Transcription initiation platforms and GTF recruitment at tissue-specific enhancers and promoters. 2011

Frederic Koch, and Romain Fenouil, and Marta Gut, and Pierre Cauchy, and Thomas K Albert, and Joaquin Zacarias-Cabeza, and Salvatore Spicuglia, and Albane Lamy de la Chapelle, and Martin Heidemann, and Corinna Hintermair, and Dirk Eick, and Ivo Gut, and Pierre Ferrier, and Jean-Christophe Andrau
Centre d'Immunologie de Marseille-Luminy, Université Aix-Marseille, Campus de Luminy, Marseille, France.

Recent work has shown that RNA polymerase (Pol) II can be recruited to and transcribe distal regulatory regions. Here we analyzed transcription initiation and elongation through genome-wide localization of Pol II, general transcription factors (GTFs) and active chromatin in developing T cells. We show that Pol II and GTFs are recruited to known T cell-specific enhancers. We extend this observation to many new putative enhancers, a majority of which can be transcribed with or without polyadenylation. Importantly, we also identify genomic features called transcriptional initiation platforms (TIPs) that are characterized by large areas of Pol II and GTF recruitment at promoters, intergenic and intragenic regions. TIPs show variable widths (0.4-10 kb) and correlate with high CpG content and increased tissue specificity at promoters. Finally, we also report differential recruitment of TFIID and other GTFs at promoters and enhancers. Overall, we propose that TIPs represent important new regulatory hallmarks of the genome.

