Evidence for Directed Evolution of Larger Size Motif in Arabidopsis thaliana Genome
Transcription control of gene expression depends on a variety of interactions mediated by the core promoter region, sequence specific DNA-binding proteins, and their cognate promoter elements. The prominent group of cis acting elements in plants contains an ACGT core. The cis element with this core...
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doaj-abb4b8b0f6804855af4ed788be00364b2020-11-25T02:01:16ZengHindawi LimitedThe Scientific World Journal1537-744X2012-01-01201210.1100/2012/983528983528Evidence for Directed Evolution of Larger Size Motif in Arabidopsis thaliana GenomeRajesh Mehrotra0Amit Yadav1Purva Bhalothia2Ratna Karan3Sandhya Mehrotra4Department of Biological Sciences, Birla Institute of Technology and Science, Pilani, Rajasthan 333031, IndiaDepartment of Biological Sciences, Birla Institute of Technology and Science, Pilani, Rajasthan 333031, IndiaDepartment of Biological Sciences, Birla Institute of Technology and Science, Pilani, Rajasthan 333031, IndiaDepartment of Plant Environmentand Soil Sciences, Louisiana State University, Baton Rouge, LA 70894, USADepartment of Biological Sciences, Birla Institute of Technology and Science, Pilani, Rajasthan 333031, IndiaTranscription control of gene expression depends on a variety of interactions mediated by the core promoter region, sequence specific DNA-binding proteins, and their cognate promoter elements. The prominent group of cis acting elements in plants contains an ACGT core. The cis element with this core has been shown to be involved in abscisic acid, salicylic acid, and light response. In this study, genome-wide comparison of the frequency of occurrence of two ACGT elements without any spacers as well as those separated by spacers of different length was carried out. In the first step, the frequency of occurrence of the cis element sequences across the whole genome was determined by using BLAST tool. In another approach the spacer sequence was randomized before making the query. As expected, the sequence ACGTACGT had maximum occurrence in Arabidopsis thaliana genome. As we increased the spacer length, one nucleotide at a time, the probability of its occurrence in genome decreased. This trend continued until an unexpectedly sharp rise in frequency of (ACGT)N25(ACGT). The observation of higher probability of bigger size motif suggests its directed evolution in Arabidopsis thaliana genome.http://dx.doi.org/10.1100/2012/983528 |
collection |
DOAJ |
language |
English |
format |
Article |
sources |
DOAJ |
author |
Rajesh Mehrotra Amit Yadav Purva Bhalothia Ratna Karan Sandhya Mehrotra |
spellingShingle |
Rajesh Mehrotra Amit Yadav Purva Bhalothia Ratna Karan Sandhya Mehrotra Evidence for Directed Evolution of Larger Size Motif in Arabidopsis thaliana Genome The Scientific World Journal |
author_facet |
Rajesh Mehrotra Amit Yadav Purva Bhalothia Ratna Karan Sandhya Mehrotra |
author_sort |
Rajesh Mehrotra |
title |
Evidence for Directed Evolution of Larger Size Motif in Arabidopsis thaliana Genome |
title_short |
Evidence for Directed Evolution of Larger Size Motif in Arabidopsis thaliana Genome |
title_full |
Evidence for Directed Evolution of Larger Size Motif in Arabidopsis thaliana Genome |
title_fullStr |
Evidence for Directed Evolution of Larger Size Motif in Arabidopsis thaliana Genome |
title_full_unstemmed |
Evidence for Directed Evolution of Larger Size Motif in Arabidopsis thaliana Genome |
title_sort |
evidence for directed evolution of larger size motif in arabidopsis thaliana genome |
publisher |
Hindawi Limited |
series |
The Scientific World Journal |
issn |
1537-744X |
publishDate |
2012-01-01 |
description |
Transcription control of gene expression depends on a variety of interactions mediated by the core promoter region, sequence specific DNA-binding proteins, and their cognate promoter elements. The prominent group of cis acting elements in plants contains an ACGT core. The cis element with this core has been shown to be involved in abscisic acid, salicylic acid, and light response. In this study, genome-wide comparison of the frequency of occurrence of two ACGT elements without any spacers as well as those separated by spacers of different length was carried out. In the first step, the frequency of occurrence of the cis element sequences across the whole genome was determined by using BLAST tool. In another approach the spacer sequence was randomized before making the query. As expected, the sequence ACGTACGT had maximum occurrence in Arabidopsis thaliana genome. As we increased the spacer length, one nucleotide at a time, the probability of its occurrence in genome decreased. This trend continued until an unexpectedly sharp rise in frequency of (ACGT)N25(ACGT). The observation of higher probability of bigger size motif suggests its directed evolution in Arabidopsis thaliana genome. |
url |
http://dx.doi.org/10.1100/2012/983528 |
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