Identification of the Promoter Region and the Transcriptional Regulatory Sequence of theevgASOperon ofEscherichia coli

1998 ◽  
Vol 62 (2) ◽  
pp. 286-290 ◽  
Author(s):  
Hiroyuki TANABE ◽  
Katsuhide YAMASAKI ◽  
Akinori KATOH ◽  
Sachiko YOSHIOKA ◽  
Ryutaro UTSUMI
Keyword(s):  
Promoter Region ◽  
Ofescherichia Coli ◽  
Regulatory Sequence ◽  
Transcriptional Regulatory ◽  
Transcriptional Regulatory Sequence

scholarly journals Putative cis-Acting Stem-Loops in the 5′ Untranslated Region of the Severe Acute Respiratory Syndrome Coronavirus Can Substitute for Their Mouse Hepatitis Virus Counterparts

2006 ◽  
Vol 80 (21) ◽  
pp. 10600-10614 ◽  
Author(s):  
Hyojeung Kang ◽  
Min Feng ◽  
Megan E. Schroeder ◽  
David P. Giedroc ◽  
Julian L. Leibowitz
Keyword(s):  
Severe Acute Respiratory Syndrome ◽  
Hepatitis Virus ◽  
Mouse Hepatitis Virus ◽  
Regulatory Sequence ◽  
Stem Loop ◽  
Cis Acting ◽  
Transcriptional Regulatory ◽  
Similar Phenotype ◽  
Transcriptional Regulatory Sequence

ABSTRACT Consensus covariation-based secondary structural models for the 5′ 140 nucleotides of the 5′ untranslated regions (5′UTRs) from mouse hepatitis virus (MHV) and severe acute respiratory syndrome coronavirus (SCoV) were developed and predicted three major helical stem-loop structures, designated stem-loop 1 (SL1), SL2, and SL4. The SCoV 5′UTR was predicted to contain a fourth stem-loop, named SL3, in which the leader transcriptional regulatory sequence (TRS) is folded into a hairpin loop. cDNAs corresponding to MHV/SCoV chimeric genomes were constructed by replacing the complete MHV 5′UTR with the corresponding SCoV sequence and by separately replacing MHV 5′UTR putative SL1, putative SL2, TRS, and putative SL4 with the corresponding SCoV sequences. Chimeric genomes were transcribed in vitro, and viruses were recovered after electroporation into permissive cells. Genomes in which the MHV 5′UTR SL1, SL2, and SL4 were individually replaced by their SCoV counterparts were viable. Chimeras containing the complete SCoV 5′UTR or the predicted SCoV SL3 were not viable. A chimera containing the SCoV 5′UTR in which the SCoV TRS was replaced with the MHV TRS was also not viable. The chimera containing the entire SCoV 5′UTR failed to direct the synthesis of any virus-specific RNA. Replacing the SCoV TRS with the MHV TRS in the MHV/5′UTR SCoV chimera permitted the synthesis of minus-sense genome-sized RNA but did not support the production of positive- or minus-sense subgenomic RNA7. A similar phenotype was obtained with the MHV/SCoV SL3 chimera. These results suggest a role for the TRS in the replication of minus-sense genomic RNA in addition to its known function in subgenomic RNA synthesis.

scholarly journals Transcriptional regulatory sequence divergence between mouse and bat modifies forelimb length

2008 ◽  
Vol 319 (2) ◽  
pp. 470
Author(s):  
Chris J. Cretekos ◽  
Ying Wang ◽  
Eric D. Green ◽  
James F. Martin ◽  
John J. Rasweiler ◽  
...  
Keyword(s):  
Sequence Divergence ◽  
Regulatory Sequence ◽  
Transcriptional Regulatory ◽  
Transcriptional Regulatory Sequence

MCM1 binds to a transcriptional control element in Ty1

1993 ◽  
Vol 13 (1) ◽  
pp. 57-62
Author(s):  
B Errede
Keyword(s):  
Gene Expression ◽  
Transcriptional Control ◽  
Control Element ◽  
Regulatory Sequence ◽  
Gene Promoters ◽  
Adjacent Gene ◽  
Transposable Element Insertion ◽  
Transcriptional Regulatory ◽  
Transcriptional Regulatory Sequence ◽  
Insertion Mutations

Some Ty1 transposable-element insertion mutations of Saccharomyces cerevisiae activate adjacent-gene expression. These Ty1-activated genes are regulated similarly to certain mating genes. This report shows that the MCM1 protein, which binds to several mating genes, also binds to a transcriptional regulatory sequence in Ty1. The binding of MCM1 to Ty1 correlates with the ability of its binding site to function as a component of the Ty1 transcriptional activator. This correlation supports the idea that MCM1 is important for Ty1-activated gene expression. At mating-gene promoters, MCM1 binds with coactivators or repressors such as STE12, alpha 1, or alpha 2. In contrast, MCM1 binds without these associated DNA-binding proteins at its site in Ty1. This finding suggests that its role in Ty1-mediated transcription is different from that at mating genes.

