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Universality of core promoter elements?

Matthias Siebert, Johannes Söding
2014 Nature  
How cells locate the regions to initiate transcription is an open question, because core promoter elements (CPEs) are found in only a small fraction of core promoters [1] [2] [3] [4] .  ...  We tested the predictive power of the 'core promoter consensus pattern' 5 but found no enrichment around the TFIIB peaks.  ... 
doi:10.1038/nature13587 pmid:25056067 fatcat:ukbfkkrnbffgraj6n42ph4edyi

Nucleotide Resolution Comparison of Transcription of Human Cytomegalovirus and Host Genomes Reveals Universal Use of RNA Polymerase II Elongation Control Driven by Dissimilar Core Promoter Elements

Mrutyunjaya Parida, Kyle A. Nilson, Ming Li, Christopher B. Ball, Harrison A. Fuchs, Christine K. Lawson, Donal S. Luse, Jeffery L. Meier, David H. Price, Thomas Shenk
2019 mBio  
The deep, nucleotide resolution identification of transcription start sites (TSSs) enabled an extensive analysis of core promoter elements.  ...  After a thorough analysis of productive elongation and of core promoter element usage, we found that some mechanisms of regulating transcription are shared between the host and HCMV but that others are  ...  of the deficiency in the PRO-Cap method caused by high levels of viral productive elongation.  ... 
doi:10.1128/mbio.02047-18 pmid:30755505 pmcid:PMC6372792 fatcat:4temnf7bczfcznmmiqcynzqqyy

ElemeNT: a computational tool for detecting core promoter elements

Anna Sloutskin, Yehuda M Danino, Yaron Orenstein, Yonathan Zehavi, Tirza Doniger, Ron Shamir, Tamar Juven-Gershon
2015 Transcription  
Eli Sloutskin for invaluable assistance in ElemeNT development and web execution. We thank Gal Nuta for assisting with optimization of ElemeNT parameters. We thank Dr.  ...  YO was supported by the Edmond J Safra Center for Bioinformatics at Tel-Aviv University and the Israeli Center for Research Excellence (I-CORE), Gene Regulation in Complex Human Disease, center 41/11.  ...  This highlights the importance of the core promoter elements annotation of individual genes, revealing distinct functions associated with a core promoter element.  ... 
doi:10.1080/21541264.2015.1067286 pmid:26226151 pmcid:PMC4581360 fatcat:bmgsh6h43rbxrkunfyhuor6tky

Ni-Silica-based Catalysts for CH4 Reforming by CO2 with Enhanced Stability: Recent Designs and the Impacts of Ni Confinement, Promoters, and Core-Shell Structures

Oscar Daoura, Lebanese University, Laboratoire de Chimie Physique des Matériaux (LCPM/PR2N), Faculté des Sciences II, Campus Fanar, BP 90696 Jdeideh, Lebanon, Maya Boutros, Franck Launay, Sorbonne Université, CNRS, Laboratoire de Réactivité de Surface, LRS, Campus Pierre et Marie Curie, F-75005 Paris, France
2021 Journal of Energy and Power Technology  
CO2 reforming of CH4, also referred to as the Dry Reforming of Methane (DRM), is considered an excellent method to produce H2 and CO (syngas), which are known to be used for the production of higher alkanes  ...  The present review summarizes the progress in the design of Ni/silica-based catalysts for the dry reforming of methane between the years 2015 and 2018.  ...  Another rare-earth element, gadolinium has been tested successfully for the promotion of Ni/ZSM-5 in DRM (Table 2 , entry 23) [82] .  ... 
doi:10.21926/jept.2101007 fatcat:migqn5bb6fbtdfzpr7znuf74v4

