FASCIATED EAR4 encodes a bZIP transcription factor that controls shoot meristem size in maize
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ABSTRACT:
ORGANISM(S): Zea mays
PROVIDER: GSE61954 | GEO | 2015/01/21
SECONDARY ACCESSION(S): PRJNA262781
REPOSITORIES: GEO
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Project description:fasciated ear4 (fea4) is a semi-dwarfed mutant with fasciated ears and tassels, and greatly enlarged vegetative and inflorescence meristems. Chromatin Immunoprecipitation-sequencing (ChIP-seq) and expression profiling by RNA-seq suggest that fea4 is required to regulate the auxin response and leaf differentiation programs in the periphery of the meristem, suggesting a new mechanism of meristem size regulation that is spatially and mechanistically distinct from the CLV-WUS model. To gain insight into transcriptional regulation by FEA4, we used RNA-seq to profile genome-wide expression changes in developing ear primordia of fea4 loss-of-function mutants compared to fea4/+ wild-type (wt) siblings. To map genome-wide occupancy of FEA4 and define its putative transcriptional targets, we performed ChIP-seq using the pFEA4-YFP::FEA4 transgenic lines.
2015-01-21 | E-GEOD-61954 | biostudies-arrayexpress
Project description:Meristem maintenance, achieved through the highly conserved CLAVATA-WUSCHEL (CLV-WUS) regulatory circuit, is fundamental in balancing stem cell proliferation with cellular differentiation. Disruptions to meristem homeostasis can alter meristem size, leading to enlarged organs. Cotton, the world’s most important fiber crop, shows inherent variation in fruit size. Leveraging meristem regulation could benefit cotton agriculture and increase yields of high-quality fibers. Using virus-based gene manipulation in cotton, we altered expression of genes functioning in the CLV-WUS circuit to perturb meristem regulation and increase fruit size. Targeted alteration of individual components of the CLV-WUS circuit only modestly fasciated flowers and fruits. Unexpectedly, controlled expression of meristem regulator SELF-PRUNING (SP) dramatically increased the impacts of altered CLV-WUS expression on flower and fruit fasciation. Meristem transcriptomics show SP and genes of the CLV-WUS circuit are expressed independently from each other, suggesting these gene products are not acting in the same path. Virus-induced silencing of GhSP facilitated delivery of other signals to the meristem to dramatically alter organ specification. SELF-PRUNING has a role in cotton meristem homeostasis, and changes in GhSP expression increased access of virus-based signals to the meristem.
2023-03-01 | GSE206189 | GEO
Project description:KNOTTED1(KN1)-like homeobox (KNOX) transcription factors function in plant meristems, self-renewing structures consisting of stem cells and their immediate daughters. Despite their importance for plant development, the genomic network targeted by KNOX proteins is poorly understood. Using ChIP-seq, we defined the KN1 cistrome in maize inflorescences and found that KN1 binds to several thousand loci. To understand how these binding occupancies correlate with changes in transcriptional regulation, we performed RNA-seq on immature ears and tassels, and compared expression profiles between normal and loss-of-function kn1 plants, in addition to immature leaves from normal and gain-of-function Kn1 plants. We found that 643 of the KN1 targets were modulated in one or multiple tissues, with a strong enrichment for transcription factors (including other homeobox genes) and genes participating in several hormonal pathways, most significantly auxin, implicating KN1 at the crossroads of plant hormone signaling. The loss-of-function kn1 phenotype is reminiscent of auxin mutants and kn1 mis-expression in leaves correlates with increased auxin signaling. Our results demonstrate that KN1 plays a key role in orchestrating the upper levels of a hierarchical gene regulatory network that impacts plant meristem identity and function. For loss-of-function mutant, kn1-e1 homozygote were compared to heterozygote or wild-type siblings (ears, tassels and shoot apical meristem). For gain-of-function mutant, Kn1-N homozygote were compared to wild-type siblings.Kn1-N heterozygote were compared to wild-type siblings. For each genotype and tissue, 2 biological replicates were sequenced, except for tassels (3 biological replicates). The whole data set thus includes a total of 20 samples/libraries.
