Stalled Hox promoters as chromosomal boundaries

Chopra, Vivek S.; Cande, Jessica; Hong, Joung-Woo; Levine, Michael

doi:10.1101/gad.1807309

Cited by 97 publications

(107 citation statements)

References 40 publications

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“…Nonetheless, only ladybird exhibits insulator activity in these assays. Similar results were observed in a recent study using the same white/lacZ expression vectors (Chopra et al, 2009). Most, but not all, stalled promoters were found to possess an insulator activity.…”

Section: Research Articlesupporting

confidence: 79%

“…For example, the gooseberry promoter contains stalled Pol II, whereas the linked gooseberry-neuro promoter does not. Neither promoter was found to contain insulator activity, suggesting that only a subset of stalled promoters mediate enhancer blocking (Chopra et al, 2009) (see Discussion).…”

Section: Research Articlementioning

confidence: 99%

“…4A). A recent study suggests that promoters containing stalled Pol II can function as insulators (Chopra et al, 2009). Consequently, the lbe promoter, which contains stalled Pol II C-F).…”

Section: Regulation Of Enhancer-promoter Interactionsmentioning

confidence: 99%

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Evolving enhancer-promoter interactions within the tinman complex of the flour beetle,Tribolium castaneum

2009

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Modifications of cis-regulatory DNAs, particularly enhancers, underlie changes in gene expression during animal evolution. Here, we present evidence for a distinct mechanism of regulatory evolution, whereby a novel pattern of gene expression arises from altered gene targeting of a conserved enhancer. The tinman gene complex (Tin-C) controls the patterning of dorsal mesodermal tissues, including the dorsal vessel or heart in Drosophila. Despite broad conservation of Tin-C gene expression patterns in the flour beetle (Tribolium castaneum), the honeybee (Apis mellifera) and the fruit fly (Drosophila melanogaster), the expression of a key pericardial determinant, ladybird, is absent from the dorsal mesoderm of Tribolium embryos. Evidence is presented that this loss in expression is replaced by expression of C15, the neighboring gene in the complex. This switch in expression from ladybird to C15 appears to arise from an inversion within the tinman complex, which redirects a conserved ladybird 3Ј enhancer to regulate C15. In Drosophila, this enhancer fails to activate C15 expression owing to the activity of an insulator at the intervening ladybird early promoter. By contrast, a chromosomal inversion allows the cardiac enhancer to bypass the ladybird insulator in Tribolium. Given the high frequency of genome rearrangements in insects, it is possible that such enhancer switching might be widely used in the diversification of the arthropods.

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Section: Research Articlesupporting

confidence: 79%

Section: Research Articlementioning

confidence: 99%

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Evolving enhancer-promoter interactions within the tinman complex of the flour beetle,Tribolium castaneum

2009

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“…exert enhancer functions directly 21 or by binding to histone modifiers like many large intergenic non-coding RNAs (lincRNAs) 22 or Polycomb-associated RNAs. 23 Finally, it was recently shown that paused RNAP II can act as an insulator 24 in Drosophila, indicating its diverse roles in transcription regulation not only at the promoter or across gene bodies, but also indirectly via association to cis-regulatory elements. Overall, we propose the use of RNAP II recruitment as a means to isolate active and tissue-specific enhancers, and that this tissue-specificity both Figure 2.…”

Section: Tips and Tissue-specificitymentioning

confidence: 99%

Initiating RNA Polymerase II and TIPs as hallmarks of enhancer activity and tissue-specificity

Koch¹,

Andrau²

2011

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“…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). It is possible that a similar scenario is occurring in this system; however, further studies will be required to ascertain whether this is the case with the TBS element.…”

Section: Discussionmentioning

confidence: 99%

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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Stalled Hox promoters as chromosomal boundaries

Cited by 97 publications

References 40 publications

Evolving enhancer-promoter interactions within the tinman complex of the flour beetle,Tribolium castaneum

Evolving enhancer-promoter interactions within the tinman complex of the flour beetle,Tribolium castaneum

Initiating RNA Polymerase II and TIPs as hallmarks of enhancer activity and tissue-specificity

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

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