Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

The GATA transcription factor GtaC regulates early developmental gene expression dynamics in Dictyostelium

ABSTRACT: In many developmental systems, morphogenesis is coupled with dramatic changes in spatiotemporal gene expression, often orchestrated by the coordinated action of transcription factors. Development of the social soil amoebae Dictyostelium discoideum proceeds through a sequence of morphological and transcriptional changes, but the role of transcription factors in development is not well understood. GtaC, a GATA-type zinc-finger transcription factor, is essential for Dictyostelium development. It decodes pulsatile extracellular cAMP signals during early development and mediates cell-type differentiation at later stages. Here, we studied the developmental regulatory roles of GtaC through the concerted analysis of temporal ChIP- and RNA-sequencing data from strains that carry different alleles of gtaC. We show that GtaC exhibits temporally distinctive DNA-binding patterns throughout early development, accompanied by largely cotemporaneous expression of its target genes. We also show that GtaC binds DNA in two modes. One of these modes exhibits binding preferences for canonical GATA-like sequences, the regulatory consequences accompanying which is predominantly up-regulation of target gene expression. The other binding mode is mostly associated with down-regulation. Among its targets we find transcription factors that are essential for development as well as genes involved in cAMP signaling and cell-type specification. Our results suggest that GtaC is a master regulator that regulates multiple physiological processes during early development, when Dictyostelium transitions from a group of unicellular amoebae to an integrated multicellular organism. Cotemporaneous transcriptional profiling and ChIP sequencing during early Dictyostelium development

ORGANISM(S): Dictyostelium discoideum

SUBMITTER: Gad Shaulsky

PROVIDER: E-GEOD-63151 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Publications

The GATA transcription factor GtaC regulates early developmental gene expression dynamics in Dictyostelium.

Santhanam Balaji B Cai Huaqing H Devreotes Peter N PN Shaulsky Gad G Katoh-Kurasawa Mariko M

Nature communications 20150706

In many systems, including the social amoeba Dictyostelium discoideum, development is often marked by dynamic morphological and transcriptional changes orchestrated by key transcription factors. However, efforts to examine sequential genome-wide changes of gene regulation in developmental processes have been fairly limited. Here we report the developmental regulatory dynamics of GtaC, a GATA-type zinc-finger transcription factor, through the analyses of serial ChIP- and RNA-sequencing data. GtaC ...[more]

PMID: 26144553

Similar Datasets

Project description:Cross species comparison of genomes and transcriptomes is a powerful tool for understanding underlying biological processes, accurate functional classification of genes, and discovery of novel elements. The shift to next-generation sequencing platforms has tremendously accelerated the analysis of genomes and transcriptomes. The use of this technology for transcriptome analysis has many advantages over hybridization based technologies, including higher sensitivity and specificity, and eliminates the need for probe design. Using Illumina sequencing of mRNAs, we have captured the global transcriptional profiles of the developmental cycles of D. discoideum and D. purpureum. The morphology and transcriptional profiles in these two species have been largely conserved even after greater than 300 million years of divergence. We also captured the transcriptional profiles of prespore and prestalk cells from both species. The RNA-seq results correlate well with previously known markers and reveal many new transcripts with unique developmental regulation and cell type enrichment. Our analysis provides the first complete picture of the transcriptional landscape in both D. discoideum and D. purpureum. Transcriptional abundance of over 13,900 genome elements from seven time points of development, and prespore/prestalk cell types will be available through a graphical, highly-interactive, explorative web interface at: http://www.ailab.si/dictyexpress , which currently displays all of our published microarray data. Sequence coverage at a single nucleotide resolution will also be available through an interactive genome browser. These data, from morphology to genome to transcriptome, provide a global picture of the developmental cycles of D. discoideum and D. purpureum and will facilitate the functional classification of genes, as well as discovery of novel genes, splice variants, regulatory elements and non-coding RNAs. Keywords: Transcriptome Analysis Examination of 7 developmental time points in two cell types with 2 biological replicates for each sample.

Project description:The analysis of fungi secreted proteins has been increasingly employed as a powerful strategy in the prospecting of new catalysts with potential biotechnological application. Since enzyme production is strongly modulated by several factors such as pH, available nutrients, water content, oxygen levels and temperature, the evaluation of growth conditions is of utmost importance to achieve optimal enzyme production. Here, a non-sequenced wood-rotting fungus, L. crinitus, was selected as a model organism for secretome analysis by means of in vitro enzymatic assays and in-depth characterization via proteomics. For enzyme production, the fungus was cultured with several types and concentrations of carbon and nitrogen sources and variable water content. Five different carbon substrates (glucose, maltose, starch, sucrose, carboxymethylcellulose (CMC), glycerol and fructose) and three nitrogen containing compounds (urea, sodium nitrate and ammonium chloride) were used as substitutes of the original carbon and nitrogen sources in culture media. Interestingly, the biomass yield as well as the array of secreted proteins differed drastically under different growing conditions. A mixture of soluble secreted extracts derived from different culture conditions was analyzed both by shotgun mass spectrometry and through protein separation by two-dimensional gel electrophoresis (2DE) prior to identification via LC-MS/MS. Proteins were identified by sequence homology searches using mass spectrometry (MS)-driven BLAST. The spectrum of secreted enzymes comprised various types of CAZymes (carbohydrate-active enzymes), oxidase/reductases, proteases, lipase/esterases, proteins with non-related functions thereby classified as miscellany proteins and hypothetical or unknown predicted proteins. Although pre-separation by 2DE improved the number of identifications (protein map of 150 spots corresponding to 171 identifications) compared to the shotgun approach (98 identifications) both strategies revealed similar distribution of proteins within the functional categories described above. Culture media with reduced water content stimulated the expression of oxidases/reductases such as Lac, MnP, GMC oxidoreductases and glyoxal oxidase while hydrolases were induced during submerged fermentation. The diversity of proteins observed within both the CAZyme and oxidoreductase groups revealed in this fungus a powerful arsenal of enzymes dedicated to the breakdown and consumption of lignocellulose. Moreover, further secretome characterization after sequencing and analysis of the L. crinitus genome can potentially lead to the discovery of novel enzymes of industrial and biotechnological interest. Importantly, information on sequencing data could also reveal novel enzymes which production is strongly stimulated only in specific growing conditions.

Dataset Information

The GATA transcription factor GtaC regulates early developmental gene expression dynamics in Dictyostelium

Publications

The GATA transcription factor GtaC regulates early developmental gene expression dynamics in Dictyostelium.

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets