The block to transcriptional elongation within the human c-myc gene is determined in the promoter-proximal region.

Krumm, Anton; Meulia, Tea; Brunvand, Mark W.; Groudine, Mark

doi:10.1101/gad.6.11.2201

Cited by 249 publications

(216 citation statements)

References 59 publications

(62 reference statements)

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“…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 . Similar data for mammalian c-Myc and c-Fos were augmented with in vitro studies that suggested initially a termination control further downstream, but more thorough characterizations in vivo showed these genes to have properties like those of Drosophila Hsp70 paused Pol II 33,34 .…”

Section: How General Is Paused Pol Ii?supporting

confidence: 57%

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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Section: How General Is Paused Pol Ii?supporting

confidence: 57%

Imaging Drosophila gene activation and polymerase pausing in vivo

Lis

2007

Nature

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“…The c-myc gene can be expressed from four promoters (P0, P1, P2, P3), all of which appear to be regulated independently (Eick et al, 1990), with RNA initiated at the P2 promoter usually contributing 80-90% of total steady-state c-myc RNA in normal cells (Spencer and Groudine, 1991). RNA pol II pauses in the P2 promoter region, causing premature attenuation of P1 transcripts (Krumm et al, 1992), with the rate of RNA pol II release from the P2 pause site shown to regulate c-myc transcriptional activity (Strobl and Eick, 1992;Kohlhuber et al, 1993 resulted from P2 initiation alone, no increases in P1 transcript levels would have been observed. Our data therefore suggest that the enhanced c-myc mRNA levels observed after HGF/SF stimulation are mediated through both P1-and P2-initiated transcripts, following closely similar patterns of change.…”

Section: Discussionmentioning

confidence: 99%

Hepatocyte growth factor-stimulated renal tubular mitogenesis: effects on expression of c-myc, c-fos, c-met, VEGF and the VHL tumour-suppressor and related genes

Clifford

Czapla²,

Richards³

et al. 1998

Br J Cancer

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Hepatocyte growth factor (HGF/SF) is a potent renal proximal tubular cell (PTEC) mitogen involved in renal development. HGF/SF is the functional ligand for the c-met proto-oncogene, and germline c-met mutations are associated with familial papillary renal cell carcinoma. Somatic von Hippel-Lindau disease tumour-suppressor gene (VHL) mutations are frequently detected in sporadic clear cell renal cell carcinomas (RCC), and germline VHL mutations are the commonest cause of familial clear cell RCC. pVHL binds to the positive regulatory components of the trimeric elongin (SIII) complex (elongins B and C) and has been observed to deregulate expression of the vascular endothelial growth factor (VEGF) gene. HGF/SF has similarly been reported to up-regulate expression of the VEGF gene in non-renal experimental systems. To investigate the mechanism of HGF/SF action in PTECs and, specifically, to examine potential interactions between the HGF/c-met and the VHL-mediated pathways for renal tubular growth control, we have isolated untransformed PTECs from normal kidneys, developed conditions for their culture in vitro and used these cells to investigate changes in mRNA levels of the VHL, elongin A, B and C, VEGF, c-myc, c-fos and c-met genes after HGF/SF exposure. Significant elevations in the mRNA levels of VEGF, c-myc, c-fos, c-met and elongins A, B and C, but not VHL, were detected after HGF/SF stimulation of human PTECs (P < 0.02), with a consistent order of peak levels observed over successive replicates (c-fos at 1 h, VEGF at 2-4 h, c-myc, at 4 h, followed by c-met and all three elongin subunits at 8 h). This study highlights the spectrum of changes in gene expression observed in PTECs after HGF/SF stimulation and has identified possible candidate mediators of the HGF/SF-induced mitogenic response. Our evidence would suggest that the changes in PTEC VEGF expression induced by HGF/SF are mediated by a VHL-independent pathway. Images Figure 1

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“…Upon activation by heat shock, Pol II is able to rapidly transcribe these genes. Regulation of Pol II activity after recruitment has also been described in bacteria 23 , yeast 13 and mammalian cell lines 3,[6][7][8][9][10][11][12] , and includes instances where Pol II is found in an inactive pre-initiation complex 24,25 . We will collectively refer to inactive Pol II near the transcription start site as stalled Pol II.…”

mentioning

confidence: 95%

RNA polymerase stalling at developmental control genes in the Drosophila melanogaster embryo

et al. 2007

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It is widely assumed that the key rate-limiting step in gene activation is the recruitment of RNA polymerase II (Pol II) to the core promoter 2 . Although there are well-documented examples where Pol II is recruited to a gene but stalls3 -14, a general role for Pol II stalling in development has not been established. We have performed comprehensive Pol II ChIP-chip assays in Drosophila embryos and identified three distinct Pol II binding behaviors: active (uniform binding across the entire transcription unit), no binding, and stalled (binding at the transcription start site). The striking feature of the ~10% genes that are stalled is that they are highly enriched for developmental control genes that are repressed at the time of analysis or poised for activation during subsequent stages of development. We propose that Pol II stalling facilitates rapid temporal and spatial changes in gene activity during development.Pol II stalling is probably best studied at heat shock genes in Drosophila, where Pol II engages in transcription but pauses immediately downstream of the transcriptional start site 3,4,22 . Upon activation by heat shock, Pol II is able to rapidly transcribe these genes. Regulation of Pol II activity after recruitment has also been described in bacteria 23 , yeast 13 and mammalian cell lines 3,[6][7][8][9][10][11][12] , and includes instances where Pol II is found in an inactive pre-initiation complex 24,25 . We will collectively refer to inactive Pol II near the transcription start site as stalled Pol II.To determine at which genes Pol II stalling occurs during development, we analyzed global Pol II occupancy in whole Drosophila embryos. While this is one of the few systems where The results show that many genes known to be repressed in Toll 10b embryos display strikingly high levels of Pol II near the transcription start site (Fig.1A-D). In some cases the prominent Pol II peak is tightly restricted to the promoter region (e.g. at the tup gene in Fig. 1A), while at other genes Pol II is also found at low levels throughout the transcription unit (e.g. the sog and brk genes Fig. 1C,D). This is consistent with previous evidence that some genes such as sog are transiently activated but then repressed at later stages 26 , while other genes such as tup are never activated in Toll 10b mutants 19,20 .The Pol II profile of repressed genes is clearly distinct from those of active genes ( Fig. 1E, F). For example, the Hbr gene, which encodes an FGF receptor specifically expressed in mesodermal precursors ( Fig. 1E), and ribosomal genes such as RpL3 (Fig.1F), show uniformly high levels of Pol II throughout the transcription unit. Furthermore, genes that are silent in the early embryo simply lack Pol II binding altogether ( Fig. 1G, H). Thus, there appears to be three distinct classes of genes: those with Pol II distributed throughout the transcription unit, those genes with preferential enrichment of Pol II at the transcription site, and genes that lack Pol II binding altogether.To further characterize t...

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The block to transcriptional elongation within the human c-myc gene is determined in the promoter-proximal region.

Cited by 249 publications

References 59 publications

Imaging Drosophila gene activation and polymerase pausing in vivo

Imaging Drosophila gene activation and polymerase pausing in vivo

Hepatocyte growth factor-stimulated renal tubular mitogenesis: effects on expression of c-myc, c-fos, c-met, VEGF and the VHL tumour-suppressor and related genes

RNA polymerase stalling at developmental control genes in the Drosophila melanogaster embryo

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