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https://read.qxmd.com/read/30696368/identify-gene-expression-pattern-change-at-transcriptional-and-post-transcriptional-levels
#1
Ji-Gang Zhang, Chao Xu, Lan Zhang, Wei Zhu, Hui Shen, Hong-Wen Deng
Gene transcription is regulated with distinct sets of regulatory factors at multiple levels. Transcriptional and post-transcriptional regulation constitute two major regulation modes of gene expression to either activate or repress the initiation of transcription and thereby control the number of proteins synthesized during translation. Disruptions of the proper regulation patterns at transcriptional and post-transcriptional levels are increasingly recognized as causes of human diseases. Consequently, identifying the differential gene expression at transcriptional and post-transcriptional levels respectively is vital to identify potential disease-associated and/or causal genes and understand their roles in the disease development...
January 30, 2019: Transcription
https://read.qxmd.com/read/30663929/balanced-between-order-and-disorder-a-new-phase-in-transcription-elongation-control-and-beyond
#2
Huasong Lu, Rongdiao Liu, Qiang Zhou
We recently reported that the cyclin T1 histidine-rich domain creates a phase-separated environment to promote hyperphosphorylation of RNA polymerase II C-terminal domain and robust transcriptional elongation by P-TEFb. Here, we discuss this and several other recent discoveries to demonstrate that phase separation is important for controlling various aspects of transcription.
January 21, 2019: Transcription
https://read.qxmd.com/read/30585107/regulatory-functions-of-the-mediator-kinases-cdk8-and-cdk19
#3
Charli B Fant, Dylan J Taatjes
The Mediator-associated kinases CDK8 and CDK19 function in the context of three additional proteins: CCNC and MED12, which activate CDK8/CDK19 kinase function, and MED13, which enables their association with the Mediator complex. The Mediator kinases affect RNA polymerase II (pol II) transcription indirectly, through phosphorylation of transcription factors and by controlling Mediator structure and function. In this review, we discuss cellular roles of the Mediator kinases and mechanisms that enable their biological functions...
December 26, 2018: Transcription
https://read.qxmd.com/read/30556762/rna-processing-in-skeletal-muscle-biology-and-disease
#4
Emma R Hinkle, Hannah J Wiedner, Adam J Black, Jimena Giudice
RNA processing encompasses the capping, cleavage, polyadenylation and alternative splicing of pre-mRNA. Proper muscle development relies on precise RNA processing, driven by the coordination between RNA-binding proteins. Recently, skeletal muscle biology has been intensely investigated in terms of RNA processing. High throughput studies paired with deletion of RNA-binding proteins have provided a high-level understanding of the molecular mechanisms controlling the regulation of RNA-processing in skeletal muscle...
December 17, 2018: Transcription
https://read.qxmd.com/read/30488763/cdk7-a-kinase-at-the-core-of-transcription-and-in-the-crosshairs-of-cancer-drug-discovery
#5
Robert P Fisher
The transcription cycle of RNA polymerase II (Pol II) is regulated by a set of cyclin-dependent kinases (CDKs). Cdk7, associated with the transcription initiation factor TFIIH, is both an effector CDK that phosphorylates Pol II and other targets within the transcriptional machinery, and a CDK-activating kinase (CAK) for at least one other essential CDK involved in transcription. Recent studies have illuminated Cdk7 functions that are executed throughout the Pol II transcription cycle, from promoter clearance and promoter-proximal pausing, to co-transcriptional chromatin modification in gene bodies, to mRNA 3'-end formation and termination...
November 29, 2018: Transcription
https://read.qxmd.com/read/30409083/therapeutic-targeting-of-transcriptional-cyclin-dependent-kinases
#6
Matthew D Galbraith, Heather Bender, Joaquín M Espinosa
The fact that many cancer types display transcriptional addiction driven by dysregulation of oncogenic enhancers and transcription factors has led to increased interest in a group of protein kinases, known as transcriptional cyclin dependent kinases (tCDKs), as potential therapeutic targets. Despite early reservations about targeting a process that is essential to healthy cell types, there is now evidence that targeting tCDKs could provide enough therapeutic window to be effective in the clinic. Here, we discuss recent developments in this field, with an emphasis on highly-selective inhibitors and the challenges to be addressed before these inhibitors could be used for therapeutic purposes...
November 9, 2018: Transcription
https://read.qxmd.com/read/30375921/share-and-share-alike-the-role-of-tra1-from-the-saga-and-nua4-coactivator-complexes
#7
Alan C M Cheung, Luis Miguel Díaz-Santín
SAGA and NuA4 are coactivator complexes required for transcription on chromatin. Although they contain different enzymatic and biochemical activities, both contain the large Tra1 subunit. Recent electron microscopy studies have resolved the complete structure of Tra1 and its integration in SAGA/NuA4, providing important insight into Tra1 function.
