Promoter-associated Pausing in Promoter Architecture and Postinitiation Transcriptional Regulation

J, Lis

doi:10.1101/sqb.1998.63.347

Cited by 157 publications

(152 citation statements)

References 2 publications

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“…Yet, recent studies have begun to paint a very different picture of transcriptional regulation, whereby a sizable fraction of promoters are constitutively occupied by Pol II, and it is the polymerase release into productive elongation that is rate limiting. The notion that the rate-limiting step in transcription does not need to be Pol II recruitment is not in itself novel: Years ago, elegant studies from J. Lis's group demonstrated that the Drosophila heat-shock genes were regulated during early elongation (32). A surprise, however, came from the recent genomewide studies in Drosophila revealing that up to 20% of genes may be controlled in a similar manner (19,20).…”

Section: Discussionmentioning

confidence: 97%

Immediate mediators of the inflammatory response are poised for gene activation through RNA polymerase II stalling

Adelman

Kennedy

Nechaev

et al. 2009

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

138

140

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The kinetics and magnitude of cytokine gene expression are tightly regulated to elicit a balanced response to pathogens and result from integrated changes in transcription and mRNA stability. Yet, how a single microbial stimulus induces peak transcription of some genes (TNF␣) within minutes whereas others (IP-10) require hours remains unclear. Here, we dissect activation of several lipopolysaccharide (LPS)-inducible genes in macrophages, an essential cell type mediating inflammatory response in mammals. We show that a key difference between the genes is the step of the transcription cycle at which they are regulated. Specifically, at TNF␣, RNA Polymerase II initiates transcription in resting macrophages, but stalls near the promoter until LPS triggers rapid and transient release of the negative elongation factor (NELF) complex and productive elongation. In contrast, no NELF or polymerase is detectible near the IP-10 promoter before induction, and LPS-dependent polymerase recruitment is rate limiting for transcription. We further demonstrate that this strategy is shared by other immune mediators and is independent of the inducer and signaling pathway responsible for gene activation. Finally, as a striking example of evolutionary conservation, the Drosophila homolog of the TNF␣ gene, eiger, displayed all of the hallmarks of NELF-dependent polymerase stalling. We propose that polymerase stalling ensures the coordinated, timely activation the inflammatory gene expression program from Drosophila to mammals. cytokine gene expression ͉ inflammation ͉ TNF␣ ͉ transcription initiation and elongation ͉ NELF

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Section: Discussionmentioning

confidence: 97%

Immediate mediators of the inflammatory response are poised for gene activation through RNA polymerase II stalling

Adelman

Kennedy

Nechaev

et al. 2009

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

138

140

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“…However, such regulation in eukaryotic systems has been appreciated only recently. Indeed, RNAPII is engaged on many regulated but silent promoters in organisms from Drosophila melanogaster to humans (25). P-TEFb is also required for the transcription of many activated genes transcribed by RNAPII in cells (7).…”

Section: Discussionmentioning

confidence: 99%

AIRE Recruits P-TEFb for Transcriptional Elongation of Target Genes in Medullary Thymic Epithelial Cells

Oven

Brdičková

Kohoutek

et al. 2007

Molecular and Cellular Biology

141

131

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AIRE is a transcriptional activator that directs the ectopic expression of many tissue-specific genes in medullary thymic epithelial cells, which plays an important role in the negative selection of autoreactive T cells. However, its mechanism of action remains poorly understood. In this study, we found that AIRE regulates the step of elongation rather than initiation of RNA polymerase II. For these effects, AIRE bound and recruited P-TEFb to target promoters in medullary thymic epithelial cells. In these cells, AIRE activated the ectopic transcription of insulin and salivary protein 1 genes. Indeed, by chromatin immunoprecipitation, we found that RNA polymerase II was already engaged on these promoters but was unable to elongate in the absence of AIRE. Moreover, the genetic inactivation of cyclin T1 from P-TEFb abolished the transcription of AIRE-responsive genes and led to lymphocytic infiltration of lacrimal and salivary glands in the CycT1 ؊/؊ mouse. Our findings reveal critical steps by which AIRE regulates the transcription of genes that control central tolerance in the thymus.

