scholarly journals Regulation of Gene Expression under Hypoxic Conditions

2019 ◽  
Vol 20 (13) ◽  
pp. 3278 ◽  
Author(s):  
Koh Nakayama ◽  
Naoyuki Kataoka
Keyword(s):  
Gene Expression ◽  
Rna Processing ◽  
Rna Splicing ◽  
Regulation Of Gene Expression ◽  
Splicing Factors ◽  
Rna Transport ◽  
Regulate Gene Expression ◽  
Hypoxic Conditions ◽  
Eukaryotic Gene Expression ◽  
Eukaryotic Gene

Eukaryotes are often subjected to different kinds of stress. In order to adjust to such circumstances, eukaryotes activate stress–response pathways and regulate gene expression. Eukaryotic gene expression consists of many different steps, including transcription, RNA processing, RNA transport, and translation. In this review article, we focus on both transcriptional and post-transcriptional regulations of gene expression under hypoxic conditions. In the first part of the review, transcriptional regulations mediated by various transcription factors including Hypoxia-Inducible Factors (HIFs) are described. In the second part, we present RNA splicing regulations under hypoxic conditions, which are mediated by splicing factors and their kinases. This work summarizes and discusses the emerging studies of those two gene expression machineries under hypoxic conditions.

scholarly journals RNA Epigenetics: Fine-Tuning Chromatin Plasticity and Transcriptional Regulation, and the Implications in Human Diseases

Genes ◽  
2021 ◽  
Vol 12 (5) ◽  
pp. 627
Author(s):  
Amber Willbanks ◽  
Shaun Wood ◽  
Jason X. Cheng
Keyword(s):  
Gene Expression ◽  
Chromatin Structure ◽  
Fine Tuning ◽  
Human Diseases ◽  
Rna Modifications ◽  
Regulate Gene Expression ◽  
Eukaryotic Gene Expression ◽  
Eukaryotic Gene ◽  
Fine Tune

Chromatin structure plays an essential role in eukaryotic gene expression and cell identity. Traditionally, DNA and histone modifications have been the focus of chromatin regulation; however, recent molecular and imaging studies have revealed an intimate connection between RNA epigenetics and chromatin structure. Accumulating evidence suggests that RNA serves as the interplay between chromatin and the transcription and splicing machineries within the cell. Additionally, epigenetic modifications of nascent RNAs fine-tune these interactions to regulate gene expression at the co- and post-transcriptional levels in normal cell development and human diseases. This review will provide an overview of recent advances in the emerging field of RNA epigenetics, specifically the role of RNA modifications and RNA modifying proteins in chromatin remodeling, transcription activation and RNA processing, as well as translational implications in human diseases.

scholarly journals SPATIAL ORGANIZATION OF TRANSCRIBED EUKARYOTIC GENES

2020 ◽  
Author(s):  
Susanne Leidescher ◽  
Johannes Nübler ◽  
Yana Feodorova ◽  
Erica Hildebrand ◽  
Simon Ullrich ◽  
...  
Keyword(s):  
Gene Expression ◽  
Spatial Organization ◽  
Regulation Of Gene Expression ◽  
Spatial Arrangement ◽  
Eukaryotic Genes ◽  
Eukaryotic Gene Expression ◽  
Eukaryotic Gene ◽  
Intrinsic Stiffness ◽  
Established Role

SUMMARYDespite the well established role of nuclear organization in the regulation of gene expression, little is known about the reverse: how transcription shapes the spatial organization of the genome. In particular, given the relatively small sizes of genes and the limited resolution of light microscopy, the structure and spatial arrangement of a single transcribed gene are still poorly understood. Here, we make use of several long highly expressed mammalian genes and demonstrate that they form Transcription Loops (TLs) with polymerases moving along the loops and carrying nascent RNAs that undergo co-transcriptional splicing. TLs dynamically modify their harboring loci and extend into the nuclear interior suggesting an intrinsic stiffness. Both experimental evidence and polymer modeling support the hypothesis that TL stiffness is caused by the dense decoration of transcribed genes with multiple voluminous nascent RNPs. We propose that TL formation is a universal principle of eukaryotic gene expression.

