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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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Average PWM score of different core promoter elements at specific positions. The average PWM score of elements (dInr, DPE, TATA and dTCT) at the allowed positions relative to the determined TSS is presented. The +1 position is the predicted TSS location. Black squares depict the average score of discovered elements using CAGE whereas red circles depict the average score of discovered elements using RNA-seq. For both CAGE and RNA-seq data, some enrichment of the mean score is detected at the expected positions (-30 for TATA, -2 for dInr and dTCT and 28 for DPE). Error bars represent the standard errors of the means (SEM).
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f0004: Average PWM score of different core promoter elements at specific positions. The average PWM score of elements (dInr, DPE, TATA and dTCT) at the allowed positions relative to the determined TSS is presented. The +1 position is the predicted TSS location. Black squares depict the average score of discovered elements using CAGE whereas red circles depict the average score of discovered elements using RNA-seq. For both CAGE and RNA-seq data, some enrichment of the mean score is detected at the expected positions (-30 for TATA, -2 for dInr and dTCT and 28 for DPE). Error bars represent the standard errors of the means (SEM).

Mentions: The distribution of elements found among the allowed positions peaked around the expected relative position (Fig. 3). This peak was observed in both CAGE and RNA-seq data, suggesting that the detected elements are biologically functional. Extending the allowed range around the relative position from ±5 bp to ±10 bp did not reveal additional elements (Fig. S3); hence, a ±5 bp range was used for all downstream analyses. Additionally, the distribution of detected elements among the CAGE defined peaked, broad and unclassified promoters did not differ greatly from the overall distribution (Fig. S4). Reassuringly, the average PWM score also peaked at the biologically relevant positions, although the observed peaks were less profound than the distribution peaks (Fig. 4). Notably, the PWMs were constructed based on completely different data sets obtained by entirely different experimental approaches, as compared to the CAGE and RNA-seq datasets.Figure 3.


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)

Average PWM score of different core promoter elements at specific positions. The average PWM score of elements (dInr, DPE, TATA and dTCT) at the allowed positions relative to the determined TSS is presented. The +1 position is the predicted TSS location. Black squares depict the average score of discovered elements using CAGE whereas red circles depict the average score of discovered elements using RNA-seq. For both CAGE and RNA-seq data, some enrichment of the mean score is detected at the expected positions (-30 for TATA, -2 for dInr and dTCT and 28 for DPE). Error bars represent the standard errors of the means (SEM).
© Copyright Policy - open-access
Related In: Results  -  Collection

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

f0004: Average PWM score of different core promoter elements at specific positions. The average PWM score of elements (dInr, DPE, TATA and dTCT) at the allowed positions relative to the determined TSS is presented. The +1 position is the predicted TSS location. Black squares depict the average score of discovered elements using CAGE whereas red circles depict the average score of discovered elements using RNA-seq. For both CAGE and RNA-seq data, some enrichment of the mean score is detected at the expected positions (-30 for TATA, -2 for dInr and dTCT and 28 for DPE). Error bars represent the standard errors of the means (SEM).
Mentions: The distribution of elements found among the allowed positions peaked around the expected relative position (Fig. 3). This peak was observed in both CAGE and RNA-seq data, suggesting that the detected elements are biologically functional. Extending the allowed range around the relative position from ±5 bp to ±10 bp did not reveal additional elements (Fig. S3); hence, a ±5 bp range was used for all downstream analyses. Additionally, the distribution of detected elements among the CAGE defined peaked, broad and unclassified promoters did not differ greatly from the overall distribution (Fig. S4). Reassuringly, the average PWM score also peaked at the biologically relevant positions, although the observed peaks were less profound than the distribution peaks (Fig. 4). Notably, the PWMs were constructed based on completely different data sets obtained by entirely different experimental approaches, as compared to the CAGE and RNA-seq datasets.Figure 3.

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