October 30, 2018: Transcription
https://read.qxmd.com/read/30375919/roles-of-cdks-in-rna-polymerase-ii-transcription-of-the-hiv-1-genome
#8
Andrew P Rice
Studies of RNA Polymerase II (Pol II) transcription of the HIV-1 genome are of clinical interest, as the insight gained may lead to strategies to selectively reactivate latent viruses in patients in whom viral replication is suppressed by antiviral drugs. Such a targeted reactivation may contribute to a functional cure of infection. This review discusses five Cyclin-dependent kinases - CDK7, CDK9, CDK11, CDK2, and CDK8 - involved in transcription and processing of HIV-1 RNA. CDK7 is required for Pol II promoter clearance of reactivated viruses; CDK7 also functions as an activating kinase for CDK9 when resting CD4+ T cells harboring latent HIV-1 are activated...
October 30, 2018: Transcription
https://read.qxmd.com/read/30319007/human-cdk12-and-cdk13-multi-tasking-ctd-kinases-for-the-new-millennium
#9
Arno L Greenleaf
As the new millennium began, CDK12 and CDK13 were discovered as nucleotide sequences that encode protein kinases related to cell cycle CDKs. By the end of the first decade both proteins had been qualified as CTD kinases, and it was emerging that both are heterodimers containing a Cyclin K subunit. Since then, many studies on CDK12 have shown that, through phosphorylating the CTD of transcribing RNAPII, it plays critical roles in several stages of gene expression, notably RNA processing; it is also crucial for maintaining genome stability...
October 14, 2018: Transcription
https://read.qxmd.com/read/30299209/global-role-for-coactivator-complexes-in-rna-polymerase-ii-transcription
#10
Veronique Fischer, Kenny Schumacher, Laszlo Tora, Didier Devys
SAGA and TFIID are related transcription complexes, which were proposed to alternatively deliver TBP at different promoter classes. Recent genome-wide studies in yeast revealed that both complexes are required for the transcription of a vast majority of genes by RNA polymerase II raising new questions about the role of coactivators.
October 9, 2018: Transcription
https://read.qxmd.com/read/30227759/cdk9-a-signaling-hub-for-transcriptional-control
#11
Curtis W Bacon, Iván D'Orso
Cyclin-dependent kinase 9 (CDK9) is critical for RNA Polymerase II (Pol II) transcription initiation, elongation, and termination in several key biological processes including development, differentiation, and cell fate responses. A broad range of diseases are characterized by CDK9 malfunction, illustrating its importance in maintaining transcriptional homeostasis in basal- and signal-regulated conditions. Here we provide a historical recount of CDK9 discovery and the current models suggesting CDK9 is a central hub necessary for proper execution of different steps in the transcription cycle...
September 19, 2018: Transcription
https://read.qxmd.com/read/30205741/molecular-dissection-of-charge-syndrome-highlights-the-vulnerability-of-neural-crest-cells-to-problems-with-alternative-splicing-and-other-transcription-related-processes
#12
Félix-Antoine Bérubé-Simard, Nicolas Pilon
CHARGE syndrome is characterized by co-occurrence of multiple malformations due to abnormal development of neural crest cells. Here, we review the phenotypic and molecular overlap between CHARGE syndrome and similar pathologies, and further discuss the observation that neural crest cells appear especially sensitive to malfunction of the chromatin-transcription-splicing molecular hub.
September 11, 2018: Transcription
https://read.qxmd.com/read/30105929/poor-codon-optimality-as-a-signal-to-degrade-transcripts-with-frameshifts
#13
Miquel Àngel Schikora-Tamarit, Lucas B Carey
Frameshifting errors are common and mRNA quality control pathways, such as nonsense-mediated decay (NMD), exist to degrade these aberrant transcripts. Recent work has shown the existence of a genetic link between NMD and codon-usage mediated mRNA decay. Here we present computational evidence that these pathways are synergic for removing frameshifts.
2018: Transcription
https://read.qxmd.com/read/30063880/r1-retrotransposons-in-the-nucleolar-organizers-of-drosophila-melanogaster-are-transcribed-by-rna-polymerase-i-upon-heat-shock
#14
Himanshu S Raje, Molly E Lieux, Patrick J DiMario
The ribosomal RNA genes (rDNA) of Drosophila melanogaster reside within centromere-proximal nucleolar organizers on both the X and Y chromosomes. Each locus contains between 200-300 tandem repeat rDNA units that encode 18S, 5.8S, 2S, and 28S ribosomal RNAs (rRNAs) necessary for ribosome biogenesis. In arthropods like Drosophila, about 60% of the rDNA genes have R1 and/or R2 retrotransposons inserted at specific sites within their 28S regions; these units likely fail to produce functional 28S rRNA. We showed earlier that R2 expression increases upon nucleolar stress caused by the loss of the ribosome assembly factor, Nucleolar Phosphoprotein of 140 kDa (Nopp140)...
