scholarly journals RNA Pol II Length and Disorder Enable Cooperative Scaling of Transcriptional Bursting

2019 ◽  
Author(s):  
Porfirio Quintero-Cadena ◽  
Tineke L. Lenstra ◽  
Paul W. Sternberg
Keyword(s):  
Rna Polymerase Ii ◽  
Transcriptional Activity ◽  
Quantitative Model ◽  
Data Driven ◽  
Rna Seq ◽  
Rna Pol Ii ◽  
Eukaryotic Transcription ◽  
New Perspective ◽  
Transcriptional Bursting ◽  
Promoter Recruitment

AbstractRNA Polymerase II contains a disordered C-terminal domain (CTD) whose length enigmatically correlates with genome size. The CTD is crucial to eukaryotic transcription, yet the functional and evolutionary relevance of this variation remains unclear. Here, we use smFISH, live imaging, and RNA-seq to investigate how CTD length and disorder influence transcription. We find that length modulates the size and frequency of transcriptional bursting. Disorder is highly conserved and mediates CTD-CTD interactions, an ability we show is separable from protein sequence and necessary for efficient transcription. We build a data-driven quantitative model, simulations of which recapitulate experiments and support CTD length promotes initial polymerase recruitment to the promoter but slows down its release from it, and that CTD-CTD interactions enable promoter recruitment of multiple polymerases. Our results reveal how these tunable parameters provide access to a range of transcriptional activity, offering a new perspective for the mechanistic significance of CTD length and disorder in transcription across eukaryotes.

scholarly journals The gammaherpesviral TATA-box-binding protein directly interacts with the CTD of host RNA Pol II to direct late gene transcription

2020 ◽  
Author(s):  
Angelica F. Castañeda ◽  
Allison L. Didychuk ◽  
Robert K. Louder ◽  
Chloe O. McCollum ◽  
Zoe H. Davis ◽  
...  
Keyword(s):  
Rna Polymerase Ii ◽  
Gene Transcription ◽  
Binding Protein ◽  
Tata Box ◽  
Late Gene ◽  
Rna Pol Ii ◽  
Eukaryotic Transcription ◽  
Pol Ii ◽  
Terminal Domain ◽  
Tata Box Binding Protein

ABSTRACTβ- and γ-herpesviruses include the oncogenic human viruses Kaposi’s sarcoma-associated virus (KSHV) and Epstein-Barr virus (EBV), and human cytomegalovirus (HCMV), which is a significant cause of congenital disease. Near the end of their replication cycle, these viruses transcribe their late genes in a manner distinct from host transcription. Late gene transcription requires six virally-encoded proteins, one of which is a functional mimic of host TATA-box-binding protein (TBP) that is also involved in recruitment of RNA polymerase II (Pol II) via unknown mechanisms. Here, we applied biochemical protein interaction studies together with electron microscopy-based imaging of a reconstituted human preinitiation complex to define the mechanism underlying Pol II recruitment. These data revealed that the herpesviral TBP, encoded by ORF24 in KSHV, makes a direct protein-protein contact with the C-terminal domain of host RNA polymerase II (Pol II), which is a unique feature that functionally distinguishes viral from cellular TBP. The interaction is mediated by the N-terminal domain (NTD) of ORF24 through a conserved motif that is shared in its β- and γ-herpesvirus homologs. Thus, these herpesviruses employ an unprecedented strategy in eukaryotic transcription, wherein promoter recognition and polymerase recruitment are facilitated by a single transcriptional activator with functionally distinct domains.SIGNIFICANCE STATEMENTThe β- and γ-herpesviruses mediate their late gene transcription through a set of viral transcriptional activators (vTAs). One of these vTAs, ORF24 in Kaposi’s sarcoma-associated herpesvirus (KSHV), is a mimic of host TATA-box-binding protein (TBP). We demonstrate that the N-terminal domain of ORF24 and its homologs from other β- and γ-herpesviruses directly bind the unstructured C-terminal domain (CTD) of RNA Pol II. This functionally distinguishes the viral TBP mimic from cellular TBP, which does not bind Pol II. Thus, herpesviruses encode a transcription factor that has the dual ability to directly interact with promoter DNA and the polymerase, a property which is unique in eukaryotic transcription and is conceptually akin to prokaryotic transcription factors.

