Plant Cell
HOME HELP FEEDBACK SUBSCRIPTIONS ARCHIVE SEARCH
QUICK SEARCH:   [advanced]


     

Plant Cell Advance Online Publication
Published on May 11, 2007; 10.1105/tpc.107.050419

This Article
Right arrow Full Text - TPC Advance Online Pub. (PDF)
Right arrow Supplemental Data
Right arrow All Versions of this Article:
19/5/1441    most recent
tpc.107.050419v1
Right arrow Alert me when this article is cited
Right arrow Alert me if a correction is posted
Services
Right arrow Email this article to a friend
Right arrow Similar articles in this journal
Right arrow Similar articles in PubMed
Right arrow Alert me to new issues of the journal
Right arrow Download to citation manager
Right arrow reprints & permissions
Citing Articles
Right arrow Citing Articles via Google Scholar
Google Scholar
Right arrow Articles by Freeling, M.
Right arrow Articles by Thomas, B. C.
Right arrow Search for Related Content
PubMed
Right arrow PubMed Citation
Right arrow Articles by Freeling, M.
Right arrow Articles by Thomas, B. C.
Agricola
Right arrow Articles by Freeling, M.
Right arrow Articles by Thomas, B. C.

Received January 18, 2007
Returned for revision March 10, 2007
Accepted April 19, 2007

G-Boxes, Bigfoot Genes, and Environmental Response: Characterization of Intragenomic Conserved Noncoding Sequences in Arabidopsis

Michael Freeling 1*, Lakshmi Rapaka 1, Eric Lyons 1, Brent Pedersen 2, and Brian C. Thomas 2

1 Department of Plant and Microbial Biology, University of California, Berkeley, California 94720
2 College of Natural Resources, University of California, Berkeley, California 94720

* To whom correspondence should be addressed. E-mail: freeling{at}nature.berkeley.edu.

A tetraploidy left Arabidopsis thaliana with 6358 pairs of homeologs 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 homeolog only and with no other gene, suggesting that binding site turnover impedes detection. Bigfoot genes may function in adaptation to environmental change.






HOME HELP FEEDBACK SUBSCRIPTIONS ARCHIVE SEARCH
ASPB Publications THE PLANT CELL PLANT PHYSIOLOGY
Copyright © 2007 by the American Society of Plant Biologists