Translating the Untranslated Region

Schwerk, Johannes; Savan, Ram

doi:10.4049/jimmunol.1500756

Cited by 77 publications

(53 citation statements)

References 148 publications

(142 reference statements)

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“…Numerical and statistical data related to the human genome are typically mentioned as general knowledge without citing a proper updated reference (11, 12) or from genome browser websites (13, 14). This is also due to a lack of a systematic reanalysis of these values which date back to February 2001 (15–17) in the recent literature, while the reanalysis of data provided by regularly updated genome browser websites is hampered by limitations presented above.…”

Section: Introductionmentioning

confidence: 99%

GeneBase 1.1: a tool to summarize data from NCBI gene datasets and its application to an update of human gene statistics

et al. 2016

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We release GeneBase 1.1, a local tool with a graphical interface useful for parsing, structuring and indexing data from the National Center for Biotechnology Information (NCBI) Gene data bank. Compared to its predecessor GeneBase (1.0), GeneBase 1.1 now allows dynamic calculation and summarization in terms of median, mean, standard deviation and total for many quantitative parameters associated with genes, gene transcripts and gene features (exons, introns, coding sequences, untranslated regions). GeneBase 1.1 thus offers the opportunity to perform analyses of the main gene structure parameters also following the search for any set of genes with the desired characteristics, allowing unique functionalities not provided by the NCBI Gene itself. In order to show the potential of our tool for local parsing, structuring and dynamic summarizing of publicly available databases for data retrieval, analysis and testing of biological hypotheses, we provide as a sample application a revised set of statistics for human nuclear genes, gene transcripts and gene features. In contrast with previous estimations strongly underestimating the length of human genes, a ‘mean’ human protein-coding gene is 67 kbp long, has eleven 309 bp long exons and ten 6355 bp long introns. Median, mean and extreme values are provided for many other features offering an updated reference source for human genome studies, data useful to set parameters for bioinformatic tools and interesting clues to the biomedical meaning of the gene features themselves.Database URL: http://apollo11.isto.unibo.it/software/

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Section: Introductionmentioning

confidence: 99%

GeneBase 1.1: a tool to summarize data from NCBI gene datasets and its application to an update of human gene statistics

et al. 2016

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“…It is well known that the 3′-UTR plays a critical role in translation and posttranscriptional gene modification. 15,16 Indeed, one of the SNPs in the 3′-UTR of the NR3C1 gene, 9β, is known to cause relative GC resistance. 4 …”

Section: Discussionmentioning

confidence: 99%

Iatrogenic Cushing’s Syndrome Due to Topical Ocular Glucocorticoid Treatment

et al. 2017

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Iatrogenic Cushing’s syndrome (CS) is a severe adverse effect of systemic glucocorticoid (GC) therapy in children, but is extremely rare in the setting of topical ocular GC therapy. In this article, we report the case of a 9-year-old girl suffering from idiopathic uveitis who developed CS due to topical ocular GC treatment. She was referred to the ophthalmology department with a complaint of painful eyes, at which time she was diagnosed with bilateral iridocyclitis and started on a treatment of betamethasone sodium phosphate eye drops. Six months after the initiation of topical ocular GC treatment, she was referred to our pediatric department with stunted growth, truncal obesity, purple skin striate, buffalo hump, and moon face. Because her serum cortisol and plasma adrenocorticotropic hormone levels were undetectable, she was diagnosed with iatrogenic CS. After the doses of topical ocular GC were reduced, the clinical symptoms of CS were improved. The fact that the amount of topical ocular GC with our patient was apparently less than that of similar previous cases tempted us to perform genetic analysis of her NR3C1 gene. We found that our patient had a single heterozygous nucleotide substitution in the 3′ untranslated region of the NR3C1 gene, which may explain why she developed CS. However, additional investigations are required to determine if our findings can be extrapolated to other patients. In conclusion, clinicians should be aware that even extremely low doses of topical ocular steroid therapy can cause iatrogenic CS.

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“…Interleukins, interferons, and chemokines encode mRNA-instability motifs, such as AUUUA sequences, constitutive decay elements, and stem loops, which are targeted by specific RNAbinding proteins to destabilize the mRNA [28]. It is possible that alpinone 3-acetate and/or hydrocortisone regulate ribosomal loading on these mRNAs through trans factor binding to the AUUUA sequence [29,30].…”

Section: Discussionmentioning

confidence: 99%

Anti-inflammatory effects of alpinone 3-acetate from Alpinia japonica seeds

2016

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We aimed to investigate the bioactive components of Alpinia japonica as anti-inflammatory compounds using searches of the Alpinia genus, and subsequently demonstrated that alpinone 3-acetate markedly inhibits 12-O-tetradecanoyiphorbol 13-acetate-induced inflammation in a mouse model of ear edema. To assess other bioactivities of alpinone 3-acetate, we performed translatome analyses and compared them with those of hydrocortisone. Polysome-associated mRNAs were prepared from alpinone 3-acetate- or hydrocortisone-treated and control cells from 12-O-tetradecanoyiphorbol 13-acetate-induced THP-1-derived macrophages cultured in the presence of Escherichia coli O-111 lipopolysaccharide. Subsequent microarray analysis revealed that alpinone 3-acetate and hydrocortisone upregulated and downregulated the same 155 and 41 genes, respectively. Moreover, direct comparisons of translationally regulated genes indicated 5 and 10 gene probes that were upregulated and downregulated by alpinone 3-acetate and hydrocortisone, respectively. In conclusion, assays of 12-O-tetradecanoyiphorbol 13-acetate-induced inflammation ear edema in mice and polysome profiling of alpinone 3-acetate bioactivities indicated similar medicinal possibilities to those of hydrocortisone.

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Translating the Untranslated Region

Cited by 77 publications

References 148 publications

GeneBase 1.1: a tool to summarize data from NCBI gene datasets and its application to an update of human gene statistics

GeneBase 1.1: a tool to summarize data from NCBI gene datasets and its application to an update of human gene statistics

Iatrogenic Cushing’s Syndrome Due to Topical Ocular Glucocorticoid Treatment

Anti-inflammatory effects of alpinone 3-acetate from Alpinia japonica seeds

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