Insulators and promoters: closer than we think

Raab, Jesse R.; Kamakaka, Rohinton T.

doi:10.1038/nrg2765

Cited by 149 publications

(163 citation statements)

References 63 publications

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“…This indicates that an unknown mechanism blocks the capacity of NLP at NIA1-NRE1 to promote transcription from the RPS13 promoter. In animals, insulator sequences and interacting proteins play such roles (Gaszner and Felsenfeld 2006;Raab and Kamakaka 2010). Plants may also harbor such DNA elements and proteins that contribute to the selected activation of particular genes by NLPs.…”

Section: Discussionmentioning

confidence: 99%

An NLP-binding site in the 3' flanking region of the nitrate reductase gene confers nitrate-inducible expression inArabidopsis thaliana(L.) Heynh.

Konishi

Yanagisawa

2013

Soil Science and Plant Nutrition

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As a signaling molecule, nitrate induces the expression of multiple genes involved in nitrate assimilation in plants. We previously showed that the expression of the Arabidopsis thaliana (L.) Heynh. nitrite reductase gene (NIR1) was activated by nitrate signaling through an interaction between NODULE INCEPETIONlike protein (NLP) transcription factors (NLP1-9) and a nitrate-responsive cis-element (NRE) in the NIR1 promoter. By in vitro binding assays, we have also demonstrated the binding of NLP6 to an NRE-like sequence, designated NIA1-NRE1, in the 3' flanking region of an A. thaliana nitrate reductase gene, NIA1.In our current study, we characterize the role of NIA1-NRE1 in NIA1 expression. Deletion analysis of the 3' flanking region of NIA1 revealed that a 345-bp sequence containing NIA1-NRE1 has a dominant role in nitrate-inducible NIA1 expression. We also found that the 35S minimal promoter fused to the 345-bp sequence, or to NIA1-NRE1, can confer nitrate-inducible expression. Furthermore, the NIA1-NRE1-fused 35S minimal promoter is transactivated by NLP6 in vivo. These results suggest that NIA1-NRE1 alone is sufficient to direct nitrate-responsive gene expression and that nitrate-inducible NIA1 expression is regulated through the interaction between NLPs and NIA1-NRE1. Additionally, we show that the distance between the NRE and the gene under the control of the NRE is not critical for this process.

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Section: Discussionmentioning

confidence: 99%

An NLP-binding site in the 3' flanking region of the nitrate reductase gene confers nitrate-inducible expression inArabidopsis thaliana(L.) Heynh.

Konishi

Yanagisawa

2013

Soil Science and Plant Nutrition

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“…While it appears that several different mechanisms may exist by which enhancer-blocking insulators function, it has been suggested that the addition of a promoter upstream of the target promoter can result in trapping of the enhancer and will prevent transcriptional activation of the target promoter (Geyer 1997). Similarities have been found to exist between insulators and promoters, including distinct chromatin modification signatures, the binding of specific transcription factors and localization to particular nuclear regions (reviewed by Raab and Kamakaka 2010), and several Drosophila insulators have been found to contain promoters Drewell et al 2002;Geyer 1997). Recently, it has been shown that promoters containing stalled polymerase II are more likely to display enhancer-blocking insulator activity than non-stalled promoters in Drosophila Chopra et al 2009), which may result from enhancer preference for components of the stalled transcriptional complex or an inherent selectivity of enhancers for particular types of promoters (Butler and Kadonaga 2001;Juven-Gershon et al 2008).…”

Section: Discussionmentioning

confidence: 99%

“…The TBS initiates transcription of a downstream GUS gene in both the forward and reverse orientations It has been suggested previously that one possible mechanism by which enhancer-blocking insulators exert their function is through their inclusion of promoter-like sequences, which either act as a decoy by interacting directly with the enhancer, or through the attenuation of a signal that travels from enhancer to promoter (reviewed by Raab and Kamakaka 2010). To determine whether the TBS element possessed any promoter activity, we generated vectors in which full-length forward-and reverse-oriented TBS fragments were fused directly to a downstream GUS reporter gene (Fig.…”

