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Atlas of Genetics and Cytogenetics in Oncology and Haematology, 2011
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The Transcription Factor Encyclopedia
Genome Biology, 2012
Here we present the Transcription Factor Encyclopedia (TFe), a new web-based compendium of mini review articles on transcription factors (TFs) that is founded on the principles of open access and collaboration. Our consortium of over 100 researchers has collectively contributed over 130 mini review articles on pertinent human, mouse and rat TFs. Notable features of the TFe website include a high-quality PDF generator and web API for programmatic data retrieval. TFe aims to rapidly educate scientists about the TFs they encounter through the delivery of succinct summaries written and vetted by experts in the field. TFe is available at http://www.cisreg.ca/tfe.
Landscape of transcription in human cells
Nature, 2012
Supplementary Figure S1 Sample Flowchart. The ENCODE transcriptome data are obtained from several cell lines which have been cultured in replicates. They were either left intact (whole cell) and/or fractionated into cytoplasm and nucleus prior to RNA isolation. Total RNA was then isolated and partitioned into RNA ¿ 200bp (long) and ¡ 200bp (short). The long RNA was further partitioned over an oligo-dT column into polyA+ and polyA-fractions. The K562 cell line also underwent additional fractionation into nucleoli, nucleoplasm and chromatin, but no further partition into polyA+ and polyA-was done. RNA-seq was conducted on polyA+, polyA-and total (K562) RNA samples. CAGE was conducted primarily on polyA+ and total RNA but also on some polyA-samples. RNA-PET was conducted on PolyA+ samples only (not shown here are RNA-seq experiments performed at CalTech on polyA+ whole cell RNA extracts).
GTRD: an integrated view of transcription regulation
Nucleic Acids Research, 2020
The Gene Transcription Regulation Database (GTRD; http://gtrd.biouml.org/) contains uniformly annotated and processed NGS data related to gene transcription regulation: ChIP-seq, ChIP-exo, DNase-seq, MNase-seq, ATAC-seq and RNA-seq. With the latest release, the database has reached a new level of data integration. All cell types (cell lines and tissues) presented in the GTRD were arranged into a dictionary and linked with different ontologies (BRENDA, Cell Ontology, Uberon, Cellosaurus and Experimental Factor Ontology) and with related experiments in specialized databases on transcription regulation (FANTOM5, ENCODE and GTEx). The updated version of the GTRD provides an integrated view of transcription regulation through a dedicated web interface with advanced browsing and search capabilities, an integrated genome browser, and table reports by cell types, transcription factors, and genes of interest.
TRANSFAC®: transcriptional regulation, from patterns to profiles
Nucleic acids …, 2003
The TRANSFAC 1 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. Structured fields for expression patterns have been introduced for transcription factors from human and mouse, using the CYTOMER 1 database on anatomical structures and developmental stages. The functionality of Match TM , a tool for matrix-based search of transcription factor binding sites, has been enhanced. For instance, the program now comes along with a number of tissue-(or state-)specific profiles and new profiles can be created and modified with Match TM Profiler. The GENE table was extended and gained in importance, containing amongst others links to LocusLink, RefSeq and OMIM now. Further, (direct) links between factor and target gene on one hand and between gene and encoded factor on the other hand were introduced. The TRANSFAC 1 public release is available at http://www.gene-regulation.com. For yeast an additional release including the latest data was made available separately as TRANSFAC 1 Saccharomyces Module (TSM) at http://transfac. gbf.de. For CYTOMER 1 free download versions are available at http://www.biobase.de:8080/index.html.
Lecture Notes in Computer Science, 1996
Two new databases have been developed to provide the comprehensive research on mechanisms controlling eukaryotic gene expression on the transcription level: TRRD (Transcription Regulatory Region Database) for accumulation of data about structural and functional organisation of gene regulatory regions, and COMPEL -the database on composite regulatory elements that contains contiguous or overlapping binding sites for different transcription factors. Link between TRRD, COMPEL and TRANSFAC through the common table "GENES" has been established. Computer analysis of the transcription regulatory sequences collected in the databases have been carried out by means of SITEVIDEO system. SITEVIDEO offers the following programs: search for significant oligonucleotides in a 15letter code; dinucleotide weight consensus; analysis of DNA conformation parameters.
