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https://www.readbyqxmd.com/read/28920762/measuring-dynamics-of-eukaryotic-transcription-initiation-challenges-insights-and-opportunities
#1
Zhengjian Zhang, Robert Tjian
Transcription of protein-encoding genes in eukaryotic cells is a dynamically coordinated process. Many of the key transcription regulators contain functionally essential intrinsically disordered regions (IDRs), the dynamic nature of which creates extra challenges to traditional biochemical analyses. Recent advances in single-molecule fluorescence imaging technology have enabled direct visualization of these rapid, complex and dynamic molecular interactions in real time.
September 18, 2017: Transcription
https://www.readbyqxmd.com/read/28886303/helicases-as-transcription-termination-factors-different-solutions-for-a-common-problem
#2
Zhong Han, Odil Porrua
Helicases are enzymes that remodel nucleic acids or protein-nucleic acid complexes in an ATP-dependent manner. They are ubiquitous and can play many diverse functions related to the metabolism of nucleic acids. A few helicases from both the prokaryotic and the eukaryotic worlds have the ability to induce transcription termination. Here we discuss how the same biological function is achieved by different helicases with quite divergent structures and mechanisms of action.
September 8, 2017: Transcription
https://www.readbyqxmd.com/read/28886274/the-plant-rna-polymerase-ii-elongation-complex-a-hub-coordinating-transcript-elongation-and-mrna-processing
#3
Marion Grasser, Klaus D Grasser
Characterisation of the Arabidopsis RNA polymerase II (RNAPII) elongation complex revealed an assembly of a conserved set of transcript elongation factors associated with chromatin remodellers, histone modifiers as well as with various pre-mRNA splicing and polyadenylation factors. Therefore, transcribing RNAPII streamlines the processes of mRNA synthesis and processing in plants.
September 8, 2017: Transcription
https://www.readbyqxmd.com/read/28854119/new-tricks-for-an-old-dog-brf2-dependent-rna-polymerase-iii-transcription-in-oxidative-stress-and-cancer
#4
Jerome Gouge, Alessandro Vannini
Here, we discuss the role of Brf2, an RNA Polymerase III core transcription factor, as a master switch of the oxidative stress response. We highlight the interplay of Brf2 with the Nrf2/Keap1 pathway, as well as the role of Brf2 in cancer and other possible regulations.
August 30, 2017: Transcription
https://www.readbyqxmd.com/read/28853995/hinge-action-versus-grip-in-translocation-by-rna-polymerase
#5
Yuri A Nedialkov, Kristopher Opron, Hailey L Caudill, Fadi Assaf, Amanda J Anderson, Robert I Cukier, Guowei Wei, Zachary F Burton
Based on molecular dynamics simulations and functional studies, a conformational mechanism is posited for forward translocation by RNA polymerase (RNAP). In a simulation of a ternary elongation complex, the clamp and downstream cleft were observed to close. Hinges within the bridge helix and trigger loop supported generation of translocation force against the RNA-DNA hybrid resulting in opening of the furthest upstream i-8 RNA-DNA bp, establishing conditions for RNAP sliding. The β flap tip helix and the most N-terminal β' Zn finger engage the RNA, indicating a path of RNA threading out of the exit channel...
August 30, 2017: Transcription
https://www.readbyqxmd.com/read/28853990/sub1-and-rnapii-until-termination-does-them-part
#6
Olga Calvo
Sub1 was initially identified as a coactivator factor with a role during transcription initiation. However, over the last years, many evidences showed that it influences processes downstream during mRNA biogenesis, such as elongation, termination, and RNAPII phosphorylation. The recent discover that Sub1 directly interacts with the RNAPII stalk adds new insights into how it achieves all these tasks.
August 30, 2017: Transcription
https://www.readbyqxmd.com/read/28841365/taf10-and-taf10b-partially-redundant-roles-during-drosophila-melanogaster-morphogenesis
#7
Z Pahi, B N Borsos, B Vedelek, Y V Shidlovskii, S G Georgieva, I M Boros, T Pankotai
Transcription of eukaryotic genes requires the cooperative action of the RNA polymerase complex, the general transcription factors (TFIIB, TFIID, TFIIE, TFIIF and TFIIH) and chromatin modifiers. The TFIID complex contributes to transcriptional activation by several mechanisms and has a subunit with associated histone acetyltransferase (HAT) activity. The histone modifier SAGA complex has both HAT and deubiquitylase (DUB) activities. TFIID and SAGA share several TBP-associated factors (TAFs), but not their HAT subunit...
