Role of Epigenetics in Unicellular to Multicellular Transition in Dictyostelium
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA565988 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR10133900.fastq.gz | Fastqsanger.gz | |||
| SRR10133901.fastq.gz | Fastqsanger.gz | |||
| SRR10133902.fastq.gz | Fastqsanger.gz | |||
| SRR10133903.fastq.gz | Fastqsanger.gz | |||
| SRR10133904.fastq.gz | Fastqsanger.gz |
Items per page: 5 1 - 5 of 234 |
Similar Datasets
Project description:The evolution of multicellularity is a critical event that remains incompletely understood. We use the social amoeba, Dictyostelium discoideum, one of the rare organisms that exists in both unicellular and multicellular stages, to examine the role of epigenetics in regulating multicellularity. While transitioning to multicellular states, patterns of H3K4 methylation and H3K27 acetylation significantly change. By combining transcriptomics, epigenomics, chromatin accessibility, and syntenic analyses with other unicellular and multicellular organisms, we identify 52 conserved genes, which are specifically accessible and expressed during multicellular states. We validated that four of these genes, including the H3K27 deacetylase hdaD, are necessary and that an SMC-like gene, smcl1, is sufficient for multicellularity. These results highlight the importance of epigenetics in reorganizing chromatin architecture to facilitate the evolution of multicellularity.
2021-06-15 | PXD024225 | panorama
Project description:BackgroundThe evolution of multicellularity is a critical event that remains incompletely understood. We use the social amoeba, Dictyostelium discoideum, one of the rare organisms that readily transits back and forth between both unicellular and multicellular stages, to examine the role of epigenetics in regulating multicellularity.ResultsWhile transitioning to multicellular states, patterns of H3K4 methylation and H3K27 acetylation significantly change. By combining transcriptomics, epigenomics, chromatin accessibility, and orthologous gene analyses with other unicellular and multicellular organisms, we identify 52 conserved genes, which are specifically accessible and expressed during multicellular states. We validated that four of these genes, including the H3K27 deacetylase hdaD, are necessary and that an SMC-like gene, smcl1, is sufficient for multicellularity in Dictyostelium.ConclusionsThese results highlight the importance of epigenetics in reorganizing chromatin architecture to facilitate multicellularity in Dictyostelium discoideum and raise exciting possibilities about the role of epigenetics in the evolution of multicellularity more broadly.
| S-EPMC8094536 | biostudies-literature
Project description:This SuperSeries is composed of the SubSeries listed below.
2021-04-21 | GSE137604 | GEO
Project description:Dictyostelium discoideum is a unicellular slime mold, developing into a multicellular fruiting body upon starvation. Development is accompanied by large-scale shifts in gene expression program, but underlying features of chromatin spatial organization remain unknown. Here, we report that the Dictyostelium 3D genome is organized into largely consecutive, non-hierarchical and weakly insulated loops positionally conserved at the onset of multicellular development. The transcription level within loops tends to be higher than in adjacent regions. Loops frequently contain functionally linked genes and genes which coherently change expression level during development. Genes at loop anchors are predominantly in the convergent orientation. Our data suggest that the loop profile may arise from the interplay between transcription and cohesin-driven chromatin extrusion. In particular, a convergent gene pair serves as a bidirectional extrusion barrier or a “diode” that controls passage of the cohesin extruder by relative transcription level of paired genes.
2024-12-31 | GSE247397 | GEO
Project description:Dictyostelium discoideum is a unicellular slime mold developing into a multicellular fruiting body upon starvation. Development is accompanied by large-scale shifts in gene expression program, but underlying rearrangements of chromatin structure remain unknown. Here, we report a unique Dictyostelium 3D genome organization represented by largely consecutive, non-hierarchical and weakly insulated loops of diverse morphology conserved at the onset of multicellular development. Loops are chromosomal neighborhoods facilitating transcription and frequently containing functionally-linked genes which coherently change expression level during development. Loop anchors are enriched with convergent gene pairs, putative enhancers and boundaries of synteny gene blocks that point at their role in genome function and evolution. Our data suggest that the loop profile arises from the interplay between transcription and cohesin-driven chromatin extrusion. In this confunction, a convergent gene pair serves as a “diode” effectively passing the extruder from upstream or downstream direction in dependence on transcription level of the paired genes.
