scholarly journals A versatile tRNA modification-sensitive northern blot method with enhanced performance

RNA ◽  
2021 ◽  
pp. rna.078929.121
Author(s):  
Abdul Khalique ◽  
Sandy Mattijssen ◽  
Richard J. Maraia
Keyword(s):  
Northern Blot ◽  
Assay Method ◽  
Trna Modification ◽  
Altered Gene Expression ◽  
Trna Modifications ◽  
Molecular Studies ◽  
Quantitative Validation ◽  
Base Modifications ◽  
Altered Gene ◽  
Positive Hybridization

The ~22 mitochondrial and ~45 cytosolic tRNAs contain several dozen different posttranscriptional modified nucleotides such that each carries a unique constellation that complements its function. Many tRNA modifications are linked to altered gene expression and their deficiencies due to mutations in tRNA modification enzymes (TMEs) are responsible for numerous diseases. Easily accessible methods to detect tRNA hypomodifications can facilitate progress in advancing such molecular studies. Our lab developed a northern blot method that can quantify relative levels of base modifications on multiple specific tRNAs ~10 years ago which has been used to characterize four different TME deficiencies and is likely further extendable. The assay method depends on differential annealing efficiency of an DNA-oligo probe to the modified versus unmodified tRNA. The signal of this probe is then normalized by a second probe elsewhere on the same tRNA. This positive hybridization in the absence of modification (PHAM) assay has proven useful for i6A37, t6A37, m3C32 and m2,2G26 in multiple laboratories. Yet, over the years we have observed idiosyncratic inconsistency and variability in the assay. Here we document these for some tRNAs and probes and illustrate principles and practices for improved reliability and uniformity in performance. We provide an overview of the method and illustrate benefits of the improved conditions. This is followed by data that demonstrate quantitative validation of PHAM using a TME deletion control, and that nearby modifications can falsely alter the calculated apparent modification efficiency. Finally, we include a calculator tool for matching probe and hybridization conditions.

Molecular and Microscopic Analysis of Altered Gene Expression in Transgenic and Gene Targeted Mice

1996 ◽  
Vol 54 ◽  
pp. 12-13
Author(s):  
W. K. Jones ◽  
J. Robbins
Keyword(s):  
Gene Expression ◽  
Pulmonary Veins ◽  
Microscopic Analysis ◽  
Mouse Tissue ◽  
Adult Heart ◽  
Heavy Chains ◽  
Altered Gene Expression ◽  
Altered Gene ◽  
Pulmonary Myocardium

Two myosin heavy chains (MyHC) are expressed in the mammalian heart and are differentially regulated during development. In the mouse, the α-MyHC is expressed constitutively in the atrium. At birth, the β-MyHC is downregulated and replaced by the α-MyHC, which is the sole cardiac MyHC isoform in the adult heart. We have employed transgenic and gene-targeting methodologies to study the regulation of cardiac MyHC gene expression and the functional and developmental consequences of altered α-MyHC expression in the mouse.We previously characterized an α-MyHC promoter capable of driving tissue-specific and developmentally correct expression of a CAT (chloramphenicol acetyltransferase) marker in the mouse. Tissue surveys detected a small amount of CAT activity in the lung (Fig. 1a). The results of in situ hybridization analyses indicated that the pattern of CAT transcript in the adult heart (Fig. 1b, top panel) is the same as that of α-MyHC (Fig. 1b, lower panel). The α-MyHC gene is expressed in a layer of cardiac muscle (pulmonary myocardium) associated with the pulmonary veins (Fig. 1c). These studies extend our understanding of α-MyHC expression and delimit a third cardiac compartment.