scholarly journals Identification and quantification of SARS-CoV-2 leader subgenomic mRNA gene junctions in nasopharyngeal samples shows phasic transcription in animal models of COVID-19 and dysregulation at later time points that can also be identified in humans

2021 ◽  
Author(s):  
Xiaofeng Dong ◽  
Rebekah Penrice-Randal ◽  
Hannah Goldswain ◽  
Tessa Prince ◽  
Nadine Randle ◽  
...  
Keyword(s):  
Nucleic Acid ◽  
Animal Models ◽  
Clinical Samples ◽  
Regulatory Sequence ◽  
Transcriptional Regulatory ◽  
Culture Models ◽  
Mrna Gene ◽  
Transcriptional Regulatory Sequence ◽  
Cell Culture Models ◽  
Gene Junction

AbstractIntroductionSARS-CoV-2 has a complex strategy for the transcription of viral subgenomic mRNAs (sgmRNAs), which are targets for nucleic acid diagnostics. Each of these sgRNAs has a unique 5’ sequence, the leader-transcriptional regulatory sequence gene junction (leader-TRS-junction), that can be identified using sequencing.ResultsHigh resolution sequencing has been used to investigate the biology of SARS-CoV-2 and the host response in cell culture models and from clinical samples. LeTRS, a bioinformatics tool, was developed to identify leader-TRS-junctions and be used as a proxy to quantify sgmRNAs for understanding virus biology. This was tested on published datasets and clinical samples from patients and longitudinal samples from animal models with COVID-19.DiscussionLeTRS identified known leader-TRS-junctions and identified novel species that were common across different species. The data indicated multi-phasic abundance of sgmRNAs in two different animal models, with spikes in sgmRNA abundance reflected in human samples, and therefore has implications for transmission models and nucleic acid-based diagnostics.

scholarly journals Coronavirus N Protein N-Terminal Domain (NTD) Specifically Binds the Transcriptional Regulatory Sequence (TRS) and Melts TRS-cTRS RNA Duplexes

2009 ◽  
Vol 394 (3) ◽  
pp. 544-557 ◽  
Author(s):  
Nicholas E. Grossoehme ◽  
Lichun Li ◽  
Sarah C. Keane ◽  
Pinghua Liu ◽  
Charles E. Dann ◽  
...  
Keyword(s):  
Regulatory Sequence ◽  
N Protein ◽  
Terminal Domain ◽  
Transcriptional Regulatory ◽  
Rna Duplexes ◽  
Transcriptional Regulatory Sequence

scholarly journals MCM1 binds to a transcriptional control element in Ty1.

1993 ◽  
Vol 13 (1) ◽  
pp. 57-62 ◽  
Author(s):  
B Errede
Keyword(s):  
Gene Expression ◽  
Transcriptional Control ◽  
Control Element ◽  
Regulatory Sequence ◽  
Gene Promoters ◽  
Adjacent Gene ◽  
Transposable Element Insertion ◽  
Transcriptional Regulatory ◽  
Transcriptional Regulatory Sequence ◽  
Insertion Mutations

Some Ty1 transposable-element insertion mutations of Saccharomyces cerevisiae activate adjacent-gene expression. These Ty1-activated genes are regulated similarly to certain mating genes. This report shows that the MCM1 protein, which binds to several mating genes, also binds to a transcriptional regulatory sequence in Ty1. The binding of MCM1 to Ty1 correlates with the ability of its binding site to function as a component of the Ty1 transcriptional activator. This correlation supports the idea that MCM1 is important for Ty1-activated gene expression. At mating-gene promoters, MCM1 binds with coactivators or repressors such as STE12, alpha 1, or alpha 2. In contrast, MCM1 binds without these associated DNA-binding proteins at its site in Ty1. This finding suggests that its role in Ty1-mediated transcription is different from that at mating genes.

scholarly journals PAP: a comprehensive workbench for mammalian transcriptional regulatory sequence analysis

2007 ◽  
Vol 35 (Web Server) ◽  
pp. W238-W244 ◽  
Author(s):  
L.-W. Chang ◽  
B. R. Fontaine ◽  
G. D. Stormo ◽  
R. Nagarajan
Keyword(s):  
Sequence Analysis ◽  
Regulatory Sequence ◽  
Transcriptional Regulatory ◽  
Transcriptional Regulatory Sequence
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