title: Advances in understanding cis regulation of the plant gene with an emphasis on comparative genomics.
abstract: The plant gene model remains largely an extrapolation from animals, with the cis functional unit, the gene, cast as a dynamic looping structure. Molecular genetics with model plants continues to make advances; highlighted here are quantitative-occupancy results from the Arabidopsis thaliana (Arabidopsis) Phytochrome-Interacting bHLH transcription Factors (PIF) quartet. Compared to this complex snapshot, results from chromatin occupancy and other Encyclopedia of DNA Elements (ENCODE)-like approaches increase our transcription factor-motif cognate library, but regulation cannot by itself be inferred from binding. Complementary published Arabidopsis conserved noncoding sequence lists are compared, evaluated, merged, and released. Comparative genomic approaches have identified a cis modifier of a gene's expression-hypothetically, a transposon-based 'rheostat'-that works in all cells, times and places.
authors.affiliation: Department of Plant and Microbial Biology, University of California, Berkeley 94720, United States. Electronic address: dburgess@berkeley.edu.
authors.forename: Diane G
authors.initials: DG
authors.lastname: Burgess
authors.affiliation: Maize Research Institute, Sichuan Agricultural University, Wenjiang, Sichuan 611130, China.
authors.forename: Jie
authors.initials: J
authors.lastname: Xu
authors.affiliation: Department of Plant and Microbial Biology, University of California, Berkeley 94720, United States.
authors.forename: Michael
authors.initials: M
authors.lastname: Freeling
mesh_terms: D017360:Arabidopsis / Q000235:genetics* / Q000378:metabolism; D029681:Arabidopsis Proteins / Q000235:genetics* / Q000378:metabolism; D051792:Basic Helix-Loop-Helix Proteins / Q000235:genetics* / Q000378:metabolism; D018506:Gene Expression Regulation, Plant; D018745:Genome, Plant
chemical_list: D029681:Arabidopsis Proteins; D051792:Basic Helix-Loop-Helix Proteins