Drosophila OVO regulates ovarian tumor transcription by binding unusually near the transcription start site

Development ◽  
2001 ◽  
Vol 128 (9) ◽  
pp. 1671-1686 ◽  
Author(s):  
J. Lu ◽  
B. Oliver

Evolutionarily conserved ovo loci encode developmentally regulated, sequence-specific, DNA-binding, C(2)H(2)-zinc-finger proteins required in the germline and epidermal cells of flies and mice. The direct targets of OVO activity are not known. Genetic experiments suggest that ovo acts in the same regulatory network as ovarian tumor (otu), but the relative position of these genes in the pathway is controversial. Three OVO-binding sites exist in a compact regulatory region that controls germline expression of the otu gene. Interestingly, the strongest OVO-binding site is very near the otu transcription start, where basal transcriptional complexes must function. Loss-of-function, gain-of-function and promoter swapping constructs demonstrate that OVO binding near the transcription start site is required for OVO-dependent otu transcription in vivo. These data unambiguously identify otu as a direct OVO target gene and raise the tantalizing possibility that an OVO site, at the location normally occupied by basal components, functions as part of a specialized core promoter.

2018 ◽  
Author(s):  
Christoph S. Börlin ◽  
Nevena Cvetesic ◽  
Petter Holland ◽  
David Bergenholm ◽  
Verena Siewers ◽  
...  

ABSTRACTOne of the fundamental processes that determine cellular fate is regulation of gene transcription. Understanding these regulatory processes is therefore essential for understanding cellular responses to changes in environmental conditions. At the core promoter, the regulatory region containing the transcription start site (TSS), all inputs regulating transcription are integrated. Here, we used Cap Analysis of Gene Expression (CAGE) to analyze the pattern of transcription start sites at four different environmental conditions (limited in ethanol, limited in nitrogen, limited in glucose and limited in glucose under anaerobic conditions) using the Saccharomyces cerevisiae strain CEN.PK113-7D. With this experimental setup we were able to show that the TSS landscape in yeast is stable at different metabolic states of the cell. We also show that the shape index, a characteristic feature of each TSS describing the spatial distribution of transcription initiation events, has a surprisingly strong negative correlation with the measured expression levels. Our analysis supplies a set of high quality TSS annotations useful for metabolic engineering and synthetic biology approaches in the industrially relevant laboratory strain CEN.PK113-7D, and provides novel insights into yeast TSS dynamics and gene regulation.


2016 ◽  
Vol 113 (21) ◽  
pp. E2899-E2905 ◽  
Author(s):  
Irina O. Vvedenskaya ◽  
Hanif Vahedian-Movahed ◽  
Yuanchao Zhang ◽  
Deanne M. Taylor ◽  
Richard H. Ebright ◽  
...  

During transcription initiation, RNA polymerase (RNAP) holoenzyme unwinds ∼13 bp of promoter DNA, forming an RNAP-promoter open complex (RPo) containing a single-stranded transcription bubble, and selects a template-strand nucleotide to serve as the transcription start site (TSS). In RPo, RNAP core enzyme makes sequence-specific protein–DNA interactions with the downstream part of the nontemplate strand of the transcription bubble (“core recognition element,” CRE). Here, we investigated whether sequence-specific RNAP–CRE interactions affect TSS selection. To do this, we used two next-generation sequencing-based approaches to compare the TSS profile of WT RNAP to that of an RNAP derivative defective in sequence-specific RNAP–CRE interactions. First, using massively systematic transcript end readout, MASTER, we assessed effects of RNAP–CRE interactions on TSS selection in vitro and in vivo for a library of 47 (∼16,000) consensus promoters containing different TSS region sequences, and we observed that the TSS profile of the RNAP derivative defective in RNAP–CRE interactions differed from that of WT RNAP, in a manner that correlated with the presence of consensus CRE sequences in the TSS region. Second, using 5′ merodiploid native-elongating-transcript sequencing, 5′ mNET-seq, we assessed effects of RNAP–CRE interactions at natural promoters in Escherichia coli, and we identified 39 promoters at which RNAP–CRE interactions determine TSS selection. Our findings establish RNAP–CRE interactions are a functional determinant of TSS selection. We propose that RNAP–CRE interactions modulate the position of the downstream end of the transcription bubble in RPo, and thereby modulate TSS selection, which involves transcription bubble expansion or transcription bubble contraction (scrunching or antiscrunching).


