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The dicerlike1 homologue, fuzzy tassel, is required for the regulation of meristem determinacy in the inflorescence and vegetative growth in maize

ABSTRACT: We have characterized a maize mutant, fuzzy tassel (fzt) with striking inflorescence and pleiotropic defects. fzt contains a mutation in the maize dicer-like1 homolog, a key enzyme required for microRNA (miRNA) biogenesis. By profiling the small RNA population in fzt mutants, we investigated the impact of fzt mutation on miRNA abundance in seedling and tassel primordia. We also investigated the transcript abundance of potential target genes of miRNA that were impacted in fzt mutant by transcriptome profiling. The result provides an avenue for future research to link specific miRNAs and their targets to discrete phenotypes and developmental roles.

ORGANISM(S): Zea mays

PROVIDER: GSE52879 | GEO | 2015/02/20

SECONDARY ACCESSION(S): PRJNA230402

REPOSITORIES: GEO

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The dicerlike1 homologue, fuzzy tassel, is required for the regulation of meristem determinacy in the inflorescence and vegetative growth in maize

Project description:We have characterized a maize mutant, fuzzy tassel (fzt) with striking inflorescence and pleiotropic defects. fzt contains a mutation in the maize dicer-like1 homolog, a key enzyme required for microRNA (miRNA) biogenesis. By profiling the small RNA population in fzt mutants, we investigated the impact of fzt mutation on miRNA abundance in seedling and tassel primordia. We also investigated the transcript abundance of potential target genes of miRNA that were impacted in fzt mutant by transcriptome profiling. The result provides an avenue for future research to link specific miRNAs and their targets to discrete phenotypes and developmental roles. Genome-wide small RNA profiling was done by Illumina TruSeq sample preparation followed by high-throughput sequencing with Illumina HiSeq 2000 platform.

2015-02-20 | E-GEOD-52879 | biostudies-arrayexpress

The dicerlike1 homologue, fuzzy tassel, is required for the regulation of meristem determinacy in the inflorescence and vegetative growth in maize

2016-10-20 | E-GEOD-52879 | ExpressionAtlas

Boron homeostasis functions in meristem maintenance in maize by regulating knotted1, cell cycle, and hormone signaling pathways

Project description:Here we report, that levels of the micronutrient boron are instrumental for meristem maintenance by integration into specific meristem maintenance pathways. We used RNA-seq analysis of the boron deficient maize mutant tassel-less1 to identify early molecular defects induced by boron deficiency in maize reproductive (tassel) meristems. RNA-seq results were independently verified through downstream in silico, double mutant, microscopy, proteomic, and molecular analyses.

2022-08-31 | GSE169600 | GEO

Genome-wide identification of AGO18b-bound miRNAs and phasiRNAs in maize by cRIP-seq

Project description:As a key member of the grass-specific subclade of argonaute proteins, AGO18b protein has been proposed to bind 24-nt meiotic phasiRNAs based on their co-expression in tapetal and meiotic cells. Here we show that expression of in maize tassels is strictly induced by developmental stages. Interestingly, reduced expression of AGO18b in both Mutator-mediated (ago18b::mum) and RNAi mutants leads to an increase in plant height and tassel length, suggesting its non-meiotic function as a negative regulator of SAM/IM maintenance. During the premiotic stage, AGO18b primarily binds to 21-nt phasiRNAs with 5’-uridine and less binds to 24-nt phasiRNAs with 5’-adenosine, coincident with its enrichment of miR2275 required for the 24-nt phasiRNA production. MiR166a, the negative regulator of SAM, is mostly enriched among AGO18b-bound miRNAs, implicating a novel negative regulator of IM. We suggest that AGO18b regulates maize tassel development via both phasiRNAs and miRNA pathways.

