The word landscape of the non-coding segments of the Arabidopsis thaliana genome

Background Genome sequences can be conceptualized as arrangements of motifs or words. The frequencies and positional distributions of these words within particular non-coding genomic segments provide important insights into how the words function in processes such as mRNA stability and regulation of...

Full description

Saved in:
Bibliographic Details
Published in:BMC genomics Vol. 10; no. 1; p. 463
Main Authors: Lichtenberg, Jens, Yilmaz, Alper, Welch, Joshua D, Kurz, Kyle, Liang, Xiaoyu, Drews, Frank, Ecker, Klaus, Lee, Stephen S, Geisler, Matt, Grotewold, Erich, Welch, Lonnie R
Format: Journal Article
Language:English
Published: London BioMed Central 08.10.2009
BioMed Central Ltd
Springer Nature B.V
BMC
Subjects:
3' Untranslated Regions
5' Untranslated Regions
Algorithms
Animal Genetics and Genomics
Arabidopsis - genetics
Arabidopsis thaliana
Bacteria
Binding sites
Biology
Biomedical and Life Sciences
Biotechnology
Computational Biology - methods
Computer engineering
Computer science
DNA, Plant - genetics
Gene expression
Gene Expression Regulation, Plant
Genetic aspects
Genome, Plant
Genomes
Genomics
Hypothesis testing
Introns
Life Sciences
Markov Chains
Messenger RNA
Methods
Microarrays
Microbial Genetics and Genomics
Models, Statistical
Physiological aspects
Plant Genetics and Genomics
Promoter Regions, Genetic
Promoters (Genetics)
Proteins
Proteomics
R&D
Regulation
Research & development
Research Article
Sequence Analysis, DNA
United States
Core Promoter
Proximal Promoter
Transcription Start Site
Word Pair
Arabidopsis Genome
ISSN:1471-2164, 1471-2164
Online Access:Get full text
Tags: Add Tag
No Tags, Be the first to tag this record!
Description
Summary:Background Genome sequences can be conceptualized as arrangements of motifs or words. The frequencies and positional distributions of these words within particular non-coding genomic segments provide important insights into how the words function in processes such as mRNA stability and regulation of gene expression. Results Using an enumerative word discovery approach, we investigated the frequencies and positional distributions of all 65,536 different 8-letter words in the genome of Arabidopsis thaliana . Focusing on promoter regions, introns, and 3' and 5' untranslated regions (3'UTRs and 5'UTRs), we compared word frequencies in these segments to genome-wide frequencies. The statistically interesting words in each segment were clustered with similar words to generate motif logos. We investigated whether words were clustered at particular locations or were distributed randomly within each genomic segment, and we classified the words using gene expression information from public repositories. Finally, we investigated whether particular sets of words appeared together more frequently than others. Conclusion Our studies provide a detailed view of the word composition of several segments of the non-coding portion of the Arabidopsis genome. Each segment contains a unique word-based signature. The respective signatures consist of the sets of enriched words, 'unwords', and word pairs within a segment, as well as the preferential locations and functional classifications for the signature words. Additionally, the positional distributions of enriched words within the segments highlight possible functional elements, and the co-associations of words in promoter regions likely represent the formation of higher order regulatory modules. This work is an important step toward fully cataloguing the functional elements of the Arabidopsis genome.
Bibliography:ObjectType-Article-1
SourceType-Scholarly Journals-1
ObjectType-Feature-2
content type line 14
content type line 23
ISSN:1471-2164
1471-2164
DOI:10.1186/1471-2164-10-463