Transcriptional control signals of a eukaryotic protein-coding gene

Science ◽  
1982 ◽  
Vol 217 (4557) ◽  
pp. 316-324 ◽  
Author(s):  
S. McKnight ◽  
R Kingsbury
Keyword(s):  
Transcriptional Control ◽  
Protein Coding ◽  
Eukaryotic Protein ◽  
Control Signals

Riboregulators in plant development

2007 ◽  
Vol 35 (6) ◽  
pp. 1638-1642 ◽  
Author(s):  
P. Laporte ◽  
F. Merchan ◽  
B.B. Amor ◽  
S. Wirth ◽  
M. Crespi
Keyword(s):  
Large Scale ◽  
Transcriptional Control ◽  
Rna Binding ◽  
Bioinformatic Analysis ◽  
Nodule Development ◽  
Small Interfering Rnas ◽  
Cortical Cells ◽  
Protein Coding ◽  
Early Nodulin ◽  
Model Plant Arabidopsis Thaliana

npcRNA (non-protein-coding RNAs) are an emerging class of regulators, so-called riboregulators, and include a large diversity of small RNAs [miRNAs (microRNAs)/siRNAs (small interfering RNAs)] that are involved in various developmental processes in plants and animals. In addition, several other npcRNAs encompassing various transcript sizes (up to several kilobases) have been identified using different genomic approaches. Much less is known about the mechanism of action of these other classes of riboregulators also present in the cell. The organogenesis of nitrogen-fixing nodules in legume plants is initiated in specific root cortical cells that express the npcRNA MtENOD40 (Medicago truncatula early nodulin 40). We have identified a novel RBP (RNA-binding protein), MtRBP1 (M. truncatula RBP 1), which interacts with the MtENOD40 RNA, and is exported into the cytoplasm during legume nodule development in the region expressing MtENOD40. A direct involvement of the MtENOD40 RNA in the relocalization of this RBP into cytoplasmic granules could be demonstrated, revealing a new RNA function in the cell. To extend these results, we searched for npcRNAs in the model plant Arabidopsis thaliana whose genome is completely known. We have identified 86 novel npcRNAs from which 27 corresponded to antisense RNAs of known coding regions. Using a dedicated ‘macroarray’ containing these npcRNAs and a collection of RBPs, we characterized their regulation in different tissues and plants subjected to environmental stresses. Most of the npcRNAs showed high variations in gene expression in contrast with the RBP genes. Recent large-scale analysis of the sRNA component of the transcriptome revealed an enormous diversity of siRNAs/miRNAs in the Arabidopsis genome. Bioinformatic analysis revealed that 34 large npcRNAs are precursors of siRNAs/miRNAs. npcRNAs, which are a sensitive component of the transcriptome, may reveal novel riboregulatory mechanisms involved in post-transcriptional control of differentiation or environmental responses.

An efficient sliding window strategy for accurate location of eukaryotic protein coding regions

2009 ◽  
Vol 39 (4) ◽  
pp. 392-395 ◽  
Author(s):  
Nini Rao ◽  
Xu Lei ◽  
Jianxiu Guo ◽  
Hao Huang ◽  
Zhenglong Ren
Keyword(s):  
Sliding Window ◽  
Protein Coding ◽  
Eukaryotic Protein ◽  
Coding Regions

scholarly journals Post-transcriptional control of cellular differentiation by the RNA exosome complex

2020 ◽  
Vol 48 (21) ◽  
pp. 11913-11928
Author(s):  
Isabela Fraga de Andrade ◽  
Charu Mehta ◽  
Emery H Bresnick
Keyword(s):  
Cellular Differentiation ◽  
Transcriptional Control ◽  
Cell Type ◽  
Protein Coding ◽  
Regulatory Machinery ◽  
Regulatory Complex ◽  
Cell Type Specific ◽  
Rna Exosome ◽  
Post Transcriptional Regulation ◽  
Exosome Complex

Abstract Given the complexity of intracellular RNA ensembles and vast phenotypic remodeling intrinsic to cellular differentiation, it is instructive to consider the role of RNA regulatory machinery in controlling differentiation. Dynamic post-transcriptional regulation of protein-coding and non-coding transcripts is vital for establishing and maintaining proteomes that enable or oppose differentiation. By contrast to extensively studied transcriptional mechanisms governing differentiation, many questions remain unanswered regarding the involvement of post-transcriptional mechanisms. Through its catalytic activity to selectively process or degrade RNAs, the RNA exosome complex dictates the levels of RNAs comprising multiple RNA classes, thereby regulating chromatin structure, gene expression and differentiation. Although the RNA exosome would be expected to control diverse biological processes, studies to elucidate its biological functions and how it integrates into, or functions in parallel with, cell type-specific transcriptional mechanisms are in their infancy. Mechanistic analyses have demonstrated that the RNA exosome confers expression of a differentiation regulatory receptor tyrosine kinase, downregulates the telomerase RNA component TERC, confers genomic stability and promotes DNA repair, which have considerable physiological and pathological implications. In this review, we address how a broadly operational RNA regulatory complex interfaces with cell type-specific machinery to control cellular differentiation.

scholarly journals Dysregulated Transcriptional Control in Prostate Cancer

2019 ◽  
Vol 20 (12) ◽  
pp. 2883 ◽  
Author(s):  
Simon J. Baumgart ◽  
Ekaterina Nevedomskaya ◽  
Bernard Haendler
Keyword(s):  
Prostate Cancer ◽  
Drug Targets ◽  
Transcriptional Control ◽  
Regulatory Elements ◽  
Protein Coding ◽  
Coding Regions ◽  
Super Enhancer ◽  
Position Coding ◽  
Transcription Dysregulation ◽  
Dna Regulatory Elements

