A New Approach to Sequence Analysis Exemplified by Identification of cis-Elements in Abscisic Acid Inducible Promoters

Peter Kamp Busk, Peter Fischer Hallin, Jesper Salomon, Lene Lange

Research output: Contribution to conference without publisher/journalPosterResearch

Abstract

Identification of cis-regulatory elements in DNA promoters by computational approaches are a great help in genome-wide elucidation of signal transduction, transcriptional regulation and gene expression. However, to accomplish this has proven a difficult problem in computational genomics in part due to the redundant nature of cis-regulatory elements1. Moreover, promoter context and chromatin structure have an important influence on the function of cis-elements and does further complicate the identification of functional cis-elements2,3.
A related computational approach to promoter studies is to use the sequences of known cis-elements for promoter prediction4. This is a computational alternative to genome-wide DNA array analysis of gene expression and can be used to confirm the importance of known promoter elements on a genome level. Unfortunately, this approach does not yield information about new cis-regulatory elements.
We have developed a method for identifying short, conserved motifs in biological sequences such as proteins, DNA and RNA5.
This method was used for analysis of approximately 2000 Arabidopsis thaliana promoters that have been shown by DNA array analysis to be induced by abscisic acid6. These promoters were compared to 28000 promoters that are not induced by abscisic acid.
The analysis identified previously described ABA-inducible promoter elements such as ABRE, CE3 and CRT1 but also new cis-elements were found. Furthermore, the list of DNA elements could be used to predict ABA-inducible promoter with more than 70 % accuracy for the top 40 predictions, which is better than previously described methods4.
In conclusion, identification of short, conserved motifs is a useful computational approach for identification of cis-elements in DNA promoters and for promoter prediction in genome analysis.
Original languageEnglish
Publication date31 Jan 2013
Publication statusPublished - 31 Jan 2013
EventPlant Biotech Denmark, Annual Meeting 2013 - Copenhagen University, Frederiksberg Campus, Copenhagen, Denmark
Duration: 31 Jan 20131 Feb 2013

Conference

ConferencePlant Biotech Denmark, Annual Meeting 2013
LocationCopenhagen University, Frederiksberg Campus
CountryDenmark
CityCopenhagen
Period31/01/201301/02/2013

Cite this

Busk, P. K., Hallin, P. F., Salomon, J., & Lange, L. (2013). A New Approach to Sequence Analysis Exemplified by Identification of cis-Elements in Abscisic Acid Inducible Promoters. Poster session presented at Plant Biotech Denmark, Annual Meeting 2013, Copenhagen, Denmark.
Busk, Peter Kamp ; Hallin, Peter Fischer ; Salomon, Jesper ; Lange, Lene. / A New Approach to Sequence Analysis Exemplified by Identification of cis-Elements in Abscisic Acid Inducible Promoters. Poster session presented at Plant Biotech Denmark, Annual Meeting 2013, Copenhagen, Denmark.
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abstract = "Identification of cis-regulatory elements in DNA promoters by computational approaches are a great help in genome-wide elucidation of signal transduction, transcriptional regulation and gene expression. However, to accomplish this has proven a difficult problem in computational genomics in part due to the redundant nature of cis-regulatory elements1. Moreover, promoter context and chromatin structure have an important influence on the function of cis-elements and does further complicate the identification of functional cis-elements2,3. A related computational approach to promoter studies is to use the sequences of known cis-elements for promoter prediction4. This is a computational alternative to genome-wide DNA array analysis of gene expression and can be used to confirm the importance of known promoter elements on a genome level. Unfortunately, this approach does not yield information about new cis-regulatory elements. We have developed a method for identifying short, conserved motifs in biological sequences such as proteins, DNA and RNA5. This method was used for analysis of approximately 2000 Arabidopsis thaliana promoters that have been shown by DNA array analysis to be induced by abscisic acid6. These promoters were compared to 28000 promoters that are not induced by abscisic acid. The analysis identified previously described ABA-inducible promoter elements such as ABRE, CE3 and CRT1 but also new cis-elements were found. Furthermore, the list of DNA elements could be used to predict ABA-inducible promoter with more than 70 {\%} accuracy for the top 40 predictions, which is better than previously described methods4. In conclusion, identification of short, conserved motifs is a useful computational approach for identification of cis-elements in DNA promoters and for promoter prediction in genome analysis.",
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Busk, PK, Hallin, PF, Salomon, J & Lange, L 2013, 'A New Approach to Sequence Analysis Exemplified by Identification of cis-Elements in Abscisic Acid Inducible Promoters', Copenhagen, Denmark, 31/01/2013 - 01/02/2013, .

