Enhancer Control of Transcriptional Bursting

Fukaya, Takashi; Lim, Bomyi; Levine, Michael

doi:10.1016/j.cell.2016.05.025

Cited by 629 publications

(724 citation statements)

References 49 publications

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“…S7). As expected, placing the enhancer further away from the target gene's promoter (GFP) led to a reduction in the level of gene expression (Fukaya et al 2016). However, notably, the spatio-temporal pattern of the enhancer's activity in the somatic muscle is the same in both constructs (Supplemental Fig.…”

Section: Highly Transcribed Developmental Enhancers Have Weak Promotementioning

confidence: 99%

The degree of enhancer or promoter activity is reflected by the levels and directionality of eRNA transcription

et al. 2018

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Gene expression is regulated by promoters, which initiate transcription, and enhancers, which control their temporal and spatial activity. However, the discovery that mammalian enhancers also initiate transcription questions the inherent differences between enhancers and promoters. Here, we investigate the transcriptional properties of enhancers during Drosophila embryogenesis using characterized developmental enhancers. We show that while the timing of enhancer transcription is generally correlated with enhancer activity, the levels and directionality of transcription are highly varied among active enhancers. To assess how this impacts function, we developed a dual transgenic assay to simultaneously measure enhancer and promoter activities from a single element in the same embryo. Extensive transgenic analysis revealed a relationship between the direction of endogenous transcription and the ability to function as an enhancer or promoter in vivo, although enhancer RNA (eRNA) production and activity are not always strictly coupled. Some enhancers (mainly bidirectional) can act as weak promoters, producing overlapping spatio-temporal expression. Conversely, bidirectional promoters often act as strong enhancers, while unidirectional promoters generally cannot. The balance between enhancer and promoter activity is generally reflected in the levels and directionality of eRNA transcription and is likely an inherent sequence property of the elements themselves.

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Section: Highly Transcribed Developmental Enhancers Have Weak Promotementioning

confidence: 99%

The degree of enhancer or promoter activity is reflected by the levels and directionality of eRNA transcription

et al. 2018

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“…4). In addition to mitotic silencing, many genes exhibit transcriptional bursts (e.g., see Bothma et al 2014;Fukaya et al 2016). It is possible that repressors like Snail get the upper hand during the refractory periods between bursts.…”

Section: Snail Exploits Intrinsic Discontinuities In Transcriptionmentioning

confidence: 99%

Mitosis-associated repression in development

et al. 2016

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Transcriptional repression is a pervasive feature of animal development. Here, we employ live-imaging methods to visualize the Snail repressor, which establishes the boundary between the presumptive mesoderm and neurogenic ectoderm of early Drosophila embryos. Snail target enhancers were attached to an MS2 reporter gene, permitting detection of nascent transcripts in living embryos. The transgenes exhibit initially broad patterns of transcription but are refined by repression in the mesoderm following mitosis. These observations reveal a correlation between mitotic silencing and Snail repression. We propose that mitosis and other inherent discontinuities in transcription boost the activities of sequence-specific repressors, such as Snail.

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“…The interpretation of this finding is that a burst of RNA synthesis from either gene can happen only as a result of a promoter-enhancer contact, and this enhancer can contact only one promoter at a time. In contrast, two genes driven from a single enhancer showed coordinated bursting, challenging the view that every burst arises from a stable enhancer-promoter contact (Fukaya et al 2016). Finally, TFs (both sequence-specific and general factors) show temporal variability in occupancy that is consistent with their role in controlling bursting dynamics.…”

Section: Transcriptional Burstingmentioning

confidence: 81%

What have single-molecule studies taught us about gene expression?

Chen

Larson

2016

Genes Dev.

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The production of a single mRNA is the result of many sequential steps, from docking of transcription factors to polymerase initiation, elongation, splicing, and, finally, termination. Much of our knowledge about the fundamentals of RNA synthesis and processing come from ensemble in vitro biochemical measurements. Single-molecule approaches are very much in this same reductionist tradition but offer exquisite sensitivity in space and time along with the ability to observe heterogeneous behavior and actually manipulate macromolecules. These techniques can also be applied in vivo, allowing one to address questions in living cells that were previously restricted to reconstituted systems. In this review, we examine the unique insights that single-molecule techniques have yielded on the mechanisms of gene expression.Single-molecule experiments are now pervasive in biology. What started out as an experimental approach for characterizing ion channels in the 1970s (Neher and Sakmann 1976) has now become a fixture in hundreds of laboratories addressing fundamental questions in biochemistry, cell biology, genetics, and development. The methodology is nearly as diverse as the problems that are addressed and encompasses imaging, optical tweezers, atomic force microscopy, electrophysiology, and cryo-electron microscopy (cryo-EM), to list a few. The unifying principle behind these approaches is straightforward: the ability to observe the heterogeneous, rare, or fleeting behavior of macromolecules that is normally masked by ensemble techniques. In this review, we focus on the role that single-molecule approaches have played in advancing our understanding of the early steps in gene expression.In general, transcription by RNA polymerase (RNAP) in bacteria or RNA polymerase II (Pol II) in eukaryotes begins when transcription factors (TFs) are recruited to the promoter. This leads to the assembly of the preinitiation complex (PIC) that contains a semicompetent polymerase. The PIC is necessary for unwinding duplex DNA and setting the stage for processive elongation by the polymerase. After conformational changes in the PIC, the polymerase escapes the promoter region and enters into productive elongation. In eukaryotes, the nascent RNA undergoes further modifications such as addition of a 5 ′ cap, synthesis of a poly-A tail, and splicing before the mature mRNA is formed. These early steps of gene expression are uniquely suited to elucidation through singlemolecule methods. For example, single-molecule experimental approaches allow one to visualize the order of assembly for molecular complexes (i.e., the PIC) and observe the variety of pathways that can result in initiation of RNAP. The ability to observe kinetics in unperturbed systems can provide clues to the mechanisms of transcription. RNAPs can also be manipulated by singlemolecule optical trapping to reveal the inner workings of force generation by this enzyme. Furthermore, singlemolecule imaging has also revealed the heterogeneity of gene expression that exists among cells in ...

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Enhancer Control of Transcriptional Bursting

Cited by 629 publications

References 49 publications

The degree of enhancer or promoter activity is reflected by the levels and directionality of eRNA transcription

The degree of enhancer or promoter activity is reflected by the levels and directionality of eRNA transcription

Mitosis-associated repression in development

What have single-molecule studies taught us about gene expression?

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