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PMID: 17496117 Published · ppublish English Journal Article Research Support, U.S. Gov't, Non-P.H.S.

G-boxes, bigfoot genes, and environmental response: characterization of intragenomic conserved noncoding sequences in Arabidopsis.

The Plant cell ·Vol. 19 ·No. 5 ·2007-05-00 ·Pages 1441-57

Freeling M, Rapaka L, Lyons E, Pedersen B, Thomas BC

Abstract

A tetraploidy left Arabidopsis thaliana with 6358 pairs of homoeologs that, when aligned, generated 14,944 intragenomic conserved noncoding sequences (CNSs). Our previous work assembled these phylogenetic footprints into a database. We show that known transcription factor (TF) binding motifs, including the G-box, are overrepresented in these CNSs. A total of 254 genes spanning long lengths of CNS-rich chromosomes (Bigfoot) dominate this database. Therefore, we made subdatabases: one containing Bigfoot genes and the other containing genes with three to five CNSs (Smallfoot). Bigfoot genes are generally TFs that respond to signals, with their modal CNS positioned 3.1 kb 5' from the ATG. Smallfoot genes encode components of signal transduction machinery, the cytoskeleton, or involve transcription. We queried each subdatabase with each possible 7-nucleotide sequence. Among hundreds of hits, most were purified from CNSs, and almost all of those significantly enriched in CNSs had no experimental history. The 7-mers in CNSs are not 5'- to 3'-oriented in Bigfoot genes but are often oriented in Smallfoot genes. CNSs with one G-box tend to have two G-boxes. CNSs were shared with the homoeolog only and with no other gene, suggesting that binding site turnover impedes detection. Bigfoot genes may function in adaptation to environmental change.

MeSH Terms
Arabidopsis/genetics Base Pairing/genetics Base Sequence Conserved Sequence DNA, Intergenic/genetics Databases, Genetic Environment Genes, Plant Molecular Sequence Data Regulatory Sequences, Nucleic Acid/genetics Software Transcription Factors/metabolism
Chemicals
DNA, Intergenic Transcription Factors
Authors & Affiliations
5 authors, click to expand affiliations / ORCID
Freeling Michael
Department of Plant and Microbial Biology, University of California, Berkeley, California 94720, USA. freeling@nature.berkeley.edu
Rapaka Lakshmi
Lyons Eric
Pedersen Brent
Thomas Brian C
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Article Info
Journal
The Plant cell
Abbr.
Plant Cell
ISSN
1040-4651
DOI
10.1105/tpc.107.050419
Email
freeling@nature.berkeley.edu
Published
2007-05-00
Epub
2007-00-11
Pages
1441-57
Language
English
Region
England
NLM ID
9208688
PMCID
PMC1913728
Subset
IM
External Links
PubMed source DOI: 10.1105/tpc.107.050419 PMC Full Text View journal details
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