TRANSFAC® and its module TRANSCompel®: transcriptional gene regulation in eukaryotes
V. Matys,Olga V. Kel-Margoulis,Ellen Fricke,Ines Liebich,Sigrid Land,A. Barre-Dirrie,Ingmar Reuter,D. Chekmenev,Mathias Krull,Klaus Hornischer,Nico Voss,Philip Stegmaier,Birgit Lewicki-Potapov,H. Saxel,Alexander E. Kel,Edgar Wingender +15 more
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TLDR
The TRANSFAC® database on transcription factors, their binding sites, nucleotide distribution matrices and regulated genes as well as the complementing database TRANSCompel® on composite elements have been further enhanced on various levels.Abstract:
The TRANSFAC database on transcription factors, their binding sites, nucleotide distribution matrices and regulated genes as well as the complementing database TRANSCompel on composite elements have been further enhanced on various levels. A new web interface with different search options and integrated versions of Match and Patch provides increased functionality for TRANSFAC. The list of databases which are linked to the common GENE table of TRANSFAC and TRANSCompel has been extended by: Ensembl, UniGene, EntrezGene, HumanPSD and TRANSPRO. Standard gene names from HGNC, MGI and RGD, are included for human, mouse and rat genes, respectively. With the help of InterProScan, Pfam, SMART and PROSITE domains are assigned automatically to the protein sequences of the transcription factors. TRANSCompel contains now, in addition to the COMPEL table, a separate table for detailed information on the experimental EVIDENCE on which the composite elements are based. Finally, for TRANSFAC, in respect of data growth, in particular the gain of Drosophila transcription factor binding sites (by courtesy of the Drosophila DNase I footprint database) and of Arabidopsis factors (by courtesy of DATF, Database of Arabidopsis Transcription Factors) has to be stressed. The here described public releases, TRANSFAC 7.0 and TRANSCompel 7.0, are accessible under http://www.gene-regulation.com/pub/databases.html.read more
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Review Article Before It Gets Started: Regulating Translation at the 5 UTR
Patrícia R. Araújo,Kihoon Yoon,Daijin Ko,Andrew D. Smith,Mei Qiao,Uthra Suresh,Suzanne C. Burns,Luiz O. F. Penalva +7 more
TL;DR: Araujo et al. as mentioned in this paper discuss important aspects of 5 UTR-mediated regulation by providing an overview of the characteristics and the function of the mainelements present in this region, like uORF (upstream open reading frame), secondary structures, and RNA binding motifs.
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Brg1 directly regulates Olig2 transcription and is required for oligodendrocyte progenitor cell specification.
S. G. Matsumoto,Fatima Banine,Kerstin Feistel,Scott Foster,Rubing Xing,Jaime Struve,Larry S. Sherman,Larry S. Sherman +7 more
TL;DR: Findings support a model whereby Brg1 promotes neurogenic radial glial progenitor cell specification but is dispensable for neuronal differentiation, and that Brg 1 is necessary for neuroepithelial-to-radial glial cell transition, but not neuronal differentiation.
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Functional annotation of structural ncRNAs within enhancer RNAs in the human genome: implications for human disease.
Chao Ren,Feng Liu,Zhangyi Ouyang,Gaole An,Chenghui Zhao,Jun Shuai,Shuhong Cai,Xiaochen Bo,Wenjie Shu +8 more
TL;DR: A catalogue of eRNAs in a broad range of human cell/tissue types is identified and understanding of e RNAs is extended by demonstrating their multi-omic signatures, and valuable insights are offered into the function ofeRNAs are offered.
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Deciphering the modulation of gene expression by type I and II interferons combining 4sU-tagging, translational arrest and in silico promoter analysis
Mirko Trilling,Nicolás Bellora,Andrzej J. Rutkowski,Miranda de Graaf,Paul Dickinson,Kevin A. Robertson,Olivia Prazeres da Costa,Peter Ghazal,Caroline C. Friedel,M. Mar Albà,Lars Dölken +10 more
TL;DR: In this paper, the authors implemented the combination of high-resolution gene-expression profiling of nascent RNA with translational inhibition of secondary feedback by cycloheximide, which revealed a prominent role of negative feedback mechanisms during the immediate (≤60 min) IFNα response.
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Sorting the nuclear proteome
Denis C. Bauer,Kai Willadsen,Fabian A. Buske,Kim-Anh Lê Cao,Timothy L. Bailey,Graham Dellaire,Mikael Bodén +6 more
TL;DR: This study investigates determinants of associations between eight intra-nuclear compartments and their proteins in heterogeneous genome-wide data and develops a model based on a range of candidate determinants, capable of mapping the intra- nuclear organization of proteins.
References
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TRANSFAC®: transcriptional regulation, from patterns to profiles
V. Matys,Ellen Fricke,Robert Geffers,Ellen Gößling,Martin Haubrock,Reinhard Hehl,Klaus Hornischer,Dagmar Karas,Alexander E. Kel,Olga V. Kel-Margoulis,Dorothee-U. Kloos,Sigrid Land,Birgit Lewicki-Potapov,Holger Michael,Richard Münch,Ingmar Reuter,Stella Rotert,H. Saxel,Maurice Scheer,S. Thiele,Edgar Wingender +20 more
TL;DR: The TRANSFAC database on eukaryotic transcriptional regulation, comprising data on transcription factors, their target genes and regulatory binding sites, has been extended and further developed, both in number of entries and in the scope and structure of the collected data.
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