2018: Transcription
https://read.qxmd.com/read/30035655/an-end-in-sight-xrn2-and-transcriptional-termination-by-rna-polymerase-ii
#15
Joshua D Eaton, Steven West
Every transcription cycle ends in termination when RNA polymerase dissociates from the DNA. Although conceptually simple, the mechanism has proven somewhat elusive in eukaryotic systems. Gene-editing and high resolution polymerase mapping now offer clarification of important steps preceding transcriptional termination by RNA polymerase II in human cells.
2018: Transcription
https://read.qxmd.com/read/29929421/transcription-infidelity-and-genome-integrity-the-parallax-view
#16
Alasdair J E Gordon, Priya Sivaramakrishnan, Jennifer A Halliday, Christophe Herman
It was recently shown that removal of GreA, a transcription fidelity factor, enhances DNA break repair. This counterintuitive result, arising from unresolved backtracked RNA polymerase impeding DNA resection and thereby facilitating RecA-loading, leads to an interesting corollary: error-free full-length transcripts and broken chromosomes. Therefore, transcription fidelity may compromise genomic integrity.
2018: Transcription
https://read.qxmd.com/read/29895219/transcription-factors-in-eukaryotic-cells-can-functionally-regulate-gene-expression-by-acting-in-oligomeric-assemblies-formed-from-an-intrinsically-disordered-protein-phase-transition-enabled-by-molecular-crowding
#17
Mark C Leake
High-speed single-molecule fluorescence microscopy in vivo shows that transcription factors in eukaryotes can act in oligomeric clusters mediated by molecular crowding and intrinsically disordered protein. This finding impacts on the longstanding puzzle of how transcription factors find their gene targets so efficiently in the complex, heterogeneous environment of the cell. Abbreviations CDF - cumulative distribution function; FRAP - fluorescence recovery after photobleaching; GFP - Green fluorescent protein; STORM - stochastic optical reconstruction microscopy; TF - Transcription factor; YFP - Yellow fluorescent protein...
2018: Transcription
https://read.qxmd.com/read/29889606/transcriptional-regulation-by-promoters-with-enhancer-function
#18
Lan T M Dao, Salvatore Spicuglia
Promoters with enhancer activity have been described recently. In this point of view, we will discuss current findings highlighting the commonality of this type of regulatory elements, their genetic and epigenetic characteristics, their potential biological roles in the regulation of gene expression and the underlining molecular mechanisms. ABBREVIATIONS: TSS: transcription start site; IFN: interferon; STARR-seq: Self-Transcribing Active Regulatory Region sequencing; MPRA: Massively Parallel Reporter Assay; ChIP: chromatin immunoprecipitation; CRISPR: Clustered Regularly Interspaced Short Palindromic Repeats; lncRNA: long non-coding RNA...
2018: Transcription
https://read.qxmd.com/read/29727262/aminoacyl-trna-synthetase-evolution-and-sectoring-of-the-genetic-code
#19
Daewoo Pak, Yunsoo Kim, Zachary F Burton
The genetic code sectored via tRNA charging errors, and the code progressed toward closure and universality because of evolution of aminoacyl-tRNA synthetase (aaRS) fidelity and translational fidelity mechanisms. Class I and class II aaRS folds are identified as homologs. From sequence alignments, a structurally conserved Zn-binding domain common to class I and class II aaRS was identified. A model for the class I and class II aaRS alternate folding pathways is posited. Five mechanisms toward code closure are highlighted: 1) aaRS proofreading to remove mischarged amino acids from tRNA; 2) accurate aaRS active site specification of amino acid substrates; 3) aaRS-tRNA anticodon recognition; 4) conformational coupling proofreading of the anticodon-codon interaction; and 5) deamination of tRNA wobble adenine to inosine...
2018: Transcription
https://read.qxmd.com/read/29624124/architecture-of-the-rna-polymerase-ii-elongation-complex-new-insights-into-spt4-5-and-elf1
#20
Haruhiko Ehara, Shun-Ichi Sekine
Transcription by RNA polymerase II (Pol II) is accomplished with the aid of numerous accessory factors specific to each transcriptional stage. The structure of the Pol II elongation complex (EC) bound with Spt4/5, Elf1, and TFIIS unveiled the sophisticated basal EC architecture essential for transcription elongation and other transcription-related events.
2018: Transcription
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