Gene Expression I (Transcription and RNA Processing): How Is Information Transferred from DNA to RNA?

2013 ◽  
pp. 205-233
Author(s):  
Charles C. Tseng ◽  
Xiaoli Yang
Keyword(s):  
Gene Expression ◽  
Rna Processing

Alternative translation and alternative RNA processing mechanism in parvovirus RNA processing

2014 ◽  
Author(s):  
◽  
Olufemi Fasina
Keyword(s):  
Gene Expression ◽  
Rna Processing ◽  
Viral Genome ◽  
Transcription Initiation ◽  
Alternative Polyadenylation ◽  
Open Reading Frames ◽  
Genome Replication ◽  
University Of Missouri ◽  
Diverse Range ◽  
Viral Genome Replication

[ACCESS RESTRICTED TO THE UNIVERSITY OF MISSOURI AT AUTHOR'S REQUEST.] Viruses as obligate intracellular metabolic parasite require the capacity to orchestrate and modulate the host environment either in the nucleus or cytoplasm for their efficient reproductive life cycle. This warrants the use of diverse range of proteins expressed from the viral genome with the ability of regulating viral genome replication, transcription and translation, in addition antagonizing host factors inhibitory to the virus. Therefore, in order to achieve these goals, viruses utilizes gene expression strategies to expand their coding capacity. Gene expression mechanism such as transcription initiation, capping, splicing and 3�-end processing afford viruses the opportunities to utilize the eukaryotic metabolic machineries for generating proteome diversity. Parvoviruses and other DNA viruses effectively capitalize on their use of nuclear eukaryotic metabolic machineries to co-opt host cell factors for optimal replication and gene expression. Parvoviruses with small genome size and overlapping open reading frames utilize alternative transcription initiation, alternative splicing and alternative polyadenylation to co-ordinate the expression of its non-structural and structural proteins. In this work, we have characterized how two parvoviruses; Dependovirus AAV5 and Bocavirus Minute virus of canine (MVC) utilize alternative gene expression mechanisms and strategies to optimize expression of viral proteins from their genome.

scholarly journals Coordination of RNA Processing Regulation by Signal Transduction Pathways

Biomolecules ◽  
2021 ◽  
Vol 11 (10) ◽  
pp. 1475
Author(s):  
Veronica Ruta ◽  
Vittoria Pagliarini ◽  
Claudio Sette
Keyword(s):  
Gene Expression ◽  
Signal Transduction ◽  
Rna Processing ◽  
Translational Regulation ◽  
Rna Binding ◽  
Rna Binding Proteins ◽  
Regulation Of Gene Expression ◽  
Signal Transduction Pathways ◽  
Challenges And Opportunities ◽  
Common Signal

Signal transduction pathways transmit the information received from external and internal cues and generate a response that allows the cell to adapt to changes in the surrounding environment. Signaling pathways trigger rapid responses by changing the activity or localization of existing molecules, as well as long-term responses that require the activation of gene expression programs. All steps involved in the regulation of gene expression, from transcription to processing and utilization of new transcripts, are modulated by multiple signal transduction pathways. This review provides a broad overview of the post-translational regulation of factors involved in RNA processing events by signal transduction pathways, with particular focus on the regulation of pre-mRNA splicing, cleavage and polyadenylation. The effects of several post-translational modifications (i.e., sumoylation, ubiquitination, methylation, acetylation and phosphorylation) on the expression, subcellular localization, stability and affinity for RNA and protein partners of many RNA-binding proteins are highlighted. Moreover, examples of how some of the most common signal transduction pathways can modulate biological processes through changes in RNA processing regulation are illustrated. Lastly, we discuss challenges and opportunities of therapeutic approaches that correct RNA processing defects and target signaling molecules.

The role of a conserved dodecamer sequence in yeast mitochondrial gene expression

Genome ◽  
1989 ◽  
Vol 31 (2) ◽  
pp. 757-760 ◽  
Author(s):  
Ronald A. Butow ◽  
Hong Zhu ◽  
Philip Perlman ◽  
Heather Conrad-Webb
Keyword(s):  
Gene Expression ◽  
Rna Processing ◽  
Mitochondrial Gene ◽  
Rna Stability ◽  
Rrna Gene ◽  
Mitochondrial Gene Expression ◽  
Reading Frame ◽  
Multicomponent Complex ◽  
Var1 Gene

All mRNAs on the yeast mitochondrial genome terminate at a conserved dodecamer sequence 5′-AAUAAUAUUCUU-3′. We have characterized two mutants with altered dodecamers. One contains a deletion of the dodecamer at the end of the var1 gene, and the other contains two adjacent transversions in the dodecamer at the end of the reading frame of fit1, a gene within the ω+ allele of the 21S rRNA gene. In each mutant, expression of the respective gene is blocked completely. A dominant nuclear suppressor, SUV3-1, was isolated that suppresses the var1 deletion but is without effect on the fit1 dodecamer mutations. Unexpectedly, however, we found that SUV3-1 blocks expression of the wild-type fit1 allele by blocking processing at its dodecamer. SUV3-1 has pleiotropic effects on mitochondrial gene expression, affecting RNA processing, RNA stability, and translation. Our results suggest that RNA metabolism and translation may be part of a multicomponent complex within mitochondria.Key words: mitochondria, yeast, mRNA, RNA processing, 3′ dodecamer.

scholarly journals Alternative RNA processing events in human calcitonin/calcitonin gene-related peptide gene expression.

