Tissue-specific in vivo transcription start sites of the human and murine cystic fibrosis genes

White, Nina L.; Higgins, Christopher F.; Trezise, A. E. O.

doi:10.1093/hmg/7.3.363

Cited by 42 publications

(36 citation statements)

References 35 publications

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“…18,19 Consequently, previous CFTR gene expression studies needed complex analysis methods and were mainly focused on the splicing efficiency of exon 9. 20,21 Currently, these initial adverse conditions surrounding the CFTR expression analysis can be overcome using more sensitive tools, such as the RT-qPCR technology.…”

Section: Discussionmentioning

confidence: 99%

Assessing the residual CFTR gene expression in human nasal epithelium cells bearing CFTR splicing mutations causing cystic fibrosis

et al. 2013

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The major purpose of the present study was to quantify correctly spliced CFTR transcripts in human nasal epithelial cells from cystic fibrosis (CF) patients carrying the splicing mutations c.580-1G4T (712-1G4T) and c.2657 þ 5G4A (2789 þ 5G4A) and to assess the applicability of this model in CFTR therapeutic approaches. We performed the relative quantification of CFTR mRNA by reverse transcription quantitative PCR (RT-qPCR) of these splicing mutations in four groups (wild type, CF-F508del controls, CF patients and CF carriers) of individuals. In addition, in vitro assays using minigene constructs were performed to evaluate the effect of a new CF complex allele c.[2657 þ 5G4A; 2562T4G]. Ex vivo qPCR data show that the primary consequence of both mutations at the RNA level is the skipping of their neighboring exon (6 and 16, respectively). The CFTR minigenes results mimicked the ex vivo data, as exon 16 skipping is the main aberrant transcript, and the correctly spliced transcript level was observed in a similar proportion when the c.2657 þ 5G4A mutation is present. In summary, we provide evidence that ex vivo quantitative transcripts analysis using RT-qPCR is a robust technology that could be useful for measuring the efficacy of therapeutic approaches that attempt to achieve an increase in CFTR gene expression.

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Section: Discussionmentioning

confidence: 99%

Assessing the residual CFTR gene expression in human nasal epithelium cells bearing CFTR splicing mutations causing cystic fibrosis

et al. 2013

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“…Lack of this 5'-most exon in differentiated myotubes could contribute to the increased Cryab protein production. 120,121 Because alternative TSS usage is common during vertebrate embryogenesis 122,123 and in different cell types, [124][125][126][127] such a transcription-based control of uORF regulation could have broad implications in developmental regulation of gene expression.…”

Section: Uorfs As Widespread Repressive Genetic Elementsmentioning

confidence: 99%

Decoding sORF translation – from small proteins to gene regulation

2016

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Translation is best known as the fundamental mechanism by which the ribosome converts a sequence of nucleotides into a string of amino acids. Extensive research over many years has elucidated the key principles of translation, and the majority of translated regions were thought to be known. The recent discovery of wide-spread translation outside of annotated protein-coding open reading frames (ORFs) came therefore as a surprise, raising the intriguing possibility that these newly discovered translated regions might have unrecognized protein-coding or gene-regulatory functions. Here, we highlight recent findings that provide evidence that some of these newly discovered translated short ORFs (sORFs) encode functional, previously missed small proteins, while others have regulatory roles. Based on known examples we will also speculate about putative additional roles and the potentially much wider impact that these translated regions might have on cellular homeostasis and gene regulation.

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“…[22][23][24][25] These data suggest that the binding of these factors putatively modifies the use of the major TSS essential for CFTR transcription during lung development. 26,27 The identification of alterations in non-coding regions and the determination of the impact of each allele component have several important consequences for recessive disorders such as CF. They permit a better understanding of the complex genotype-phenotype relationships and the opportunity to offer personalized genetic counseling or adapted therapy.…”

Section: Discussionmentioning

confidence: 99%

Functional analysis of a promoter variant identified in the CFTR gene in cis of a frameshift mutation

et al. 2011

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In monogenic diseases, the presence of several sequence variations in the same allele may complicate our understanding of genotype-phenotype relationships. We described new alterations identified in a cystic fibrosis (CF) patient harboring a 48C4G promoter sequence variation associated in cis of a 3532AC4GTA mutation and in trans with the F508del mutation. Functional analyses including in vitro experiments confirmed the deleterious effect of the 3532GTA frameshift mutation through the creation of a premature termination codon. The analyses also revealed that the 48G promoter variant has a negative effect on both transcription and mRNA level, thus demonstrating the importance of analyzing all mutations or sequence variations with potential impact on CF transmembrane conductance regulator processing, even when the two known disease-causing mutations have already been detected. Our results emphasize the need to perform, wherever possible, functional studies that may greatly assist the interpretation of the disease-causing potential of rare mutation-associated sequence variations.

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Tissue-specific in vivo transcription start sites of the human and murine cystic fibrosis genes

Cited by 42 publications

References 35 publications

Assessing the residual CFTR gene expression in human nasal epithelium cells bearing CFTR splicing mutations causing cystic fibrosis

Assessing the residual CFTR gene expression in human nasal epithelium cells bearing CFTR splicing mutations causing cystic fibrosis

Decoding sORF translation – from small proteins to gene regulation

Functional analysis of a promoter variant identified in the CFTR gene in cis of a frameshift mutation

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