2003 ◽  
Vol 185 (20) ◽  
pp. 5993-6004 ◽  
Author(s):  
Anne M. L. Barnard ◽  
Jeffrey Green ◽  
Stephen J. W. Busby

ABSTRACT FNR is an Escherichia coli transcription factor that regulates the transcription of many genes in response to anaerobiosis. We have constructed a series of artificial FNR-dependent promoters, based on the melR promoter, in which a consensus FNR binding site was centered at position −41.5 relative to the transcription start site. A second consensus FNR binding site was introduced at different upstream locations, and promoter activity was assayed in vivo. FNR can activate transcription from these promoters when the upstream FNR binding site is located at many different positions. However, sharp repression is observed when the upstream-bound FNR is located near positions −85 or −95. This repression is relieved by the FNR G74C substitution mutant, previously identified as being defective in transcription repression at the yfiD promoter. A parallel series of artificial FNR-dependent promoters, carrying a consensus FNR binding site at position −61.5 and a second upstream DNA site for FNR, was also constructed. Again, promoter activity was repressed by FNR when the upstream-bound FNR was located at particular positions.


Epigenetics ◽  
2009 ◽  
Vol 4 (1) ◽  
pp. 1-4 ◽  
Author(s):  
Zhuo Zhou ◽  
I-Ju Lin ◽  
Russell P. Darst ◽  
Jörg Bungert

2002 ◽  
Vol 22 (19) ◽  
pp. 6697-6705 ◽  
Author(s):  
Jennifer A. Fairley ◽  
Rachel Evans ◽  
Nicola A. Hawkes ◽  
Stefan G. E. Roberts

ABSTRACT The general transcription factor TFIIB plays a central role in the selection of the transcription initiation site. The mechanisms involved are not clear, however. In this study, we analyze core promoter features that are responsible for the susceptibility to mutations in TFIIB and cause a shift in the transcription start site. We show that TFIIB can modulate both the 5′ and 3′ parameters of transcription start site selection in a manner dependent upon the sequence of the initiator. Mutations in TFIIB that cause aberrant transcription start site selection concentrate in a region that plays a pivotal role in modulating TFIIB conformation. Using epitope-specific antibody probes, we show that a TFIIB mutant that causes aberrant transcription start site selection assembles at the promoter in a conformation different from that for wild-type TFIIB. In addition, we uncover a core promoter-dependent effect on TFIIB conformation and provide evidence for novel sequence-specific TFIIB promoter contacts.


2008 ◽  
Vol 190 (15) ◽  
pp. 5224-5229 ◽  
Author(s):  
Jean Bouvier ◽  
Patrick Stragier ◽  
Violette Morales ◽  
Elisabeth Rémy ◽  
Claude Gutierrez

ABSTRACT The Escherichia coli dapB gene encodes one of the enzymes of the biosynthetic pathway leading to lysine and its immediate precursor, diaminopimelate. Expression of dapB is repressed by lysine, but no trans-acting regulator has been identified so far. Our analysis of the dapB regulatory region shows that sequences located in the −81/−118 interval upstream of the transcription start site are essential for full expression of dapB, as well as for lysine repression. Screening a genomic library for a gene that could alleviate lysine repression when present in multicopy led to the recovery of argP, a gene encoding an activating protein of the LysR-type family, known to use lysine as an effector. An argP null mutation strongly decreases dapB transcription that becomes insensitive to lysine. Purified His6-tagged ArgP protein binds with an apparent K d of 35 nM to the dapB promoter in a gel retardation assay, provided that sequences up to −103 are present. In the presence of l-lysine and l-arginine, the binding of ArgP to dapB is partly relieved. These results fit with a model in which ArgP contributes to enhanced transcription of dapB when lysine becomes limiting.


2019 ◽  
Author(s):  
Edwige Belotti ◽  
Nicolas Lacoste ◽  
Thomas Simonet ◽  
Christophe Papin ◽  
Kiran Padmanabhan ◽  
...  

ABSTRACTThe histone variant H2A.Z is enriched in nucleosomes surrounding the transcription start site of active promoters, suggesting that it might be implicated in transcription. It is also required during mitosis. However, evidences obtained so far mainly rely on correlative evidences obtained in actively dividing cells. We have defined a paradigm in which cell cycle cannot interfere with H2A.Z transcriptional studies by developing an in vivo systems to invalidate H2A.Z in terminally differentiated post-mitotic muscle cells to dissociate its role during transcription from its role during mitosis. ChIP-seq, RNA-seq and ATAC-seq experiments performed on H2A.Z KO post-mitotic muscle cells show that this histone variant is neither required to maintain nor to activate transcription. Altogether, this study provides in vivo evidence that in the absence of mitosis H2A.Z is dispensable for transcription and that the enrichment of H2A.Z on active promoters is rather a marker than an actor of transcriptional activity.