Redefining the p53 response element

B. Wang, Z. Xiao, E. C. Ren
2009 Proceedings of the National Academy of Sciences of the United States of America  
Z.X. is supported by a President Graduate Fellowship, National University of Singapore.  ...  The authors note that, due to a printer's error, on page 14652, left column, in line 3 of the abstract and line 8 of the first paragraph, ''dynamic linear filter static nonlinearity Poisson spike encoder  ...  138648; and b Department of Microbiology, Yong Loo Lin School of Medicine, National University of Singapore, MD4, 5 Science Drive 2, Singapore 119260 Edited by Alan Fersht, University of Cambridge, Cambridge  ... 
doi:10.1073/pnas.0903284106 pmid:19597154 pmcid:PMC2709670 fatcat:2dv5eltngfdzxb7bs7sqyxkpxu

An AC-Rich Bean Element Serves as an Ethylene-Responsive Element in Arabidopsis

Chunying Wang, Tingting Lin, Mengqi Wang, Xiaoting Qi
2020 Plants  
Our previous work identified a 19-bp AC-rich element (ACE) in the promoter of bean (Phaseolus vulgaris) metal response element-binding transcription factor 1 (PvMTF-1).  ...  It conferred the minimal promoter to respond to the ethylene stress and inhibition of ethylene. Moreover, the cis-acting element ACE could specifically bind the nuclear proteins in vitro.  ...  We also thank Yan Li and Xudong Shang (Capital Normal University, China) for technical assistance. Conflicts of Interest: The authors declare no conflict of interest. Plants 2020, 9, 1033  ... 
doi:10.3390/plants9081033 pmid:32823972 fatcat:yny63j4ykjalpboz2thtonjska

Core Element Cloning, Cis-Element Mapping and Serum Regulation of the Human EphB4 Promoter: A Novel TATA-Less Inr/MTE/DPE-Like Regulated Gene

Scalia, Williams, Giordano
2019 Genes  
The present study describes the core promoter elements' identification and cloning, the cis-regulatory elements' mapping and the serum regulation of the human EphB4 gene promoter region.  ...  with dispersed regulatory elements characterized by a novel motif-of-ten element (MTE) at positions +18/+28, and a DPE-like motif and a DPE-like-repeated motif (DRM) spanning nt +27/+30 and +32 +35, respectively  ...  Acknowledgments: We thank Carmen Urbich at University of Frankfurt for providing hEphB4 promoter constructs −7/1509 and −7/−1028.  ... 
doi:10.3390/genes10120997 pmid:31810288 pmcid:PMC6947382 fatcat:yv653bfmx5cy7ikosri7rgpcu4

Core element cloning, Cis-element mapping and serum regulation of the human EphB4 promoter: A novel TATA-less Inr/MTE/DPE-like regulated gene

(:Unkn) Unknown, University, My
The present study describes the core promoter elements' identification and cloning, the cis-regulatory elements' mapping and the serum regulation of the human EphB4 gene promoter region.  ...  reporter assay to characterize its regulation by serum and IGF-II using EphB4 promoter deletion constructs with or without the identified new DNA-binding elements.  ...  Acknowledgments: We thank Carmen Urbich at University of Frankfurt for providing hEphB4 promoter constructs −7/1509 and −7/−1028.  ... 
doi:10.34944/dspace/4502 fatcat:wocvb4lkvrfkxnfj4ivo3ehj6u

Functional distinctions between yeast TATA elements

P A Harbury, K Struhl
1989 Molecular and Cellular Biology  
Although the yeast his3 promoter region contains two functional TATA elements, TR and TC, the GCN4 and GAL4 upstream activator proteins stimulate transcription only through TR.  ...  Further analysis of these and other mutations of the TR element led to the following conclusions. First, sequences downstream of the TATAAA sequence are important for TR function.  ...  ACKNOWLEDGMENTS We thank Wei Chen for DNAs, yeast strains, and advice during the early stages of the experiments.  ... 
doi:10.1128/mcb.9.12.5298 pmid:2685558 pmcid:PMC363694 fatcat:7v2xfnbndba6bjj6nkfz44rbbi