A New Approach to Sequence Analysis Exemplified by Identification of cis-Elements in Abscisic Acid Inducible Promoters. / Busk, Peter Kamp; Hallin, Peter Fischer; Salomon, Jesper; Lange, Lene.

2013. Poster session presented at Plant Biotech Denmark, Annual Meeting 2013, Copenhagen, Denmark.

Research output: Contribution to conference without publisher/journalPosterResearch

TY - CONF

T1 - A New Approach to Sequence Analysis Exemplified by Identification of cis-Elements in Abscisic Acid Inducible Promoters

AU - Busk, Peter Kamp

AU - Hallin, Peter Fischer

AU - Salomon, Jesper

AU - Lange, Lene

PY - 2013/1/31

Y1 - 2013/1/31

N2 - Identification of cis-regulatory elements in DNA promoters by computational approaches are a great help in genome-wide elucidation of signal transduction, transcriptional regulation and gene expression. However, to accomplish this has proven a difficult problem in computational genomics in part due to the redundant nature of cis-regulatory elements1. Moreover, promoter context and chromatin structure have an important influence on the function of cis-elements and does further complicate the identification of functional cis-elements2,3. A related computational approach to promoter studies is to use the sequences of known cis-elements for promoter prediction4. This is a computational alternative to genome-wide DNA array analysis of gene expression and can be used to confirm the importance of known promoter elements on a genome level. Unfortunately, this approach does not yield information about new cis-regulatory elements. We have developed a method for identifying short, conserved motifs in biological sequences such as proteins, DNA and RNA5. This method was used for analysis of approximately 2000 Arabidopsis thaliana promoters that have been shown by DNA array analysis to be induced by abscisic acid6. These promoters were compared to 28000 promoters that are not induced by abscisic acid. The analysis identified previously described ABA-inducible promoter elements such as ABRE, CE3 and CRT1 but also new cis-elements were found. Furthermore, the list of DNA elements could be used to predict ABA-inducible promoter with more than 70 % accuracy for the top 40 predictions, which is better than previously described methods4. In conclusion, identification of short, conserved motifs is a useful computational approach for identification of cis-elements in DNA promoters and for promoter prediction in genome analysis.

AB - Identification of cis-regulatory elements in DNA promoters by computational approaches are a great help in genome-wide elucidation of signal transduction, transcriptional regulation and gene expression. However, to accomplish this has proven a difficult problem in computational genomics in part due to the redundant nature of cis-regulatory elements1. Moreover, promoter context and chromatin structure have an important influence on the function of cis-elements and does further complicate the identification of functional cis-elements2,3. A related computational approach to promoter studies is to use the sequences of known cis-elements for promoter prediction4. This is a computational alternative to genome-wide DNA array analysis of gene expression and can be used to confirm the importance of known promoter elements on a genome level. Unfortunately, this approach does not yield information about new cis-regulatory elements. We have developed a method for identifying short, conserved motifs in biological sequences such as proteins, DNA and RNA5. This method was used for analysis of approximately 2000 Arabidopsis thaliana promoters that have been shown by DNA array analysis to be induced by abscisic acid6. These promoters were compared to 28000 promoters that are not induced by abscisic acid. The analysis identified previously described ABA-inducible promoter elements such as ABRE, CE3 and CRT1 but also new cis-elements were found. Furthermore, the list of DNA elements could be used to predict ABA-inducible promoter with more than 70 % accuracy for the top 40 predictions, which is better than previously described methods4. In conclusion, identification of short, conserved motifs is a useful computational approach for identification of cis-elements in DNA promoters and for promoter prediction in genome analysis.

M3 - Poster

ER -

Busk PK, Hallin PF, Salomon J, Lange L. A New Approach to Sequence Analysis Exemplified by Identification of cis-Elements in Abscisic Acid Inducible Promoters. 2013. Poster session presented at Plant Biotech Denmark, Annual Meeting 2013, Copenhagen, Denmark.