2012-09-04 | E-GEOD-38487 | biostudies-arrayexpress
Project description:In this study we used the maize (Zea mays) inflorescence to investigate gene networks that modulate determinacy, specifically the decision to allow branch growth. We characterized developmental transitions by associating spatiotemporal expression profiles with morphological changes resulting from genetic perturbations that disrupt steps in a pathway controlling branching. These are the RNA-seq datasets used in this study. We profiled changes in gene expression during normal maize ear and tassel development and in developing maize ear primordia upon genetic perturbation of the RAMOSA branching pathway. For the wild-type ear and tassel developmental series, greenhouse-grown B73 inbred plants were used. 10mm ears were collected and sectioned as follows from tip to base along the developmental gradient: tip 1mm sampled (tip; Inflorescence Meristem/Spikelet Pair Meristem), next 1mm discarded, next 1mm sampled (mid; Spikelet Meristem), next 2mm discarded, next 2 mm sampled (base; Floral Meristem), and immediately frozen in liquid nitrogen. Sections from ~30 sampled ears were pooled for each of 2 biological replicates to represent tip, mid, and base stages. Tassels were hand-dissected, measured, separated by stage: 1-2mm (stg1), 3-4mm (stg2), and 5-7mm (stg3), and immediately frozen in liquid N. For each stage, ~20-30 tassels were pooled for each of 2 biological replicates. For ramosa mutant series, segregating families (1:1) of ra1-R, ra2-R, and ra3-fea1 mutant alleles, all introgressed at least 6 times into the B73 inbred background, were grown at CSHL Uplands Farm. Field-grown plants were genotyped and collected 6-7 weeks after germination (V7-V8 stage). First and second ear primordia were immediately hand-dissected, measured, and frozen in liquid nitrogen. For ra1, ra2 and ra3 mutants and wild-type controls, ears were pooled into two size classes: 1) 1mm class included a range of 0.7-1.5mm sized ears and nine ears were pooled for each of 2 biological replicates; 2) 2mm class included a range of 1.8-2.5mm sized ears and six ears were pooled for each of three biological replicates. Wild-type samples were proportional mixtures of heterozygote siblings segregating in ra1, ra2, and ra3 populations. Variability factors (e.g. ear size within class, ear rank on the plant, and time of collection) were distributed evenly across pooled samples.
2013-11-27 | E-GEOD-51047 | biostudies-arrayexpress
Project description:We sequenced cDNA synthesized from mRNA from 3 time points of a time course of Arabidopsis thaliana shoot apical meristems. Plants were grown two weeks in short days (time point +0LD) and then exposed to long days for 1 day (time point +1LD) and 3 days (time point +3LD). Meristem cells were collected using laser capture microdissection, to generate a meristem-specific time course of gene expression in the early stages of floral induction. The experiment was done in three biological replicates (called A, B, and C). Some repetitions of sequencing on a few samples (technical replicates) were also done Examination of mRNA levels in shoot apical meristems at 3 time points from the stage of vegetative meristem to the stage of a transition meristem, before the formation of floral meristems.
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Project description:The root apical meristems (RAM) is established during embryogenesis and serves as a source of stem cells for plant growth and organogenesis. Young roots have a simple structure and meristeamtic and non-meristematic cells can be differentiated based on their location. We have used the Affymetrix Medicago Genome Array GeneChip to compare tissue from the root meristem and non-meristematic tissue to identify meristem specific candidate genes based on changes in gene expression before and after differentiation Keywords: Cell type comparison
2007-07-01 | GSE8115 | GEO
Project description:The root apical meristems (RAM) is established during embryogenesis and serves as a source of stem cells for plant growth and organogenesis. Young roots have a simple structure and meristeamtic and non-meristematic cells can be differentiated based on their location. We have used the Affymetrix Medicago Genome Array GeneChip to compare tissue from the root meristem and non-meristematic tissue to identify meristem specific candidate genes based on changes in gene expression before and after differentiation Experiment Overall Design: Roots were sectioned separating meristematic (root-tip) and non-meristematic root tissue; total RNA was extracted and used for hybridization to Affymetrix arrays
2008-06-16 | E-GEOD-8115 | biostudies-arrayexpress
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.
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Project description:To determine the effect of the fon2 and asp1 mutations on meristem maintenance, we carried out microarray analysis using Rice (US) gene 1.0 ST array. We analyzed gene expression profiles of the inflorescence meristems of WT, fon2-3, asp1-10, and fon2-3 asp1-fe.
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Project description:The shoot apical meristem (SAM) contains undifferentiated stem cells that are responsible for the initiation of above-ground organs, and eventually the general architecture of the plant. To gain insight into the nature of genetic programs and the regulatory networks underlying SAM function in soybean, we have used Affymetrix soybean GeneChip® to investigate the transcript profiles associated with micro-dissected SAMs or axillary meristems (AMs). While the microarray data disclosed the conservation of transcriptional signature between the two types of meristems, subsequent comparison of SAM transcript profile with that of non-meristem (NM) tissue revealed a total of 1090 and 1523 transcripts that are significantly up- or down-regulated in the SAM. Further in situ hybridization analysis on selected transcripts has implicated their roles in SAM maintenance and the establishment of organ polarity. We also identified a gene that could potentially serve as a novel marker that distinguishes the differentiating cells in the meristem from the pluripotent stem cells. Along with many unknowns, transcripts with putative annotation have also been identified that has allowed us to infer SAM regulatory roles for various families of transcription factors as well as products associated with auxin-mediated responses, cell division and proliferation, epigenetic regulation, miRNA regulation and protein turnover. Computational analysis on the promoter regions of Arabidopsis orthologs of genes with high expression in the soybean SAM revealed a conserved over-representation of three cis-acting regulatory motifs. Our microarray data thus represents a rich source of target genes for further study into the meristem function and maintenance. Keywords: meristem transcript profile
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