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Deeply conserved gene-regulatory functions of carboxy-terminal domains in dictyostelid C-module-binding factors

ABSTRACT: We describe the gene expression pattern of a Dictyostelium discoideum mutant depleted in the C-module-binding factor (CbfA) and autonomous gene-regulatory activities of CbfA carboxy-terminal domains (CbfA-CTDs)

ORGANISM(S): Dictyostelium discoideum

PROVIDER: GSE38418 | GEO | 2012/06/03

SECONDARY ACCESSION(S): PRJNA167805

REPOSITORIES: GEO

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Deeply conserved gene-regulatory functions of carboxy-terminal domains in dictyostelid C-module-binding factors

Project description:We describe the gene expression pattern of a Dictyostelium discoideum mutant depleted in the C-module-binding factor (CbfA) and autonomous gene-regulatory activities of CbfA carboxy-terminal domains (CbfA-CTDs) Comparison of gene expression in growing cells of a CbfA mutant compared to wild-type

2012-06-03 | E-GEOD-38418 | biostudies-arrayexpress

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Project description:The intent of the experiment was to gather transcriptomic data from terminally differentiated cell types --spore, stalk, and cup cells-- in a simple multicellular model system, Dictyostelium discoideum, in order to characterize the cell-type specific gene expression patterns. Specifically, we dissociated and collected each cell type from the fruiting bodies of D. discoideum at 24 hours of development. We also collected exponentially growing vegetative cells of D. discoideum.

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Conserved gene regulatory function of the carboxy-terminal domain of dictyostelid C-module-binding factor.

Project description:C-module-binding factor A (CbfA) is a jumonji-type transcription regulator that is important for maintaining the expression and mobility of the retrotransposable element TRE5-A in the social amoeba Dictyostelium discoideum. CbfA-deficient cells have lost TRE5-A retrotransposition, are impaired in the ability to feed on bacteria, and do not enter multicellular development because of a block in cell aggregation. In this study, we performed Illumina RNA-seq of growing CbfA mutant cells to obtain a list of CbfA-regulated genes. We demonstrate that the carboxy-terminal domain of CbfA alone is sufficient to mediate most CbfA-dependent gene expression. The carboxy-terminal domain of CbfA from the distantly related social amoeba Polysphondylium pallidum restored the expression of CbfA-dependent genes in the D. discoideum CbfA mutant, indicating a deep conservation in the gene regulatory function of this domain in the dictyostelid clade. The CbfA-like protein CbfB displays ?25% sequence identity with CbfA in the amino-terminal region, which contains a JmjC domain and two zinc finger regions and is thought to mediate chromatin-remodeling activity. In contrast to CbfA proteins, where the carboxy-terminal domains are strictly conserved in all dictyostelids, CbfB proteins have completely unrelated carboxy-terminal domains. Outside the dictyostelid clade, CbfA-like proteins with the CbfA-archetypical JmjC/zinc finger arrangement and individual carboxy-terminal domains are prominent in filamentous fungi but are not found in yeasts, plants, and metazoans. Our data suggest that two functional regions of the CbfA-like proteins evolved at different rates to allow the occurrence of species-specific adaptation processes during genome evolution.

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Project description:A sequencing-based profiling method (RiboMeth-seq) for ribose methylations was applied to study methylation patterns in Dictyostelium discoideum

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