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

AbstractThe recruitment of RNA-Pol-II to the transcription start site (TSS) is an important step in gene regulation in all organisms. Core promoter elements (CPE) are conserved sequence motifs that guide Pol-II to the TSS by interacting with specific transcription factors (TFs). However, only a minority of animal promoters contains CPEs. It is still unknown how Pol-II selects the TSS in their absence. Here we present a comparative analysis of promoters’ sequence composition and chromatin architecture in five eukaryotic model organisms, which shows the presence of common and unique DNA-encoded features used to organize chromatin. Analysis of Pol-II initiation patterns uncovers that, in the absence of certain CPEs, there is a strong correlation between the spread of initiation and the intensity of the 10 bp periodic signal in the nearest downstream nucleosome. Moreover, promoters’ primary and secondary initiation sites show a characteristic 10 bp periodicity in the absence of CPEs. We also show that DNA natural variants in the region immediately downstream the TSS are able to affect both the nucleosome-DNA affinity and Pol-II initiation pattern. These findings support the notion that, in addition to CPEs mediated selection, sequence-induced nucleosome positioning could be a common and conserved mechanismof TSS selection in animals.Author SummaryGene transcription is a complex process that starts with the recruitment and positioning of Pol-II enzyme at the transcription start site (TSS). Specific promoter sequences, known as core promoter elements (CPEs) facilitate this process. Surprisingly, only a fraction of promoters contain them. It is still unknown how Pol-II choses the start site in their absence. Arecently proposed alternative mechanism implicates positioned nucleosomes in the TSS selection. Here, we provide new evidence of the existence of such mechanism with a comparative analysis of promoter’s features across the animal kingdom. We analysed the promoter’s DNA sequence composition in 5 organisms and found conserved and unique consensus sequencesused to organize chromatin in the region of the first nucleosome downstream the TSS (N+1). Moreover, we found that all organisms show a strong correlation between the spread of Pol-II initiation and the strength of the DNA-encoded signal in the N+1 region. A detailed analysis of Pol-II initiation sites reveals also the presence of a 10 bp periodicity that is correlated with the intensity of the DNA signal in the N+1 region. Importantly, we report that genetic variants that alter the DNA-nucleosome affinity in that region alter Pol-II initiation spread as well.

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

Molecular and Cellular Biology ◽

10.1128/mcb.22.19.6697-6705.2002 ◽

2002 ◽

Vol 22 (19) ◽

pp. 6697-6705 ◽

Cited By ~ 24

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.

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

Development ◽

10.1242/dev.128.9.1671 ◽

2001 ◽

Vol 128 (9) ◽

pp. 1671-1686 ◽

Cited By ~ 1

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.

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

Nucleic Acids Research ◽

10.1093/nar/gky244 ◽

2018 ◽

Vol 46 (11) ◽

pp. 5455-5469 ◽

Cited By ~ 21

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

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

Canadian Journal of Microbiology ◽

10.1139/w06-073 ◽

2006 ◽

Vol 52 (11) ◽

pp. 1136-1140 ◽

Cited By ~ 5

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.

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

10.1101/393447 ◽

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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