Section: Quantification Of Enhancer-blocking Activity In Various Tranmentioning

confidence: 99%

“…Alternatively, the binding of proteins to the insulator sequence could result in a physical blockage of an activating signal, such as histone modification or intergenic transcription initiated at the enhancer and progressing toward the target promoter (reviewed by Wallace and Felsenfeld 2007). It has also been suggested that enhancer-blocking insulators may function as decoy promoters by directly interacting with the enhancer or through the attenuation of a putative signal that progresses from enhancer to promoter, thus inhibiting communication between the enhancer and target promoter (reviewed by Raab and Kamakaka 2010). Since evidence exists to support each of these models, it is probable that one single model is not applicable to all enhancer-blocking activity.…”

Section: Introductionmentioning

confidence: 99%

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Analysis of the enhancer-blocking function of the TBS element from Petunia hybrida in transgenic Arabidopsis thaliana and Nicotiana tabacum

2011

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Transcriptional enhancers possess the ability to override the tissue-specificity and efficiency of nearby promoters, which is of concern when generating transgenic constructs bearing multiple cassettes. One means of preventing these inappropriate interactions is through the use of enhancer-blocking insulators. The 2-kb transformation booster sequence (TBS) from Petunia hybrida has been shown previously to exhibit this function when inserted between an enhancer and promoter in transgenic Arabidopsis thaliana. In this study, we attempted to further characterize the ability of this fragment to impede enhancer-promoter interference through an analysis of transgenic Arabidopsis and Nicotiana tabacum lines bearing various permutations of the TBS element between the cauliflower mosaic virus (CaMV) 35S enhancer and an assortment of tissue-specific promoters fused to the b-glucuronidase (GUS) reporter gene. The full-length TBS fragment was found to function in both orientations, although to a significantly lesser degree in the reverse orientation, and was operational in both plant species tested. While multiple deletion fragments were found to exhibit activity, it appeared that several regions of the TBS were required for maximal enhancer-blocking function. Furthermore, we found that this element exhibited promoter-like activity, which has implications in terms of possible mechanisms behind its ability to impede enhancer-promoter communication in plants.

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“…Previous studies have found that a number of the heterochromatin boundaries in yeast are associated with gene promoters [111]. Epigenomic profiling is also beginning to reveal that a considerable fraction of heterochromatin boundaries in mammals are marked by active promoters [22].…”

Section: Barrier-like Activity At Gene Regulatory Elementsmentioning

confidence: 99%

Chromatin Insulator Elements: Establishing Barriers to Set Heterochromatin Boundaries

Barkess

West

2012

Epigenomics

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Epigenomic profiling has revealed that substantial portions of genomes in higher eukaryotes are organized into extensive domains of transcriptionally repressive chromatin. The boundaries of repressive chromatin domains can be fixed by DNA elements known as barrier insulators, to both shield neighboring gene expression and to maintain the integrity of chromosomal silencing. Here, we examine the current progress in identifying vertebrate barrier elements and their binding factors. We overview the design of the reporter assays used to define enhancer-blocking and barrier insulators. We look at the mechanisms vertebrate barrier proteins, such as USF1 and VEZF1, employ to counteract Polycomb- and heterochromatin-associated repression. We also undertake a critical analysis of whether CTCF could also act as a barrier protein. There is good evidence that barrier elements in vertebrates can form repressive chromatin domain boundaries. Future studies will determine whether barriers are frequently used to define repressive domain boundaries in vertebrates.

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Insulators and promoters: closer than we think

Cited by 149 publications

References 63 publications

An NLP-binding site in the 3' flanking region of the nitrate reductase gene confers nitrate-inducible expression inArabidopsis thaliana(L.) Heynh.

An NLP-binding site in the 3' flanking region of the nitrate reductase gene confers nitrate-inducible expression inArabidopsis thaliana(L.) Heynh.

Analysis of the enhancer-blocking function of the TBS element from Petunia hybrida in transgenic Arabidopsis thaliana and Nicotiana tabacum

Chromatin Insulator Elements: Establishing Barriers to Set Heterochromatin Boundaries

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