The RNA Polymerase II Core Promoter in <i>Drosophila</i>

Ngoc, Long Vo; Kassavetis, George A.; Kadonaga, James T.

doi:10.1534/genetics.119.302021

Cited by 74 publications

(82 citation statements)

References 100 publications

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“…A comparison of the average base distributions for the TATA promoters ( Supplementary Figure S3B ) with all MaxTSS to MaxTPS promoters indicates that some of the downstream sequence preferences are not as strong for the TATA group (note in particular G at +28/+29). This is consistent with earlier proposals that consensus TATA promoters are less dependent on downstream elements ( 10 , 13 , 16 , 17 ). Interestingly, the gradual rise in GC content with promoter strength does not affect the −30 to −25 region.…”

Section: Resultssupporting

confidence: 93%

A unified view of the sequence and functional organization of the human RNA polymerase II promoter

Luse

Parida

Spector

et al. 2020

Nucleic Acids Research

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To better understand human RNA polymerase II (Pol II) promoters in the context of promoter-proximal pausing and local chromatin organization, 5′ and 3′ ends of nascent capped transcripts and the locations of nearby nucleosomes were accurately identified through sequencing at exceptional depth. High-quality visualization tools revealed a preferred sequence that defines over 177 000 core promoters with strengths varying by >10 000-fold. This sequence signature encompasses and better defines the binding site for TFIID and is surprisingly invariant over a wide range of promoter strength. We identified a sequence motif associated with promoter-proximal pausing and demonstrated that cap methylation only begins once transcripts are about 30 nt long. Mapping also revealed a ∼150 bp periodic downstream sequence element (PDE) following the typical pause location, strongly suggestive of a +1 nucleosome positioning element. A nuclear run-off assay utilizing the unique properties of the DNA fragmentation factor (DFF) coupled with sequencing of DFF protected fragments demonstrated that a +1 nucleosome is present downstream of paused Pol II. Our data more clearly define the human Pol II promoter: a TFIID binding site with built-in downstream information directing ubiquitous promoter-proximal pausing and downstream nucleosome location.

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Section: Resultssupporting

confidence: 93%

A unified view of the sequence and functional organization of the human RNA polymerase II promoter

Luse

Parida

Spector

et al. 2020

Nucleic Acids Research

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“…Thus, in Drosophila , the enhancer–promoter specificity is achieved within a TAD with the use of a compatibility code between enhancers and classes of core promoters [ 251 , 252 ]; special enhancer-bound and promoter-bound architectural proteins that interact with each other [ 253 ]; and tethering elements, which are specific parts of proximal promoters or enhancers and provide for enhancer–promoter communication over great distances (reviewed in [ 254 ]).…”

Section: Global Genome Organization Of Eukaryotes and Enhancer Funmentioning

confidence: 99%

Evolution of Regulated Transcription

Bylino

Ibragimov

Shidlovskii

2020

Cells

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The genomes of all organisms abound with various cis-regulatory elements, which control gene activity. Transcriptional enhancers are a key group of such elements in eukaryotes and are DNA regions that form physical contacts with gene promoters and precisely orchestrate gene expression programs. Here, we follow gradual evolution of this regulatory system and discuss its features in different organisms. In eubacteria, an enhancer-like element is often a single regulatory element, is usually proximal to the core promoter, and is occupied by one or a few activators. Activation of gene expression in archaea is accompanied by the recruitment of an activator to several enhancer-like sites in the upstream promoter region. In eukaryotes, activation of expression is accompanied by the recruitment of activators to multiple enhancers, which may be distant from the core promoter, and the activators act through coactivators. The role of the general DNA architecture in transcription control increases in evolution. As a whole, it can be seen that enhancers of multicellular eukaryotes evolved from the corresponding prototypic enhancer-like regulatory elements with the gradually increasing genome size of organisms.

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“…Conversely, in yeast and other eukaryotes, core promoters with TATA elements can lack stereotypical nucleosome organization and may have nucleosomes positioned over the TATA box in the absence of gene activation. While there have been a number of additional core promoter elements identified in other organisms, especially Drosophila melanogaster [29], we will focus on the distinction provided by presence or absence of TATA-elements.…”

Section: Introductionmentioning

confidence: 99%

Promoter scanning during transcription initiation inSaccharomyces cerevisiae: Pol II in the “shooting gallery”

Qiu

Huang

Vvedenskaya

et al. 2019

Preprint

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34Background 35 The majority of eukaryotic promoters utilize multiple transcription start sites (TSSs). How 36 multiple TSSs are specified at individual promoters across eukaryotes is not understood for 37 most species. In S. cerevisiae, a preinitiation complex comprised of Pol II and conserved 38 general transcription factors (GTFs) assembles and opens DNA upstream of TSSs. Evidence 39 from model promoters indicates that the PIC scans from upstream to downstream to identify 40TSSs. Prior results suggest that TSS distributions at promoters where scanning occurs shift in a 41 polar fashion upon alteration in Pol II catalytic activity or GTF function. 42Results 43 To determine extent of promoter scanning across promoter classes in S. cerevisiae, we 44perturbed Pol II catalytic activity and GTF function and analyzed their effects on TSS usage 45 genome-wide. We find that alterations to Pol II, TFIIB, or TFIIF function widely alter the initiation 46 landscape consistent with promoter scanning operating at all yeast promoters, regardless of 47 promoter class. Promoter architecture, however, can determine extent of promoter sensitivity to 48 altered Pol II activity in ways that are predicted by a scanning model. 49Conclusions 50Our observations coupled with previous data validate this scanning model for Pol II initiation in 51yeast -which we term the "shooting gallery". In this model, Pol II catalytic activity, and the rate 52 and processivity of Pol II scanning together with promoter sequence determine the distribution 53of TSSs and their usage. Comparison of TSS distributions and their relationship to promoter 54 sequence among other eukaryotes suggest some, but not all, share characteristics of S. 55 cerevisiae. 56 57 58 157

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The RNA Polymerase II Core Promoter in Drosophila

Cited by 74 publications

References 100 publications

A unified view of the sequence and functional organization of the human RNA polymerase II promoter

A unified view of the sequence and functional organization of the human RNA polymerase II promoter

Evolution of Regulated Transcription

Promoter scanning during transcription initiation inSaccharomyces cerevisiae: Pol II in the “shooting gallery”

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