Blood ◽  
2015 ◽  
Vol 126 (23) ◽  
pp. 2437-2437 ◽  
Author(s):  
Kerstin Maria Kampa-Schittenhelm ◽  
Hans-Joerg Buehring ◽  
Michael Bonin ◽  
Wichard Vogel ◽  
Lothar Kanz ◽  
...  

Abstract The O-linked β-N-acetyl glucosamine (O-GlcNAc) transferase (OGT) is a master regulator enzyme adding O-GlcNAc to serine or threonine residues in a multitude of target proteins. Aberrant O-GlcNAc modification is implicated in pathologies of metabolic and neurodegenerative diseases as well as cancers and autoimmunity. We herein provide evidence that dronabinol (FDA approval as Marinol), the natural (−)-Δ9-Tetrahydrocannabinol, is a potent inducer of OGT via epigenetic hypomethylation of the transcription start site -thereby exerting antileukemic activity in acute leukemia in vivo. We have recently shown, that dronabinol, the natural (−)-Δ9-Tetrahydrocannabinol, has growth-inhibiting antitumor efficacy - including acute leukemia. We now reveal a novel mechanism-of-action via epigenetic modulation of OGT, an enzyme linked to genes involved in leukemogenesis such as AKT, MLL5, TET2 or ASXL1, releasing leukemia blasts from differentiation blockage in vivo and sensitizing cells towards induction of apoptosis. gDNA methylation gene arrays using Jurkat leukemia cells revealed global modulation of methylation patterns upon dronabinol treatment. OGT was identified as the highest altered gene (-42%, pval 3,68E-38) - correlating with an increase of OGT protein expression in Western immunoblots. Consistently, hypomethylation of the transcription start site of OGT and induction of OGT protein expression upon dronabinol were confirmed in an independent array using native patient samples. To study whether epigenetic activity is driven via the cannabinoid receptors, Jurkat cells were pretreated with CB1 (LY320135) and/or CB2 (JTE-907) antagonists, and exposed to dronabinol. Importantly, upregulation of OGT protein expression upon dronabinol was suppressed by inhibition of either receptor. Even more, inhibition of CB1 and/or CB2 reduced induction of apoptosis - and was most profound when inhibiting both receptors simultaneously. Similarly, retroviral knockdown of OGT in Jurkat and native leukemia blasts rendered cells less susceptible towards induction of apoptosis. Furthermore, we have evidence, that OGT has lead to release of the differentiation block in leukemia cells in vivo. Supportive treatment with dronabinol of an unfit patient with secondary acute myeloid leukemia resulted in direct disease control: Tantalizingly, besides a proapoptotic effect, the leukemic clone was maturing - with loss of CD34 and upregulation of CD11c, CD14 and CD15. Remarkably, immunophenotypic and genotypic (using NGS) profiling of the predominant monocyte population present two months after start of treatment, revealed that these mature monocytes derived from the leukemia clone (presenting mutations in EZH2 and ASXL1 among others - both known candidate genes of OGT). Mimicking this observation, we treated cells of this and other patients as well as defined leukemia models such as MOLM14 with dronabinol ex vivo and revealed upregulation of differentiation markers, such as CD11c, CD15 or CEBPA by flow cytometry and immunoblots - which was abrogated by lentiviral OGT-interference. Our findings provide a strong rationale for further exploring dronabinol as an agent with remarkable antileukemic efficacy achievable in vivo. In specific, overriding the differentiation blockage in leukemia cells may open up alternative therapeutic approaches similar to promyelocytic leukemia. Disclosures Off Label Use: Marinol: FDA approved for chemotherapy related nausea... here we demonstrate significant anti-leukemic effects.


2018 ◽  
Vol 46 (11) ◽  
pp. 5455-5469 ◽  
Author(s):  
Sarah Rennie ◽  
Maria Dalby ◽  
Marta Lloret-Llinares ◽  
Stylianos Bakoulis ◽  
Christian Dalager Vaagensø ◽  
...  

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