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Transcriptional elongation

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https://www.readbyqxmd.com/read/29222445/model-based-genome-wide-determination-of-rna-chain-elongation-rates-in-escherichia-coli
#1
Peter Großmann, Anja Lück, Christoph Kaleta
Dynamics in the process of transcription are often simplified, yet they play an important role in transcript folding, translation into functional protein and DNA supercoiling. While the modulation of the speed of transcription of individual genes and its role in regulation and proper protein folding has been analyzed in depth, the functional relevance of differences in transcription speeds as well as the factors influencing it have not yet been determined on a genome-wide scale. Here we determined transcription speeds for the majority of E...
December 8, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29221437/evolutionary-characterization-and-transcript-profiling-of-%C3%AE-tubulin-genes-in-flax-linum-usitatissimum-l-during-plant-development
#2
Floriana Gavazzi, Gaia Pigna, Luca Braglia, Silvia Gianì, Diego Breviario, Laura Morello
BACKGROUND: Microtubules, polymerized from alpha and beta-tubulin monomers, play a fundamental role in plant morphogenesis, determining the cell division plane, the direction of cell expansion and the deposition of cell wall material. During polarized pollen tube elongation, microtubules serve as tracks for vesicular transport and deposition of proteins/lipids at the tip membrane. Such functions are controlled by cortical microtubule arrays. Aim of this study was to first characterize the flax β-tubulin family by sequence and phylogenetic analysis and to investigate differential expression of β-tubulin genes possibly related to fibre elongation and to flower development...
December 8, 2017: BMC Plant Biology
https://www.readbyqxmd.com/read/29221126/the-clinicopathological-and-prognostic-significances-of-cdc73-expression-in-cancers-a-bioinformatics-analysis
#3
Hua-Chuan Zheng, Bao-Cheng Gong, Shuang Zhao
CDC73 interacts with human PAF1 complex, histone methyltransferase complex and RNA polymerase II for transcription elongation and 3' end processing. Its down-regulated expression was immunohistochemically detected in gastric, colorectal, ovarian and head and neck cancers, and positively correlated with aggressive behaviors and unfavorable prognosis of malignancies. We performed a bioinformatics analysis by using Oncomine, TCGA and KM plotter databases. It was found that CDC73 mRNA was overexpressed in gastric, lung, breast and ovarian cancers, even stratified by histological subtypes (p<0...
November 10, 2017: Oncotarget
https://www.readbyqxmd.com/read/29219750/a-role-for-histone-acetylation-in-regulating-transcription-elongation
#4
Michael C Church, Alastair B Fleming
Recently, we reported that a major function of histone acetylation at the yeast FLO1 gene was to regulate transcription elongation. Here, we discuss possible mechanisms by which histone acetylation might regulate RNA polymerase II processivity, and comment on the contribution to transcription of chromatin remodelling at gene coding regions and promoters.
December 8, 2017: Transcription
https://www.readbyqxmd.com/read/29217648/the-interaction-of-enl-with-paf1-mitigates-polycomb-silencing-and-facilitates-murine-leukemogenesis
#5
Katrin Hetzner, Maria-Paz Garcia-Cuellar, Christian Büttner, Robert K Slany
ENL is a chromatin reader present in complexes stimulating transcriptional elongation. It is fused to MLL in leukemia and missense mutations have been identified in Wilms' tumor and AML. Here we demonstrate that ENL overcomes polycomb silencing through recruitment of PAF1 via the conserved YEATS domain that recognizes acetylated histone H3. PAF1 was responsible for anti-repressive activities of ENL in vitro and it determined the transforming potential of MLL-ENL. MLL-ENL target loci showed supraphysiological PAF1 binding, hyper-ubiquitination of histone H2B and hypomodification with H2AUb resulting in accelerated transcription rates...
