Postdoc, Sanford Burnham Prebys Medical Discovery Institute
Identification of novel drug-targetable epigenomic components of stress tolerance in neurons
Mature neurons are post-mitotic cells and represent a unique cell population in our body as in contrast with other cells these are not replaced during the life time of an organism. Little is understand about the adaptative mechanisms that allow these cells to coope with age-related cellular stress (e.g. oxidative stress). Understanding mechanisms that employ neurons to be resilient to cell death has great significance to find cures for neurodegenerative disorders, which impact an increasing number of elderly people and lack adequate treatment. My work aim to identify drug-targetable components that can decrease the vulnerability of neurons against age-related stress. Specifically, we identified a protein as a tissue-specific regulator of cellular stress-response in motoneurons. Transgenic mice (lacking this protein) mice develop normally, however aged mice show hallmarks of late-onset neurodegenerative diseases, suggesting that the identified protein is per se not needed for neurogenesis but required for neuroprotection against age-related increase of cellular stress. Tissue-restricted expression and enzymatic nature of this protein makes it an attractive target for drug development to treat neurodegenerative disorders.
Abstract: Embryonic development is a multistep process involving activation and repression of many genes. Enhancer elements in the genome are known to contribute to tissue and cell-type specific regulation of gene expression during the cellular differentiation. Thus, their identification and further investigation is important in order to understand how cell fate is determined. Integration of gene expression data (e.g., microarray or RNA-seq) and results of chromatin immunoprecipitation (ChIP)-based genome-wide studies (ChIP-seq) allows large-scale identification of these regulatory regions. However, functional validation of cell-type specific enhancers requires further in vitro and in vivo experimental procedures. Here we describe how active enhancers can be identified and validated experimentally. This protocol provides a step-by-step workflow that includes: 1) identification of regulatory regions by ChIP-seq data analysis, 2) cloning and experimental validation of putative regulatory potential of the identified genomic sequences in a reporter assay, and 3) determination of enhancer activity in vivo by measuring enhancer RNA transcript level. The presented protocol is detailed enough to help anyone to set up this workflow in the lab. Importantly, the protocol can be easily adapted to and used in any cellular model system.
Pub.: 13 Jul '16, Pinned: 28 Jun '17
Abstract: Retinoids are morphogens and have been implicated in cell fate commitment of embryonic stem cells (ESCs) to neurons. Their effects are mediated by RAR and RXR nuclear receptors. However, transcriptional cofactors required for cell and gene-specific retinoid signaling are not known. Here we show that protein arginine methyl transferase (PRMT) 1 and 8 have key roles in determining retinoid regulated gene expression and cellular specification in a multistage neuronal differentiation model of murine ESCs. PRMT1 acts as a selective modulator, providing the cells with a mechanism to reduce the potency of retinoid signals on regulatory "hotspots." PRMT8 is a retinoid receptor target gene itself and acts as a cell type specific transcriptional coactivator of retinoid signaling at later stages of differentiation. Lack of either of them leads to reduced nuclear arginine methylation, dysregulated neuronal gene expression, and altered neuronal activity. Importantly, depletion of PRMT8 results in altered expression of a distinct set of genes, including markers of gliomagenesis. PRMT8 is almost entirely absent in human glioblastoma tissues. We propose that PRMT1 and PRMT8 serve as a rheostat of retinoid signaling to determine neuronal cell specification in a context-dependent manner and might also be relevant in the development of human brain malignancy.
Pub.: 13 Nov '14, Pinned: 28 Jun '17
Abstract: Cell type specification relies on the capacity of undifferentiated cells to properly respond to specific differentiation-inducing signals. Using genomic approaches along with loss- and gain-of-function genetic models, we identified OCT4-dependent mechanisms that provide embryonic stem cells with the means to customize their response to external cues. OCT4 binds a large set of low-accessible genomic regions. At these sites, OCT4 is required for proper enhancer and gene activation by recruiting co-regulators and RAR:RXR or β-catenin, suggesting an unexpected collaboration between the lineage-determining transcription factor and these differentiation-initiating, signal-dependent transcription factors. As a proof of concept, we demonstrate that overexpression of OCT4 in a kidney cell line is sufficient for signal-dependent activation of otherwise unresponsive genes in these cells. Our results uncover OCT4 as an integral and necessary component of signal-regulated transcriptional processes required for tissue-specific responses.
Pub.: 04 Aug '16, Pinned: 28 Jun '17
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