Linking transcription, RNA polymerase II elongation and alternative splicing

2020 ◽  
Vol 477 (16) ◽  
pp. 3091-3104 ◽  
Author(s):  
Luciana E. Giono ◽  
Alberto R. Kornblihtt
Keyword(s):  
Gene Expression ◽  
Alternative Splicing ◽  
Rna Polymerase Ii ◽  
Environmental Changes ◽  
Transcription Elongation ◽  
Single Gene ◽  
Regulation Of Gene Expression ◽  
Regulation Of Transcription ◽  
Stepping Stones ◽  
Eukaryotic Transcription

Gene expression is an intricately regulated process that is at the basis of cell differentiation, the maintenance of cell identity and the cellular responses to environmental changes. Alternative splicing, the process by which multiple functionally distinct transcripts are generated from a single gene, is one of the main mechanisms that contribute to expand the coding capacity of genomes and help explain the level of complexity achieved by higher organisms. Eukaryotic transcription is subject to multiple layers of regulation both intrinsic — such as promoter structure — and dynamic, allowing the cell to respond to internal and external signals. Similarly, alternative splicing choices are affected by all of these aspects, mainly through the regulation of transcription elongation, making it a regulatory knob on a par with the regulation of gene expression levels. This review aims to recapitulate some of the history and stepping-stones that led to the paradigms held today about transcription and splicing regulation, with major focus on transcription elongation and its effect on alternative splicing.

scholarly journals treeclimbR pinpoints the data-dependent resolution of hierarchical hypotheses

2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Ruizhu Huang ◽  
Charlotte Soneson ◽  
Pierre-Luc Germain ◽  
Thomas S.B. Schmidt ◽  
Christian Von Mering ◽  
...  
Keyword(s):  
Single Cell ◽  
Synthetic Data ◽  
Cell Types ◽  
Data Driven ◽  
Rna Seq ◽  
Hierarchical Trees

AbstracttreeclimbR is for analyzing hierarchical trees of entities, such as phylogenies or cell types, at different resolutions. It proposes multiple candidates that capture the latent signal and pinpoints branches or leaves that contain features of interest, in a data-driven way. It outperforms currently available methods on synthetic data, and we highlight the approach on various applications, including microbiome and microRNA surveys as well as single-cell cytometry and RNA-seq datasets. With the emergence of various multi-resolution genomic datasets, treeclimbR provides a thorough inspection on entities across resolutions and gives additional flexibility to uncover biological associations.

scholarly journals Single-nucleus RNA-seq and FISH identify coordinated transcriptional activity in mammalian myofibers

2020 ◽  
Vol 11 (1) ◽  
Author(s):  
Matthieu Dos Santos ◽  
Stéphanie Backer ◽  
Benjamin Saintpierre ◽  
Brigitte Izac ◽  
Muriel Andrieu ◽  
...  
Keyword(s):  
Gene Expression ◽  
Skeletal Muscle ◽  
Transcription Factors ◽  
Neuromuscular Junction ◽  
Heavy Chain ◽  
Transcriptional Activity ◽  
Rna Seq ◽  
Hybrid Fibers ◽  
Adult Mice ◽  
Single Nucleus

Abstract Skeletal muscle fibers are large syncytia but it is currently unknown whether gene expression is coordinately regulated in their numerous nuclei. Here we show by snRNA-seq and snATAC-seq that slow, fast, myotendinous and neuromuscular junction myonuclei each have different transcriptional programs, associated with distinct chromatin states and combinations of transcription factors. In adult mice, identified myofiber types predominantly express either a slow or one of the three fast isoforms of Myosin heavy chain (MYH) proteins, while a small number of hybrid fibers can express more than one MYH. By snRNA-seq and FISH, we show that the majority of myonuclei within a myofiber are synchronized, coordinately expressing only one fast Myh isoform with a preferential panel of muscle-specific genes. Importantly, this coordination of expression occurs early during post-natal development and depends on innervation. These findings highlight a previously undefined mechanism of coordination of gene expression in a syncytium.

scholarly journals N-Terminal Truncated Myb with New Transcriptional Activity Produced Through Use of an Alternative MYB Promoter in Salivary Gland Adenoid Cystic Carcinoma

Cancers ◽  
2019 ◽  
Vol 12 (1) ◽  
pp. 45
Author(s):  
Candace A. Frerich ◽  
Hailey N. Sedam ◽  
Huining Kang ◽  
Yoshitsugu Mitani ◽  
Adel K. El-Naggar ◽  
...  
Keyword(s):  
Salivary Gland ◽  
Adenoid Cystic Carcinoma ◽  
Transcriptional Activity ◽  
Perineural Invasion ◽  
Salivary Gland Tumor ◽  
Rna Seq ◽  
Gland Tumor ◽  
Adenoid Cystic ◽  
Myb Proteins ◽  
Tumor Types

