RNA Polymerase II Accumulation in the Promoter-Proximal Region of the Dihydrofolate Reductase and γ-Actin Genes

Cheng, Chonghui; Sharp, Phillip A.

doi:10.1128/mcb.23.6.1961-1967.2003

Cited by 75 publications

(64 citation statements)

References 37 publications

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“…3). The maximum occupancy of capping factors on c-Myc and GAPDH coincided with the peaks of pol II and Spt5 at the transcription start sites, as previously reported for DHFR 22 , but they were also detected at low levels within the genes (Fig. 3B, D).…”

Section: ′ and 3′ Pol II Pausing With Capping Factors On Multiple Genessupporting

confidence: 86%

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RNA polymerase II pauses and associates with pre-mRNA processing factors at both ends of genes

Glover-Cutter

Kim

Espinosa

et al. 2007

Nat Struct Mol Biol

302

336

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We investigated co-transcriptional recruitment of pre-mRNA processing factors to human genes. Capping factors associate with paused RNA pol II at the 5′ ends of quiescent genes. They also track throughout actively transcribed genes, and accumulate with paused polymerase in the 3′ flanking region. 3′ processing factors CstF and CPSF are maximally recruited 0.5-1.5 kb downstream of poly (A) sites where they coincide with capping factors, Spt5, and Ser2 hyperphosphorylated, paused pol II. 3′ end processing factors also localize at transcription start sites, and this early recruitment is enhanced after polymerase arrest with DRB. These results suggest that promoters may help specify recruitment of 3′ end processing factors. We propose a dual pausing model where elongation arrests near the transcription start site and in the 3′ flank to allow co-transcriptional processing by factors recruited to the pol II ternary complex.

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Section: ′ and 3′ Pol II Pausing With Capping Factors On Multiple Genessupporting

confidence: 86%

“…In support of this idea, pol II pauses at the 5′ end of the DHFR gene, and HCE localizes in the same region 22 . Promoter-proximal pausing is mediated by negative elongation factor (NELF) and DRB sensitivity inducing factor (DSIF) comprising Spt4 and Spt5.…”

Section: Introductionmentioning

confidence: 72%

RNA polymerase II pauses and associates with pre-mRNA processing factors at both ends of genes

Glover-Cutter

Kim

Espinosa

et al. 2007

Nat Struct Mol Biol

302

336

View full text Add to dashboard Cite

show abstract

“…This result was observed for both M-I and M-IV cells, and indicated that Pol II loading on the promoters does not necessarily correlate with transcription. This lack of correlation between Pol II loading and gene transcription has been reported previously (Komarnitsky et al, 2000;Cheng and Sharp, 2003); in fact, the accumulation of paused Pol II in the proximal promoter was suggested to be a common feature of mammalian transcriptional regulation (Cheng and Sharp, 2003). As a control for Pol II ChIP, we examined Pol II binding to the a-actin and b-actin promoters.…”

Section: Direct Target Genes Of Atf3mentioning

confidence: 66%

A potential dichotomous role of ATF3, an adaptive-response gene, in cancer development

2007

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Activating transcription factor 3 (ATF3) is a member of the ATF/cyclic AMP response element-binding family of transcription factors. We present evidence that ATF3 has a dichotomous role in cancer development. By both gain-and loss-of-function approaches, we found that ATF3 enhances apoptosis in the untransformed MCF10A mammary epithelial cells, but protects the aggressive MCF10CA1a cells and enhances its cell motility. Array analyses indicated that ATF3 upregulates the expression of several genes in the tumor necrosis factor pathway in the MCF10A cells but upregulates the expression of several genes implicated in tumor metastasis, including TWIST1, fibronectin (FN)-1, plasminogen activator inhibitor-1, urokinase-type plasminogen activator, caveolin-1 and Slug, in the MCF10CA1a cells. We present evidence that ATF3 binds to the endogenous promoters and regulates the transcription of the TWIST1, FN-1, Snail and Slug genes. Furthermore, conditioned medium experiments indicated that ATF3 has a paracrine/autocrine effect, consistent with its upregulation of genes encoding secreted factors. Finally, ATF3 gene copy number is >2 in B80% of the breast tumors examined (N ¼ 48) and its protein level is elevated in B50% of the tumors. These results provided a correlative argument that it is advantageous for the malignant cancer cells to express ATF3, consistent with its oncogenic roles suggested by the MCF10CA1a cell data.

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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.…”

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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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RNA Polymerase II Accumulation in the Promoter-Proximal Region of the Dihydrofolate Reductase and γ-Actin Genes

Cited by 75 publications

References 37 publications

RNA polymerase II pauses and associates with pre-mRNA processing factors at both ends of genes

RNA polymerase II pauses and associates with pre-mRNA processing factors at both ends of genes

A potential dichotomous role of ATF3, an adaptive-response gene, in cancer development

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

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