Conserved transcriptional regulation of a cone phototransduction gene in vertebrates

Viczian, Andrea S.; Verardo, Mark R.; Zuber, Michael E.; Knox, Barry E.; Farber, Débora B.

doi:10.1016/j.febslet.2004.10.008

Cited by 7 publications

(5 citation statements)

References 31 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…However, in all of these cases the alternate transcripts were identified in non-retinal tissue, and therefore the alternate start sites do not pertain to our present application. In addition, 8/23 promoters that we selected for analysis are validated experimentally ( Arr3 [ 38 , 41 ], Pde6c [ 42 ], Opn1mw [ 24 , 43 ], Pde6a [ 44 ], Gnat2 [ 45 ], Sag [ 46 , 47 ], Rho [ 23 ], and Nrl [ 48 ]). Those considerations expressed above give us confidence in the promoter regions selected for this study.…”

Section: Discussionmentioning

confidence: 99%

Bioinformatic identification of novel putative photoreceptor specific cis-elements

et al. 2007

View full text Add to dashboard Cite

Background: Cell specific gene expression is largely regulated by different combinations of transcription factors that bind cis-elements in the upstream promoter sequence. However, experimental detection of cis-elements is difficult, expensive, and time-consuming. This provides a motivation for developing bioinformatic methods to identify cis-elements that could prioritize future experimental studies. Here, we use motif discovery algorithms to predict transcription factor binding sites involved in regulating the differences between murine rod and cone photoreceptor populations.

show abstract

Section: Discussionmentioning

confidence: 99%

Bioinformatic identification of novel putative photoreceptor specific cis-elements

et al. 2007

View full text Add to dashboard Cite

show abstract

“…The R2R1 PCR product was TA-subcloned into the pGEMT-easy vector (Promega) to generate pGEMT-easy.R2R1. pGEMT-easy+R2R1 was digested with EcoR1 and the R2R1 containing fragment was subcloned into the EcoR1 site of the pEGFP- plasmid (Viczian et al, 2004) to generate pEGFP-R2R1→GFP. The HindIII/NotI fragment of pEGFP-.R2R1→GFP containing R2R1→GFP was subcloned into the HindIII/NotI site of I-SceI-pBSII-SK+ (Ogino et al, 2006) to generate Xtr six6 R2R1→GFP.…”

Section: Methodsmentioning

confidence: 99%

Distinct cis-acting regions control six6 expression during eye field and optic cup stages of eye formation

Ledford

Luna

Theisen

et al. 2017

Developmental Biology

View full text Add to dashboard Cite

The eye field transcription factor, Six6, is essential for both the early (specification and proliferative growth) phase of eye formation, as well as for normal retinal progenitor cell differentiation. While genomic regions driving six6 optic cup expression have been described, the sequences controlling eye field and optic vesicle expression are unknown. Two evolutionary conserved regions 5′ and a third 3′ to the six6 coding region were identified, and together they faithfully replicate the endogenous X. laevis six6 expression pattern. Transgenic lines were generated and used to determine the onset and expression patterns controlled by the regulatory regions. The conserved 3′ region was necessary and sufficient for eye field and optic vesicle expression. In contrast, the two conserved enhancer regions located 5′ of the coding sequence were required together for normal optic cup and mature retinal expression. Gain-of-function experiments indicate endogenous six6 and GFP expression in F1 transgenic embryos are similarly regulated in response to candidate trans-acting factors. Importantly, CRISPR/CAS9-mediated deletion of the 3′ eye field/optic vesicle enhancer in X. laevis, resulted in a reduction in optic vesicle size. These results identify the cis-acting regions, demonstrate the modular nature of the elements controlling early versus late retinal expression, and identify potential regulators of six6 expression during the early stages of eye formation.

show abstract

“…Recently, several publications have provided evidence that human 15,41 and mouse 14 enhancer sequences are functionally orthologous to frogs and fish and can be used to generate transgenic frogs and zebrafish that express transgenic constructs in the same tissues as transgenic mice. 42 Evolutionarily conserved sequences from the rhodopsin promoter region of Fugu are able to drive photoreceptor rod cell-specific expression of a reporter gene in both the frog and the mouse, 43 suggesting that evolutionarily conserved sequences are compatible between distantly related species.…”

Section: Multiple Methods Of Generating Transgenicmentioning

confidence: 99%

Strategies for characterising cis-regulatory elements in Xenopus

Khokha

Loots

2005

Briefings in Functional Genomics and Proteomics

View full text Add to dashboard Cite

Understanding the cis-regulatory architecture of metazoan organisms is the greatest challenge facing genome biology today. In vertebrate organisms, distinct sequence elements mediate transcriptional regulation and are scattered throughout the genome, either proximal or distal to promoters. The identification of transcriptional enhancers has proven rather difficult by conventional experimental approaches. In the past decade, the rapid generation of genomic sequences for multiple vertebrate organisms, accompanied by sophisticated comparative tools, has facilitated the identification of non-coding evolutionarily conserved regions that may encode cis-regulatory elements. Validating computational predictions and characterising cis-regulatory elements in vivo, however, has been a major bottleneck, mainly because the most commonly used organism for these experiments has been the mouse, and generating transgenic mice or modifying the mouse genome continues to be a labour-intensive, low-throughput, expensive process. This has led to the use of Xenopus, which holds great promise for high-throughput interrogation of putative cis-regulatory elements. In particular, Xenopus tropicalis may become particularly powerful for elucidating regulatory networks, chiefly because it is amenable to genetic manipulations, and its genome is being sequenced.

show abstract

Conserved transcriptional regulation of a cone phototransduction gene in vertebrates

Cited by 7 publications

References 31 publications

Bioinformatic identification of novel putative photoreceptor specific cis-elements

Bioinformatic identification of novel putative photoreceptor specific cis-elements

Distinct cis-acting regions control six6 expression during eye field and optic cup stages of eye formation

Strategies for characterising cis-regulatory elements in Xenopus

Contact Info

Product

Resources

About