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ElemeNT: a computational tool for detecting core promoter elements.

Sloutskin A, Danino YM, Orenstein Y, Zehavi Y, Doniger T, Shamir R, Juven-Gershon T - Transcription (2015)

Bottom Line: Second, the CORE database summarizes ElemeNT-predicted core promoter elements near CAGE and RNA-seq-defined Drosophila melanogaster transcription start sites (TSSs).ElemeNT's predictions are based on biologically-functional core promoter elements, and can be used to infer core promoter compositions.ElemeNT does not assume prior knowledge of the actual TSS position, and can therefore assist in annotation of any given sequence.

View Article: PubMed Central - PubMed

Affiliation: a The Mina and Everard Goodman Faculty of Life Sciences ; Bar-Ilan University ; Ramat Gan , Israel.

ABSTRACT
Core promoter elements play a pivotal role in the transcriptional output, yet they are often detected manually within sequences of interest. Here, we present 2 contributions to the detection and curation of core promoter elements within given sequences. First, the Elements Navigation Tool (ElemeNT) is a user-friendly web-based, interactive tool for prediction and display of putative core promoter elements and their biologically-relevant combinations. Second, the CORE database summarizes ElemeNT-predicted core promoter elements near CAGE and RNA-seq-defined Drosophila melanogaster transcription start sites (TSSs). ElemeNT's predictions are based on biologically-functional core promoter elements, and can be used to infer core promoter compositions. ElemeNT does not assume prior knowledge of the actual TSS position, and can therefore assist in annotation of any given sequence. These resources, freely accessible at http://lifefaculty.biu.ac.il/gershon-tamar/index.php/resources, facilitate the identification of core promoter elements as active contributors to gene expression.

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Schematic representation of the major core promoter elements. The region of the core promoter area (−40 to +40 relative to the TSS) is illustrated. The diagram is roughly to scale, and each element is colored according to its color in the output table (see Fig. 2B).
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f0001: Schematic representation of the major core promoter elements. The region of the core promoter area (−40 to +40 relative to the TSS) is illustrated. The diagram is roughly to scale, and each element is colored according to its color in the output table (see Fig. 2B).

Mentions: The focused core promoter area encompasses distinct DNA sequence motifs, termed core promoter elements or motifs. These elements are recognized by the basal transcription machinery to recruit RNAP II and to form the preinitiation complex.16-18 The TFIID multi-subunit complex is a key basal transcription factor that recognizes the core promoter in the process of transcription initiation.16-19 Distinct TFIID subunits, namely TATA box-binding protein (TBP) and TBP-associated factors (TAFs), recognize specific core promoter sequences.2-4,16,20-23Table 1 and Figure 1 provide a summary of the characteristics of the known core promoter elements of focused promoters. Remarkably, the MTE, DPE and Bridge elements are exclusively dependent on the presence of a functional initiator with a strict spacing requirement, and are typically enriched in TATA-less promoters.2-4,20,21,23-25Table 1.


ElemeNT: a computational tool for detecting core promoter elements.

Sloutskin A, Danino YM, Orenstein Y, Zehavi Y, Doniger T, Shamir R, Juven-Gershon T - Transcription (2015)

Schematic representation of the major core promoter elements. The region of the core promoter area (−40 to +40 relative to the TSS) is illustrated. The diagram is roughly to scale, and each element is colored according to its color in the output table (see Fig. 2B).
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4581360&req=5

f0001: Schematic representation of the major core promoter elements. The region of the core promoter area (−40 to +40 relative to the TSS) is illustrated. The diagram is roughly to scale, and each element is colored according to its color in the output table (see Fig. 2B).
Mentions: The focused core promoter area encompasses distinct DNA sequence motifs, termed core promoter elements or motifs. These elements are recognized by the basal transcription machinery to recruit RNAP II and to form the preinitiation complex.16-18 The TFIID multi-subunit complex is a key basal transcription factor that recognizes the core promoter in the process of transcription initiation.16-19 Distinct TFIID subunits, namely TATA box-binding protein (TBP) and TBP-associated factors (TAFs), recognize specific core promoter sequences.2-4,16,20-23Table 1 and Figure 1 provide a summary of the characteristics of the known core promoter elements of focused promoters. Remarkably, the MTE, DPE and Bridge elements are exclusively dependent on the presence of a functional initiator with a strict spacing requirement, and are typically enriched in TATA-less promoters.2-4,20,21,23-25Table 1.

Bottom Line: Second, the CORE database summarizes ElemeNT-predicted core promoter elements near CAGE and RNA-seq-defined Drosophila melanogaster transcription start sites (TSSs).ElemeNT's predictions are based on biologically-functional core promoter elements, and can be used to infer core promoter compositions.ElemeNT does not assume prior knowledge of the actual TSS position, and can therefore assist in annotation of any given sequence.

View Article: PubMed Central - PubMed

Affiliation: a The Mina and Everard Goodman Faculty of Life Sciences ; Bar-Ilan University ; Ramat Gan , Israel.

ABSTRACT
Core promoter elements play a pivotal role in the transcriptional output, yet they are often detected manually within sequences of interest. Here, we present 2 contributions to the detection and curation of core promoter elements within given sequences. First, the Elements Navigation Tool (ElemeNT) is a user-friendly web-based, interactive tool for prediction and display of putative core promoter elements and their biologically-relevant combinations. Second, the CORE database summarizes ElemeNT-predicted core promoter elements near CAGE and RNA-seq-defined Drosophila melanogaster transcription start sites (TSSs). ElemeNT's predictions are based on biologically-functional core promoter elements, and can be used to infer core promoter compositions. ElemeNT does not assume prior knowledge of the actual TSS position, and can therefore assist in annotation of any given sequence. These resources, freely accessible at http://lifefaculty.biu.ac.il/gershon-tamar/index.php/resources, facilitate the identification of core promoter elements as active contributors to gene expression.

Show MeSH