Adenoid cystic carcinoma (ACC) is an aggressive salivary gland tumor that frequently displays perineural invasion and is often associated with translocations or overexpression of the MYB oncogene. Detailed analyses of MYB transcripts from ACC patient samples revealed that ACC tumors utilize an alternative MYB promoter, which is rarely used in normal cells or other tumor types. The alternative promoter transcripts produce N-terminally truncated Myb proteins lacking a highly conserved and phosphorylated domain, which includes the pS11 epitope that is frequently used to detect Myb proteins. In RNA-seq assays, Myb isoforms lacking the N-terminal domain displayed unique transcriptional activities, regulating many genes differently than full-length Myb. Thus, a regulatory pathway unique to ACC activates the alternative MYB promoter, leading to the production of a truncated Myb protein with altered transcriptional activities. This could provide new therapeutic opportunities for ACC patients.

scholarly journals Mechanism of RNA polymerase II stalling by DNA alkylation

2017 ◽  
Vol 114 (46) ◽  
pp. 12172-12177 ◽  
Author(s):  
Stefano Malvezzi ◽  
Lucas Farnung ◽  
Claudia M. N. Aloisi ◽  
Todor Angelov ◽  
Patrick Cramer ◽  
...  
Keyword(s):  
Rna Polymerase ◽  
Rna Polymerase Ii ◽  
Anticancer Agents ◽  
Excision Repair ◽  
Minor Groove ◽  
Dna Alkylation ◽  
Drug Induced ◽  
Rna Pol Ii ◽  
Pol Ii

Several anticancer agents that form DNA adducts in the minor groove interfere with DNA replication and transcription to induce apoptosis. Therapeutic resistance can occur, however, when cells are proficient in the removal of drug-induced damage. Acylfulvenes are a class of experimental anticancer agents with a unique repair profile suggesting their capacity to stall RNA polymerase (Pol) II and trigger transcription-coupled nucleotide excision repair. Here we show how different forms of DNA alkylation impair transcription by RNA Pol II in cells and with the isolated enzyme and unravel a mode of RNA Pol II stalling that is due to alkylation of DNA in the minor groove. We incorporated a model for acylfulvene adducts, the stable 3-deaza-3-methoxynaphtylethyl-adenosine analog (3d-Napht-A), and smaller 3-deaza-adenosine analogs, into DNA oligonucleotides to assess RNA Pol II transcription elongation in vitro. RNA Pol II was strongly blocked by a 3d-Napht-A analog but bypassed smaller analogs. Crystal structure analysis revealed that a DNA base containing 3d-Napht-A can occupy the +1 templating position and impair closing of the trigger loop in the Pol II active center and polymerase translocation into the next template position. These results show how RNA Pol II copes with minor-groove DNA alkylation and establishes a mechanism for drug resistance.

Heat shock-induced alterations in phosphorylation of the largest subunit of RNA polymerase II as revealed by monoclonal antibodies CC-3 and MPM-2

1999 ◽  
Vol 77 (4) ◽  
pp. 367-374 ◽  
Author(s):  
Sébastien B Lavoie ◽  
Alexandra L Albert ◽  
Alain Thibodeau ◽  
Michel Vincent
Keyword(s):  
Heat Shock ◽  
Rna Polymerase ◽  
Rna Polymerase Ii ◽  
Transcriptional Activity ◽  
Phosphorylation Sites ◽  
Stress Genes ◽  
Terminal Domain ◽  
Carboxy Terminal Domain ◽  
Heat Shocks ◽  
Carboxy Terminal

The phosphorylation of the carboxy-terminal domain of the largest subunit of RNA polymerase II plays an important role in the regulation of transcriptional activity and is also implicated in pre-mRNA processing. Different stresses, such as a heat shock, induce a marked alteration in the phosphorylation of this domain. The expression of stress genes by RNA polymerase II, to the detriment of other genes, could be attributable to such modifications of the phosphorylation sites. Using two phosphodependent antibodies recognizing distinct hyperphosphorylated forms of RNA polymerase II largest subunit, we studied the phosphorylation state of the subunit in different species after heat shocks of varying intensities. One of these antibodies, CC-3, preferentially recognizes the carboxy-terminal domain of the largest subunit under normal conditions, but its reactivity is diminished during stress. In contrast, the other antibody used, MPM-2, demonstrated a strong reactivity after a heat shock in most species studied. Therefore, CC-3 and MPM-2 antibodies discriminate between phosphoisomers that may be functionally different. Our results further indicate that the pattern of phosphorylation of RNA polymerase II in most species varies in response to environmental stress.Key words: RNA polymerase II, heat shock, phosphorylation, CC-3, MPM-2.