December 7, 2017: Blood
https://www.readbyqxmd.com/read/29212533/subtracting-the-sequence-bias-from-partially-digested-mnase-seq-data-reveals-a-general-contribution-of-tfiis-to-nucleosome-positioning
#6
Gabriel Gutiérrez, Gonzalo Millán-Zambrano, Daniel A Medina, Antonio Jordán-Pla, José E Pérez-Ortín, Xenia Peñate, Sebastián Chávez
BACKGROUND: TFIIS stimulates RNA cleavage by RNA polymerase II and promotes the resolution of backtracking events. TFIIS acts in the chromatin context, but its contribution to the chromatin landscape has not yet been investigated. Co-transcriptional chromatin alterations include subtle changes in nucleosome positioning, like those expected to be elicited by TFIIS, which are elusive to detect. The most popular method to map nucleosomes involves intensive chromatin digestion by micrococcal nuclease (MNase)...
December 7, 2017: Epigenetics & Chromatin
https://www.readbyqxmd.com/read/29209639/enhancer-remodeling-regulates-epigenetic-adaptation-and-resistance-to-mek1-2-inhibition-in-triple-negative-breast-cancer
#7
Samantha M Bevill, Jon S Zawistowski, Gary L Johnson
Kinase inhibitors targeting the mitogen/extracellular signal-regulated kinase kinase (MEK)- extracellular signal related kinase (ERK) signaling pathway have limited durability in inhibiting growth of triple-negative breast cancer. We defined genome wide enhancer remodeling following MEK inhibition capable of driving adaptive gene transcription. Targeting positive elongation factor (P-TEFb) transcriptional regulatory complex members can block enhancer remodeling making the response to MEK-ERK inhibition durable...
2017: Molecular & Cellular Oncology
https://www.readbyqxmd.com/read/29208012/pho-dynamically-interacts-with-spt5-to-facilitate-transcriptional-switches-at-the-hsp70-locus
#8
Allwyn Pereira, Renato Paro
BACKGROUND: Numerous target genes of the Polycomb group (PcG) are transiently activated by a stimulus and subsequently repressed. However, mechanisms by which PcG proteins regulate such target genes remain elusive. RESULTS: We employed the heat shock-responsive hsp70 locus in Drosophila to study the chromatin dynamics of PRC1 and its interplay with known regulators of the locus before, during and after heat shock. We detected mutually exclusive binding patterns for HSF and PRC1 at the hsp70 locus...
December 6, 2017: Epigenetics & Chromatin
https://www.readbyqxmd.com/read/29207313/regulation-of-host-pathogen-interactions-via-the-post-transcriptional-csr-rsm-system
#9
REVIEW
Maria Kusmierek, Petra Dersch
A successful colonization of specific hosts requires a rapid and efficient adaptation of the virulence-relevant gene expression program by bacterial pathogens. An important element in this endeavor is the Csr/Rsm system. This multi-component, post-transcriptional control system forms a central hub within complex regulatory networks and coordinately adjusts virulence properties with metabolic and physiological attributes of the pathogen. A key function is elicited by the RNA-binding protein CsrA/RsmA. CsrA/RsmA interacts with numerous target mRNAs, many of which encode crucial virulence factors, and alters their translation, stability or elongation of transcription...
December 2, 2017: Current Opinion in Microbiology
https://www.readbyqxmd.com/read/29203770/the-transcript-cleavage-factor-paralogue-tfs4-is-a-potent-rna-polymerase-inhibitor
#10
Thomas Fouqueau, Fabian Blombach, Ross Hartman, Alan C M Cheung, Mark J Young, Finn Werner
TFIIS-like transcript cleavage factors enhance the processivity and fidelity of archaeal and eukaryotic RNA polymerases. Sulfolobus solfataricus TFS1 functions as a bona fide cleavage factor, while the paralogous TFS4 evolved into a potent RNA polymerase inhibitor. TFS4 destabilises the TBP-TFB-RNAP pre-initiation complex and inhibits transcription initiation and elongation. All inhibitory activities are dependent on three lysine residues at the tip of the C-terminal zinc ribbon of TFS4; the inhibition likely involves an allosteric component and is mitigated by the basal transcription factor TFEα/β...
