scholarly journals Bayesian weighing of electron cryo-microscopy data for integrative structural modeling

2017 ◽  
Author(s):  
Massimiliano Bonomi ◽  
Samuel Hanot ◽  
Charles H. Greenberg ◽  
Andrej Sali ◽  
Michael Nilges ◽  
...  
Keyword(s):  
Rna Polymerase ◽  
Rna Polymerase Ii ◽  
Synthetic Data ◽  
Scoring Function ◽  
Structural Modeling ◽  
List Type ◽  
Sources Of Information ◽  
Macromolecular System ◽  
Microscopy Data

SummaryCryo-electron microscopy (cryo-EM) has become a mainstream technique for determining the structures of complex biological systems. However, accurate integrative structural modeling has been hampered by the challenges in objectively weighing cryo-EM data against other sources of information due to the presence of random and systematic errors, as well as correlations, in the data. To address these challenges, we introduce a Bayesian scoring function that efficiently and accurately ranks alternative structural models of a macromolecular system based on their consistency with a cryo-EM density map and other experimental and prior information. The accuracy of this approach is benchmarked using complexes of known structure and illustrated in three applications: the structural determination of the GroEL/GroES, RNA polymerase II, and exosome complexes. The approach is implemented in the open-source Integrative Modeling Platform (http://integrativemodeling.org), thus enabling integrative structure determination by combining cryo-EM data with other sources of information.HighlightsWe present a modeling approach to integrate cryo-EM data with other sources of informationWe benchmark our approach using synthetic data on 21 complexes of known structureWe apply our approach to the GroEL/GroES, RNA polymerase II, and exosome complexes

Structural Biology of RNA Polymerase II Transcription: 20 Years On

2020 ◽  
Vol 36 (1) ◽  
pp. 1-34 ◽  
Author(s):  
Sara Osman ◽  
Patrick Cramer
Keyword(s):  
Rna Polymerase ◽  
Rna Polymerase Ii ◽  
Transcription Initiation ◽  
Focal Point ◽  
Dna Lesions ◽  
Cellular Regulation ◽  
Pol Ii ◽  
Associated Proteins ◽  
Rna Polymerase Ii Transcription

Gene transcription by RNA polymerase II (Pol II) is the first step in the expression of the eukaryotic genome and a focal point for cellular regulation during development, differentiation, and responses to the environment. Two decades after the determination of the structure of Pol II, the mechanisms of transcription have been elucidated with studies of Pol II complexes with nucleic acids and associated proteins. Here we provide an overview of the nearly 200 available Pol II complex structures and summarize how these structures have elucidated promoter-dependent transcription initiation, promoter-proximal pausing and release of Pol II into active elongation, and the mechanisms that Pol II uses to navigate obstacles such as nucleosomes and DNA lesions. We predict that future studies will focus on how Pol II transcription is interconnected with chromatin transitions, RNA processing, and DNA repair.

scholarly journals Integrator terminates promoter-proximal Pol II to generate C. elegans piRNA precursors

2020 ◽  
Author(s):  
Toni Beltran ◽  
Elena Pahita ◽  
Subhanita Ghosh ◽  
Boris Lenhard ◽  
Peter Sarkies
Keyword(s):  
Catalytic Activity ◽  
Rna Polymerase ◽  
Rna Polymerase Ii ◽  
Transcription Termination ◽  
List Type ◽  
Germline Development ◽  
Pol Ii ◽  
C Elegans

AbstractPiwi-interacting RNAs (piRNAs) play key roles in germline development and genome defence in metazoans. In C. elegans, piRNAs are transcribed from >15000 discrete genomic loci by RNA polymerase II, resulting in 28 nt short-capped piRNA precursors. Here we investigate transcription termination at piRNA loci. We show that the Integrator complex, which terminates snRNA transcription, is recruited to piRNA loci. We show that the catalytic activity of Integrator cleaves nascent capped piRNA precursors associated with promoter-proximal Pol II, resulting in termination of transcription. Loss of Integrator activity, however, does not result in transcriptional readthrough at the majority of piRNA loci. Our results draw new parallels between snRNA and piRNA biogenesis in nematodes, and provide evidence of a role for the Integrator complex as a terminator of promoter-proximal RNA polymerase II.Highlights- Integrator localises to sites of piRNA biogenesis in nematodes- Integrator cleaves nascent RNAs associated with promoter-proximal Pol II at piRNA loci to release short capped piRNA precursors from chromatin- Repression of Pol II elongation at the majority of piRNA loci is independent of Integrator