UI MeSH Term Description Entries
D011401 Promoter Regions, Genetic DNA sequences which are recognized (directly or indirectly) and bound by a DNA-dependent RNA polymerase during the initiation of transcription. Highly conserved sequences within the promoter include the Pribnow box in bacteria and the TATA BOX in eukaryotes. rRNA Promoter,Early Promoters, Genetic,Late Promoters, Genetic,Middle Promoters, Genetic,Promoter Regions,Promoter, Genetic,Promotor Regions,Promotor, Genetic,Pseudopromoter, Genetic,Early Promoter, Genetic,Genetic Late Promoter,Genetic Middle Promoters,Genetic Promoter,Genetic Promoter Region,Genetic Promoter Regions,Genetic Promoters,Genetic Promotor,Genetic Promotors,Genetic Pseudopromoter,Genetic Pseudopromoters,Late Promoter, Genetic,Middle Promoter, Genetic,Promoter Region,Promoter Region, Genetic,Promoter, Genetic Early,Promoter, rRNA,Promoters, Genetic,Promoters, Genetic Middle,Promoters, rRNA,Promotor Region,Promotors, Genetic,Pseudopromoters, Genetic,Region, Genetic Promoter,Region, Promoter,Region, Promotor,Regions, Genetic Promoter,Regions, Promoter,Regions, Promotor,rRNA Promoters
D004247 DNA A deoxyribonucleotide polymer that is the primary genetic material of all cells. Eukaryotic and prokaryotic organisms normally contain DNA in a double-stranded state, yet several important biological processes transiently involve single-stranded regions. DNA, which consists of a polysugar-phosphate backbone possessing projections of purines (adenine and guanine) and pyrimidines (thymine and cytosine), forms a double helix that is held together by hydrogen bonds between these purines and pyrimidines (adenine to thymine and guanine to cytosine). DNA, Double-Stranded,Deoxyribonucleic Acid,ds-DNA,DNA, Double Stranded,Double-Stranded DNA,ds DNA
D004742 Enhancer Elements, Genetic Cis-acting DNA sequences which can increase transcription of genes. Enhancers can usually function in either orientation and at various distances from a promoter. Enhancer Elements,Enhancer Sequences,Element, Enhancer,Element, Genetic Enhancer,Elements, Enhancer,Elements, Genetic Enhancer,Enhancer Element,Enhancer Element, Genetic,Enhancer Sequence,Genetic Enhancer Element,Genetic Enhancer Elements,Sequence, Enhancer,Sequences, Enhancer
D000818 Animals Unicellular or multicellular, heterotrophic organisms, that have sensation and the power of voluntary movement. Under the older five kingdom paradigm, Animalia was one of the kingdoms. Under the modern three domain model, Animalia represents one of the many groups in the domain EUKARYOTA. Animal,Metazoa,Animalia
D012319 RNA Polymerase II A DNA-dependent RNA polymerase present in bacterial, plant, and animal cells. It functions in the nucleoplasmic structure and transcribes DNA into RNA. It has different requirements for cations and salt than RNA polymerase I and is strongly inhibited by alpha-amanitin. EC 2.7.7.6. DNA-Dependent RNA Polymerase II,RNA Pol II,RNA Polymerase B,DNA Dependent RNA Polymerase II
D051379 Mice The common name for the genus Mus. Mice, House,Mus,Mus musculus,Mice, Laboratory,Mouse,Mouse, House,Mouse, Laboratory,Mouse, Swiss,Mus domesticus,Mus musculus domesticus,Swiss Mice,House Mice,House Mouse,Laboratory Mice,Laboratory Mouse,Mice, Swiss,Swiss Mouse,domesticus, Mus musculus
D018899 CpG Islands Areas of increased density of the dinucleotide sequence cytosine--phosphate diester--guanine. They form stretches of DNA several hundred to several thousand base pairs long. In humans there are about 45,000 CpG islands, mostly found at the 5' ends of genes. They are unmethylated except for those on the inactive X chromosome and some associated with imprinted genes. CpG Clusters,CpG-Rich Islands,Cluster, CpG,Clusters, CpG,CpG Cluster,CpG Island,CpG Rich Islands,CpG-Rich Island,Island, CpG,Island, CpG-Rich,Islands, CpG,Islands, CpG-Rich
D024363 Transcription Initiation Site The first nucleotide of a transcribed DNA sequence where RNA polymerase (DNA-DIRECTED RNA POLYMERASE) begins synthesizing the RNA transcript. Transcription Start Site,Initiation Site, Transcription,Initiation Sites, Transcription,Site, Transcription Initiation,Site, Transcription Start,Sites, Transcription Initiation,Sites, Transcription Start,Start Site, Transcription,Start Sites, Transcription,Transcription Initiation Sites,Transcription Start Sites
D026723 Polyadenylation The addition of a tail of polyadenylic acid (POLY A) to the 3' end of mRNA (RNA, MESSENGER). Polyadenylation involves recognizing the processing site signal, (AAUAAA), and cleaving of the mRNA to create a 3' OH terminal end to which poly A polymerase (POLYNUCLEOTIDE ADENYLYLTRANSFERASE) adds 60-200 adenylate residues. The 3' end processing of some messenger RNAs, such as histone mRNA, is carried out by a different process that does not include the addition of poly A as described here. Polyadenylations
D035165 Transcription Factors, General Transcription factors that form transcription initiation complexes on DNA, bind to specific DNA-DIRECTED RNA POLYMERASES and are required to initiate transcription. Although their binding may be localized to distinct sequence and structural motifs within the DNA they are considered non-specific with regard to the specific gene being transcribed. General Transcription Factors,General Transcription Initiation Complex Proteins

