Genome wide binding sites of the Arabidopsis B3 domain protein FUSCA3
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ABSTRACT:
ORGANISM(S): Arabidopsis thaliana
PROVIDER: GSE43291 | GEO | 2013/01/11
SECONDARY ACCESSION(S): PRJNA185307
REPOSITORIES: GEO
Similar Datasets
Project description:FUSCA3 (FUS3) is a B3 domain transcription factor that is a member of the LEAFY COTYLEDON (LEC) group of genes. The LEC genes encode proteins that also include LEC2, a B3 domain factor related to FUS3, and LEC1, a CCAAT box binding factor. LEC1, LEC2 and FUS3 are essential for plant embryo development. We report ChIP-chip experiments using the Affymetrix tiling array to globally map binding sites for FUS3. Fangfang Wang and Sharyn E. Perry (2013) Plant Physiology preview FUSCA3 was expressed by the native promoter and included a C-terminal 10x-c-myc tag. This transgene was able to rescue the fus3-3 mutant. A second transgene (35S:AGL15) was present to allow establishment of stable somatic embryo cultures. ChIP was performed using anti-c-myc antibody (Myc-Tag (9B11) Mouse mAb; Cell Signaling 2276S) on tissue expressing FUS3-myc (three biological replicates) and on three controls of tissue expressing FUS3 (no epitope tag).
2013-01-11 | E-GEOD-43291 | biostudies-arrayexpress
Project description:During seed maturation, the embryo accumulates nutrition storage compounds such as oil and reserve proteins, and acquires dormancy and desiccation tolerance. Arabidopsis transcription factors LEC1, LEC2, FUS3 and ABI3 are known as the master regulators of seed maturation because all these events during the seed maturation are severely affected by the respective mutants. In addition, the lec1, lec2 and fus3 mutants exhibit some heterochronic characteristics, as exemplified by the development of true leaf-like cotyledons during embryogenesis. To characterize these mutants at the whole genome expression level, microarray experiments were performed. Developing seeds were dissected from the siliques of the lec1-1, lec2-1, or fus3-3 homozygous plants or the respective wild type plants (Col-0 for fus3-3, WS for lec1-1 and lec2-1) at 8 and 12 days after flowering. Seeds samples were obtained from triplicate batches of plants and used for RNA preparation.
2014-10-01 | E-GEOD-61684 | biostudies-arrayexpress
Project description:During seed maturation, the embryo accumulates nutrition storage compounds such as oil and reservve proteins, and acquires dormancy and desiccation tolerance. Arabidopsis transcription factors LEC1, LEC2, FUS3 and ABI3 are known as the master regulators of seed maturation because all these events during the seed maturation are severely affected by the respective mutants. In addition, the lec1, lec2 and fus3 mutants exhibit some heterochronic characteristics, as exemplified by the development of true leaf-like cotyledons during embryogenesis. To characterize these mutants at the whole genome expression level, microarray experiments were performed.
2014-10-01 | GSE61685 | GEO
Project description:During seed maturation, the embryo accumulates nutrition storage compounds such as oil and reservve proteins, and acquires dormancy and desiccation tolerance. Arabidopsis transcription factors LEC1, LEC2, FUS3 and ABI3 are known as the master regulators of seed maturation because all these events during the seed maturation are severely affected by the respective mutants. In addition, the lec1, lec2 and fus3 mutants exhibit some heterochronic characteristics, as exemplified by the development of true leaf-like cotyledons during embryogenesis. To characterize these mutants at the whole genome expression level, microarray experiments were performed.
2014-10-01 | GSE61684 | GEO
Project description:During seed maturation, the embryo accumulates nutrition storage compounds such as oil and reserve proteins, and acquires dormancy and desiccation tolerance. Arabidopsis transcription factors LEC1, LEC2, FUS3 and ABI3 are known as the master regulators of seed maturation because all these events during the seed maturation are severely affected by the respective mutants. In addition, the lec1, lec2 and fus3 mutants exhibit some heterochronic characteristics, as exemplified by the development of true leaf-like cotyledons during embryogenesis. To characterize these mutants at the whole genome expression level, microarray experiments were performed. Developing seeds were dissected from the siliques of the abi3-6 homozygous plants or the respective wild type plants (Col-0) at 12 and 16 days after flowering. Seeds samples were obtained from triplicate batches of plants and used for RNA preparation.
