviral mRNA 3’UTRs as negative regulators of translation that can be inactivated by innate immune responses that induce ADAR1. Importance UTRs comprise a large percentage of filovirus genomes and are apparent targets of editing by ADAR1, an enzyme with pro- and antiviral activities. However, the functional significance of the UTRs and of ADAR1 editing have been uncertain. This study demonstrates that MARV and EBOV 3’UTRs can modulate translation, in some cases negatively. ADAR1 editing or deletion of select regions within the translation suppressing 3’UTRs, relieves the negative effects of the UTRs. These data indicate that filovirus 3’UTRs contain translation regulatory elements that are modulated by activation of ADAR1, suggesting a complex interplay between filovirus gene expression and innate immunity.

Post-Transcriptional Regulation of Cardiac Sarcomere Protein Titin Through 3’ Untranslated Regions

2013 ◽  
Vol 9 ◽  
Author(s):  
Tara A Shrout
Keyword(s):  
Gene Expression ◽  
Transcriptional Control ◽  
Striated Muscle ◽  
Binding Capacity ◽  
Structural Features ◽  
Neonatal Rat ◽  
Regulatory Control ◽  
Untranslated Regions ◽  
Luciferase Reporter ◽  
Regulatory Effects

Titin is the largest known protein in the human body, and forms the backbone of all striated muscle sarcomeres. The elastic nature of titin is an important component of muscle compliance and functionality. A significant amount of energy is expended to synthesize titin, thus we postulate that titin gene expression is under strict regulatory control in order to conserve cellular resources. In general, gene expression is mediated in part by post-transcriptional control elements located within the 5’ and 3’ untranslated regions (UTRs) of mature mRNA. The 3’UTR in particular contains structural features that affect binding capacity to other RNA components, such as MicroRNA, which control mRNA localization, translation, and degradation. The degree and significance of the regulatory effects mediated by two determined variants of titin’s 3’ UTR were evaluated in Neonatal Rat Ventricular Myocyte and Human Embryonic Kidney cell lines. Recombinant plasmids to transfect these cells lines were engineered by insertion of the variant titin 3’UTR 431- and 1047-base pairs sequences into luciferase reporter vectors. Expression due to an unaltered reporter vector served as the control. Quantitative changes in luciferase activity due to the recombinants proportionally represented the effect titin’s respective 3’UTR conferred on downstream post-transcriptional expression relative to the control. The effect due to titin’s shorter 3’UTR sequence was inconclusive; however, results illustrated that titin’s longer 3’UTR sequence caused a 35 percent decrease in protein expression. Secondary structural analysis of the two sequences revealed differential folding patterns that affect the stability and degree of MicroRNA-binding within titin’s variant 3’UTR sequences.

Effects of Saccharomyces Cerevisiae Strains on Chemical Profiles of Cabernet Sauvignon Wines: Based on the Combined Results of 1H NMR, HS-SPME/GC-MS and HPLC-DAD-ESI-MS/MS

2018 ◽  
Vol 18 (2) ◽  
pp. 115-131
Author(s):  
Liang Heng-Yu ◽  
Su Ning ◽  
Guo Kun ◽  
Wang Yuan ◽  
Yang De-Yu
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Principal Component ◽  
Grape Juice ◽  
Pilot Scale ◽  
Ethyl Esters ◽  
Cabernet Sauvignon ◽  
Esi Ms ◽  
H Nmr ◽  
Chemical Profiles ◽  
Indigenous Yeasts

Five Saccharomyces cerevisiae strains (Chinese indigenous yeasts SC5, WC5, SC8, CC17 and commercial starter F15) were inoculated into Cabernet sauvignon grape must and fermented at pilot scale. For the first time, combination of 1H NMR, HS-SPME/GC-MS and HPLC-DAD-ESI-MS/MS metabonomic profiling techniques was performed to analyze the global chemical fingerprints of sampled wines at the end of alcoholic and malolactic fermentation respectively, then 13 non-volatile flavor compounds, 52 volatile organic aromas and 43 polyphenolic molecules were identified and determined correspondently. All principal component analysis (PCA) of two fermentation stages based on the analytical results of 1H NMR, HS-SPME/GC-MS and HPLC-DAD-ESI-MS/MS divided these strains into three clusters: (1) SC5 and SC8, (2) WC5 and F15 and (3) CC17. The wine fermented by indigenous yeast, CC17, showed a very unique chemical profile, such as low pH and high color intensity, reduced amino acids (including proline) and the lowest total higher alcohols levels, most of the fixed acids, glycerol, ethyl esters and anthocyanins concentrations. The statistical results indicate that CC17 strain possesses very special anabolism and catabolism abilities on such substances in grape juice and has potentiality to produce characteristic wines with high qualities.

scholarly journals Mapping chromatin accessibility and active regulatory elements reveals pathological mechanisms in human gliomas

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Karolina Stępniak ◽  
Magdalena A. Machnicka ◽  
Jakub Mieczkowski ◽  
Anna Macioszek ◽  
Bartosz Wojtaś ◽  
...  
Keyword(s):  
Gene Expression ◽  
Chromatin Structure ◽  
Molecular Mechanisms ◽  
Genome Mapping ◽  
Malignant Gliomas ◽  
Regulatory Elements ◽  
Chromatin Accessibility ◽  
Multiple Tumor ◽  
Genes Encoding ◽  
Methylation Patterns

AbstractChromatin structure and accessibility, and combinatorial binding of transcription factors to regulatory elements in genomic DNA control transcription. Genetic variations in genes encoding histones, epigenetics-related enzymes or modifiers affect chromatin structure/dynamics and result in alterations in gene expression contributing to cancer development or progression. Gliomas are brain tumors frequently associated with epigenetics-related gene deregulation. We perform whole-genome mapping of chromatin accessibility, histone modifications, DNA methylation patterns and transcriptome analysis simultaneously in multiple tumor samples to unravel epigenetic dysfunctions driving gliomagenesis. Based on the results of the integrative analysis of the acquired profiles, we create an atlas of active enhancers and promoters in benign and malignant gliomas. We explore these elements and intersect with Hi-C data to uncover molecular mechanisms instructing gene expression in gliomas.

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