Unraveling RNA-mediated networks: new insights from new technologies

2014 ◽  
Vol 395 (1) ◽  
pp. 51-60 ◽  
Author(s):  
Oliver Rossbach ◽  
Albrecht Bindereif
Keyword(s):  
Rna Processing ◽  
New Technologies ◽  
Mrna Processing ◽  
Mrna Splicing ◽  
Cross Linking ◽  
Splicing Factors ◽  
Epigenetic Mechanisms ◽  
Rna Targets ◽  
Eukaryotic Gene Expression ◽  
Eukaryotic Gene

Abstract Eukaryotic gene expression is regulated in a combinatorial manner and on several interconnected layers, ranging from epigenetic mechanisms, transcription, RNA processing to protein stages. mRNA processing plays a major role in tissue- and development-dependent regulation, in particular alternative pre-mRNA splicing, which greatly enhances the capacity and composition of the proteome. Within the last decade, novel methods have been developed to systematically study the complex networks between regulatory alternative splicing factors and their RNA targets. This minireview focuses on cross-linking and immunoprecipitation methods, which – in combination with deep RNA sequencing – have made an important contribution in unraveling these networks.

scholarly journals Extensive splicing across the Saccharomyces cerevisiae genome

2019 ◽  
Author(s):  
Stephen M. Douglass ◽  
Calvin S. Leung ◽  
Tracy L. Johnson
Keyword(s):  
Gene Expression ◽  
Saccharomyces Cerevisiae ◽  
Alternative Splice ◽  
Rna Splicing ◽  
Model Organism ◽  
Growth Conditions ◽  
Mrna Splicing ◽  
Eukaryotic Gene Expression ◽  
Eukaryotic Gene ◽  
Splice Forms

AbstractPre-mRNA splicing is vital for the proper function and regulation of eukaryotic gene expression. Saccharomyces cerevisiae has been used as a model organism for studies of RNA splicing because of the striking conservation of the spliceosome components and its catalytic activity. Nonetheless, there are relatively few annotated alternative splice forms, particularly when compared to higher eukaryotes. Here, we describe a method to combine large scale RNA sequencing data to accurately discover novel splice isoforms in Saccharomyces cerevisiae. Using our method, we find extensive evidence for novel splicing of annotated intron-containing genes as well as genes without previously annotated introns and splicing of transcripts that are antisense to annotated genes. By incorporating several mutant strains at varied temperatures, we find conditions which lead to differences in alternative splice form usage. Despite this, every class and category of alternative splicing we find in our datasets is found, often at lower frequency, in wildtype cells under normal growth conditions. Together, these findings show that there is widespread splicing in Saccharomyces cerevisiae, thus expanding our view of the regulatory potential of RNA splicing in yeast.Author SummaryPre-mRNA splicing is a fundamental step in eukaryotic gene expression. Saccharomyces cerevisiae, also known as brewer’s yeast, is a model organism for the study of pre-mRNA splicing in eukaryotes. Through the process of pre-mRNA splicing, a single gene is capable of encoding multiple mature mRNA products, but it is often difficult to identify the splice events that lead to these mRNA products. Here, we describe a method to accurately discover novel splice events in Saccharomyces cerevisiae and find evidence for extensive splicing in Saccharomyces. By utilizing a variety of strains and growth conditions, we are able to characterize many splice forms and correlate cellular conditions with prevalence of novel splice events.