1985 ◽  
Vol 82 (7) ◽  
pp. 1994-1998 ◽  
Author(s):  
V. Jonas ◽  
C. R. Lin ◽  
E. Kawashima ◽  
D. Semon ◽  
L. W. Swanson ◽  
...  
Keyword(s):  
Gene Expression ◽  
Rna Processing ◽  
Calcitonin Gene Related Peptide ◽  
Human Calcitonin ◽  
Related Peptide ◽  
Calcitonin Gene ◽  
Peptide Gene

Bone Marrow Cells from Patients with Shwachman-Diamond Syndrome Abnormally Express Ribosomal Protein and Ribosomal Biogenesis-Related Genes.

Blood ◽  
2007 ◽  
Vol 110 (11) ◽  
pp. 3303-3303
Author(s):  
Piya Rujkijyanont ◽  
Joseph Beyene ◽  
Yigal Dror
Keyword(s):  
Gene Expression ◽  
Ribosomal Protein ◽  
Rna Processing ◽  
Real Time Pcr ◽  
Ribosomal Proteins ◽  
Ribosomal Biogenesis ◽  
Rrna Processing ◽  
Rrna Transcription ◽  
Shwachman Diamond Syndrome ◽  
Marrow Cells

Abstract Background and rational: Shwachman-Diamond syndrome (SDS) is an autosomal recessive disorder characterized by varying degrees of cytopenia and high propensity for myelodysplastic syndrome and acute leukemia. SBDS, the gene associated with SDS, has recently been identified and is postulated to play a role in ribosomal biogenesis and RNA processing, but its functions are still unknown. Defects in ribosomal biogenesis can be characterized by abnormal synthesis of rRNA synthesis or ribosomal proteins or both. Determining the mRNA expression pattern of the various RP genes in SBDS deficient cells will help deciphering the role of SBDS in ribosomal biogenesis. Objectives: To determine whether the primary SDS marrow cells which carry homozygous SBDS mutations abnormally express genes which code for ribosomal proteins (RP) or for proteins that are involved in its transcription. Methods: Total RNA from marrow cells from 9 SDS patients who had hypocellular marrow with normal differential and no malignant transformation and 7 healthy age-matched donors of bone marrows for transplantation was extracted. RNA was labeled and hybridized to Affymetrix HG_U133_Plus2.0 GeneChip. Data were pre-processed using robust multichip analysis (RMA) and differentially expressed genes were identified with permutation-based methods. False discovery rate (FDR)-adjusted p-values were used to rank genes and cluster analysis grouped genes and samples. T-statistic values were used to screen for differentially expressed RP-related genes. Real-time PCR was performed to confirm differential expression of genes found by oligonucleotide microarray. Results: Of the 38,500 genes on the HG_133_Plus2.0 we analyzed 375 known ribosomal protein and RNA processing-related genes. Interestingly, there were differences in the expression pattern of the RP genes, suggesting differential regulation of these genes in Sbds-deficient cells. Interestingly, despite uniform decrease in RP gene expression in reduced cell growth conditions, only 27 of the 85 RP genes were downregulated. Downregulation of representative 2 genes was confirmed by real-time PCR. Further, one of the RP genes, RPL27L was upregulated. This gene, which is a target of p53, has a non-ribosomal function and lead to accelerated apoptosis. It is noteworthy that several genes involved in mRNA transcription such as GABPA and YY1were downregulated without dysregulation of genes involved in mRNA degradation, suggesting that the downregulation of the RP gene expression is at the transcription level. In addition to dysregulation of the RP mRNA we also found dysregulation of genes involved in rRNA transcription (e.g. MKI67IP) and pre rRNA processing (e.g. FBL). Conclusions: SBDS-deficiency results in dysregulation of selective group of RP genes as well as genes related to rRNA processing and rRNA transcription. Future studies should focus on the mechanism of the abnormal expression as well as its biological consequences.

Removal of a terminator structure by RNA processing regulates int gene expression

1984 ◽  
Vol 176 (1) ◽  
pp. 39-53 ◽  
Author(s):  
Ursula Schmeissner ◽  
Keith McKenney ◽  
Martin Rosenberg ◽  
Donald Court
Keyword(s):  
Gene Expression ◽  
Rna Processing

scholarly journals Gene expression control by selective RNA processing and stabilization in bacteria

2013 ◽  
Vol 344 (2) ◽  
pp. 104-113 ◽  
Author(s):  
Tatiana Rochat ◽  
Philippe Bouloc ◽  
Francis Repoila
Keyword(s):  
Gene Expression ◽  
Rna Processing ◽  
Expression Control ◽  
Gene Expression Control

Regulation of cyclin D1 gene expression

2010 ◽  
Vol 38 (1) ◽  
pp. 217-222 ◽  
Author(s):  
Ini-Isabée Witzel ◽  
Li Fang Koh ◽  
Neil D. Perkins
Keyword(s):  
Gene Expression ◽  
Cyclin D1 ◽  
Rna Processing ◽  
Dominant Role ◽  
Rna Stability ◽  
Transcriptional Regulator ◽  
Nuclear Factor Κb ◽  
Nuclear Factor ◽  
Post Transcriptional Regulation

Cyclin D1 is a key regulator of cell proliferation and its expression is subject to both transcriptional and post-transcriptional regulation. In different cellular contexts, different pathways assume a dominant role in regulating its expression, whereas their disregulation can contribute to overexpression of cyclin D1 in tumorigenesis. Here, we discuss the ability of the NF-κB (nuclear factor κB)/IKK [IκB (inhibitor of NF-κB) kinase] pathways to regulate cyclin D1 gene transcription and also consider the newly discovered role of the SNARP (SNIP1/SkIP-associated RNA processing) complex as a co-transcriptional regulator of cyclin D1 RNA stability.

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