Two haplotypes of 5' untranslated region in L-myc gene with different internal ribosome entry site activity

Kumimoto, Hiroshi; Yamane, Yoshihiro; Ishizaki, Kanji

doi:10.3892/ijo.26.1.287

Int J Oncol

2005

DOI: 10.3892/ijo.26.1.287

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Two haplotypes of 5' untranslated region in L-myc gene with different internal ribosome entry site activity

Hiroshi Kumimoto

Yoshihiro Yamane²,

Kanji Ishizaki³

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“…For example, promoter SNPs (also called regulatory SNPs or rSNPs) may change the gene expression by affecting the transcriptional factor binding sites 29. In addition, SNPs located in the 5′‐UTRs (5′‐SNPs) can affect the gene expression and initiation of translation 30, 31. Furthermore, mRNA stability and translation can be modified by the SNPs influencing the microRNA binding sites (miRSNPs) or other elements along the 3′‐UTRs 32–34.…”

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confidence: 99%

A comprehensive catalogue of functional genetic variations in the EGFR pathway: Protein–protein interaction analysis reveals novel genes and polymorphisms important for cancer research

Savas

Geraci

Jurišica

et al. 2009

Intl Journal of Cancer

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The EGFR pathway is a critical signaling pathway deregulated in many solid tumors. In addition to the initiation and progression of cancer, the EGFR pathway is also implicated in variable treatment responses and prognoses. Genetic variation in the form of Single Nucleotide Polymorphisms (SNPs) can affect the function/expression of the EGFR pathway genes. Here, we applied a systematic and comprehensive approach utilizing diverse public databases and in silico analysis tools to select putative functional genetic variations from 244 genes involved in the EGFR pathway. Our data comprises 649 SNPs. Three hundred sixty SNPs are predicted to have biological consequences (functional SNPs). These SNPs can be directly used in further studies to test their association with risk, treatment response and prognosis in cancer. To systematically cover the EGFR pathway, we also performed a network‐based analysis to further select putative functional SNPs from the genes whose protein products physically interact with the EGFR pathway proteins. We utilized protein–protein interaction information and focused on 14 proteins that have a high degree of connectivity (interacting with ≥10 proteins) with the EGFR pathway genes identified to have functional SNPs (f‐EGFR genes). Two of these proteins (FYN and LCK) had interactions with 17 of the f‐EGFR genes, yet both lacked any putative functional SNP. However, our analysis indicated the presence of potentially functional SNPs in 9 other highly interactive proteins. The genes and their SNPs identified in the network‐based analysis represent potential candidates for gene–gene and SNP–SNP interaction studies in cancer research. © 2009 UICC

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confidence: 99%

A comprehensive catalogue of functional genetic variations in the EGFR pathway: Protein–protein interaction analysis reveals novel genes and polymorphisms important for cancer research

Savas

Geraci

Jurišica

et al. 2009

Intl Journal of Cancer

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Current Practice in Bicistronic IRES Reporter Use: A Systematic Review

Akker

Zacchini

Housmans

et al. 2021

IJMS

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Bicistronic reporter assays have been instrumental for transgene expression, understanding of internal ribosomal entry site (IRES) translation, and identification of novel cap-independent translational elements (CITE). We observed a large methodological variability in the use of bicistronic reporter assays and data presentation or normalization procedures. Therefore, we systematically searched the literature for bicistronic IRES reporter studies and analyzed methodological details, data visualization, and normalization procedures. Two hundred fifty-seven publications were identified using our search strategy (published 1994–2020). Experimental studies on eukaryotic adherent cell systems and the cell-free translation assay were included for further analysis. We evaluated the following methodological details for 176 full text articles: the bicistronic reporter design, the cell line or type, transfection methods, and time point of analyses post-transfection. For the cell-free translation assay, we focused on methods of in vitro transcription, type of translation lysate, and incubation times and assay temperature. Data can be presented in multiple ways: raw data from individual cistrons, a ratio of the two, or fold changes thereof. In addition, many different control experiments have been suggested when studying IRES-mediated translation. In addition, many different normalization and control experiments have been suggested when studying IRES-mediated translation. Therefore, we also categorized and summarized their use. Our unbiased analyses provide a representative overview of bicistronic IRES reporter use. We identified parameters that were reported inconsistently or incompletely, which could hamper data reproduction and interpretation. On the basis of our analyses, we encourage adhering to a number of practices that should improve transparency of bicistronic reporter data presentation and improve methodological descriptions to facilitate data replication.

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Two haplotypes of 5' untranslated region in L-myc gene with different internal ribosome entry site activity

Cited by 2 publications

References 0 publications

A comprehensive catalogue of functional genetic variations in the EGFR pathway: Protein–protein interaction analysis reveals novel genes and polymorphisms important for cancer research

A comprehensive catalogue of functional genetic variations in the EGFR pathway: Protein–protein interaction analysis reveals novel genes and polymorphisms important for cancer research

Current Practice in Bicistronic IRES Reporter Use: A Systematic Review

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