Out or decay: fate determination of nuclear RNAs

2020 ◽  
Vol 64 (6) ◽  
pp. 895-905 ◽  
Author(s):  
Jianshu Wang ◽  
Hong Cheng
Keyword(s):  
Rna Polymerase ◽  
Rna Polymerase Ii ◽  
Fate Determination ◽  
Biological Relevance ◽  
Nuclear Rna ◽  
Nuclear Degradation ◽  
Processing Steps ◽  
Mammalian System

Abstract In eukaryotes, RNAs newly synthesized by RNA polymerase II (RNAPII) undergo several processing steps prior to transport to the cytoplasm. It has long been known that RNAs with defects in processing or export are removed in the nucleus. Recent studies revealed that RNAs without apparent defects are also subjected to nuclear degradation, indicating that nuclear RNA fate is determined in a more complex and dynamic way than previously thought. Nuclear RNA sorting directly determines the quality and quantity of RNA pools for future translation and thus is of significant importance. In this essay, we will summarize recent studies on this topic, mainly focusing on findings in mammalian system, and discuss about important remaining questions and possible biological relevance for nuclear RNA fate determination.

scholarly journals Extensive 5’-Surveillance Guards Against Non-Canonical NAD-Caps of Nuclear mRNAs in Yeast

2020 ◽  
Author(s):  
Yaqing Zhang ◽  
David Kuster ◽  
Tobias Schmidt ◽  
Daniel Kirrmaier ◽  
Gabriele Nübel ◽  
...  
Keyword(s):  
Rna Polymerase ◽  
Rna Polymerase Ii ◽  
Budding Yeast ◽  
Yeast Cells ◽  
List Type ◽  
Core Motif ◽  
Ribonucleic Acids ◽  
Initiation Step ◽  
Decapping Enzymes

SummaryThe ubiquitous redox coenzyme nicotinamide adenine dinucleotide (NAD) acts as a non-canonical cap structure on prokaryotic and eukaryotic ribonucleic acids. Here we find that in budding yeast, NAD-RNAs are abundant (>1400 species), short (<170 nt), and mostly correspond to mRNA 5’-ends. The modification percentage is low (<5%). NAD is incorporated during the initiation step by RNA polymerase II, which uses distinct promoters with a YAAG core motif for this purpose. Most NAD-RNAs are 3’-truncated. At least three decapping enzymes, Rai1, Dxo1, and Npy1, guard against NAD-RNA at different cellular locations, targeting overlapping transcript populations. NAD-mRNAs do not support translation in vitro. Our work indicates that in budding yeast, most of the NAD incorporation into RNA seems to be accidental and undesirable to the cell, which has evolved a diverse surveillance machinery to prematurely terminate, decap and reject NAD-RNAs.In BriefIn budding yeast, most of the NAD incorporation into RNA seems to be accidental and undesirable to the cell, which has evolved a diverse surveillance machinery to prematurely terminate, decap and reject NAD-RNAs.Graphical AbstractHighlightsYeast cells have thousands of short NAD-RNAs related to the 5’-ends of mRNAsRNA polymerase II prefers a YAAG promoter motif for NAD incorporation into RNANAD-RNA is strongly guarded against by Rai1, Dxo1, and Npy1 decapping enzymes at different subcellular sitesIn vitro, NAD-mRNAs are rejected from translation

scholarly journals Alteration of epigenetic landscape by lamin A mutations: Hallmark of Dilated Cardiomyopathy

2020 ◽  
Author(s):  
Avinanda Banerjee ◽  
Kaushik Sengupta
Keyword(s):  
Rna Polymerase ◽  
Dilated Cardiomyopathy ◽  
Rna Polymerase Ii ◽  
Fibroblast Cell ◽  
C2c12 Cells ◽  
Lamin A ◽  
List Type ◽  
Epigenetic Landscape ◽  
Mutant Proteins ◽  
First Time

AbstractMutations in lamin A have been reported to be associated with over 16 human diseases including dilated cardiomyopathy (DCM). We have focused on three such DCM causing mutants of lamin A which have to address the contribution of lamins in the pathogenesis of DCM at molecular level. We have elucidated the effect of these mutants for the first time on the epigenetic landscape of a myogenic fibroblast cell line C2C12. C2C12 cells expressing these mutant proteins exhibited alterations in some histone modification marks like H3K4me3, H3K9me3, H3K27me3, H3K36me3 and RNA Polymerase II activity compared to its wild type variants. This report paves the way for further studies involving epigenetic regulation in laminopathies which would be an important step in explaining the molecular mechanism and pathophysiology of the diseases like dilated cardiomyopathy.High Lightslamin A K97E mutation predominantly alters H3K9me3 histone modifications landscapelamin A K97E aggregates within nucleus also sequester the HP1γlamin A K97E mutation affects RNA polymerase II distribution pattern

scholarly journals Hyperosmotic stress induces downstream-of-gene transcription and alters the RNA Polymerase II interactome despite widespread transcriptional repression