August 25, 2017: Transcription
https://www.readbyqxmd.com/read/28841355/topological-requirements-of-the-mitochondrial-heavy-strand-promoters
#8
Ornella Zollo, Neal Sondheimer
In vitro studies of mitochondrial transcription often use linear templates that fail to replicate key features of transcription on a circular genome. We developed a plasmid-based system for the analysis of heavy-strand promoters that recapitulates key features of native mtDNA to study topological and protein requirements of promoter activation. The heavy-strand promoters (HSP1 and HSP2) are simultaneously active on a circular template. HSP2 requires supercoiling for maximal activation. Increasing TFAM concentrations suppress HSP2 at levels that result in HSP1 stimulation...
August 25, 2017: Transcription
https://www.readbyqxmd.com/read/28841352/toward-understanding-of-the-mechanisms-of-mediator-function-in-vivo-focus-on-the-preinitiation-complex-assembly
#9
Thomas Eychenne, Michel Werner, Julie Soutourina
Mediator is a multisubunit complex conserved in eukaryotes that plays an essential coregulator role in RNA polymerase (Pol) II transcription. Despite intensive studies of the Mediator complex, the molecular mechanisms of its function in vivo remain to be fully defined. In this review, we will discuss the different aspects of Mediator function starting with its interactions with specific transcription factors, its recruitment to chromatin and how, as a coregulator, it contributes to the assembly of transcription machinery components within the preinitiation complex (PIC) in vivo and beyond the PIC formation...
August 25, 2017: Transcription
https://www.readbyqxmd.com/read/28820318/7sk-small-nuclear-rna-a-multifunctional-transcriptional-regulatory-rna-with-gene-specific-features
#10
Sylvain Egloff, Cécilia Studniarek, Tamás Kiss
The 7SK small nuclear RNA is a multifunctional transcriptional regulatory RNA that controls the nuclear activity of the positive transcription elongation factor b (P-TEFb), specifically targets P-TEFb to the promoter regions of selected protein-coding genes and promotes transcription of RNA polymerase II-specific spliceosomal small nuclear RNA genes.
August 18, 2017: Transcription
https://www.readbyqxmd.com/read/28795863/a-new-era-of-studying-p53-mediated-transcription-activation
#11
Wei-Li Liu, Robert A Coleman, Sameer K Singh
To prevent tumorigenesis, p53 stimulates transcription by facilitating the recruitment of the transcription machinery on target gene promoters. Cryo-Electron Microscopy studies on p53-bound RNA Polymerase II (Pol II) reveal that p53 structurally regulates Pol II to affect its DNA binding and elongation, providing new insights into p53-mediated transcriptional regulation.
August 10, 2017: Transcription
https://www.readbyqxmd.com/read/28795861/lnc00673-errlr01-is-a-prognostic-indicator-of-overall-survival-in-breast-cancer
#12
Ubaidat Abdul-Rahman, Balázs Gyoörffy, Brian D Adams
LncRNAs are novel noncoding RNAs involved in the epigenetic regulation of gene expression by recruiting ribonucleoprotein complexes to specific genomic loci to initiate histone methylation and/or other chromatin modifications. LncRNAs themselves function as tumor suppressors or oncogenes, depending on the gene regulatory networks they govern. We identified lnc00673 (ERRLR01) as a marker of overall survival (OS) in breast cancer patients. Specifically, ERRLR01 levels were elevated in triple-negative breast cancer (TNBC) as compared to Luminal- A, Luminal-B, and HER2 breast cancer subtypes...
August 10, 2017: Transcription
https://www.readbyqxmd.com/read/28792271/is-tfiih-the-new-achilles-heel-of-cancer-cells
#13
Pietro Berico, Frédéric Coin
TFIIH is a ten-subunit complex involved in transcription and DNA repair. It contains several enzymatic activities including a ATP-dependent DNA translocase in XPB and a cyclin-dependent kinase in CDK7. Recently the discovery of several XPB and CDK7 inhibitors with specific impact on the transcriptional addiction of many tumors pinpointed these activities as potential target in cancer chemotherapy. Unexpectedly a basal transcription factor involved in global mRNA expression now emerges a one of the most clinically promising Achilles heels of cancerous cells...
August 9, 2017: Transcription
https://www.readbyqxmd.com/read/28771071/the-rna-polymerase-ii-ctd-orphan-residues-emerging-insights-into-the-functions-of-tyr-1-thr-4-and-ser-7
#14
Nathan M Yurko, James L Manley
The C-terminal domain of the RNA polymerase II largest subunit (CTD) consists of a unique repeated heptad sequence of the consensus Tyr1-Ser2-Pro3-Thr4-Ser5-Pro6-Ser7. An important function of the CTD is to couple transcription with RNA processing reactions that occur during the initiation, elongation and termination phases of transcription. During this transcription cycle, the CTD is subject to extensive modification, primarily phosphorylation, on its non-proline residues. Reversible phosphorylation of Ser2 and Ser5 is well known to play important and general functions during transcription in all eukaryotes...