December 4, 2017: Nature Communications
https://www.readbyqxmd.com/read/29199514/rna-polymerases-iv-and-v-influence-the-3-boundaries-of-polymerase-ii-transcription-units-in-arabidopsis
#11
Anastasia McKinlay, Ram Podicheti, Jered M Wendte, Ross Cocklin, Douglas B Rusch
Nuclear multisubunit RNA polymerases IV and V (Pol IV and Pol V) evolved in plants as specialized forms of Pol II. Their functions are best understood in the context of RNA-directed DNA methylation (RdDM), a process in which Pol IV-dependent 24 nt siRNAs direct the de novo cytosine methylation of regions transcribed by Pol V. Pol V has additional functions, independent of Pol IV and 24 nt siRNA biogenesis, in maintaining the repression of transposons and genomic repeats whose silencing depends on maintenance cytosine methylation...
December 4, 2017: RNA Biology
https://www.readbyqxmd.com/read/29197941/heterogeneous-functional-expression-of-the-sustained-inward-na-current-in-guinea-pig-sinoatrial-node-cells
#12
Futoshi Toyoda, Ding Wei-Guang, Hiroshi Matsuura
The sustained inward Na+ current (I st) identified in the sinoatrial node (SAN) cell has been suggested to play a pivotal role in cardiac pacemaking. However, the composition of cells in the SAN is heterogeneous and cell-to-cell variability in the magnitude of I st remains to be fully characterized. The present study investigated the current density of I st in morphologically different types of pacemaker cells dissociated from guinea pig SAN. I st was preferentially detected in spontaneously active spindle or spider-shaped cells, but was less well expressed in larger-sized elongated spindle-type cells and practically absent in clearly striated atrial-like cells, despite clear expression of the funny current (I f)...
December 3, 2017: Pflügers Archiv: European Journal of Physiology
https://www.readbyqxmd.com/read/29194659/a-stress-associated-protein-atsap13-from-arabidopsis-thaliana-provides-tolerance-to-multiple-abiotic-stresses
#13
Anirudha Dixit, Parul Tomar, Evan Vaine, Hesham Abdullah, Samuel Hazen, Om Parkash Dhankher
Members of Stress Associated Protein (SAP) family in plants have been shown to impart tolerance to multiple abiotic stresses, however, their mode of action in providing tolerance to multiple abiotic stresses is largely unknown. There are 14 SAP genes in Arabidopsis thaliana containing A20, AN1, and Cys2-His2 zinc finger domains. AtSAP13, a member of the SAP family, carries two AN1 zinc finger domains and an additional Cys2-His2 domain. AtSAP13 transcripts showed upregulation in response to Cd, ABA and salt stresses...
November 30, 2017: Plant, Cell & Environment
https://www.readbyqxmd.com/read/29192133/synthetic-transcription-elongation-factors-license-transcription-across-repressive-chromatin
#14
Graham S Erwin, Matthew P Grieshop, Asfa Ali, Jun Qi, Matthew Lawlor, Deepak Kumar, Istaq Ahmad, Anna McNally, Natalia Teider, Katie Worringer, Rajeev Sivasankaran, Deeba N Syed, Asuka Eguchi, Md Ashraf, Justin Jeffery, Mousheng Xu, Paul M C Park, Hasan Mukhtar, Achal K Srivastava, Mohammed Faruq, James E Bradner, Aseem Z Ansari
Releasing a paused RNA polymerase II into productive elongation is tightly-regulated, especially at genes that impact human development and disease. To exert control over this rate-limiting step, we designed sequence-specific synthetic transcription elongation factors (Syn-TEFs). These molecules are composed of programmable DNA-binding ligands flexibly tethered to a small molecule that engages the transcription elongation machinery. By limiting activity to targeted loci, Syn-TEFs convert constituent modules from broad-spectrum inhibitors of transcription into gene-specific stimulators...
November 30, 2017: Science
https://www.readbyqxmd.com/read/29191170/the-arabidopsis-elp3-elo3-and-elp4-elo1-genes-enhance-disease-resistance-in-fragaria-vesca-l
#15
Katchen Julliany P Silva, Asha M Brunings, Juliana A Pereira, Natalia A Peres, Kevin M Folta, Zhonglin Mou
BACKGROUND: Plant immune response is associated with a large-scale transcriptional reprogramming, which is regulated by numerous transcription regulators such as the Elongator complex. Elongator is a multitasking protein complex involved in diverse cellular processes, including histone modification, DNA methylation, and tRNA modification. In recent years, Elongator is emerging as a key regulator of plant immune responses. However, characterization of Elongator's function in plant immunity has been conducted only in the model plant Arabidopsis thaliana...