Identifying Metadata Elements with URIs

Thomas Baker, Makx Dekkers
2003 D-Lib Magazine  
maintained in the context of IFLA's Universal Bibliographic Control and International MARC Core Activity [UBCIM].  ...  The Uniform Resource Identifier, defined in the IETF RFC 2396 as "a compact string of characters for identifying an abstract or physical resource", has been promoted for use as a universal form of identification  ... 
doi:10.1045/july2003-baker fatcat:dqxpbr2vijezjafknwoph7wtny

Cross Element Evaluation of Insurance Product'S Brand Positioning, Cultural Elements and Client Decision Dilemmas

Gaurav Sahni, Prakash Hemraj Karmadkar
2018 Journal of Advances and Scholarly Researches in Allied Education  
Abstratct -There is an increasing desire for new information, concepts and models of Web client behavior because of the advancement of digital marketing as it turns into a crucial element of client associations  ...  As a number of scientific studies have pinpointed, the important thing to long-term achievement for organization is always to construct client confidence and brand name rank however the second option is  ...  elements.  ... 
doi:10.29070/15/57936 fatcat:ptbybgd4i5fv5onkzxmj6x4hzi

Permutational analysis of Saccharomyces cerevisiae regulatory elements

Namrita Dhillon, Robert Shelansky, Brent Townshend, Miten Jain, Hinrich Boeger, Drew Endy, Rohinton Kamakaka
2020 Synthetic Biology  
Genomic and epigenomic mapping of transcription factors and chromatin factors has led to the delineation of various modular regulatory elements – Enhancers (UAS), core promoters, 5' untranslated regions  ...  We describe a simple and rapid approach to build a combinatorial library of regulatory elements and have used this library to study 26 different enhancers, core promoters, 5'UTRs and transcription terminators  ...  TATA-containing core promoters are labeled in red. Figure 6 .Figure 7 . 67 PCA of pairwise combinations of regulatory elements.  ... 
doi:10.1093/synbio/ysaa007 pmid:32775697 pmcid:PMC7402160 fatcat:jebcio7ruredxpisst27g4wuou

The unexpected traits associated with core promoter elements

Rivka Dikstein
2011 Transcription  
The core promoter of eukaryotic coding and non-coding genes that are transcribed by RNA polymerase II (RNAP II) is composed of DNA elements surrounding the transcription start site.  ...  This review summarizes the current knowledge about core promoter elements and focuses on several unexpected links between core promoter structure and certain gene features.  ...  core promoter elements; the interplay between new core promoter elements and the succeeding stages of gene expression; the association of core promoter elements, other than the TATA-box, and gene features  ... 
doi:10.4161/trns.2.5.17271 pmid:22231114 pmcid:PMC3265775 fatcat:kiuu3ke3wvhtfmzf6r7zqmqhzm

Transcriptional Regulatory Elements in the Human Genome

Glenn A. Maston, Sara K. Evans, Michael R. Green
2006 Annual review of genomics and human genetics (Print)  
Here we review the various classes of transcriptional regulatory elements (core promoters, proximal promoters, distal enhancers, silencers, insulators/boundary elements, and locus control regions) and  ...  Finally, we discuss the methods currently used to identify transcriptional regulatory elements, and the ability of these methods to be scaled up for the purpose of annotating the entire human genome. 29  ...  A statistical analysis of ∼10,000 predicted human promoters revealed that these known core promoter sequence motifs may not be as universal as previously thought (68) .  ... 
doi:10.1146/annurev.genom.7.080505.115623 pmid:16719718 fatcat:22zd77fewbgzpbsyb3vg7sagry

Common Data Elements for Neurological Registries

Janet Warner, Megan Johnston, Lawrence Korngut, Nathalie Jette, Tamara Pringsheim
2013 Canadian Journal of Neurological Sciences  
Core data elements will require a national group of registry leaders and experts to provide oversight and updating of core data elements to ensure validity and relevance over time.  ...  of Calgary, Calgary, Alberta; 2 Institute of Public Health, University of Calgary, Calgary, Alberta.  ... 
doi:10.1017/s0317167100017212 fatcat:fcezckwbkzhfxhbuxrgd2mq2ci
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