August 3, 2017: Transcription
https://www.readbyqxmd.com/read/28632998/trna-structure-and-evolution-and-standardization-to-the-three-nucleotide-genetic-code
#15
Daewoo Pak, Robert Root-Bernstein, Zachary F Burton
Cloverleaf tRNA with a 75 nucleotide (nt) core is posited to have evolved from ligation of three 31 nt minihelices followed by symmetric internal deletions of 9 nt within ligated acceptor stems. Statistical tests strongly support the model. Although the tRNA anticodon loop and T loop are homologs, their U-turns have been treated as distinct motifs. An appropriate comparison, however, shows that intercalation of D loop G19 between T loop bases 4 and 5 causes elevation of T loop base 5 and flipping of T loop bases 6 and 7 out of the 7 nt loop...
August 8, 2017: Transcription
https://www.readbyqxmd.com/read/28598255/the-regulatory-role-of-mirnas-on-vdr-in-breast-cancer
#16
Tatyana Singh, Brian D Adams
Triple negative breast cancer (TNBC) has been associated with the lack of three hormone receptors; estrogen receptor (ER), progesterone receptor (PR), and human epidermal growth factor receptor 2 (HER-2). However, a host of other steroid hormone receptors such as vitamin D receptor (VDR) is present in TNBC, and the role of these hormone receptors in breast tumorigenesis is unclear. The levels of microRNAs (miRNAs) are also expressed differently than in normal mammary epithelial cells. miRNAs are regulatory RNAs involved in various cellular functions, mainly gene silencing...
August 8, 2017: Transcription
https://www.readbyqxmd.com/read/28598247/a-long-range-flexible-billboard-model-of-gene-activation
#17
Christopher M Vockley, Ian C McDowell, Antony M D'Ippolito, Timothy E Reddy
Gene regulation is fundamentally important for the coordination of diverse biologic processes including homeostasis and responses to developmental and environmental stimuli. Transcription factor (TF) binding sites are one of the major functional subunits of gene regulation. They are arranged in cis-regulatory modules (CRMs) that can be more active than the sum of their individual effects. Recently, we described a mechanism of glucocorticoid (GC)-induced gene regulation in which the glucocorticoid receptor (GR) binds coordinately to multiple CRMs that are 10s of kilobases apart in the genome...
August 8, 2017: Transcription
https://www.readbyqxmd.com/read/28548879/ras-and-rho-gtpase-regulation-of-pol-ii-transcription-a-shortcut-model-revisited
#18
Zhi-Liang Zheng
Transcriptional control is critical in relaying signals mediated by Ras and Rho family small GTPases to effect gene expression. In the classical model, signaling components such as MAP kinase target sequence-specific transcription factors, which in turn recruit RNA polymerase (Pol) II holoenzyme to the promoter and activate transcription. Findings in recent years have led to the proposal of a shortcut model in which the Mediator components of the Pol II holoenzyme are regulated by signaling pathways. A very recent finding shows that an evolutionarily conserved Rho GTPase signaling pathway can directly modulate the Pol II C-terminal domain (CTD) phosphorylation by inhibiting the CTD phosphatase in yeast and Arabidopsis...
August 8, 2017: Transcription
https://www.readbyqxmd.com/read/28448767/transcriptional-control-of-yeast-ribosome-biogenesis-a-multifaceted-role-for-general-regulatory-factors
#19
Maria Cristina Bosio, Beatrice Fermi, Giorgio Dieci
In Saccharomyces cerevisiae, a group of more than 200 co-regulated genes (Ribi genes) is involved in ribosome biogenesis. This regulon has recently been shown to rely on a small set of transcriptional regulators (mainly Abf1, but also Reb1, Tbf1 and Rap1) previously referred to as general regulatory factors (GRFs) because of their widespread binding and action at many promoters and other specialized genomic regions. Intriguingly, Abf1 binding to Ribi genes is differentially modulated in response to distinct nutrition signaling pathways...
August 8, 2017: Transcription
https://www.readbyqxmd.com/read/28379052/regulation-of-transcription-factors-by-sumoylation
#20
Emanuel Rosonina, Akhi Akhter, Yimo Dou, John Babu, Veroni S Sri Theivakadadcham
Transcription factors (TFs) are among the most frequently detected targets of sumoylation, and effects of the modification have been studied for about 200 individual TFs to date. TF sumoylation is most often associated with reduced target gene expression, which can be mediated by enhanced interactions with corepressors or by interference with protein modifications that promote transcription. However, recent studies show that sumoylation also regulates gene expression by controlling the levels of TFs that are associated with chromatin...
August 8, 2017: Transcription
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