2014-10-01 | E-GEOD-61685 | biostudies-arrayexpress
Project description:The embryonic temporal regulator FUSCA3 (FUS3) plays major roles in the establishment of embryonic leaf identity and regulation of developmental timing. Loss-of-function mutations of this B3-domain transcription factor result in replacement of cotyledons with leaves and precocious germination, while constitutive misexpression causes the conversion of leaves into cotyledon-like organs and delays vegetative and reproductive phase transitions. To identify downstream targets of FUS3 involved in vegetative phase transitions, we performed microarray analysis on seedlings that transiently activate FUS3 using the AtML1:FUS3-GR-DEX inducible system. Using this construct, FUS3 is ectopically expressed in the ML1 or epidermal layer and becomes activated upon addition of dexamethasone. We found that activation of FUS3 after germination dampens the expression of genes involved in the biosynthesis and response to the plant hormone ethylene, while a loss-of-function fus3 mutant shows many phenotypes consistent with increased ethylene signaling. This FUS3-dependent regulation of ethylene signaling also impinges on timing functions outside of embryogenesis. Loss of FUS3 function results in accelerated vegetative phase change and this is again partially dependent on functional ethylene action. This alteration in vegetative phase transition is dependent on both embryonic and vegetative FUS3 function, suggesting that this important transcriptional regulator controls both embryonic and vegetative developmental timing. This study indicates that the embryonic regulator FUS3 not only regulates the embryonic-to-vegetative phase transition through hormonal regulation, but also functions postembryonically to modulate vegetative phase transitions by negatively regulating ethylene action.
2011-12-11 | E-MEXP-3465 | biostudies-arrayexpress
Project description:Desiccation tolerance (DT) allowed seed plants to conquer ecosystems with long periods of limited water availability. This adaptive features allows seeds to remain dried for very long times without losing their ability to germinate. There is little information about all the signaling components required to achieve DT and on how transcription factors (TFs) modulate global DT processes. We performed RNA-seq experiment and carbohydrates profiles of lec1, lec2, fus3 and abi3, as well as their corresponding wild types, at three stages of seed development 15, 17 and 21 DAF (day after open flower) belonging to the seed desiccation period. A complex experimental design approach and regulatory networks prediction were used to identify differentially expressed genes specifically involved in DT process. In order to identify mechanisms involved in the acquisition of DT during seed development, we designed a comparative transcriptomic analysis between the seed desiccation intolerant (DI) mutants lec1-1, abi3-5 and fus3-3, the desiccation tolerant mutant lec2-1 and the desiccation tolerant weak allele of abi3 (abi3-1) with their respective wild type controls. This analysis should allow to identify genes that are differentially expressed in the desiccation intolerant mutants respect to tolerant mutants and WT controls.
2016-09-06 | E-GEOD-76015 | biostudies-arrayexpress
Project description:Developing Arabidopsis seeds accumulate oils and seed storage proteins synthesized by the pathways of primary metabolism. Seed development and metabolism are positively regulated by transcription factors belonging to the LAFL regulatory network. The VAL gene family encodes repressors of the seed maturation program in germinating seeds, although they are also expressed during seed maturation. VAL1 functions as a repressor of seed metabolism, as val1 mutant seeds accumulated elevated levels of storage proteins compared to the wild type. Two VAL1 splice variants were identified through RNA sequencing analysis: a full-length and a truncated form lacking the plant-homeodomain-like domain associated with epigenetic repression. None of the transcripts encoding the core LAFL network transcription factors were affected in val1 embryos. Instead, activation of VAL1 by FUSCA3 appears to result in repression of a subset of seed maturation genes downstream of core LAFL regulators as 39% of transcripts in the FUSCA3 regulon were de-repressed in the val1 mutant. The LEC1 and LEC2 regulons also responded but to a lesser extent. Additional 832 transcripts that were not LAFL targets were de-repressed in val1 mutant embryos. These transcripts are candidate targets of VAL1, acting through epigenetic and/or transcriptional repression.
2016-02-19 | GSE74692 | GEO
Project description:Developing Arabidopsis seeds accumulate oils and seed storage proteins synthesized by the pathways of primary metabolism. Seed development and metabolism are positively regulated by transcription factors belonging to the LAFL regulatory network. The VAL gene family encodes repressors of the seed maturation program in germinating seeds, although they are also expressed during seed maturation. VAL1 functions as a repressor of seed metabolism, as val1 mutant seeds accumulated elevated levels of storage proteins compared to the wild type. Two VAL1 splice variants were identified through RNA sequencing analysis: a full-length and a truncated form lacking the plant-homeodomain-like domain associated with epigenetic repression. None of the transcripts encoding the core LAFL network transcription factors were affected in val1 embryos. Instead, activation of VAL1 by FUSCA3 appears to result in repression of a subset of seed maturation genes downstream of core LAFL regulators as 39% of transcripts in the FUSCA3 regulon were de-repressed in the val1 mutant. The LEC1 and LEC2 regulons also responded but to a lesser extent. Additional 832 transcripts that were not LAFL targets were de-repressed in val1 mutant embryos. These transcripts are candidate targets of VAL1, acting through epigenetic and/or transcriptional repression. 2 genotypes, 7 time points, 3 biological and 4 technical replicates
2016-02-19 | E-GEOD-74692 | biostudies-arrayexpress