2024-12-31 | GSE247396 | GEO
Project description:Dictyostelium discoideum is a unicellular slime mold developing into a multicellular fruiting body upon starvation. Development is accompanied by large-scale shifts in gene expression program, but underlying rearrangements of chromatin structure remain unknown. Here, we report a unique Dictyostelium 3D genome organization represented by largely consecutive, non-hierarchical and weakly insulated loops of diverse morphology conserved at the onset of multicellular development. Loops are chromosomal neighborhoods facilitating transcription and frequently containing functionally-linked genes which coherently change expression level during development. Loop anchors are enriched with convergent gene pairs, putative enhancers and boundaries of synteny gene blocks that point at their role in genome function and evolution. Our data suggest that the loop profile arises from the interplay between transcription and cohesin-driven chromatin extrusion. In this confunction, a convergent gene pair serves as a “diode” effectively passing the extruder from upstream or downstream direction in dependence on transcription level of the paired genes.
2024-12-31 | GSE246367 | GEO
Project description: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
2015-07-02 | E-GEOD-63151 | biostudies-arrayexpress
Project description:Calmodulin (CaM) is an essential calcium-binding protein within eukaryotes. CaM binds to calmodulin-binding proteins (CaMBPs) and influences a variety of cellular and developmental processes. In this study, we used immunoprecipitation coupled with mass spectrometry (LC-MS/MS) to reveal over 500 putative CaM interactors in the model organism Dictyostelium discoideum. Our analysis revealed several known CaMBPs in Dictyostelium and mammalian cells (e.g., myosin, calcineurin), as well as many novel interactors (e.g., cathepsin D). Gene ontology (GO) term enrichment and Search Tool for the Retrieval of Interacting proteins (STRING) analyses linked the CaM interactors to several cellular and developmental processes in Dictyostelium including cytokinesis, gene expression, endocytosis, and metabolism. The primary localizations of the CaM interactors include the nucleus, ribosomes, vesicles, mitochondria, cytoskeleton, and extracellular space. These findings are not only consistent with previous work on CaM and CaMBPs in Dictyostelium, but they also provide new insight on their diverse cellular and developmental roles in this model organism. In total, this study provides the first in vivo catalogue of putative CaM interactors in Dictyostelium and sheds additional light on the essential roles of CaM and CaMBPs in eukaryotes.
| S-EPMC7915506 | biostudies-literature
Project description: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.
2015-07-02 | GSE63151 | GEO
Project description:Dictyostelium discoideum behavior depends on nutrients. When sufficient food is present these amoebae exist in a unicellular state (vegetative growth), but upon starvation they aggregate into a multicellular organism (developmental growth). For proteomics 30 minutes and eight hour cultures of D. discoideum under vegetative and starved growth conditions were compared by DIA-LFQ. This unique biology makes D. discoideum an ideal model for investigating how fundamental metabolism commands cell differentiation and function. We show here that reactive oxygen species (ROS), generated as a consequence of nutrient limitation, lead to the sequestration of the amino acid cysteine in the antioxidant glutathione, limiting the use of its sulfur atom for processes such as protein translation and FeS cluster-containing enzyme activity that contribute to mitochondrial metabolism and cellular proliferation. Such regulated sulfur sequestration maintains D. discoideum in a non-proliferating state that paves the way for multicellular development. This new mechanism of ROS signaling highlights oxygen and sulfur as simple, early evolutionary signaling molecules dictating cell fate, with implications for responses to nutrient fluctuations in higher eukaryotes.
2021-03-23 | PXD023404 | Pride