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Asymmetric organs and microRNA-directed DNA modification

Cell Press

A new research study published in the November issue of Developmental Cell reveals that the regulation of critical genes that guide development of asymmetric leaf patterning depends on microRNA-directed gene inhibition via DNA methylation. MicroRNAs are a class of very small genes that do not code for proteins but instead act as regulators that can inhibit gene transcription. The new paper shows that interaction between the microRNA and a newly transcribed mRNA molecule is required for DNA modification at the target gene.

The leaves of the plant Arabidopsis have top and bottom halves with different cellular morphologies and different physiological roles. Specific mutations in the Arabidopsis genes PHABULOSA (PHB) and PHAVOLUTA (PHV) interfere with normal leaf patterning. The mutations, which alter a microRNA binding site in mRNAs transcribed from the template gene, are associated with excess PHB and PHV proteins. The mechanism by which the normal microRNAs associated with the wild-type genes repress synthesis of PHB and PHV was not clear.

A research team led by Dr. M. Kathryn Barton from the Carnegie Institution of Washington in Stanford, California examined the relationship between microRNAs and DNA methylation. In general, high levels of methylation are associated with low levels of transcription while low levels of methylation are associated with high transcription rates. "To test whether the microRNA complementary site in the PHB mRNA affects the chromatin state of the PHB gene, we assayed the PHB gene for the extent of methylation in wild-type and in phb-1d mutants," explains Dr. Barton.

The researchers found that PHB and PHV coding sequences were heavily methylated downstream of the microRNA complementary site in most wild-type plant cells and that methylation was reduced in phb-1d and phv-1d mutants. According to Dr. Barton, "These results suggest a model in which the microRNA interacts with nascent, newly processed PHB mRNA to alter chromatin of the corresponding PHB template DNA predominantly in differentiated cells." The authors speculate that microRNAs provide a general repression of PHB and PHV during development and that specific regions of the plant may have the ability to overcome this repression, thus permitting varying morphologies, as is observed on the top and bottom of Arabidopsis leaves.

Ning Bao, Khar-Wai Lye, and M. Kathryn Barton: "Mutations at a microRNA Complementary Site in PHABULOSA and PHAVOLUTA mRNAs Are Associated with Decreased Methylation of the Template Chromosome"


Publishing in Developmental Cell, Volume 7, Number 5, November 2004, pages 653-662.

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