Expression data of wild type and alfa-1 null L3 stage C.elegans with and without food
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PROVIDER: PRJNA565228 | ENA |
REPOSITORIES: ENA
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Project description:The objective of this experiment was to determine changes in gene expression upon loss of alfa-1 in C.elegans under well-fed and starvation conditions. The human C9orf72 has an orthologue in C. elegans based on sequence homology, which is the F18A1.6 gene and also recently named as alfa-1 (ALS/FTD-associated gene homolog 1). We analyzed the domain structure of ALFA-1 and found that it shares the same DENN domains as human C9orf72, including the uDENN, cDENN, and dDENN domains. We obtained a mutant strain of the alfa-1 gene, which has a mutant allele (ok3062) of 486 bp deletion and 24 bp insertion in the region of exon 3 and exon 4. To understand the changes in gene expression in the alfa-1 mutant C. elegans, we performed the microarray gene expression profiling experiments under the defined conditions.
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2016-07-03 | E-MTAB-3789 | biostudies-arrayexpress
Project description:The layered compartmentalization of functionally-related synaptic connections, a common feature of nervous systems, underlies proper connectivity between neurons and enables parallel processing of neural information. However, the stepwise development of layered neuronal connections is not well understood. The medulla neuropil of the Drosophila melanogaster visual system is comprised of 10 discrete layers (M1-M10), within which neural computations underlying distinct visual features are processed. As such, the Drosophila medulla neuropil serves as a model system for understanding layered compartmentalization of synaptic connectivity. The first step leading to the establishment of neurite layer specificity in the outer medulla (M1-M6) is the innervation of one of two broad, primordial domains that will subsequently expand and transform into the M1-M6 layers. We previously found that the transcription factor dFezf cell-autonomously directs L3 neurons to their proper early broad domain before they innervate and form synapses specifically within the M3 layer of the mature medulla. Here, we examined the transcriptomes of wild type and dFezf mutant L3 neurons by RNA-seq and identified downstream target genes that are regulated by dFezf. We show that dFezf controls L3 layer specificity through temporally precise transcriptional repression of the transcription factor slp1 (sloppy paired 1). During the period of broad domain selection, dFezf limits slp1 expression in L3 neurons. Slp1 is upregulated in dFezf-null L3 neurons, and ablation of slp1 fully rescues the targeting defect observed in dFezf-null L3 growth cones. Surprisingly, L3 innervation of the M3 layer after broad domain selection requires early slp1 expression. DFezf thus functions as a transcriptional repressor to coordinate the temporal dynamics of a transcriptional cascade that orchestrates sequential steps of layer-specific synapse formation. Moreover, we performed ATAC-seq in wild type L3 neurons and identified the accessible regions in the L3 genome, where dFezf may directly bind and regulate gene expression.
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Project description:The layered compartmentalization of functionally-related synaptic connections, a common feature of nervous systems, underlies proper connectivity between neurons and enables parallel processing of neural information. However, the stepwise development of layered neuronal connections is not well understood. The medulla neuropil of the Drosophila melanogaster visual system is comprised of 10 discrete layers (M1-M10), within which neural computations underlying distinct visual features are processed. As such, the Drosophila medulla neuropil serves as a model system for understanding layered compartmentalization of synaptic connectivity. The first step leading to the establishment of neurite layer specificity in the outer medulla (M1-M6) is the innervation of one of two broad, primordial domains that will subsequently expand and transform into the M1-M6 layers. We previously found that the transcription factor dFezf cell-autonomously directs L3 neurons to their proper early broad domain before they innervate and form synapses specifically within the M3 layer of the mature medulla. Here, we examined the transcriptomes of wild type and dFezf mutant L3 neurons by RNA-seq and identified downstream target genes that are regulated by dFezf. We show that dFezf controls L3 layer specificity through temporally precise transcriptional repression of the transcription factor slp1 (sloppy paired 1). During the period of broad domain selection, dFezf limits slp1 expression in L3 neurons. Slp1 is upregulated in dFezf-null L3 neurons, and ablation of slp1 fully rescues the targeting defect observed in dFezf-null L3 growth cones. Surprisingly, L3 innervation of the M3 layer after broad domain selection requires early slp1 expression. DFezf thus functions as a transcriptional repressor to coordinate the temporal dynamics of a transcriptional cascade that orchestrates sequential steps of layer-specific synapse formation. Moreover, we performed ATAC-seq in wild type L3 neurons and identified the accessible regions in the L3 genome, where dFezf may directly bind and regulate gene expression.
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Project description:We, being members of modENCODE consortium, have established an experimetal pipeline in C.elegans that allows global identification of the binding sites for transcription factors using chromatin immunoprecipitation followed by illumina high-throughput sequencing (ChIP-seq). In current study, we identified the binding sites for HLH-8 at L3 stage, which is required for normal muscle development and normal defecation and egg-laying. For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf
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Project description:Interaction proteomics of yeast Sac1-ALFA compared to untagged control strains
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Project description:We, being members of modENCODE consortium, have established an experimetal pipeline in C.elegans that allows global identification of the binding sites for transcription factors using chromatin immunoprecipitation followed by illumina high-throughput sequencing (ChIP-seq). In current study, we identified the binding sites for EOR-1 at L3 stage, which plays important roles in regulating RAS/RAF-mediated signaling during excretory system development and RAS/RAF- and WNT-mediated signaling during P12 fate specification. For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf
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