2020 ◽  
Author(s):  
Nicolle A. Rosa-Mercado ◽  
Joshua T. Zimmer ◽  
Maria Apostolidi ◽  
Jesse Rinehart ◽  
Matthew D. Simon ◽  
...  
Keyword(s):  
Rna Polymerase ◽  
Rna Polymerase Ii ◽  
Transcriptional Repression ◽  
Transcriptional Response ◽  
Hyperosmotic Stress ◽  
Transcriptional Level ◽  
List Type ◽  
Upstream Gene ◽  
Pol Ii ◽  
Transcription Profiles

SummaryStress-induced readthrough transcription results in the synthesis of thousands of downstream-of-gene (DoG) containing transcripts. The mechanisms underlying DoG formation during cellular stress remain unknown. Nascent transcription profiles during DoG induction in human cell lines using TT-TimeLapse-seq revealed that hyperosmotic stress induces widespread transcriptional repression. Yet, DoGs are produced regardless of the transcriptional level of their upstream genes. ChIP-seq confirmed that the stress-induced redistribution of RNA Polymerase (Pol) II correlates with the transcriptional output of genes. Stress-induced alterations in the Pol II interactome are observed by mass spectrometry. While subunits of the cleavage and polyadenylation machinery remained Pol II-associated, Integrator complex subunits dissociated from Pol II under stress conditions. Depleting the catalytic subunit of the Integrator complex, Int11, using siRNAs induces hundreds of readthrough transcripts, whose parental genes partially overlap those of stress-induced DoGs. Our results provide insights into the mechanisms underlying DoG production and how Integrator activity influences DoG transcription.In briefRosa-Mercado et al. report that hyperosmotic stress causes widespread transcriptional repression in human cells, yet DoGs arise regardless of the transcriptional response of their upstream genes. They find that the interaction between Pol II and Integrator is disrupted by hypertonicity and that knocking down the Integrator nuclease leads to DoG production.HighlightsHyperosmotic stress triggers transcriptional repression of many genes.DoG RNAs arise independent of the transcriptional level of their upstream gene.The interaction between Pol II and Integrator subunits decreases after salt stress.Depletion of the Int11 nuclease subunit induces the production of hundreds of DoGs.

scholarly journals Determination of mRNA fate by different RNA polymerase II promoters.

1993 ◽  
Vol 90 (21) ◽  
pp. 10091-10095 ◽  
Author(s):  
J. Enssle ◽  
W. Kugler ◽  
M. W. Hentze ◽  
A. E. Kulozik
Keyword(s):  
Rna Polymerase ◽  
Rna Polymerase Ii ◽  
Mrna Fate

scholarly journals Dual requirement for the yeast MMS19 gene in DNA repair and RNA polymerase II transcription.

1996 ◽  
Vol 16 (12) ◽  
pp. 6783-6793 ◽  
Author(s):  
S Lauder ◽  
M Bankmann ◽  
S N Guzder ◽  
P Sung ◽  
L Prakash ◽  
...  
Keyword(s):  
Dna Repair ◽  
Rna Polymerase ◽  
Rna Polymerase Ii ◽  
Excision Repair ◽  
Regulatory Element ◽  
Pol Ii ◽  
Cellular Processes ◽  
Nucleotide Excision ◽  
Damaged Dna

Genetic and biochemical studies of Saccharomyces cerevisiae have indicated the involvement of a large number of protein factors in nucleotide excision repair (NER) of UV-damaged DNA. However, how MMS19 affects this process has remained unclear. Here, we report on the isolation of the MMS19 gene and the determination of its role in NER and other cellular processes. Genetic and biochemical evidence indicates that besides its function in NER, MMS19 also affects RNA polymerase II (Pol II) transcription. mms19delta cells do not grow at 37 degrees C, and mutant extract exhibits a thermolabile defect in Pol II transcription. Thus, Mms19 protein resembles TFIIH in that it is required for both transcription and DNA repair. However, addition of purified Mms19 protein does not alleviate the transcriptional defect of the mms19delta extract, nor does it stimulate the incision of UV-damaged DNA reconstituted from purified proteins. Interestingly, addition of purified TFIIH corrects the transcriptional defect of the mms19delta extract. Mms19 is, however, not a component of TFIIH or of Pol II holoenzyme. These and other results suggest that Mms19 affects NER and transcription by influencing the activity of TFIIH as an upstream regulatory element. It is proposed that mutations in the human MMS19 counterpart could result in syndromes in which both NER and transcription are affected.

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