Recent advances in whole-genome and transcriptome sequencing of prostate cancer at different stages indicate that a large number of mutations found in tumors are present in non-protein coding regions of the genome and lead to dysregulated gene expression. Single nucleotide variations and small mutations affecting the recruitment of transcription factor complexes to DNA regulatory elements are observed in an increasing number of cases. Genomic rearrangements may position coding regions under the novel control of regulatory elements, as exemplified by the TMPRSS2-ERG fusion and the amplified enhancer identified upstream of the androgen receptor (AR) gene. Super-enhancers are increasingly found to play important roles in aberrant oncogenic transcription. Several players involved in these processes are currently being evaluated as drug targets and may represent new vulnerabilities that can be exploited for prostate cancer treatment. They include factors involved in enhancer and super-enhancer function such as bromodomain proteins and cyclin-dependent kinases. In addition, non-coding RNAs with an important gene regulatory role are being explored. The rapid progress made in understanding the influence of the non-coding part of the genome and of transcription dysregulation in prostate cancer could pave the way for the identification of novel treatment paradigms for the benefit of patients.

Promoter sequences of eukaryotic protein-coding genes

Science ◽  
1980 ◽  
Vol 209 (4463) ◽  
pp. 1406-1414 ◽  
Author(s):  
J Corden ◽  
B Wasylyk ◽  
A Buchwalder ◽  
P Sassone-Corsi ◽  
C Kedinger ◽  
...  
Keyword(s):  
Protein Coding ◽  
Eukaryotic Protein ◽  
Promoter Sequences ◽  
Protein Coding Genes

Transcriptional control signals in the genome of bovine papillomavirus type 1

Nature ◽  
1983 ◽  
Vol 303 (5912) ◽  
pp. 77-80 ◽  
Author(s):  
M. Saveria Campo ◽  
Demetrios A. Spandidos ◽  
Jas Lang ◽  
Neil M. Wilkie
Keyword(s):  
Transcriptional Control ◽  
Bovine Papillomavirus ◽  
Control Signals

scholarly journals Human to yeast pathway transplantation: cross-species dissection of the adenine de novo pathway regulatory node

2017 ◽  
Author(s):  
Neta Agmon ◽  
Jasmine Temple ◽  
Zuojian Tang ◽  
Tobias Schraink ◽  
Maayan Baron ◽  
...  
Keyword(s):  
Yeast Strain ◽  
Transcriptional Control ◽  
De Novo ◽  
Enzyme Level ◽  
Yeast Cells ◽  
Protein Coding ◽  
Coding Regions ◽  
Human Proteins ◽  
Human Ortholog ◽  
Yeast Genes

AbstractPathway transplantation from one organism to another represents a means to a more complete understanding of a biochemical or regulatory process. The purine biosynthesis pathway, a core metabolic function, was transplanted from human to yeast. We replaced the entireSaccharomyces cerevisiaeadenine de novo pathway with the cognate human pathway components. A yeast strain was “humanized” for the full pathway by deleting all relevant yeast genes completely and then providing the human pathway in trans using a neochromosome expressing the human protein coding regions under the transcriptional control of their cognate yeast promoters and terminators. The “humanized” yeast strain grows in the absence of adenine, indicating complementation of the yeast pathway by the full set of human proteins. While the strain with the neochromosome is indeed prototrophic, it grows slowly in the absence of adenine. Dissection of the phenotype revealed that the human ortholog ofADE4, PPAT, shows only partial complementation. We have used several strategies to understand this phenotype, that point toPPAT/ADE4as the central regulatory node. Pathway metabolites are responsible for regulatingPPAT’sprotein abundance through transcription and proteolysis as well as its enzymatic activity by allosteric regulation in these yeast cells. Extensive phylogenetic analysis of PPATs from diverse organisms hints at adaptations of the enzyme-level regulation to the metabolite levels in the organism. Finally, we isolated specific mutations in PPAT as well as in other genes involved in the purine metabolic network that alleviate incomplete complementation byPPATand provide further insight into the complex regulation of this critical metabolic pathway.

scholarly journals Transcriptional control and exploitation of an immune-responsive family of plant retrotransposons

2017 ◽  
Author(s):  
Jérôme Zervudacki ◽  
Agnès Yu ◽  
Delase Amesefe ◽  
Jingyu Wang ◽  
Jan Drouaud ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Plant Defense ◽  
Transcriptional Control ◽  
Plant Immunity ◽  
Disease Resistance Gene ◽  
Loss Of Function ◽  
Long Terminal Repeats ◽  
Protein Coding ◽  
Regulatory Modules ◽  
Microrna Genes

ABSTRACTMobilization of transposable elements (TEs) in plants has been recognized as a driving force of evolution and adaptation, in particular by providing genes with regulatory modules that impact their transcription. In this study, we employed anATCOPIA93Long terminal repeats (LTR) promoter-GUSfusion to show that this retrotransposon behaves like an immune-responsive gene during plant defense in Arabidopsis. We also showed that the reactivation of the endogenousATCOPIA93copy“EVD”, in the presence of bacterial stress, is not only negatively regulated by DNA methylation but also by Polycomb-mediated silencing—a mode of repression typically found at protein-coding and microRNA genes. Interestingly, one of theATCOPIA93-derived soloLTRs is located upstream of the disease resistance geneRPP4and is devoid of either DNA methylation or H3K27m3 marks. Through loss-of-function experiments, we demonstrated that this soloLTR is required for proper expression ofRPP4during plant defense, thus linking the responsiveness ofATCOPIA93to biotic stress and the co-option of its LTR for plant immunity.

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