Structure of transcribing mammalian RNA polymerase II

Bernecky, Carrie; Herzog, Franz; Baumeister, Wolfgang; Plitzko, Jürgen M.; Cramer, Patrick

doi:10.1038/nature16482

Cited by 199 publications

(236 citation statements)

References 56 publications

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“…Since our samples were not cross-linked, heterogeneity (i.e., p53-bound Pol II vs. unbound Pol II) occurred in the data set (see the Materials and Methods). This was consistent with a previous study showing heterogeneity resulting from a mixture of free Pol II and DNA-bound Pol II (Bernecky et al 2016). To help define potential extra density within the assembly, we performed a control 3D analysis of our Pol II preparations lacking p53, generated exactly as in Figure 1A, and further compared it with previously published Pol II structures (Supplemental Fig.…”

Section: Resultssupporting

confidence: 63%

Structural visualization of the p53/RNA polymerase II assembly

et al. 2016

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The master tumor suppressor p53 activates transcription in response to various cellular stresses in part by facilitating recruitment of the transcription machinery to DNA. Recent studies have documented a direct yet poorly characterized interaction between p53 and RNA polymerase II (Pol II). Therefore, we dissected the human p53/Pol II interaction via single-particle cryo-electron microscopy, structural docking, and biochemical analyses. This study reveals that p53 binds Pol II via the Rpb1 and Rpb2 subunits, bridging the DNA-binding cleft of Pol II proximal to the upstream DNA entry site. In addition, the key DNA-binding surface of p53, frequently disrupted in various cancers, remains exposed within the assembly. Furthermore, the p53/Pol II cocomplex displays a closed conformation as defined by the position of the Pol II clamp domain. Notably, the interaction of p53 and Pol II leads to increased Pol II elongation activity. These findings indicate that p53 may structurally regulate DNA-binding functions of Pol II via the clamp domain, thereby providing insights into p53-regulated Pol II transcription.

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Section: Resultssupporting

confidence: 63%

Structural visualization of the p53/RNA polymerase II assembly

et al. 2016

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“…The mammalian transcription machinery assembles into a preinitiation complex (PIC) consisting of general transcription factors such as TFIIB and RNA polymerase II (Pol II) and strand-separated or open DNA (Kostrewa et al 2009;He et al 2013;Sainsbury et al 2015;Bernecky et al 2016;Louder et al 2016). Once Pol II initiates transcription, it then forms a paused complex (PC) 20-60 bp downstream at most genes (Core et al 2008;Adelman and Lis 2012).…”

mentioning

confidence: 99%

Genome-wide uniformity of human ‘open’ pre-initiation complexes

Lai

Pugh

2016

Genome Res.

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Transcription of protein-coding and noncoding DNA occurs pervasively throughout the mammalian genome. Their sites of initiation are generally inferred from transcript 5 ′ ends and are thought to be either locally dispersed or focused. How these two modes of initiation relate is unclear. Here, we apply permanganate treatment and chromatin immunoprecipitation (PIPseq) of initiation factors to identify the precise location of melted DNA separately associated with the preinitiation complex (PIC) and the adjacent paused complex (PC). This approach revealed the two known modes of transcription initiation. However, in contrast to prevailing views, they co-occurred within the same promoter region: initiation originating from a focused PIC, and broad nucleosome-linked initiation. PIP-seq allowed transcriptional orientation of Pol II to be determined, which may be useful near promoters where sufficient sense/anti-sense transcript mapping information is lacking. PIP-seq detected divergently oriented Pol II at both coding and noncoding promoters, as well as at enhancers. Their occupancy levels were not necessarily coupled in the two orientations. DNA sequence and shape analysis of initiation complex sites suggest that both sequence and shape contribute to specificity, but in a context-restricted manner. That is, initiation sites have the locally "best" initiator (INR) sequence and/or shape. These findings reveal a common core to pervasive Pol II initiation throughout the human genome.

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“…During transcription of actively transcribed gene regions in eukaryotic 'open' chromatin the double helix must be unwound by DNA helicases [96] and the strands must be separated to enable access to DNA-dependent RNA polymerases I, II [97,98], and III. This creates intermediate DNA single-strand regions which are prone to chemical structure damage by multiple noxious impacts like reactive oxygen species (ROS) [3] and mutagens [99].…”

Section: Discussionmentioning

confidence: 99%

The Spermine Phosphate-Bound Cyclooctaoxygen Sodium Epigenetic Shell of Euchromatin DNA Is Destroyed by the Epigenetic Poison Glyphosate

Kesel¹,

Struys²,

Cellini³

2017

Preprint

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Oxygen exists in two gaseous and six solid allotropic modifications. An additional allotropic modification of oxygen, the cyclooctaoxygen, was predicted to exist in 1990. The first synthesis and characterization of cyclooctaoxygen as its sodium crown complex, isolated in the form of three cytosine nucleoside hydrochloride complexes, was reported in 2016. Cyclooctaoxygen sodium was synthesized from atmospheric oxygen, or catalase effect-generated oxygen, under catalysis of cytosine nucleosides and either ninhydrin or eukaryotic low-molecular weight RNA. The cationic cyclooctaoxygen sodium complex was shown to bind RNA and DNA, to associate with single-stranded DNA and spermine phosphate, and to be essentially non-toxic to cultured mammalian cells at 0.1-1.0 mM concentration. We postulated that cyclooctaoxygen is formed in most eukaryotic cells from dihydrogen peroxide in a catalase reaction catalysed by cytidine and RNA. A molecular biological model was deduced for a first epigenetic shell of eukaryotic euchromatin. This model incorporates an epigenetic explanation for the interactions of the essential micronutrient selenium (as selenite) with eukaryotic euchromatin. The sperminium phosphate/cyclooctaoxygen sodium complex is calculated to cover the actively transcribed regions (2.6%) of bovine lymphocyte interphase genome. Cyclooctaoxygen seems to be naturally absent in hypoxia-induced highly condensed chromatin, taken as a model for eukaryotic metaphase/anaphase/early telophase mitotic chromatin. We hence propose that the cyclooctaoxygen sodium-bridged spermine phosphate and selenite coverage serves as an epigenetic shell of actively transcribed gene regions in eukaryotic 'open' euchromatin DNA. The total herbicide glyphosate (ROUNDUP) and its metabolite (aminomethyl)phosphonic acid (AMPA) are proved to represent 'epigenetic poisons', since they both selectively destroy the cyclooctaoxygen sodium complex. This definition is of reason, since the destruction of cyclooctaoxygen is sufficient to bring the protection shield of human euchromatin into collateral epigenetic collapse.

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Structure of transcribing mammalian RNA polymerase II

Cited by 199 publications

References 56 publications

Structural visualization of the p53/RNA polymerase II assembly

Structural visualization of the p53/RNA polymerase II assembly

Genome-wide uniformity of human ‘open’ pre-initiation complexes

The Spermine Phosphate-Bound Cyclooctaoxygen Sodium Epigenetic Shell of Euchromatin DNA Is Destroyed by the Epigenetic Poison Glyphosate

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