An element in intron 1 of the CFTR gene augments intestinal expression in vivo

Rowntree, Rebecca K.; Vassaux, Georges; McDowell, Tarra L.; Howe, Steve; McGuigan, Amanda; Phylactides, Marios; Huxley, Clare; Harris, Ann

doi:10.1093/hmg/10.14.1455

Cited by 60 publications

(53 citation statements)

References 42 publications

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“…For example, excised introns generally do not contribute to gene function, but D. melanogaster introns were aligned to and showed expression in non-melanogaster species. Here the conservation of intron sequence is consistent with functional constraint on intron evolution, possibly due to the regular presence of intronic splicing enhancers (Hare and Palumbi 2003;Xing and Lee 2006) and transcriptional enhancers (Banerji et al 1983;Rowntree et al 2001) rather than expression per se. If introns have little direct function as RNA-elements, then we might expect that the expression of most introns would be low, because most reads mapping to introns would be derived from incompletely processed transcripts.…”

Section: Caveatssupporting

confidence: 69%

Comparative validation of the D. melanogaster modENCODE transcriptome annotation

et al. 2014

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Accurate gene model annotation of reference genomes is critical for making them useful. The modENCODE project has improved the D. melanogaster genome annotation by using deep and diverse high-throughput data. Since transcriptional activity that has been evolutionarily conserved is likely to have an advantageous function, we have performed large-scale interspecific comparisons to increase confidence in predicted annotations. To support comparative genomics, we filled in divergence gaps in the Drosophila phylogeny by generating draft genomes for eight new species. For comparative transcriptome analysis, we generated mRNA expression profiles on 81 samples from multiple tissues and developmental stages of 15 Drosophila species, and we performed cap analysis of gene expression in D. melanogaster and D. pseudoobscura. We also describe conservation of four distinct core promoter structures composed of combinations of elements at three positions. Overall, each type of genomic feature shows a characteristic divergence rate relative to neutral models, highlighting the value of multispecies alignment in annotating a target genome that should prove useful in the annotation of other high priority genomes, especially human and other mammalian genomes that are rich in noncoding sequences. We report that the vast majority of elements in the annotation are evolutionarily conserved, indicating that the annotation will be an important springboard for functional genetic testing by the Drosophila community.

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Section: Caveatssupporting

confidence: 69%

Comparative validation of the D. melanogaster modENCODE transcriptome annotation

et al. 2014

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“…Both colon carcinoma cell lines, Caco2 and HT29, also showed the ϩ15.6 kb DHS. A DHS in intron 1 (185 ϩ 10 kb) that we have previously shown to contain an intestinal-specific enhancer element in vitro and in vivo (19,(25)(26)(27) was detected in both Caco2 and HT29 cells. Additional cell-line specific DHS are evident in intron 10 (1716 ϩ 13.2 kb) in Caco2 cells and intron 18 (3600 ϩ 1.6 kb) in HT29.…”

Section: Resultsmentioning

confidence: 85%

Intronic enhancers coordinate epithelial-specific looping of the active CFTR locus

Ott

Blackledge

Kerschner

et al. 2009

Proc. Natl. Acad. Sci. U.S.A.

103

211

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The regulated expression of large human genes can depend on long-range interactions to establish appropriate three-dimensional structures across the locus. The cystic fibrosis transmembrane conductance regulator (CFTR) gene, which encompasses 189 kb of genomic DNA, shows a complex pattern of expression with both spatial and temporal regulation. The flanking loci, ASZ1 and CTTNBP2, show very different tissue-specific expression. The mechanisms governing control of CFTR expression remain poorly understood, although they are known to involve intronic regulatory elements. Here, we show a complex looped structure of the CFTR locus in cells that express the gene, which is absent from cells in which the gene is inactive. By using chromatin conformation capture (3C) with a bait probe at the CFTR promoter, we demonstrate close interaction of this region with sequences in the middle of the gene about 100 kb from the promoter and with regions 3 to the locus that are about 200 kb away. We show that these interacting regions correspond to prominent DNase I hypersensitive sites within the locus. Moreover, these sequences act cooperatively in reporter gene constructs and recruit proteins that modify chromatin structure. The model for CFTR gene expression that is revealed by our data provides a paradigm for other large genes with multiple regulatory elements lying within both introns and intergenic regions. We anticipate that these observations will enable original approaches to designing regulated transgenes for tissue-specific gene therapy protocols.cis-acting elements ͉ enhancer:promoter interactions ͉ regulation of expression ͉ cystic fibrosis transmembrane conductance regulator U nderstanding the three-dimensional organization of individual loci within the human genome and how this relates to the regulation of gene expression is the focus of intense study. Many new technologies are being developed to locate and classify the functional elements of the human genome (1). These elements may contribute to the transcription of ubiquitously expressed genes and are also likely responsible for regulating genes with expression that is temporally and spatially controlled. Cis-acting regulatory elements located within noncoding regions of genomic DNA can influence the organization of chromosomes and the transcriptional activity of genes. These cis sequences include distal enhancers that may reside large distances from the gene promoters they control. Variations in these enhancer/promoter interactions and the nuclear localization of the genes they regulate are thought to be contributing factors in the diversity of transcriptional profiles between different cell types. Moreover, they are important in adjusting these profiles throughout cellular differentiation and development (2-7). These long-range associations are facilitated by the looping of chromatin, whereby regulatory elements come together with requisite nuclear factors to function within ''transcriptional hubs'' where transcriptional activity is coordinated (8).Here, we present...

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“…Another example of a tissue-specific intronic enhancer is found in the cystic fibrosis transmembrane regulator, where an element in intron 1 has been demonstrated to have an important role in regulating expression in the small intestine, but not lung, in transgenic mice [21].…”

Section: Discussionmentioning

confidence: 99%

Conserved elements within first intron of aquaporin-5 (Aqp5) function as transcriptional enhancers

Flodby

Zhou

Ann

et al. 2007

Biochemical and Biophysical Research Communications

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A 4.3-kb rat aquaporin-5 (Aqp5) promoter that directs lung and salivary cell-specific expression in vitro directs low level expression of a GFP reporter in lungs of transgenic mice. Alignment of rat, mouse and human AQP5 genomic sequences identified a highly conserved region in the 3′ portion of intron 1, here termed ci1. To investigate the role of ci1 in Aqp5 expression, transient transfections were undertaken in AQP5-expressing mouse lung epithelial (MLE-15) and rat salivary (Pa-4) cells and AQP5-non-expressing NIH/3T3 cells. A 536 bp ci1 fragment enhanced transcriptional activity of the rat Aqp5 minimal promoter specifically in MLE-15 cells in an orientation-independent manner. Enhancer activity was Aqp5 promoter-specific, since no increase in activity was detected with the TK promoter. These results suggest that expression of transgenes in mouse lungs under direction of the 4.3 kb rat Aqp5 promoter may be augmented by inclusion of ci1 in transgenic constructs.

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An element in intron 1 of the CFTR gene augments intestinal expression in vivo

Cited by 60 publications

References 42 publications

Comparative validation of the D. melanogaster modENCODE transcriptome annotation

Comparative validation of the D. melanogaster modENCODE transcriptome annotation

Intronic enhancers coordinate epithelial-specific looping of the active CFTR locus

Conserved elements within first intron of aquaporin-5 (Aqp5) function as transcriptional enhancers

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