10 research outputs found
Gene network analysis of Arabidopsis thaliana flower development through dynamic gene perturbations
Understanding how flowers develop from undifferentiated stem cells has occupied developmental biologists for decades. Key to unraveling this process is a detailed knowledge of the global regulatory hierarchies that control developmental transitions, cell differentiation and organ growth. These hierarchies may be deduced from gene perturbation experiments, which determine the effects on gene expression after specific disruption of a regulatory gene. Here, we tested experimental strategies for gene perturbation experiments during Arabidopsis thaliana flower development. We used artificial miRNAs (amiRNAs) to disrupt the functions of key floral regulators, and expressed them under the control of various inducible promoter systems that are widely used in the plant research community. To be able to perform genome‐wide experiments with stage‐specific resolution using the various inducible promoter systems for gene perturbation experiments, we also generated a series of floral induction systems that allow collection of hundreds of synchronized floral buds from a single plant. Based on our results, we propose strategies for performing dynamic gene perturbation experiments in flowers, and outline how they may be combined with versions of the floral induction system to dissect the gene regulatory network underlying flower development
Molecular basis for the specification of floral organs by APETALA3 and PISTILLATA
How different organs are formed from small sets of undifferentiated
precursor cells is a key question in developmental biology. To
understand the molecular mechanisms underlying organ specification
in plants, we studied the function of the homeotic selector
genes APETALA3 (AP3) and PISTILLATA (PI), which control the
formation of petals and stamens during Arabidopsis flower development.
To this end, we characterized the activities of the transcription
factors that AP3 and PI encode throughout flower
development by using perturbation assays as well as transcript profiling
and genomewide localization studies, in combination with
a floral induction system that allows a stage-specific analysis of
flower development by genomic technologies. We discovered considerable
spatial and temporal differences in the requirement for
AP3/PI activity during flower formation and show that they control
different sets of genes at distinct phases of flower development.
The genomewide identification of target genes revealed that
AP3/PI act as bifunctional transcription factors: they activate genes
involved in the control of numerous developmental processes required
for organogenesis and repress key regulators of carpel formation.
Our results imply considerable changes in the composition
and topology of the gene network controlled by AP3/PI during the
course of flower development. We discuss our results in light of
a model for the mechanism underlying sex-determination in seed
plants, in which AP3/PI orthologues might act as a switch between
the activation of male and the repression of female development
Analysis of the gene regulatory network underlying reproductive floral organ development through gene perturbation experiments
THESIS 9989Homeosis or homeotic transformation refers to the formation of one body
structure or organ in place of another. For more than two decades, the floral homeotic
genes have been at the center of intense studies that showed how they specify the identity of floral organs by acting in different combinations within distinct floral whorls. The specification of the floral organ identity by the homeotic genes is described by the ABCE model, which represents a milestone in the field of flower development and illustrates how the activity of different classes of transcription factors cooperate to specify the development of sepals, petals, stamens, and carpels
Molecular basis for the specification of floral organs by APETALA3 and PISTILLATA
How different organs are formed from small sets of undifferentiated
precursor cells is a key question in developmental biology. To
understand the molecular mechanisms underlying organ specification
in plants, we studied the function of the homeotic selector
genes APETALA3 (AP3) and PISTILLATA (PI), which control the
formation of petals and stamens during Arabidopsis flower development.
To this end, we characterized the activities of the transcription
factors that AP3 and PI encode throughout flower
development by using perturbation assays as well as transcript profiling
and genomewide localization studies, in combination with
a floral induction system that allows a stage-specific analysis of
flower development by genomic technologies. We discovered considerable
spatial and temporal differences in the requirement for
AP3/PI activity during flower formation and show that they control
different sets of genes at distinct phases of flower development.
The genomewide identification of target genes revealed that
AP3/PI act as bifunctional transcription factors: they activate genes
involved in the control of numerous developmental processes required
for organogenesis and repress key regulators of carpel formation.
Our results imply considerable changes in the composition
and topology of the gene network controlled by AP3/PI during the
course of flower development. We discuss our results in light of
a model for the mechanism underlying sex-determination in seed
plants, in which AP3/PI orthologues might act as a switch between
the activation of male and the repression of female development
Molecular basis for the specification of floral organs by APETALA3 and PISTILLATA
How different organs are formed from small sets of undifferentiated
precursor cells is a key question in developmental biology. To
understand the molecular mechanisms underlying organ specification
in plants, we studied the function of the homeotic selector
genes APETALA3 (AP3) and PISTILLATA (PI), which control the
formation of petals and stamens during Arabidopsis flower development.