2019-08-07 | GSE93983 | GEO

Project description:Maize Tasselseed5 developing tassel transcriptome

| PRJNA495059 | ENA

Fuzzy Logic Selection as a New Reliable Tool to Identify Gene Signatures in Breast Cancer - the INNODIAG Study

Project description:Based on fuzzy logic selection and classification algorithms, our selection method measures the contribution of each gene for each of two pre-defined classes in order to find the best discrimination. This algorithm extracts and ranks the most pertinent markers, since it is based on feature weighting according to optimal error rate, sensitivity and specificity. We applied the fuzzy logic selection on four breast cancer microarray databases to obtain new gene signatures based on histological grade. To validate these gene signatures, we designed probes for the selected genes on Nimblegen custom microarrays and tested them on a series of 151 consecutive invasive breast carcinomas displaying clinicopathological features similar to those observed in routine practice.

2014-01-12 | GSE53958 | GEO

Maize tumors caused by Ustilago maydis require organ-specific genes in host and pathogen

Project description:Two-organism transcriptome profiling of infected seedling, adult leaf, and tassel demonstrated that both the host and pathogen exhibit organ-specific expression programs. Phenotypic screening of U. maydis mutants deleted for suites of secreted protein genes and maize growth mutants demonstrated organ-restricted tumorigenesis. Two-dye, competitive hybridizations were performed on Agilent oligo arrays. Keywords: maize, pathogen, fungus, Ustilago, organ-specificity

2010-04-01 | GSE20130 | GEO

A Genome-Wide Characterization of MicroRNA Genes in Maize

Project description:MicroRNAs (miRNAs) are small non-coding RNAs that play essential roles in plant growth and development. We conducted a genome-wide survey of maize miRNA genes, characterizing their structure, expression, and evolution. Computational approaches based on homology and secondary structure modeling identified 150 high-confidence genes within 26 miRNA families. For 25 families, expression was verified by deep-sequencing of small RNA libraries that were prepared from an assortment of maize tissues. PCR-RACE amplification of 68 miRNA transcript precursors, representing 18 families conserved across several plant species, showed that splice variation and the use of alternative transcriptional start and stop sites is common within this class of genes. Comparison of sequence variation data from diverse maize inbred lines versus teosinte accessions suggest that the mature miRNAs are under strong purifying selection while the flanking sequences evolve equivalently to other genes. Since maize is derived from an ancient tetraploid, the effect of whole-genome duplication on miRNA evolution was examined. We found that, like protein-coding genes, duplicated miRNA genes underwent extensive gene-loss, with ~35% of duplicate homeologous miRNA genes retained. This number is higher than that observed with protein-coding genes. A search for putative miRNA targets indicated a bias towards genes in regulatory and metabolic pathways. As maize is one of the principal models for plant growth and development, this study will serve as a foundation for future research into the functional roles of miRNA genes. Surveying miRNA genes in 5 maize tissues (root, seedling, tassel, ear, and pollen) by sequencing small RNA libraries using the Illumina Genome Analyzer

2009-11-23 | E-GEOD-17943 | biostudies-arrayexpress

Project description:Maize tassel carpel suppression RNA-seq

| PRJNA657042 | ENA

A complete map of affinity and specificity encoding for a partially fuzzy protein interaction

Project description:Thousands of protein domains encoded in the human genome function by binding up to a million short linear motifs embedded in intrinsically disordered regions of other proteins. How affinity and specificity are encoded in these binding domains and the motifs themselves is not well understood. The evolvability of binding specificity - how rapidly and extensively it can change upon mutation - is also largely unexplored, as is the contribution of ‘fuzzy’ dynamic residues to affinity and specificity in protein-protein interactions. Here we produce the first global map of affinity and specificity encoding in a globular protein domain. Quantifying >200,000 energetic interactions between the domain and ligand allows us to identify 20 major energetically coupled pairs of sites. These are organised into six modules, with the vast majority of mutations in each module only reprogramming specificity for a single position in the ligand. Nine of the major energetic couplings encoding specificity are direct structural contacts and 11 have an allosteric mechanism of action. The dynamic tail of the ligand is more robust to mutation than the structured portion but contributes additively to binding affinity and communicates with structured residues to enable changes in specificity. Our results present how affinity and specificity are encoded in a globular protein domain interacting with a disordered peptide and a direct comparison of the encoding of affinity and specificity in structured and dynamic molecular recognition.

2024-04-25 | GSE265816 | GEO

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