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Unknown,Transcriptomics,Genomics,Proteomics

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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. 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.

ORGANISM(S): Kluyveromyces lactis

SUBMITTER: Lauren Booth

PROVIDER: E-GEOD-39027 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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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.

2012-06-30 | GSE39027 | GEO

K. lactis mating type regulator ChIP-chip

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

2012-06-25 | E-GEOD-38919 | biostudies-arrayexpress

K. lactis mating type regulator ChIP-chip

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

Project description:The hindlimb and external genitalia of present-day tetrapods are thought to derive from an ancestral common primordium that evolved to generate a wide diversity of structures adapted for efficient locomotion and mating in the ecological niche conquered by the species. We show that despite long evolutionary distance from the ancestral condition, the early primordium of the mouse external genitalia preserved the capacity to take hindlimb fates. In the absence of Tgfbr1, the pericloacal mesoderm generates an extra pair of hindlimbs at the expense of the external genitalia. It has been shown that the hindlimb and the genital primordia share many of their key regulatory factors. Tgfbr1 controls the response to those factors acting in a pioneer-like mode to modulate the accessibility status of regulatory elements that control the gene regulatory networks leading to the formation of genital or hindlimb structures. Our work uncovers a remarkable tissue plasticity with potential implications in the evolution of the hindlimb/genital area of tetrapods, and identifies a novel mechanism for Tgfbr1 activity that might also contribute to the control of other physiological or pathological processes.

2024-02-23 | GSE231592 | GEO

Significance of Immunohistochemical Expression of Fascin-1 in Colorectal Carcinoma

Project description:Colorectal carcinoma is a major health problem. As a malignant tumor, the malignant potential of colorectal carcinoma is based mainly on its ability to metastasis to different sites. Fascin-1 is an actin binding protein which is involved in reconstruction of intracellular actin network, the latter enforces the neoplastic cell to invade surrounding structures.

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Breakthrough infections by SARS-CoV-2 variants boost cross-reactive hybrid immune responses in mRNA-vaccinated Golden Syrian Hamsters

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2023-12-18 | GSE246866 | GEO

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Expression data from yeast heterologously expressing alpha-ENaC, CFTR or Kir2.1 alpha-ENaC]

Project description:Misfolded membrane proteins are retained in the endoplasmic reticulum (ER) and are subject to the ER associated degradation pathway, which clears the secretory pathway of potentially toxic species. While the transcriptional response to environmental stressors has been extensively studied, limited data exist describing the cellular response to misfolded membrane proteins. To this end, we expressed and then compared the transcriptional profiles elicited by the synthesis of three ER retained, misfolded ion channels: The Î± subunit of the epithelial sodium channel, ENaC, the cystic fibrosis transmembrane conductance regulator, CFTR, and an inwardly rectifying potassium channel, Kir2.1, which vary in their mass, membrane topologies, and quaternary structures. To examine transcriptional profiles in a null background, the proteins were expressed in yeast, which was previously used to examine the degradation requirements for each substrate. Surprisingly, the proteins failed to induce a canonical unfolded protein response or heat shock response, although messages encoding several cytosolic and ER lumenal protein folding factors rose when Î±ENaC or CFTR were expressed. In contrast, the levels of these genes were unaltered by Kir2.1 expression; instead, the yeast iron regulon was activated. Nevertheless, a significant number of genes that respond to various environmental stressors were upregulated by all three substrates, and when compared to previous microarray data we deduced the existence of a group of genes that reflect a novel misfolded membrane protein response. These data indicate that aberrant proteins in the ER elicit profound yet unique cellular responses. Yeast heterologously expressing Î±ENaC, CFTR, Kir2.1 or harboring a vector control were grown under identical conditions (at least 3 biological replicates) and subject to gene expression analysis.

2014-09-10 | E-GEOD-61243 | biostudies-arrayexpress

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