Related Publications

Frederic Koch, and Romain Fenouil, and Marta Gut, and Pierre Cauchy, and Thomas K Albert, and Joaquin Zacarias-Cabeza, and Salvatore Spicuglia, and Albane Lamy de la Chapelle, and Martin Heidemann, and Corinna Hintermair, and Dirk Eick, and Ivo Gut, and Pierre Ferrier, and Jean-Christophe Andrau
November 2022, Nature structural & molecular biology,
Frederic Koch, and Romain Fenouil, and Marta Gut, and Pierre Cauchy, and Thomas K Albert, and Joaquin Zacarias-Cabeza, and Salvatore Spicuglia, and Albane Lamy de la Chapelle, and Martin Heidemann, and Corinna Hintermair, and Dirk Eick, and Ivo Gut, and Pierre Ferrier, and Jean-Christophe Andrau
May 2017, BMC medical genomics,
Frederic Koch, and Romain Fenouil, and Marta Gut, and Pierre Cauchy, and Thomas K Albert, and Joaquin Zacarias-Cabeza, and Salvatore Spicuglia, and Albane Lamy de la Chapelle, and Martin Heidemann, and Corinna Hintermair, and Dirk Eick, and Ivo Gut, and Pierre Ferrier, and Jean-Christophe Andrau
January 2012, PloS one,
Frederic Koch, and Romain Fenouil, and Marta Gut, and Pierre Cauchy, and Thomas K Albert, and Joaquin Zacarias-Cabeza, and Salvatore Spicuglia, and Albane Lamy de la Chapelle, and Martin Heidemann, and Corinna Hintermair, and Dirk Eick, and Ivo Gut, and Pierre Ferrier, and Jean-Christophe Andrau
June 2025, Epigenetics & chromatin,
Frederic Koch, and Romain Fenouil, and Marta Gut, and Pierre Cauchy, and Thomas K Albert, and Joaquin Zacarias-Cabeza, and Salvatore Spicuglia, and Albane Lamy de la Chapelle, and Martin Heidemann, and Corinna Hintermair, and Dirk Eick, and Ivo Gut, and Pierre Ferrier, and Jean-Christophe Andrau
October 2011, Genome research,
Frederic Koch, and Romain Fenouil, and Marta Gut, and Pierre Cauchy, and Thomas K Albert, and Joaquin Zacarias-Cabeza, and Salvatore Spicuglia, and Albane Lamy de la Chapelle, and Martin Heidemann, and Corinna Hintermair, and Dirk Eick, and Ivo Gut, and Pierre Ferrier, and Jean-Christophe Andrau
December 2017, Genome biology,
Frederic Koch, and Romain Fenouil, and Marta Gut, and Pierre Cauchy, and Thomas K Albert, and Joaquin Zacarias-Cabeza, and Salvatore Spicuglia, and Albane Lamy de la Chapelle, and Martin Heidemann, and Corinna Hintermair, and Dirk Eick, and Ivo Gut, and Pierre Ferrier, and Jean-Christophe Andrau
July 1974, The Journal of biological chemistry,
Frederic Koch, and Romain Fenouil, and Marta Gut, and Pierre Cauchy, and Thomas K Albert, and Joaquin Zacarias-Cabeza, and Salvatore Spicuglia, and Albane Lamy de la Chapelle, and Martin Heidemann, and Corinna Hintermair, and Dirk Eick, and Ivo Gut, and Pierre Ferrier, and Jean-Christophe Andrau
June 1982, Journal of molecular biology,
Frederic Koch, and Romain Fenouil, and Marta Gut, and Pierre Cauchy, and Thomas K Albert, and Joaquin Zacarias-Cabeza, and Salvatore Spicuglia, and Albane Lamy de la Chapelle, and Martin Heidemann, and Corinna Hintermair, and Dirk Eick, and Ivo Gut, and Pierre Ferrier, and Jean-Christophe Andrau
September 1997, Proceedings of the National Academy of Sciences of the United States of America,
Frederic Koch, and Romain Fenouil, and Marta Gut, and Pierre Cauchy, and Thomas K Albert, and Joaquin Zacarias-Cabeza, and Salvatore Spicuglia, and Albane Lamy de la Chapelle, and Martin Heidemann, and Corinna Hintermair, and Dirk Eick, and Ivo Gut, and Pierre Ferrier, and Jean-Christophe Andrau
January 2018, Molecular and cellular biology,
Copied contents to your clipboard!