The RNA polymerase II core promoter.

By S. Smale, J. T. Kadonaga. Annual Review of Biochemistry, 2003

1,238 citations recorded by the source corpus.

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Citations in the corpus

The General Transcription Machinery and General Cofactors (2006, background): “It is interesting to note that DPE and TATA motifs not only specify the initiation site for transcription, but also act as regulatory elements for enhancer function (Butler and Kadonaga, 2001; Smale and Kadonaga, 2003).”
Genome-wide analysis of mammalian promoter architecture and evolution (2006, background): “This spacing is consistent with the structural evidence showing that the distance from the TATA box to the active center of RNA polymerase II is 30 b”
DeePromoter: Robust Promoter Predictor Using Deep Learning (2019, background): “The vast majority of studies on the TATA-box have been conducted on human, yeast, and Drosophila genomes, however, similar elements have been found in other species such as archaea and ancient eukaryotes (Smale and Kadonaga, 2003).”
Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project (2007, background): “However, in many cases, multiple TSSs resided within a single small segment (up to , 200 bases); this was due to some promoters containing TSSs with many very close precise initiation sites 47 .”
MicroRNA genes are transcribed by RNA polymerase II (2004, background): “…gene determined in this study seems to lack the known common promoter elements that are required for transcription initiation com- plex, including the TATA box, the initiator element, the downstream promoter element (DPE), or the TFIIB recog- nition element (BRE) (Smale and Kadonaga, 2003).”
JASPAR, the open access database of transcription factor-binding profiles: new content and tools in the 2008 update (2007, background): “(15) for a review on core promoter patterns].”
Distinct and predictive chromatin signatures of transcriptional promoters and enhancers in the human genome (2007, background): “Promoters are located at the 5′ ends of genes immediately surrounding the transcriptional start site (TSS) and serve as the point of assembly of the transcriptional machinery and initiation of transcriptio”
Discovery of functional elements in 12 Drosophila genomes using evolutionary signatures (2007, background): “6b), including close matches to several known core promoter motifs involved in transcription initiation 97 .”
Tools for neuroanatomy and neurogenetics in Drosophila (2008, background): “An enhancer requires the presence of specific sequence motifs in the core promoter to function properly and the core promoters of different genes vary in their content of these motifs; thus, not all enhancers function efficiently with all core promoters (9).”
Non-coding nuclear DNA markers in phylogenetic reconstruction (2009, background): “Typically, promoters consist of a set of core elements, which are necessary to facilitate transcription by providing binding sites for the RNA polymerase and essential transcription factors, and a variable number of regulatory elements (Smale and Kadonaga 2003).”
Transcription regulation and animal diversity (2003, background): “There are at least three different sequence elements that can recruit the TBP containing TFIID initiation complex: TATA, initiator element (INR) and the downstream promoter element (DPE”
Structure and mechanism of the RNA polymerase II transcription machinery (2004, background): “Sequence elements found in core promoters include the TATA element (TBP-binding site), BRE (TFIIB-recognition element), Inr (initiator element) and DPE (downstream promoter element”
hERG K(+) channels: structure, function, and clinical significance. (2012, background): “Mammalian gene promoters are typically either GC rich or contain canonical TATA box or CCAAT box motifs that bind components of the RNA polymerase complex of proteins required for initiation of transcription (581).”
Molecular mechanisms of heavy metal tolerance and evolution in invertebrates (2009, background): “…basal RNA polymerase II complex, bound to the initiator or TATA box, determine the rate of transcriptional initiation: the frequency by which the RNA polymerase II complex leaves the initiator to transcribe the downstream coding sequence into mRNA (Shopland et al., 1995; Smale & Kadonaga, 2003).”
Noncoding transcription by RNA Polymerase Pol IVb/Pol V mediates transcriptional silencing of overlapping and adjacent genes (2008, neutral): “It is noteworthy that the 50 terminal nucleotides of all RACE products were adenosine or guanosine (Figure S2), given that transcripts of eukaryotic Pol I, II, III, and bacterial RNA polymerase typically begin with purines (Smale and Kadonaga, 2003; Sollner-Webb and Reeder, 1979; Zecherle et al., 19”
Nucleosome positioning and gene regulation: advances through genomics (2009, background): “In PIC assembly, general transcription factors , such as TATA-binding protein ( TBP ) or TFIID, bind to core promoter elements and position other initiation factors, such as TFIIB and TFIIF, which then direct Pol II to initiate transcription at the initiator element (INR element) (the consens”