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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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A sample output of the ElemeNT program. (A) The input sequence annotated with the combinations of elements identified in it. ElemeNT detected a TATA box flanked by both a BREu element and a BREd element, Drosophila and mammalian initiator elements and DPE and Bridge elements. The two possible combinations result from a sequence match to both the Drosophila and mammalian initiators, due to the partial sequence redundancy of the 2 elements. (B) A table displaying all the elements identified within the input sequence, their location, PWM and consensus match scores. Note the message displayed for the TATA-box, indicating the presence of mammalian and Drosophila initiators, as well as BREu and BREd, at optimal distances for transcriptional synergy.
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f0002: A sample output of the ElemeNT program. (A) The input sequence annotated with the combinations of elements identified in it. ElemeNT detected a TATA box flanked by both a BREu element and a BREd element, Drosophila and mammalian initiator elements and DPE and Bridge elements. The two possible combinations result from a sequence match to both the Drosophila and mammalian initiators, due to the partial sequence redundancy of the 2 elements. (B) A table displaying all the elements identified within the input sequence, their location, PWM and consensus match scores. Note the message displayed for the TATA-box, indicating the presence of mammalian and Drosophila initiators, as well as BREu and BREd, at optimal distances for transcriptional synergy.

Mentions: 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).


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)

A sample output of the ElemeNT program. (A) The input sequence annotated with the combinations of elements identified in it. ElemeNT detected a TATA box flanked by both a BREu element and a BREd element, Drosophila and mammalian initiator elements and DPE and Bridge elements. The two possible combinations result from a sequence match to both the Drosophila and mammalian initiators, due to the partial sequence redundancy of the 2 elements. (B) A table displaying all the elements identified within the input sequence, their location, PWM and consensus match scores. Note the message displayed for the TATA-box, indicating the presence of mammalian and Drosophila initiators, as well as BREu and BREd, at optimal distances for transcriptional synergy.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

f0002: A sample output of the ElemeNT program. (A) The input sequence annotated with the combinations of elements identified in it. ElemeNT detected a TATA box flanked by both a BREu element and a BREd element, Drosophila and mammalian initiator elements and DPE and Bridge elements. The two possible combinations result from a sequence match to both the Drosophila and mammalian initiators, due to the partial sequence redundancy of the 2 elements. (B) A table displaying all the elements identified within the input sequence, their location, PWM and consensus match scores. Note the message displayed for the TATA-box, indicating the presence of mammalian and Drosophila initiators, as well as BREu and BREd, at optimal distances for transcriptional synergy.
Mentions: 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).

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