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Epigenetics refers to heritable changes in patterns of gene expression that occur without alterations in DNA sequence. The epigenetic mechanisms involve covalent modifications of DNA and histones, which affect transcriptional activity of chromatin. Since chromatin states can be propagated through mitotic and meiotic divisions, epigenetic mechanisms are thought to provide heritable 'cellular memory'. Here, we review selected examples of epigenetic memory in plants and briefly discuss underlying mechanisms. [ABSTRACT FROM AUTHOR]

It is necessary to use algorithms to analyze gene expression data from DNA microarrays, such as in clustering and machine learning. Previously, we developed the knowledge-based fuzzy adaptive resonance theory (KB-FuzzyART), a clustering algorithm suitable for analyzing gene expression data, to find clues for identifying gene networks. Leaf primordia form around the shoot apical meristem (SAM), which consists of indeterminate stem cells. Upon initiation of leaf development, adaxial–abaxial patterning is crucial for lateral expansion, via cellular proliferation, and the formation of flat symmetric leaves. Many regulatory genes that specify such patterning have been identified. Analysis by the KB-FuzzyART and subsequent molecular and genetic analyses previously showed that ASYMMETRIC LEAVES1 (AS1) and AS2 repress the expression of some abaxial-determinant genes, such as AUXIN RESPONSE FACTOR3 (ARF3)/ETTIN (ETT) and ARF4, which are responsible for defects in leaf adaxial–abaxial polarity in as1 and as2. In the present study, genetic analysis revealed that ARF3/ETT and ARF4 were regulated by modifier genes, BOBBER1 (BOB1) and ELONGATA3 (ELO3), together with AS1–AS2. We analyzed expression arrays with as2 elo3 and as2 bob1, and extracted genes downstream of ARF3/ETT by using KB-FuzzyART and molecular analyses. The results showed that expression of Kip-related protein (KRP) (for inhibitors of cyclin-dependent protein kinases) and Isopentenyltransferase (IPT) (for biosynthesis of cytokinin) genes were controlled by AS1–AS2 through ARF3/ETT and ARF4 functions, which suggests that the AS1–AS2–ETT pathway plays a critical role in controlling the cell division cycle and the biosynthesis of cytokinin around SAM to stabilize leaf development in Arabidopsis thaliana. [ABSTRACT FROM PUBLISHER]

The ASYMMETRIC LEAVES2 ( AS2) gene, a member of the AS2/ LOB gene family, and the ASYMMETRIC LEAVES1 ( AS1) gene of Arabidopsis thaliana participate in the development of a symmetrical, expanded lamina. We report here the patterns of expression of these genes, and the importance of the sites of such expression in leaf development. Transcripts of both genes accumulated in the entire leaf primordia at early stages, but the patterns of accumulation changed as the leaves expanded. AS2 and AS1 transcripts were detected, respectively, in the adaxial domain and in the inner domain between the adaxial and abaxial domains of leaves. The ratios of numbers of adaxial cells to abaxial cells in cotyledons of corresponding mutant lines were greater than the ratios in wild-type cotyledons. The low levels of ectopic expression of AS2 under the control of the AS1 promoter in as2 mutant plants restored an almost normal phenotype in some cases, but also resulted in flatter leaves than those of wild-type plants. Strong expression of the construct in wild-type and as2 plants, but not as1 plants, resulted in the formation of narrow, upwardly curled leaves. Our results indicate that AS2 represses cell proliferation in the adaxial domain in the presence of AS1, and that adaxial expression of AS2 at an appropriate level is critical for the development of a symmetrical, expanded lamina. Real-time RT-PCR analysis revealed that mutation of either AS2 or AS1 resulted in an increase in the levels of transcripts of ETTIN ( ETT; also known as AUXIN RESPONSE FACTOR3, ARF3) and KANADI2 ( KAN2), which are abaxial determinants, and YABBY5 ( YAB5). Thus, AS2 and AS1 might negatively regulate the expression of these genes in the adaxial domain, which might be related to the development of flat and expanded leaves. [ABSTRACT FROM AUTHOR]