To this end, we characterized the activities of the transcription
factors that AP3 and PI encode throughout flower
development by using perturbation assays as well as transcript profiling
and genomewide localization studies, in combination with
a floral induction system that allows a stage-specific analysis of
flower development by genomic technologies. We discovered considerable
spatial and temporal differences in the requirement for
AP3/PI activity during flower formation and show that they control
different sets of genes at distinct phases of flower development.
The genomewide identification of target genes revealed that
AP3/PI act as bifunctional transcription factors: they activate genes
involved in the control of numerous developmental processes required
for organogenesis and repress key regulators of carpel formation.
Our results imply considerable changes in the composition
and topology of the gene network controlled by AP3/PI during the
course of flower development. We discuss our results in light of
a model for the mechanism underlying sex-determination in seed
plants, in which AP3/PI orthologues might act as a switch between
the activation of male and the repression of female development
Molecular basis for the specification of floral organs by APETALA3 and PISTILLATA
How different organs are formed from small sets of undifferentiated
precursor cells is a key question in developmental biology. To
understand the molecular mechanisms underlying organ specification
in plants, we studied the function of the homeotic selector
genes APETALA3 (AP3) and PISTILLATA (PI), which control the
formation of petals and stamens during Arabidopsis flower development.
To this end, we characterized the activities of the transcription
factors that AP3 and PI encode throughout flower
development by using perturbation assays as well as transcript profiling
and genomewide localization studies, in combination with
a floral induction system that allows a stage-specific analysis of
flower development by genomic technologies. We discovered considerable
spatial and temporal differences in the requirement for
AP3/PI activity during flower formation and show that they control
different sets of genes at distinct phases of flower development.
The genomewide identification of target genes revealed that
AP3/PI act as bifunctional transcription factors: they activate genes
involved in the control of numerous developmental processes required
for organogenesis and repress key regulators of carpel formation.
Our results imply considerable changes in the composition
and topology of the gene network controlled by AP3/PI during the
course of flower development. We discuss our results in light of
a model for the mechanism underlying sex-determination in seed
plants, in which AP3/PI orthologues might act as a switch between
the activation of male and the repression of female development
Control of Reproductive Floral Organ Identity Specification in Arabidopsis by the C Function Regulator AGAMOUSC
The floral organ identity factor AGAMOUS (AG) is a key regulator of Arabidopsis thaliana flower development, where it is involved
in the formation of the reproductive floral organs as well as in the control of meristem determinacy. To obtain insights into
how AG specifies organ fate, we determined the genes and processes acting downstream of this C function regulator during
early flower development and distinguished between direct and indirect effects. To this end, we combined genome-wide
localization studies, gene perturbation experiments, and computational analyses. Our results demonstrate that AG controls
flower development to a large extent by controlling the expression of other genes with regulatory functions, which are involved
in mediating a plethora of different developmental processes. One aspect of this function is the suppression of the leaf development
program in emerging floral primordia. Using trichome initiation as an example, we demonstrate that AG inhibits an important
aspect of leaf development through the direct control of key regulatory genes. A comparison of the gene expression programs
controlled by AG and the B function regulators APETALA3 and PISTILLATA, respectively, showed that while they control many
developmental processes in conjunction, they also have marked antagonistic, as well as independent activities
Control of Reproductive Floral Organ Identity Specification in Arabidopsis by the C Function Regulator AGAMOUSC
The floral organ identity factor AGAMOUS (AG) is a key regulator of Arabidopsis thaliana flower development, where it is involved
in the formation of the reproductive floral organs as well as in the control of meristem determinacy. To obtain insights into
how AG specifies organ fate, we determined the genes and processes acting downstream of this C function regulator during
early flower development and distinguished between direct and indirect effects. To this end, we combined genome-wide
localization studies, gene perturbation experiments, and computational analyses. Our results demonstrate that AG controls
flower development to a large extent by controlling the expression of other genes with regulatory functions, which are involved
in mediating a plethora of different developmental processes. One aspect of this function is the suppression of the leaf development
program in emerging floral primordia. Using trichome initiation as an example, we demonstrate that AG inhibits an important
aspect of leaf development through the direct control of key regulatory genes. A comparison of the gene expression programs
controlled by AG and the B function regulators APETALA3 and PISTILLATA, respectively, showed that while they control many
developmental processes in conjunction, they also have marked antagonistic, as well as independent activities