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CHD chromatin remodelers regulate separate gene sets and distinct stages of Dictyostelium development

ABSTRACT: We utilized RNA-seq to profile expression levels in wild type AX2 cells and three mutants for the CHD family of ATP-dependent chromatin remodellers in Dictyostelium discoideum. Total RNA was polyA enriched and sequenced at two stages of development: in the growth stage (0H) and in 5H cAMP pulsed cells (5H). All mutants analysed were also in the AX2 background. Looking at mRNA levels in AX2, chdA-, chdB- and chdC-.

ORGANISM(S): Dictyostelium discoideum

SUBMITTER: James Plattt

PROVIDER: E-GEOD-47222 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Different CHD chromatin remodelers are required for expression of distinct gene sets and specific stages during development of Dictyostelium discoideum.

Platt James L JL Rogers Benjamin J BJ Rogers Kelley C KC Harwood Adrian J AJ Kimmel Alan R AR

Development (Cambridge, England) 20131201 24

Control of chromatin structure is crucial for multicellular development and regulation of cell differentiation. The CHD (chromodomain-helicase-DNA binding) protein family is one of the major ATP-dependent, chromatin remodeling factors that regulate nucleosome positioning and access of transcription factors and RNA polymerase to the eukaryotic genome. There are three mammalian CHD subfamilies and their impaired functions are associated with several human diseases. Here, we identify three CHD orth ...[more]

PMID: 24301467

Similar Datasets

CHD chromatin remodelers regulate separate gene sets and distinct stages of Dictyostelium development

Project description:We utilized RNA-seq to profile expression levels in wild type AX2 cells and three mutants for the CHD family of ATP-dependent chromatin remodellers in Dictyostelium discoideum. Total RNA was polyA enriched and sequenced at two stages of development: in the growth stage (0H) and in 5H cAMP pulsed cells (5H). All mutants analysed were also in the AX2 background.

2014-01-03 | GSE47222 | GEO

DcgA knock-out experiment in Dictyostelium discoideum

Project description:Four replicates of DcgA gene knockout D. discoideum clones were sequenced together with four replicates of random integrant clones. All clones were from the same AX2 strain.

2017-02-01 | E-MTAB-3829 | biostudies-arrayexpress

A Dictyostelium SH2 domain adaptor protein required for correct DIF-1 signaling and pattern formation

Project description:When developing in the light slug formation in LrrB null (lrrB-) mutants is delayed, relative to the parental strain, and the slugs are highly defective in phototaxis and thermotaxis. In the dark the mutant arrests development as an elongated mound, in a novel process we term dark stalling. The developmental and phototaxis defects are cell autonomous and marker analysis shows that the pstO prestalk sub-region of the slug is aberrant in the lrrB- mutant. Expression profiling reveals many other alterations in gene expression in lrrB- slugs compared to the wild-type parental Ax2 line, including greatly reduced expression of the ecmB gene.

2011-05-31 | E-TABM-1090 | biostudies-arrayexpress

The Dictyostelium retinoblastoma-like rblA gene is a major regulator of S-phase, mitotic and developmental gene expression

Project description:In metazoans, the retinoblastoma tumor suppressor has two major functions. In the first, it represses genes whose products are required for S-phase entry and S-phase progression, and thus stabilizes the G1 phase. In a second function, Rb synergizes with factors that induce cell cycle exit and terminal differentiation. Using mRNAseq and microarray transcriptional profiling, we show that rblA, the Rb ortholog of the Amebozoan Dictyostelium, has both of these functions. We characterize the action of rblA in the Dictyostelium cell cycle in detail, and in particular show that it represses not only S-phase genes but also almost all genes whose products are involved in mitosis. We compare rblA null mutants with their parent strain Ax2 at two developmental stages, vegetative growth and the preculminant stage of fruiting body formation; cell cycle genes show misregulation in the mutant at both stages.

2011-11-02 | E-TABM-1087 | biostudies-arrayexpress

A balance in the delivery of ER components and the vacuolar proton pump determines phagosome acidification

