Characterization of MiR319-Regulated TCPs in Maize Development

Maize produces two inflorescences, the tassel and the ear, that are essential for reproduction. Both inflorescences arise from similar inflorescence primordia and are patterned largely by the same developmental regulators. Some of these inflorescence regulators are also responsible for leaf development and are critical for establishing plant architecture. TEOSINTE BRANCHED1/CYCLODIA/PCF1&2 (TCPs) are a unique class of plant-specific transcription factors that control proliferation and differentiation to establish plant architecture. A subset of TCPs (CIN-TCP) are regulated by microRNA (miRNA) miR319 and are required for petal and leaf development in multiple plant species. miRNAs are short non-coding RNAs that direct cleavage of target mRNAs. The maize fuzzy tassel (fzt) mutant is a hypomorphic allele of dicer-like1, which encodes a key enzyme required for miRNA biogenesis. fzt mutants have a broad range of vegetative and reproductive defects including reduced plant and leaf size, meristem indeterminacy in the inflorescences, and sex determination defects. fzt has reduced levels of some miRNAs, including miR319. Because miR319 is significantly reduced in fzt mutants and TCP genes have well-known roles in plant development, we hypothesized that mis-expression of TCP genes might contribute to the fzt phenotype. RNA-seq analysis of tassel primordia indicated that CIN-like TCPs were expressed at similar levels in fzt mutants and normal siblings. RNA-seq at the whole tissue level cannot detect subtle changes in expression domain or timing, however, so I examined the spatiotemporal expression of miR319-targeted TCPs in shoot apices and tassel primordia using RNA in situ hybridization. Preliminary data suggests that at least two TCP genes are expressed in all inflorescence meristems and floral primordia. I also initiated experiments to establish mutant lines in several TCP genes for functional analyses.M.S

Characterization of MiR319-Regulated TCPs in Maize Development

Maize produces two inflorescences, the tassel and the ear, that are essential for reproduction. Both inflorescences arise from similar inflorescence primordia and are patterned largely by the same developmental regulators. Some of these inflorescence regulators are also responsible for leaf development and are critical for establishing plant architecture. TEOSINTE BRANCHED1/CYCLODIA/PCF1&2 (TCPs) are a unique class of plant-specific transcription factors that control proliferation and differentiation to establish plant architecture. A subset of TCPs (CIN-TCP) are regulated by microRNA (miRNA) miR319 and are required for petal and leaf development in multiple plant species. miRNAs are short non-coding RNAs that direct cleavage of target mRNAs. The maize fuzzy tassel (fzt) mutant is a hypomorphic allele of dicer-like1, which encodes a key enzyme required for miRNA biogenesis. fzt mutants have a broad range of vegetative and reproductive defects including reduced plant and leaf size, meristem indeterminacy in the inflorescences, and sex determination defects. fzt has reduced levels of some miRNAs, including miR319. Because miR319 is significantly reduced in fzt mutants and TCP genes have well-known roles in plant development, we hypothesized that mis-expression of TCP genes might contribute to the fzt phenotype. RNA-seq analysis of tassel primordia indicated that CIN-like TCPs were expressed at similar levels in fzt mutants and normal siblings. RNA-seq at the whole tissue level cannot detect subtle changes in expression domain or timing, however, so I examined the spatiotemporal expression of miR319-targeted TCPs in shoot apices and tassel primordia using RNA in situ hybridization. Preliminary data suggests that at least two TCP genes are expressed in all inflorescence meristems and floral primordia. I also initiated experiments to establish mutant lines in several TCP genes for functional analyses

A variably imprinted epiallele impacts seed development.

The contribution of epigenetic variation to phenotypic variation is unclear. Imprinted genes, because of their strong association with epigenetic modifications, represent an opportunity for the discovery of such phenomena. In mammals and flowering plants, a subset of genes are expressed from only one parental allele in a process called gene imprinting. Imprinting is associated with differential DNA methylation and chromatin modifications between parental alleles. In flowering plants imprinting occurs in a seed tissue - endosperm. Proper endosperm development is essential for the production of viable seeds. We previously showed that in Arabidopsis thaliana intraspecific imprinting variation is correlated with naturally occurring DNA methylation polymorphisms. Here, we investigated the mechanisms and function of allele-specific imprinting of the class IV homeodomain leucine zipper (HD-ZIP) transcription factor HDG3. In imprinted strains, HDG3 is expressed primarily from the methylated paternally inherited allele. We manipulated the methylation state of endogenous HDG3 in a non-imprinted strain and demonstrated that methylation of a proximal transposable element is sufficient to promote HDG3 expression and imprinting. Gain of HDG3 imprinting was associated with earlier endosperm cellularization and changes in seed weight. These results indicate that epigenetic variation alone is sufficient to explain imprinting variation and demonstrate that epialleles can underlie variation in seed development phenotypes

Nucleosome conformation dictates the histone code

Histone post-translational modifications (PTMs) play a critical role in chromatin regulation. It has been proposed that these PTMs form localized ‘codes’ that are read by specialized regions (reader domains) in chromatin-associated proteins (CAPs) to regulate downstream function. Substantial effort has been made to define [CAP: histone PTM] specificities, and thus decipher the histone code and guide epigenetic therapies. However, this has largely been done using the reductive approach of isolated reader domains and histone peptides, which cannot account for any higher-order factors. Here, we show that the [BPTF PHD finger and bromodomain: histone PTM] interaction is dependent on nucleosome context. The tandem reader selectively associates with nucleosomal H3K4me3 and H3K14ac or H3K18ac, a combinatorial engagement that despite being in cis is not predicted by peptides. This in vitro specificity of the BPTF tandem reader for PTM-defined nucleosomes is recapitulated in a cellular context. We propose that regulatable histone tail accessibility and its impact on the binding potential of reader domains necessitates we refine the ‘histone code’ concept and interrogate it at the nucleosome level