Functional Identification of the Transcription Start Site and the Core Promoter of the Juvenile Hormone Esterase Gene in Trichoplusia ni

1995 ◽  
Vol 214 (1) ◽  
pp. 286-294 ◽  
Author(s):  
D. Schelling ◽  
G. Jones
Keyword(s):  
Juvenile Hormone ◽  
Transcription Start Site ◽  
Trichoplusia Ni ◽  
Core Promoter ◽  
Start Site ◽  
Functional Identification ◽  
Transcription Start ◽  
Juvenile Hormone Esterase ◽  
The Core ◽  
Esterase Gene

scholarly journals Transcription of the juvenile hormone esterase gene under the control of both an initiator and AT-rich motif

1998 ◽  
Vol 335 (1) ◽  
pp. 79-84 ◽  
Author(s):  
Grace JONES ◽  
Maria MANCZAK ◽  
Douglas SCHELLING ◽  
Helen TURNER ◽  
Davy JONES
Keyword(s):  
Core Promoter ◽  
Tata Box ◽  
Binding Motif ◽  
Start Site ◽  
Wild Type ◽  
Transcription Start ◽  
Juvenile Hormone Esterase ◽  
A Cell ◽  
Esterase Gene ◽  
Wild Type Promoter

The binding of transcription factors to the core promoter of the juvenile hormone esterase gene was functionally characterized using both a cell-free in vitrotranscription functional assay and a cell transfection assay. A core JHE promoter (-61 to +28 bp relative to transcription start site) supported faithful transcription from the in vivo transcription start site. The nuclear extracts from the Sf9 insect cell line that provided transcription from that template also bound to that template as a probe in gel-mobility shift assays. Deletion or transversion of the initiator-binding motif (-1 to +4 bp) abolished detectable transcription either in vitro or in transfected cells. An AT-rich motif (ATATAT; -28 to -23 bp) serves another transcription factor-binding site. Mutation of the AT-rich motif to a canonical TATA-box preserved transcription, while either its deletion or complete transversion abolished or significantly reduced detectable transcriptional activity. These results indicate that, under these conditions, the functional operation of this core promoter approaches that of a composite promoter in which both the TATA- and initiator-binding protein complexes are necessary, even for basal transcription. On the other hand, these debilitating mutations to either the TATA box or initiator motif did not prevent the ability of the corresponding gel-shift competitive probes to compete with the wild-type promoter for binding by the transcription factors. Even a double transversion of both the AT-rich motif and the initiator-binding motif was able to competitively displace the protein complex that bound to the labelled wild-type probe. These data strongly indicate the presence of (an) additional core-promoter-associated transcription factor(s) (that is not the ‘downstream element ’) that contact(s) the AT-binding complex and/or initiator-binding factor with sufficient avidity to remove them from binding to the competing wild-type promoter sequence.

scholarly journals Maneuver at the transcription start site: Mot1p and NC2 navigate TFIID/TBP to specific core promoter elements

Epigenetics ◽  
2009 ◽  
Vol 4 (1) ◽  
pp. 1-4 ◽  
Author(s):  
Zhuo Zhou ◽  
I-Ju Lin ◽  
Russell P. Darst ◽  
Jörg Bungert
Keyword(s):  
Transcription Start Site ◽  
Core Promoter ◽  
Start Site ◽  
Transcription Start ◽  
Promoter Elements

scholarly journals Core Promoter-Dependent TFIIB Conformation and a Role for TFIIB Conformation in Transcription Start Site Selection

2002 ◽  
Vol 22 (19) ◽  
pp. 6697-6705 ◽  
Author(s):  
Jennifer A. Fairley ◽  
Rachel Evans ◽  
Nicola A. Hawkes ◽  
Stefan G. E. Roberts
Keyword(s):  
Transcription Start Site ◽  
Site Selection ◽  
Transcription Initiation ◽  
Core Promoter ◽  
Initiation Site ◽  
Start Site ◽  
Wild Type ◽  
Transcription Start ◽  
General Transcription Factor ◽  
Selection Of

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.

