Advances in understanding cis regulation of the plant gene with an emphasis on comparative genomics.

Diane G Burgess, Jie Xu, Michael Freeling

Current opinion in plant biology 2015 Oct

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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. Copyright © 2015 Elsevier Ltd. All rights reserved.

Citation

Diane G Burgess, Jie Xu, Michael Freeling. Advances in understanding cis regulation of the plant gene with an emphasis on comparative genomics. Current opinion in plant biology. 2015 Oct;27:141-7