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Gene expression arrays comparing Kluyveromyces lactis wild-type a cells to MATa2 knock-out a cells and wild-type alpha cells to MATalpha2 knock-out alpha cells

ABSTRACT: We examine how different transcriptional network structures can evolve from a common, ancestral network. We show that regulatory protein modularity, conversion of one cis-regulatory sequence to another, distribution of binding energy among protein-protein and protein-DNA interactions, and exploitation of ancestral network features all contribute to the evolution of a novel mode of regulation at a conserved gene set. The formation of this derived mode of regulation did not disrupt the ancestral mode and thereby created a hybrid regulatory state where both means of transcription regulation (ancestral and derived) contribute to the conserved expression pattern of the network. Finally, we show how this hybrid regulatory state has resolved in different ways in different lineages to generate the diversity of regulatory network structures observed in modern species.

ORGANISM(S): Kluyveromyces lactis

PROVIDER: GSE39027 | GEO | 2012/06/30

SECONDARY ACCESSION(S): PRJNA169630

REPOSITORIES: GEO

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Gene expression arrays comparing Kluyveromyces lactis wild-type a cells to MATa2 knock-out a cells and wild-type alpha cells to MATalpha2 knock-out alpha cells

Project description:We examine how different transcriptional network structures can evolve from a common, ancestral network. We show that regulatory protein modularity, conversion of one cis-regulatory sequence to another, distribution of binding energy among protein-protein and protein-DNA interactions, and exploitation of ancestral network features all contribute to the evolution of a novel mode of regulation at a conserved gene set. The formation of this derived mode of regulation did not disrupt the ancestral mode and thereby created a hybrid regulatory state where both means of transcription regulation (ancestral and derived) contribute to the conserved expression pattern of the network. Finally, we show how this hybrid regulatory state has resolved in different ways in different lineages to generate the diversity of regulatory network structures observed in modern species. a2 KO and alpha2 KO mRNA abundance was measured relative to a WT cell of the same mating type. 2 replicates each. Dye-swaps were performed.

2012-06-29 | E-GEOD-39027 | biostudies-arrayexpress

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Project description:We examine how different transcriptional network structures can evolve from an ancestral network. We show that regulatory protein modularity, conversion of one cis-regulatory sequence to another, distribution of binding energy among protein-protein and protein-DNA interactions, and exploitation of ancestral network features all contribute to the evolution of a novel mode of regulation at a conserved gene set. The formation of this derived mode of regulation did not disrupt the ancestral mode and thereby created a hybrid regulatory state where both means of transcription regulation (ancestral and derived) contribute to the conserved expression pattern of the network. Finally, we show how this hybrid regulatory state has resolved in different ways in different lineages to generate the diversity of regulatory network structures observed in modern species. Six samples were analyzed, three of which were controls and three of which were experimental

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K. lactis mating type regulator ChIP-chip

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Treg specific Gata3 knock out array

Project description:The transcription factor Foxp3 is indispensible for the differentiation and function of regulatory T cells (Treg cells). To gain insights into the molecular mechanisms of Foxp3 mediated gene expression we purified Foxp3 complexes and explored their composition. Biochemical and mass-spectrometric analyses revealed that Foxp3 forms multi-protein complexes of 400-800 kDa or larger and identified 361 associated proteins ~30% of which are transcription-related. Foxp3 directly regulates expression of a large proportion of the genes encoding its co-factors. Reciprocally, some transcription factor partners of Foxp3 facilitate its expression. Functional analysis of Foxp3 cooperation with one such partner, Gata3, provided further evidence for a network of transcriptional regulation afforded by Foxp3 and its associates to control distinct aspects of Treg cell biology. Gene expression profile of Treg specific knock-out of Gata3 vs. their littermate controls were analyzed to gain insight into Gata3 dependendent genes in Treg cells.

2012-08-28 | GSE39864 | GEO

Tgfbr1 controls developmental plasticity between the hindlimb and external genitalia by remodeling their regulatory landscape

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Treg specific Gata3 knock out array

2012-08-28 | E-GEOD-39864 | biostudies-arrayexpress

TSG knock out in hiPSCs

Project description:We will perform RNAseq to evaluate the effects of the loss of a list of TSGs on the transcriptome.

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Phenotypic characterization of an alpha 4 neuronal nicotinic acetylcholine receptor subunit knock-out mouse.

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Promotion of somatic CAG repeat expansion by Fan1 knock-out in Huntington's disease knock-in mice is blocked by Mlh1 knock-out.

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