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WIREs Dev Biol
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Perspectives on the RNA polymerase II core promoter

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Abstract The RNA polymerase II core promoter is sometimes referred to as the gateway to transcription. The core promoter is generally defined to be the stretch of DNA that directs the initiation of transcription. This simple description belies a complex multidimensional regulatory element, as there is considerable diversity in core promoter structure and function. Core promoters can be viewed at the levels of DNA sequences, transcription factors, and biological networks. Key DNA sequences are known as core promoter elements, which include the TATA box, initiator (Inr), polypyrimidine initiator (TCT), TFIIB recognition element (BRE), motif ten element (MTE), and downstream core promoter element (DPE) motifs. There are no universal core promoter elements that are present in all promoters. Different types of core promoters are transcribed by different sets of transcription factors and exhibit distinct properties, such as specific interactions with transcriptional enhancers, that are determined by the presence or absence of particular core promoter motifs. Moreover, some core promoter elements have been found to be associated with specific biological networks. For instance, the TCT motif is dedicated to the transcription of ribosomal protein genes in Drosophila and humans. In addition, nearly all of the Drosophila Hox genes have a DPE motif in their core promoters. The complexity of the core promoter is further seen in the relation among transcription initiation patterns, the stability or lability of transcriptional states, and the organization of the chromatin structure in the promoter region. Hence, the current data indicate that the core promoter is a critical component in the regulation of gene activity. WIREs Dev Biol 2012, 1:40–51 doi: 10.1002/wdev.21 This article is categorized under: Gene Expression and Transcriptional Hierarchies > Regulatory Mechanisms Gene Expression and Transcriptional Hierarchies > Gene Networks and Genomics

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A single T versus A nucleotide distinguishes the polypyrimidine initiator (TCT) motif from the initiator (Inr). (a) The TCT consensus sequence closely resembles the Inr consensus. The +1 start sites that are typically used with TCT‐dependent and Inr‐dependent core promoters are indicated. (b) The TCT motif cannot substitute for an Inr. The wild‐type adenovirus major late core promoter has an Inr motif. Mutation of the Inr results in the loss of transcriptional activity as well as binding by purified TFIID. Substitution of the Inr with the TCT motif also leads to the loss of transcriptional activity and TFIID binding. However, mutation of the TCT motif to fit the Inr consensus (TCA) results in the restoration of transcriptional activity and TFIID binding. These experiments reveal that a single T versus A nucleotide results in different activities of the TCT and Inr motifs.40 The inability of the TCT motif to substitute for an Inr was also observed in two different downstream core promoter element (DPE)‐containing promoters.40 (c) Sequence of the mutant TCA version of the TCT motif.

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Chromatin structure and transcriptional state. Promoters can be viewed from the perspective of the transcriptional state of the gene. In the case of housekeeping genes, the transcriptional state is stable and the flow of factors through the promoter region can be viewed as that of a steady state system. This stable transcriptional state correlates with an ordered chromatin structure in the promoter region, wherein a positioned array of nucleosomes is typically observed. Regulated genes are in a labile transcriptional state in which they are poised for rapid activation or repression. This labile state correlates with little or no apparent order in the chromatin structure in the promoter region. Focused promoters, particularly those with TATA, initiator (Inr), motif ten element (MTE), or downstream core promoter element (DPE) motifs, are generally associated with regulated genes and a lack of positioned nucleosomes in the promoter region. Dispersed promoters, on the other hand, are commonly found in housekeeping genes with positioned nucleosomes in the promoter region. One notable exception to this general trend is the polypyrimidine initiator (TCT) motif‐based transcription system, in which focused promoters mediate the transcription of ribosomal protein genes, which are housekeeping genes. Unlike the TATA, Inr, motif ten element (MTE), and downstream core promoter element (DPE)‐containing promoters, TCT‐dependent promoters exhibit strong nucleosome positioning.31 These findings suggest that the key feature that dictates the chromatin structure in the promoter region is the stability or lability of the transcriptional state.

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Hypothetical mechanisms for transcription from focused and dispersed promoters. (a) In the model for focused promoters, the transcription preinitiation complex (PIC) is assembled at a single location in the core promoter, and start site selection is determined by the preference of RNA polymerase II to initiate transcription at nearby nucleotides. In some cases, there may be a strongly favored nucleotide and a single predominant start site is observed. In other cases, transcription might initiate at multiple nucleotides that are not necessarily adjacent to one another. (b) In the model for dispersed transcription, there are multiple weak promoters that are created by the combination of a binding site of a sequence‐specific DNA‐binding factor, such as Sp1 or NF‐Y, and an initiator (Inr)‐like sequence. Thus, a single promoter unit would be a sequence‐specific factor binding site and an Inr‐like sequence. These promoter units can be arranged in tandem as well as interdigitated.

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Focused and dispersed modes of transcription initiation. In focused transcription, there is either a single predominant transcription start site or a cluster of start sites in a small region of several nucleotides. In dispersed transcription, there are multiple weak start sites that are distributed over a larger region of about 50–100 nucleotides. Focused promoters are generally associated with regulated genes, whereas dispersed promoters are typically found in housekeeping genes, which maintain steady levels of transcription.

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Some core promoter elements for transcription by RNA polymerase II. These elements include the BREu and BREd (TFIIB recognition element, upstream and downstream), TATA box, Inr (Initiator), MTE (motif ten element), DPE (downstream core promoter element), Bridge, TCT (polypyrimidine initiator), XCPE1 (X core promoter element 1), and DCE (downstream core element). The locations of the motifs are drawn roughly to scale. The BREu, TATA, Inr, MTE, DPE, and TCT motifs have been found in both Drosophila and humans. These motifs are typically found in focused core promoters, although there are probably Inr‐like elements in dispersed promoters. There are no universal core promoter elements that are found in all promoters. Moreover, it is likely that many other core promoter motifs remain to be discovered. The functional properties of a core promoter are determined by the presence or absence of specific core promoter motifs. For example, some enhancers will activate transcription from DPE‐dependent core promoters but not from TATA‐dependent core promoters.

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Core promoter motifs in biological networks. (a) The polypyrimidine initiator (TCT) motif is dedicated to the synthesis of ribosomal proteins.40 The TCT‐based transcription system for the synthesis of ribosomal proteins complements the RNA polymerase I and RNA polymerase III transcription systems for the synthesis of ribosomal RNAs and transfer RNAs. (b) The Drosophila Hox genes, except for Ubx and abd‐A, have TATA‐less, downstream core promoter element (DPE)‐dependent core promoters.22 The DPE motifs in the indicated genes are conserved from Drosophila melanogaster to Drosophila virilis. Ubx and abd‐A, the two most evolutionarily recent Hox genes, lack both TATA and DPE motifs in their core promoters. lab, labial; pb, proboscipedia; Dfd, Deformed; Scr, Sex combs reduced; Antp, Antennapedia; Ubx, Ultrabithorax; abd‐A, abdominal‐A; Abd‐B, Abdominal‐B.

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