Pterostilbene, a Bioactive Component of Blueberries, Alleviates Renal Interstitial Fibrosis by Inhibiting Macrophage-Myofibroblast Transition

2020 ◽  
Vol 48 (07) ◽  
pp. 1715-1729
Author(s):  
Yanhuan Feng ◽  
Fan Guo ◽  
Hongxia Mai ◽  
Jing Liu ◽  
Zijing Xia ◽  
...  
Keyword(s):  
Bone Marrow ◽  
Renal Fibrosis ◽  
Transcriptional Activity ◽  
Interstitial Fibrosis ◽  
Unilateral Ureteral Obstruction ◽  
Rna Seq ◽  
Renal Interstitial Fibrosis ◽  
Bioactive Component

Pterostilbene (PTB) is a derivative of resveratrol present in grapes and blueberries. PTB is structurally similar to resveratrol, possessing properties such as being analgesic, anti-aging, antidiabetic, anti-inflammatory, anti-obesity, anti-oxidation, cholesterol-reductive, and neuroprotective. However, there have not been reports on the effect of PTB on macrophage-myofibroblast transition (MMT) induced fibrosis in kidney. In this study, we investigated the antifibrotic effects of PTB on the in vivo mouse unilateral ureteral obstruction (UUO) model and in vitro MMT cells. Kidneys subjected to UUO with PTB treatment were collected for the investigation of PTB mediating MMT derived renal interstitial fibrosis. We conducted kidney RNA-seq transcriptomes and TGF-[Formula: see text]1-induced bone marrow-derived macrophages assays to determine the mechanisms of PTB. We found that PTB treatment suppressed the interstitial fibrosis in UUO mice. PTB also attenuated the number of MMT cells in vivo and in vitro. The transcriptomic analysis showed that CXCL10 may play a central role in the process of PTB-treated renal fibrosis. The siRNA-mediated CXCL10 knockdown decreased the number of MMT cells in TGF-[Formula: see text]1-induced bone marrow-derived macrophages. Our results suggested that PTB attenuated renal interstitial fibrosis by mediating MMT by regulating transcriptional activity of CXCL10.

scholarly journals Human-Centric Data Science for Urban Studies

2019 ◽  
Vol 8 (12) ◽  
pp. 584 ◽  
Author(s):  
Bernd Resch ◽  
Michael Szell
Keyword(s):  
Urban Studies ◽  
Smart City ◽  
Data Science ◽  
City Planning ◽  
Data Driven ◽  
Data Sets ◽  
Use Of Technology ◽  
New Perspective ◽  
Research Initiatives ◽  
Adequate Data

Due to the wide-spread use of disruptive digital technologies like mobile phones, cities have transitioned from data-scarce to data-rich environments. As a result, the field of geoinformatics is being reshaped and challenged to develop adequate data-driven methods. At the same time, the term "smart city" is increasingly being applied in urban planning, reflecting the aims of different stakeholders to create value out of the new data sets. However, many smart city research initiatives are promoting techno-positivistic approaches which do not account enough for the citizens’ needs. In this paper, we review the state of quantitative urban studies under this new perspective, and critically discuss the development of smart city programs. We conclude with a call for a new anti-disciplinary, human-centric urban data science, and a well-reflected use of technology and data collection in smart city planning. Finally, we introduce the papers of this special issue which focus on providing a more human-centric view on data-driven urban studies, spanning topics from cycling and wellbeing, to mobility and land use.

scholarly journals Large distances separate coregulated genes in living Drosophila embryos

2019 ◽  
Vol 116 (30) ◽  
pp. 15062-15067 ◽  
Author(s):  
Tyler Heist ◽  
Takashi Fukaya ◽  
Michael Levine
Keyword(s):  
Rna Polymerase Ii ◽  
Transcriptional Activity ◽  
Target Genes ◽  
Reporter Genes ◽  
Transcriptional Enhancers ◽  
Close Proximity ◽  
Resolution Imaging ◽  
In Cis ◽  
Target Promoters ◽  
Drosophila Embryos

Transcriptional enhancers are short segments of DNA that switch genes on and off in response to a variety of cellular signals. Many enhancers map quite far from their target genes, on the order of tens or even hundreds of kilobases. There is extensive evidence that remote enhancers are brought into proximity with their target promoters via long-range looping interactions. However, the exact physical distances of these enhancer–promoter interactions remain uncertain. Here, we employ high-resolution imaging of living Drosophila embryos to visualize the distances separating linked genes that are coregulated by a shared enhancer. Cotransvection assays (linked genes on separate homologs) suggest a surprisingly large distance during transcriptional activity: at least 100–200 nm. Similar distances were observed when a shared enhancer was placed into close proximity with linked reporter genes in cis. These observations are consistent with the occurrence of “transcription hubs,” whereby clusters (or condensates) of multiple RNA polymerase II complexes and associated cofactors are periodically recruited to active promoters. The dynamics of this process might be responsible for rapid fluctuations in the distances separating the transcription of coregulated reporter genes during transvection. We propose that enhancer-promoter communication depends on a combination of classical looping and linking models.

Sign in / Sign up

Export Citation Format

Share Document