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RNA-seq data of mammalian cells treated with artificial transcription factors

ABSTRACT: RNA-seq data of mammalian cells treated with artificial transcription factors

PROVIDER: PRJNA1198988 | ENA |

REPOSITORIES: ENA

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RNA-seq data of mammalian cells treated with artificial transcription factors

Project description:Interferon (IFN)-γ is a central regulator of cell-mediated immunity in human health and disease, but reduced expression of the target receptors impairs signaling activity and leads to immunotherapy resistance. Although intracellular expression of IFN-γ restores signaling and downstream functions, we lack tools to activate the IFNG gene instead of cell surface receptors. This work describes the design and characterization of an artificial transcription factor (ATF) protein that recognizes the IFNG gene with six zinc finger domains, which are dovetailed to a VP64 signaling domain that promotes gene transcription and translation. Biological studies with human Jurkat T cells reveal that the ATF treatment induces potent IFN-γ expression and amplifies the gene transcriptome profile for multiple class I HLA alleles and interferon-stimulated genes (ISGs). Biophysical characterization showed the recombinant ATF protein recognizes the human IFNG gene with nanomolar affinity (KD = 5.27 ± 0.3 nM), adopts a protein secondary structure associated with the ββα-fold of zinc finger domains, and is resistant to thermal denaturation. These studies demonstrate that transcriptional targeting of cytokine genes, rather than surface receptors, can activate cytokine expression and show potential for directing immune function.

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Artificial acceleration of mammalian cell reprogramming by bacterial proteins

Project description:Mammalian cell reprogramming to pluripotency can be achieved by overexpression of a set of defined transcription factors (Yamanaka factors). Various gene products regulate progression of this process. Some small molecule compounds have been identified to influence it through interacting cellular proteins by library screenings. Although such compounds are useful to reveal mechanisms underlying reprogramming as well as enhancing reprogramming efficiency, the screening usually requires huge amount of compounds to be tested to identify an effective one (ex., one effective molecule in several tens of thousands). Here, we show a case report that there are gene products that can affect efficiency of mammalian cell reprogramming in a xeno-species. Thirty genes specific for a bacterium Wolbachia pipientis, as a pilot trial, were forcedly expressed along with Yamanaka factors in mammalian cells. As a result, we found that 8 Wolbachia genes affected the reprogramming efficiency either positively or negatively. This is a surprisingly high probability compared with small molecule compounds reported. Although this study is just a case report, it shows that screenings using genes from a xenospecies can be so effective. In principle, use of genes from a xenospecies could be useful for controls of various cellular states such as induction or maintenance of a cell type of interest and development novel drugs. Our findings suggest that systems using genes from xeno-species can be novel strategies for a wide variety of cellular events possibly with a high hit rate.

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Neuronal chromatin remodeling factors in the mammalian nervous system

Project description:Neuronal chromatin remodeling factors in the mammalian nervous system

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