Determination of Transcription Start Sites (TSSs) in Yersinia pestis with a Primer Extension Assay

2018 ◽  
pp. 89-98
Author(s):  
Yanping Han
Keyword(s):  
Yersinia Pestis ◽  
Primer Extension ◽  
Transcription Start ◽  
Primer Extension Assay ◽  
Transcription Start Sites

scholarly journals Transcript Analysis of Multiple Copies ofamo (Encoding Ammonia Monooxygenase) and hao(Encoding Hydroxylamine Oxidoreductase) in Nitrosomonas europaea

2001 ◽  
Vol 183 (3) ◽  
pp. 1096-1100 ◽  
Author(s):  
Norman G. Hommes ◽  
Luis A. Sayavedra-Soto ◽  
Daniel J. Arp
Keyword(s):  
Nitrosomonas Europaea ◽  
Primer Extension ◽  
Transcript Analysis ◽  
Ammonia Monooxygenase ◽  
Transcription Start ◽  
Hydroxylamine Oxidoreductase ◽  
Transcription Start Sites ◽  
Promoter Sequences ◽  
Genes Encoding ◽  
Multiple Copies

ABSTRACT The genes encoding ammonia monooxygenase (amoCAB), hydroxylamine oxidoreductase (hao), and thec-type cytochrome c-554 (hcy) are present in multiple copies in the genome of Nitrosomonas europaea. The upstream regions of the two copies ofamoC, the three copies of hao, and one copy ofhcy were cloned and sequenced. Primer extension reactions were done to identify transcription start sites for these genes, as well as for amoA. Putative ς70 promoter sequences were found associated with all but one of the mapped transcription start sites. Primer extensions were done withamoC primers using RNA harvested from cells incubated with and without ammonium. The experiments suggested that N. europaea cells may be able to use different promoters in the presence and absence of ammonium.

scholarly journals Determination of the Secondary Structure of an RNA fragment in Solution: Selective 2`-Hydroxyl Acylation Analyzed by Primer Extension Assay (SHAPE)

BIO-PROTOCOL ◽  
2015 ◽  
Vol 5 (2) ◽  
Author(s):  
Manuel Miras ◽  
Raquel Sempere ◽  
Jelena Kraft ◽  
W. Miller ◽  
Miguel Aranda ◽  
...  
Keyword(s):  
Secondary Structure ◽  
Primer Extension ◽  
Primer Extension Assay

scholarly journals Comprehensive determination of transcription start sites derived from all RNA polymerases using ReCappable-seq

2021 ◽  
pp. gr.275784.121
Author(s):  
Bo Yan ◽  
George Tzertzinis ◽  
Ira Schildkraut ◽  
Laurence Ettwiller
Keyword(s):  
Noncoding Rna ◽  
Rna Polymerases ◽  
Transcription Start ◽  
Pol Ii ◽  
Transcription Start Sites ◽  
Cell Functions ◽  
Wide Scale ◽  
Nucleotide Resolution ◽  
Pol Iii

Determination of eukaryotic Transcription Start Sites (TSS) has been based on methods that require the cap structure at the 5-prime end of transcripts derived from Pol-II RNA polymerase. Consequently, these methods do not reveal TSS derived from the other RNA polymerases which also play critical roles in various cell functions. To address this limitation, we developed ReCappable-seq which comprehensively identifies TSS for both Pol-lI and non-Pol-II transcripts at single-nucleotide resolution. The method relies on specific enzymatic exchange of 5-prime m7G caps and 5-prime triphosphates with a selectable tag. When applied to human transcriptomes, ReCappable-seq identifies Pol-II TSS that are in agreement with orthogonal methods such as CAGE. Additionally, ReCappable-seq reveals a rich landscape of TSS associated with Pol-III transcripts which have not previously been amenable to study at genome-wide scale. Novel TSS from non-Pol-II transcription can be located in the nuclear and mitochondrial genomes. ReCappable-seq interrogates the regulatory landscape of coding and noncoding RNA concurrently and enables the classification of epigenetic profiles associated with Pol-lI and non-Pol-II TSS.

Sequence analysis reveals homology between two proteins of the flagellar radial spoke

1992 ◽  
Vol 12 (9) ◽  
pp. 3967-3977
Author(s):  
A M Curry ◽  
B D Williams ◽  
J L Rosenbaum
Keyword(s):  
Sequence Analysis ◽  
Protein Gene ◽  
Molecular Tools ◽  
Transcription Start ◽  
Mrna Accumulation ◽  
Transcription Start Sites ◽  
Radial Spoke ◽  
Radial Spokes ◽  
Flagellar Regeneration

Flagellar radial spokes contribute to the regulation of dynein arm activity and thus the pattern of flagellar bending. We have sequenced the genes for radial spoke protein 4 (RSP4) and RSP6, two of the five proteins that make up the radial spoke head in Chlamydomonas reinhardtii. The two genes, which are tightly linked genetically (B. Huang, G. Piperno, Z. Ramanis, and D.J.L. Luck, J. Cell Biol. 88:80-88, 1981), are separated by only 435 bp. They encode proline-rich polypeptides of 49.8 kDa (RSP4) and 48.8 kDa (RSP6), which are 48% identical to each other but do not resemble any previously sequenced proteins. The transcription start sites of these genes and an additional radial spoke protein gene, that for RSP3, were determined, and patterns of mRNA accumulation during flagellar regeneration were examined for the three radial spoke protein genes. These studies provide the molecular tools for a detailed analysis of radial spoke head function and assembly and for a determination of the mechanism by which the genes required to build a complex organelle are regulated.

scholarly journals Sequence analysis reveals homology between two proteins of the flagellar radial spoke.

1992 ◽  
Vol 12 (9) ◽  
pp. 3967-3977 ◽  
Author(s):  
A M Curry ◽  
B D Williams ◽  
J L Rosenbaum
Keyword(s):  
Sequence Analysis ◽  
Protein Gene ◽  
Molecular Tools ◽  
Transcription Start ◽  
Mrna Accumulation ◽  
Transcription Start Sites ◽  
Radial Spoke ◽  
Radial Spokes ◽  
Flagellar Regeneration

Flagellar radial spokes contribute to the regulation of dynein arm activity and thus the pattern of flagellar bending. We have sequenced the genes for radial spoke protein 4 (RSP4) and RSP6, two of the five proteins that make up the radial spoke head in Chlamydomonas reinhardtii. The two genes, which are tightly linked genetically (B. Huang, G. Piperno, Z. Ramanis, and D.J.L. Luck, J. Cell Biol. 88:80-88, 1981), are separated by only 435 bp. They encode proline-rich polypeptides of 49.8 kDa (RSP4) and 48.8 kDa (RSP6), which are 48% identical to each other but do not resemble any previously sequenced proteins. The transcription start sites of these genes and an additional radial spoke protein gene, that for RSP3, were determined, and patterns of mRNA accumulation during flagellar regeneration were examined for the three radial spoke protein genes. These studies provide the molecular tools for a detailed analysis of radial spoke head function and assembly and for a determination of the mechanism by which the genes required to build a complex organelle are regulated.

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