Project description:As part of a study comparing phagosome composition in wild-type Dictyostelium discoideum with mutants in two cytoskeletal/motor proteins, we compared global gene expression and proteomes between the strains to test whether differences in mRNA and protein abundance were correlated with changes in phagosomal composition. abp1 and myoK mutants in both the Ax2 and DH1 backgrounds were compared with their respective wild-type parents.Both analyses converged and confirmed the phagosome analysis (supplemental Tables). Protein differences were markedly fewer in the myoK-null mutant than in the abp1 null lysate. Proteins of known function, differential in the myoK-null lysate, were involved in remodeling of the plasma membrane and early membrane trafficking. Proteins differential in the abp1-null lysate spanned various functions at all levels of cell metabolism. Most of the proteins differential in 2D-DIGE displayed similar mutant-to-wt ratios at the mRNA level in microarrays. A prominent example of overlap is the 1.4 fold overexpression (p ??? 0.016) of Vps5, both in proteomics and microarray analyses of abp1-null cells. Like half of the proteins involved in membrane trafficking that are differential in microarray analyses of abp1-null cells, Vps5 is putatively involved in endosome-to-Golgi trafficking as a retromer sorting nexin. Therefore, one might speculate that, in addition to direct effects on phagocytic uptake, absence of Abp1 has an impact on endosome-to-Golgi trafficking.

2012-02-06 | E-MTAB-978 | biostudies-arrayexpress

Argonaute proteins affect siRNA levels and accumulation of a novel extrachromosomal DNA from the Dictyostelium retrotransposon DIRS-1

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2014-12-04 | E-GEOD-56111 | biostudies-arrayexpress

Transcription profiling of Dictyostelium discoideum strains during growth and early development

Project description:Dictyostelium discoideum is an ideal organism to study SH2-domain mediated signal transduction because not only does it provide relatively simple model cell biological and developmental processes, but also possesses a highly streamlined repertoire of SH2-containing proteins. We studied one such novel protein, LrrB, by gene deletion and protein interaction experiments. A DNA microarray experiment carried out on growing cells reveals misregulation of a small set of vegetative genes in the lrrB knockout strain when compared to the parent, Ax2. Real time PCR experiments described in the accompanying manuscript extend these observations to show how this affects gene expression during early development, and that knockouts in another SH2 protein that interacts with LrrB show misregulation of some of the same genes, suggesting that these proteins may form part of a novel adaptor complex that regulates gene expression during Dictyostelium growth and early development.

2010-06-09 | E-TABM-803 | biostudies-arrayexpress

cAR1 rescues developmental gene expression defects of rasC/rasG double mutants

Project description:It has been shown previously that rasC- cells do not aggregate, predominantly as a result of a defective cAMP relay, although there are also subtle defects in cAMP chemotaxis. There is no appreciable effect on early gene expression in response to starvation. In contrast, rasG-/rasC- cells are totally blocked in aggregation, cAMP relay and cAMP chemotaxis and, in addition, there is no induction of carA and gpaB gene expression, in response to starvation. However, expression of carA from the actin15 promoter in vegetative rasG-/rasC- cells restores the induced expression of carA and gpaB in response to starvation, but has no effect on the defects in aggregation, cAMP chemotaxis and cAMP relay. In order to determine the generality of the effect on early gene expression, micro array analysis was undertaken. These results revealed 121 genes that were significantly (p<0.05) induced in expression 5 fold or more in wild type cells, in response to starvation. Of these genes, the expression of 100 was not induced significantly in rasG-/rasC- cells, but the expression of most of these was restored in rasG-/rasC-/[act15:carA] cells, in response to starvation. These results indicate that the inhibition of early gene expression in rasG-/rasC- cells and its restoration in response to the expression of carA in vegetative cells is a fairly general phenomenon. Thus, signaling through RasG or RasC is required for the induction of expression of many genes that occurs in response to starvation, but the constitutive expression of carA is able to bypass this requirement.

2010-10-31 | E-TABM-1085 | biostudies-arrayexpress

Regulation of nucleosome positioning by a CHD Type III chromatin remodeller and its relationship to developmental gene expression in Dictyostelium [RNA-seq]

Project description:We utilized RNA-seq to profile expression levels in wild type Ax2 cells and a mutants for ChdC a member of a family of ATP-depedent chromatin remodellers in Dictyostelium discoideum. Total RNA was polyA enriched and sequenced at two stages of development: in the growth stage (0H) and loose mound stage of development (10-12H)

2017-02-26 | GSE70141 | GEO

Developmental expression profile of Dictyostelium discoideum: wild type (AX2) and polyketide synthase knock-out mutants

Project description:Knockout mutants of polyketide synthase genes were generated (pks1, pks2, pks3, pks14, pks18, pks37) and compared to wild-type AX2 strain of Dictyostelium discoideum using Agilent custom microarrays. The Dictyostelium cells were harvested at eight developmental stages (Amoeboid, Intiation of starvation, loose aggregate, Streaming, Mound, Slug, early culminant, Fruiting body) and subjected to microarray based expression profiling.

2015-07-18 | GSE71036 | GEO

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