Transcription factor IIB acetylates itself to regulate transcription
Nature, 2003
Thin-layer chromatography TLC was done on silica gel plates as previously described 17. Acetyl-CoA and CoA were visualized by UV at 254 nm. Deacetylation of acetyl-TFIIB 0.1 nmol of [ 14 C]-acetyl-CoA was incubated with 20 pmol rhTFIIB for 40 min, allowing full acetylation. A 50-fold excess of CoA over initial acetyl-CoA was added and the mixture was incubated for the number of hours shown. The results were visualized by SDS-PAGE and autoradiography. The integrity of rhTFIIB after incubation was verified by western blotting with anti-TFIIB antibodies. Proteolytic determination of acetylation sites The acetylation site was determined by proteolytic digestion and LC-MS/MS analysis. Protein bands were excised from gels and subjected to limited tryptic digestion, followed by nanoscale reverse-phase HPLC separation of the resulting peptides. Peptides were identified after electrospray ionization into a LCQ DECA ion-trap mass spectrometer. For a peptide coverage of 74% of the protein, K238 is the only acetylated lysine residue. Site-specific mutagenesis The construct was mutated using the QuikChange kit (Stratagene) and custom primers (Oligos, Etc.). Mutant constructs were verified by sequencing. Proteins were expressed in Escherichia coli and purified as previously described 12. The presence of TFIIB and its variants was verified by western blot with anti-TFIIB antibodies and a secondary antibodyperoxidase derived coloured reaction. Immunoaffinity capturing TFIIB affinity matrices were prepared as previously described 14. TFIIB and acetyl-TFIIB affinity agarose beads were mixed with highly purified recombinant TFIIB, then with rhTBP or TFIIF (Calbiochem) at ambient temperature. Binding to the TFIIB affinity matrix was monitored by western blotting with mouse monoclonal antibody against TBP (a gift from J. Flint) or rabbit polyclonal antibodies against RAP74 (C-18, Santa Cruz). In vitro transcription assays HeLa nuclear extract was depleted of TFIIB using an affinity matrix with covalently attached polyclonal antibody for hTFIIB. Transcription reactions were assembled with depleted nuclear extract, AdMLP G-less supercoiled DNA template 18 and [ 33 P]-UTP. To substitute for endogenous TFIIB different amounts of highly purified rhTFIIB or K238A were added. Activity was then quantified by autoradiography after SDS-PAGE; the 340nucleotide RNA transcript was generated from AdMLP. Transfection experiments Plasmids were purified using a CsCl gradient after Triton X14 treatment and transfected using Fugene 6 (Roche). Cell cultures were treated with lysis buffer 48 h post-transfection, and the luciferase reporter assay system (Promega Corp.) was used with the AdMLP. A b-galactosidase reporter assay system (Tropix) was used with the RSV and SV40 promoters. Cells received 3 mg total plasmid DNA. Co-transfection of 0.5 mg plasmid containing the luciferase gene in the pGL3-45S RNA promoter-EMCV vector (a gift from T. Moss), which does not require TFIIB for transcription, was used as a control to correct for varying transfection efficiencies. Galactosidase data are normalized to the activity seen with the plasmid promoter vector alone^s.e.m. Transfection experiments were performed in four triplicate sets, with consistent results (s.d.^3%). ChIP assays The amount of TFIIF and flag-TFIIB variants attached to the co-transfected AdMLP in MBP cells was measured by ChIP assay, using a protocol from Upstate Solutions (with slight modifications). The chromatin was not sonicated. T7 and luciferase primers were used for the PCR amplification of the AdMLP fragment.
A code for transcription initiation in mammalian genomes
Genome Research, 2007
Genome-wide detection of transcription start sites (TSSs) has revealed that RNA Polymerase II transcription initiates at millions of positions in mammalian genomes. Most core promoters do not have a single TSS, but an array of closely located TSSs with different rates of initiation. As a rule, genes have more than one such core promoter; however, defining the boundaries between core promoters is not trivial. These discoveries prompt a re-evaluation of our models for transcription initiation. We describe a new framework for understanding the organization of transcription initiation. We show that initiation events are clustered on the chromosomes at multiple scales-clusters within clusters-indicating multiple regulatory processes. Within the smallest of such clusters, which can be interpreted as core promoters, the local DNA sequence predicts the relative transcription start usage of each nucleotide with a remarkable 91% accuracy, implying the existence of a DNA code that determines TSS selection. Conversely, the total expression strength of such clusters is only partially determined by the local DNA sequence. Thus, the overall control of transcription can be understood as a combination of large-and small-scale effects; the selection of transcription start sites is largely governed by the local DNA sequence, whereas the transcriptional activity of a locus is regulated at a different level; it is affected by distal features or events such as enhancers and chromatin remodeling.