Role of small nuclear RNAs in eukaryotic gene expression

2013 ◽  
Vol 54 ◽  
pp. 79-90 ◽  
Author(s):  
Saba Valadkhan ◽  
Lalith S. Gunawardane
Keyword(s):  
Gene Expression ◽  
Protein Interactions ◽  
Rna Stability ◽  
Splice Sites ◽  
Branch Site ◽  
Small Nuclear Rnas ◽  
Eukaryotic Gene Expression ◽  
Eukaryotic Gene ◽  
Rna Biogenesis

Eukaryotic cells contain small, highly abundant, nuclear-localized non-coding RNAs [snRNAs (small nuclear RNAs)] which play important roles in splicing of introns from primary genomic transcripts. Through a combination of RNA–RNA and RNA–protein interactions, two of the snRNPs, U1 and U2, recognize the splice sites and the branch site of introns. A complex remodelling of RNA–RNA and protein-based interactions follows, resulting in the assembly of catalytically competent spliceosomes, in which the snRNAs and their bound proteins play central roles. This process involves formation of extensive base-pairing interactions between U2 and U6, U6 and the 5′ splice site, and U5 and the exonic sequences immediately adjacent to the 5′ and 3′ splice sites. Thus RNA–RNA interactions involving U2, U5 and U6 help position the reacting groups of the first and second steps of splicing. In addition, U6 is also thought to participate in formation of the spliceosomal active site. Furthermore, emerging evidence suggests additional roles for snRNAs in regulation of various aspects of RNA biogenesis, from transcription to polyadenylation and RNA stability. These snRNP-mediated regulatory roles probably serve to ensure the co-ordination of the different processes involved in biogenesis of RNAs and point to the central importance of snRNAs in eukaryotic gene expression.

Implications of DNA replication for eukaryotic gene expression

1991 ◽  
Vol 99 (2) ◽  
pp. 201-206 ◽  
Author(s):  
A.P. Wolffe
Keyword(s):  
Gene Expression ◽  
Dna Replication ◽  
Replication Fork ◽  
Recent Progress ◽  
Gene Activity ◽  
Nucleosome Assembly ◽  
Developmental Processes ◽  
Eukaryotic Gene Expression ◽  
Eukaryotic Gene

DNA replication has a key role in many developmental processes. Recent progress in understanding events at the replication fork suggests mechanisms for both establishing and maintaining programs of eukaryotic gene activity. In this review, I discuss the consequences of replication fork passage for preexisting chromatin structures and describe how the mechanism of nucleosome assembly at the replication fork may facilitate the formation of either transcriptionally active or repressed chromatin.

Integrated databases and computer systems for studying eukaryotic gene expression

1999 ◽  
Vol 15 (7) ◽  
pp. 669-686 ◽  
Author(s):  
N. A. Kolchanov ◽  
M. P. Ponomarenko ◽  
A. S. Frolov ◽  
E. A. Ananko ◽  
F. A. Kolpakov ◽  
...  
Keyword(s):  
Gene Expression ◽  
Computer Systems ◽  
Eukaryotic Gene Expression ◽  
Eukaryotic Gene

scholarly journals Independent Recruitment of Mediator and SAGA by the Activator Met4

2006 ◽  
Vol 26 (8) ◽  
pp. 3149-3163 ◽  
Author(s):  
Christophe Leroy ◽  
Laëtitia Cormier ◽  
Laurent Kuras
Keyword(s):  
Gene Expression ◽  
Amino Acids ◽  
Rna Polymerase Ii ◽  
Gene Network ◽  
Pol Ii ◽  
Eukaryotic Gene Expression ◽  
Eukaryotic Gene ◽  
Target Promoters ◽  
Sulfur Containing

ABSTRACT Mediator is a key RNA polymerase II (Pol II) cofactor in the regulation of eukaryotic gene expression. It is believed to function as a coactivator linking gene-specific activators to the basal Pol II initiation machinery. In support of this model, we provide evidence that Mediator serves in vivo as a coactivator for the yeast activator Met4, which controls the gene network responsible for the biosynthesis of sulfur-containing amino acids and S-adenosylmethionine. In addition, we show that SAGA (Spt-Ada-Gcn5-acetyltransferase) is also recruited to Met4 target promoters, where it participates in the recruitment of Pol II by a mechanism involving histone acetylation. Interestingly, we find that SAGA is not required for Mediator recruitment by Met4 and vice versa. Our results provide a novel example of functional interplay between Mediator and coactivators involved in histone modification.

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