December 1, 2017: BMC Plant Biology
https://www.readbyqxmd.com/read/29189719/transcriptional-and-hormonal-regulation-of-weeping-trait-in-salix-matsudana
#16
Juanjuan Liu, Yanfei Zeng, Pengcheng Yan, Caiyun He, Jianguo Zhang
Salix matsudana is a large and rapidly-growing tree, with erect or spreading branchlets (upright willow). However, S. matsudana var. pseudomatsudana is one of the varietas, with pendulous branchlets (weeping willow). It has high ornamental value for its graceful pendulous branches. In order to study the molecular basis for this weeping trait, leaves and stems collected at different developmental stages were analyzed using RNA-seq coupled with digital gene expression. Although weeping trees are used worldwide as landscape plants, little is known about the genes that control weeping...
November 30, 2017: Genes
https://www.readbyqxmd.com/read/29187597/emerging-roles-of-transcriptional-enhancers-in-chromatin-looping-and-promoter-proximal-pausing-of-rna-polymerase-ii
#17
Huan Meng, Blaine Bartholomew
Initiation and regulation of transcription by RNA polymerase II (RNAPII) in eukaryotes relies upon the control elements of promoters and enhancers. Promoters and enhancers share common architectures and functions in similar ways. The prevailing view is functional promoters and enhancers can initiate bidirectional transcription. With the acceleration of recent genome-wide studies of regulated transcription, it has become clear that transcriptional enhancers in mammalian genomes are major sources of pervasive non-coding RNA transcription...
November 29, 2017: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/29186682/control-of-gene-expression-in-senescence-through-transcriptional-read-through-of-convergent-protein-coding-genes
#18
Lisa Muniz, Maharshi Krishna Deb, Marion Aguirrebengoa, Sandra Lazorthes, Didier Trouche, Estelle Nicolas
Antisense RNAs are non-coding RNAs that can regulate their corresponding sense RNAs and are generally produced from specific promoters. We uncover here a family of antisense RNAs, named START RNAs, produced during cellular senescence by transcriptional read-through at convergent protein-coding genes. Importantly, START RNAs repress the expression of their corresponding sense RNAs. In proliferative cells, we found that the Pol II elongation rate is limited downstream of TTS at START loci, allowing transcription termination to occur before Pol II reaches the convergent genes, thus preventing antisense RNA production and interference with the expression of the convergent genes...
November 28, 2017: Cell Reports
https://www.readbyqxmd.com/read/29183994/translation-efficiency-is-maintained-at-elevated-temperature-in-e-coli
#19
Gareth J Morgan, David H Burkhardt, Jeffery W Kelly, Evan T Powers
Cellular protein levels are dictated by the balance between gene transcription, mRNA translation and protein degradation, among other factors. Translation requires the interplay of several RNA hybridization processes, which are expected to be temperature sensitive. We used ribosome profiling to monitor translation in E. coli at 30 °C and investigate how this changes after 10-20 minutes of heat shock at 42 °C. Translation efficiencies are robustly maintained after thermal heat shock and after mimicking the heat shock response transcriptional program at 30 °C by overexpressing the heat shock sigma factor encoded by the rpoH gene...
November 28, 2017: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/29180511/functions-of-the-tfiie-related-tandem-winged-helix-domain-of-rpc34-in-rna-polymerase-iii-initiation-and-elongation
#20
Yi-Yu Wei, Hung-Ta Chen
Rpc34 is a subunit of the Rpc82/34/31 subcomplex residing on the DNA-binding cleft of RNA polymerase (pol) III. Rpc34 contains a structurally flexible N-terminal tandem winged-helix (tWH) domain related to the transcription factor TFIIE. While the second WH (WH2) fold of the tWH domain is known to function in DNA melting activity during transcription initiation, the functional role of the WH1 fold is unknown. In this study, we generated a series of new Rpc34 tWH mutants conferring a cold-sensitive growth phenotype...
November 27, 2017: Molecular and Cellular Biology
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