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
Keyword(s):  
Transcription Start Site ◽  
Ovarian Tumor ◽  
Core Promoter ◽  
Regulatory Region ◽  
Start Site ◽  
Loss Of Function ◽  
Transcription Start ◽  
Germline Expression ◽  
Promoter Swapping

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.

scholarly journals Regulation of the juvenile hormone esterase gene by a composite core promoter

2000 ◽  
Vol 346 (1) ◽  
pp. 233-240 ◽  
Author(s):  
Grace JONES ◽  
Yan Xia CHU ◽  
Douglas SCHELLING ◽  
Davy JONES
Keyword(s):  
Juvenile Hormone ◽  
Mutational Analysis ◽  
Core Promoter ◽  
Tata Box ◽  
Transient Transfection Assay ◽  
Core Element ◽  
Juvenile Hormone Esterase ◽  
Transcription In Vitro ◽  
Esterase Gene

Transcription from the core promoter of the juvenile hormone esterase gene (-61 to +28) requires the presence of both an AT-rich motif (TATA box) and an initiator motif for any transcription to occur, when assayed by either transcription in vitro with lepidopteran Sf9 nuclear extracts or by transient-transfection assay in Sf9 cells. Additional gel-shift experiments indicated that at least one additional binding site is essential for transcription to occur. Mutational analysis in the transcription-in vitro and cell-transfection assays demonstrated that a 14-bp region from +13 to +27 relative to the transcription start site is also essential for transcription to occur. Whereas the wild-type core promoter is highly transcriptionally active, inclusion of additional flanking sequences to position -212 reduces that activity approx. 100-fold, and inclusion of the 5ʹ region out to position -500 reduces transcription by 200-fold. The pattern of dependence on both the AT-rich motif and the initiator for detectable transcription, and the high innate activity being repressed by 5ʹ-binding factors, was recapitulated in mosquito C7-10 cells. This study demonstrates that the cellular juvenile hormone esterase gene is organized as a composite core promoter, dependent on both TATA-box and initiator-binding factors, an organization that has been more commonly reported for viral promoters. This highly active composite core promoter is made more complex by the absolute dependence on the presence of a third site shortly downstream from the initiator, which is distinct from the ‘downstream promoter element’ described from some TATA-less genes. The juvenile hormone esterase gene thus appears to be a model of a cellular composite core promoter with a multipartite, indispensible requirement for not just both the TATA box and initiator, but also for at least a third core element as well.

scholarly journals Transcription start site analysis reveals widespread divergent transcription in D. melanogaster and core promoter-encoded enhancer activities

2018 ◽  
Vol 46 (11) ◽  
pp. 5455-5469 ◽  
Author(s):  
Sarah Rennie ◽  
Maria Dalby ◽  
Marta Lloret-Llinares ◽  
Stylianos Bakoulis ◽  
Christian Dalager Vaagensø ◽  
...  
Keyword(s):  
Transcription Start Site ◽  
Core Promoter ◽  
Start Site ◽  
Transcription Start ◽  
Site Analysis ◽  
Divergent Transcription

Role of the Sulfolobus shibatae viral T6 initiator in conferring promoter strength and in influencing transcription start site selection

2006 ◽  
Vol 52 (11) ◽  
pp. 1136-1140 ◽  
Author(s):  
Sohail A Qureshi
Keyword(s):  
Transcription Start Site ◽  
Dna Sequences ◽  
Site Selection ◽  
Core Promoter ◽  
Promoter Strength ◽  
Start Site ◽  
Transcription Start ◽  
Recognition Element ◽  
Sulfolobus Shibatae

Archaeal promoters contain a TATA-box, an adjacent upstream TFB-recognition element (BRE), and a downstream initiator (INR) region from which transcription originates. While the contribution of A-box and BRE to promoter strength is well established, the role of DNA sequences within the INR region and its vicinity on transcription efficiency and start site selection remains unclear. Here, I demonstrate using the strong Sulfolobus shibatae viral T6 promoter that either substitution of its natural sequence from –17 and beyond with plasmid DNA or introduction of point transversion mutations at +3, –2, –4, and –5 positions reduce promoter strength dramatically, whereas +1, –1, and –2 mutations influence the transcription start site. These data therefore reveal that the INR region plays a role as important as the BRE and the A-box in T6 gene transcription. Key words: Archaea, transcription, initiator (INR), Sulfolobus shibatae, core promoter.

scholarly journals Regulation of the juvenile hormone esterase gene by a composite core promoter

2000 ◽  
Vol 346 (1) ◽  
pp. 233 ◽  
Author(s):  
Grace JONES ◽  
Yan Xia CHU ◽  
Douglas SCHELLING ◽  
Davy JONES
Keyword(s):  
Juvenile Hormone ◽  
Core Promoter ◽  
Juvenile Hormone Esterase ◽  
Esterase Gene

scholarly journals Saccharomyces cerevisiae displays a stable transcription start site landscape in multiple conditions

2018 ◽  
Author(s):  
Christoph S. Börlin ◽  
Nevena Cvetesic ◽  
Petter Holland ◽  
David Bergenholm ◽  
Verena Siewers ◽  
...  
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Transcription Start Site ◽  
Environmental Conditions ◽  
Transcription Initiation ◽  
Core Promoter ◽  
Regulatory Region ◽  
Laboratory Strain ◽  
Start Site ◽  
Transcription Start ◽  
Strong Negative Correlation

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.

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