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“…A small set of randomly chosen Drosophila genes also seemed to have paused Pol II, as assessed by UV-ChIP and nuclear run-on assays 31 , though not at the full occupancy (1 Pol II per promoter) seen for Hsp70 (ref. 30). Additionally, evidence supporting some form of elongational control in specific vertebrate genes has existed since the early 1980s, for example, greater nuclear run-on signals from 59 portions than 39 regions of chicken b-globin 32 .…”

Section: How General Is Paused Pol Ii?mentioning

confidence: 99%

“…Although such a distribution is indicative of Pol II promoter recruitment not being rate limiting in transcription, this Pol II could be in a pre-initiation complex or at some other post-recruitment step that precedes pausing. Additional criteria need to be applied 30 . Nuclear run-on assays can demonstrate that the detected Pol II is trancriptionally engaged, particularly if performed in the presence of Sarkosyl or high salt, which blocks new initiation and seems to remove barriers to elongation 22 .…”

Section: Defining a Pol II As 'Promoter Paused'mentioning

confidence: 99%

Imaging Drosophila gene activation and polymerase pausing in vivo

Lis

2007

Nature

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Since the early 1960s, imaging studies of Drosophila sp. polytene chromosomes have provided unique views of gene transcription in vivo. The dramatic changes in chromatin structure that accompany gene activation can be visualized as chromosome puffs. Now, live-cell imaging techniques coupled with protein-DNA crosslinking assays on a genome-wide scale allow more detailed mechanistic questions to be addressed and are prompting the re-evaluation of models of transcription regulation in both Drosophila and mammals.D etermining the complete genome sequence of humans, Drosophila and other model higher eukaryotes was an important step in cataloguing the complete code that programmes the development and maintenance of multicellular organisms. A critical challenge that remains is to determine in molecular terms how this code is read and regulated in higher eukaryotes 1 . The regulation of transcription of the genome is a major mode by which an organism controls both its homeostasis and development. This regulation is executed mainly through the interactions of a plethora of transcription factor proteins and RNAs with each other and with DNA and associated histones 2 . These interactions then dictate when, where, and to what level specific genes are transcribed. Although biochemical and genetic approaches have identified many of the macromolecular players and their activities, a mechanistic understanding of how they operate in gene regulation can be guided and tested by direct imaging of these molecular interactions and the resulting biochemical processes in living cells.Two developments in the imaging of transcription factors at specific endogenous gene loci in vivo are providing new views of transcription mechanisms and regulation. One, currently specific to Drosophila, makes use of state-of-the-art optics combined with the natural amplification of signals in tissue containing polytene chromosomes, allowing investigation of molecular interactions and dynamics at specific loci in real time in living nuclei 3 . The other, although having a history in Drosophila 4-6 , is species-general and uses crosslinking in vivo-that is, chromatin immunoprecipitation (ChIP) assays and variants thereof-to produce a 'molecular image' of specific protein interactions and chromatin modifications with particular DNA sequences in the genome 7 . Here I describe how these optical and molecular imaging approaches are providing new insights into transcription and the rate-limiting steps in its regulation in multicellular organisms. In particular, recent genome-wide ChIP assays in Drosophila 8,9 and mammals 10 support a paradigm shift in gene regulation by indicating that control of transcription elongation by RNA polymerase II (Pol II) in a promoter-proximal pausing model (Box 1), rather than control of the recruitment or initiation of Pol II, is the rate-limiting step for a large fraction of highly regulated genes. Early insights from spread polytene nucleiOver the past several decades, Drosophila has provided extraordinary views of chromosome s...

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Promoter-associated Pausing in Promoter Architecture and Postinitiation Transcriptional Regulation

Cited by 157 publications

References 2 publications

Immediate mediators of the inflammatory response are poised for gene activation through RNA polymerase II stalling

Immediate mediators of the inflammatory response are poised for gene activation through RNA polymerase II stalling

AIRE Recruits P-TEFb for Transcriptional Elongation of Target Genes in Medullary Thymic Epithelial Cells

Imaging Drosophila gene activation and polymerase pausing in vivo

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