Polymorphism of the MTHFR Gene is Associated with Altered Gene Expression in Colorectal Cancer

Endoscopy ◽  
2004 ◽  
Vol 36 (05) ◽  
Author(s):  
K Collins ◽  
GA Doherty ◽  
MR Sweeney ◽  
SM Byrne ◽  
AA Aftab ◽  
...  
Keyword(s):  
Gene Expression ◽  
Colorectal Cancer ◽  
Mthfr Gene ◽  
Altered Gene Expression ◽  
Altered Gene

scholarly journals Altered gene expression in Chironomus riparius (insecta) in response to tire rubber and polystyrene microplastics

2021 ◽  
pp. 117462
Author(s):  
Victor Carrasco-Navarro ◽  
Ana-Belén Muñiz González ◽  
Jouni Sorvari ◽  
Jose-Luis Martínez Guitarte
Keyword(s):  
Gene Expression ◽  
Chironomus Riparius ◽  
Tire Rubber ◽  
Altered Gene Expression ◽  
Altered Gene

scholarly journals Comparative Transcriptome Atlases Reveal Altered Gene Expression Modules between Two Cleomaceae C3 and C4 Plant Species

2014 ◽  
Vol 26 (8) ◽  
pp. 3243-3260 ◽  
Author(s):  
Canan Külahoglu ◽  
Alisandra K. Denton ◽  
Manuel Sommer ◽  
Janina Maß ◽  
Simon Schliesky ◽  
...  
Keyword(s):  
Gene Expression ◽  
Plant Species ◽  
Comparative Transcriptome ◽  
C4 Plant ◽  
Altered Gene Expression ◽  
Altered Gene

Purification and characterization of the plasminogen activator inhibitors PAI-1, PAI-2, and PN-1 from the human glioblastoma U138

1993 ◽  
Vol 71 (5-6) ◽  
pp. 248-254 ◽  
Author(s):  
Patricia G. Murphy ◽  
Steven P. Lenz ◽  
Mark Dobson ◽  
Allan D. Arndt ◽  
David A. Hart
Keyword(s):  
Monoclonal Antibody ◽  
Plasminogen Activator ◽  
Concanavalin A ◽  
Northern Blot ◽  
Northern Blot Analysis ◽  
Plasminogen Activator Inhibitor ◽  
Immunoaffinity Column ◽  
Positive Hybridization ◽  
Activator Inhibitor ◽  
Pai 1

This investigation presents data which indicate that the plasminogen activator inhibitor (PAI) activity secreted from U138 cells is composed of three separate PAIs: PAI-1, PAI-2, and PN-1. It was demonstrated that the U138 PAI-1-like protein had an apparent molecular mass of 50 kilodaltons (kDa) and was purified to apparent homogeneity by elution from an anti-PAI-1 immunoaffinity column. These fractions were also reactive with a second anti-PAI-1 monoclonal antibody using immunoblotting techniques. Northern blot analysis of RNA isolated from unstimulated U138 cells demonstrated positive hybridization with the cDNA specific for human PAI-1. The U138 PAI-2-like protein was adherent to an anti-PAI-2 immunoaffinity column and was demonstrated to be nonadherent to concanavalin A – agarose, heparin–Sepharose, and the anti-PAI-1 immunoaffinity column. The eluted U138 PAI-2-like protein was demonstrated to have an apparent molecular mass of 60 kDa and was also reactive with a second anti-PAI-2 monoclonal antibody using immunoblotting techniques. Further, the cDNA specific for PAI-2 was demonstrated to hybridize to a 2.5-kilobase message from RNA isolated from U138 cells. A third PAI was detected that was nonadherent to concanavalin A – agarose and both of the anti-PAI columns. This 50-kDa PAI was adherent to heparin–Sepharose and thrombin–agarose columns, and was not reactive with any antibodies for either PAI-1 or PAI-2. Northern blot analysis of U138 RNA demonstrated positive hybridization with an oligodeoxynucleotide specific for PN-1. This investigation demonstrates with biochemical, immunological, and molecular data that the U138 glioblastoma constitutively produces three PAIs.Key words: plasminogen activator inhibitor, U138 glioblastoma, PAI purification, human tumor cell line, proteinase inhibitors.

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