NDLI: Computational Identification of Cis-regulatory Elements Associated with Pungency of Chili Peppers

Content Provider	IEEE Xplore Digital Library
Author	Tieming Ji Ranjan, D. Curry, J. O'Connell, M.
Copyright Year	2007
Description	Author affiliation: New Mexico State Univ., Las Cruces (Tieming Ji; Ranjan, D.)
Abstract	In silico characterization of promoter or regulatory regions of genomes is an important aspect of understanding gene expression regulation. Plant secondary metabolism represents an opportunity to discover promoter elements among coordinately transcribed genes on these complex pathways. We used CisFind, a software tool we developed, for finding un-extendable conserved matches among multiple DNA sequences. The underlying algorithm for this tool is a modified suffix tree. We used CisFind to detect unknown common regulatory elements in the 5' proximal regions of four genes on the capsaicinoid biosynthetic pathway. These DNA sequences were retrieved by genome walking from eight different chili peppers differing in pungency levels; tomato DNA was included as an outgroup. Nine unique candidate promoter elements were identified among these sequences. Their distribution is consistent with a role in regulating these genes for expression related to chili pungency. These candidate promoter elements were also predicted by other online software tools with different algorithms, increasing the probability that these elements are in fact biologically relevant.
Starting Page	1188
Ending Page	1192
File Size	1031076
Page Count	5
File Format	PDF
ISBN	9781424415090
DOI	10.1109/BIBE.2007.4375713
Language	English
Publisher	Institute of Electrical and Electronics Engineers, Inc. (IEEE)
Publisher Date	2007-10-14
Publisher Place	USA
Access Restriction	Subscribed
Rights Holder	Institute of Electrical and Electronics Engineers, Inc. (IEEE)
Subject Keyword	Sequences DNA Genomics Bioinformatics Software tools Gene expression Software algorithms Computer science Biochemistry Legged locomotion capsaicinoid cis-regulatory elements suffix tree algorithm biosynthetic pathway Capsicum
Content Type	Text
Resource Type	Article

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