Identification of Small Activating RNAs that Enhance Endogenous <i>OCT4</i> Expression in Human Mesenchymal Stem Cells

Wang, Ji; Huang, Vera; Ye, Lin; Bárcena, Alicia; Lin, Guiting; Lue, Tom F.; Li, Long Cheng

doi:10.1089/scd.2014.0290

Cited by 17 publications

(9 citation statements)

References 40 publications

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“…It is important to note that genes completely silenced by DNA methylation also tend to respond poorly to RNAa [8]. However, treatments with epigenetic modifying agents such as DNA demethylation agents and histone deacetylase inhibitors have been shown to restore susceptibility to or enhance RNAa [8,34] ( Fig. 1F ).…”

Section: Experimental Considerationsmentioning

confidence: 99%

“…Unbiased tiling design leads to the identification of saRNAs [9,11,34]; however, this approach can be time-consuming, expensive, and inefficient. Based on empirical observations, we have generated a set of rules that have improved the chance of identifying functional saRNA targets [18].…”

Section: Experimental Considerationsmentioning

confidence: 99%

“…In some cases, certain areas of a gene promoter support ‘hotspots’ in which several neighboring saRNAs induce variable levels of gene expression. Such regions can be identified by creating additional candidate saRNAs targeting overlapping or neighboring sequence [34]. These duplexes should also adhere to design rules as best as possible, although they may likely be less desirable by design standards.…”

Section: Experimental Considerationsmentioning

confidence: 99%

“…It is unclear if all genes are susceptible to activation if all possible targets on their promoters are exhausted. It has been shown that genes completely silenced by DNA methylation [8] and/or genes silenced in a tissue- or cell type-specific manner are less accessible to RNAa [34]. In such cases, treating cells with subtoxic doses of demethylating agents (e.g.…”

Section: Experimental Considerationsmentioning

confidence: 99%

“…5-AzaC) [8] or histone deacetylase inhibitors [e.g. valproic acid (VPA)]) [34] may restore/promote susceptibility to RNAa ( Fig. 1F ).…”

Section: Experimental Considerationsmentioning

confidence: 99%

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Inducing gene expression by targeting promoter sequences using small activating RNAs

et al. 2015

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Vector-based systems comprised of exogenous nucleic acid sequences remain the standard for ectopic expression of a particular gene. Such systems offer robust overexpression, but have inherent drawbacks such as the tedious process of construction, excluding sequences (e.g. introns and untranslated regions) important for gene function and potential insertional mutagenesis of host genome associated with the use of viral vectors. We and others have recently reported that short double-stranded RNAs (dsRNAs) can induce endogenous gene expression by targeting promoter sequences in a phenomenon referred to as RNA activation (RNAa) and such dsRNAs are termed small activating RNAs (saRNAs). To date, RNAa has been successfully utilized to induce the expression of different genes such as tumor suppressor genes. Here, we describe a detailed protocol for target selection and dsRNA design with associated experiments to facilitate RNAa in cultured cells. This technique may be applied to selectively activate endogenous gene expression for studying gene function, interrogating molecular pathways and reprogramming cell fate.

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Section: Experimental Considerationsmentioning

confidence: 99%

Section: Experimental Considerationsmentioning

confidence: 99%

Section: Experimental Considerationsmentioning

confidence: 99%

Section: Experimental Considerationsmentioning

confidence: 99%

“…5-AzaC) [8] or histone deacetylase inhibitors [e.g. valproic acid (VPA)]) [34] may restore/promote susceptibility to RNAa ( Fig. 1F ).…”

Section: Experimental Considerationsmentioning

confidence: 99%

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Inducing gene expression by targeting promoter sequences using small activating RNAs

et al. 2015

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Regulation of Oct4 in stem cells and neural crest cells

Patel

Parchem

2022

Birth Defects Research

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During embryonic development, cells gradually restrict their developmental potential as they exit pluripotency and differentiate into various cell types. The POU transcription factor Oct4 (encoded by Pou5f1) lies at the center of the pluripotency machinery that regulates stemness and differentiation in stem cells, and is required for reprogramming of somatic cells into induced pluripotent stem cells (iPSCs). Several studies have revealed that Oct4 and other stemness genes are also expressed in multipotent cell populations such as neural crest cells (NCCs), and are required to expand the NCC developmental potential. Transcriptional regulation of Oct4 has been studied extensively in stem cells during early embryonic development and reprogramming, but not in NCCs. Here, we review how Oct4 is regulated in pluripotent stem cells, and address some of the gaps in knowledge about regulation of the pluripotency network in NCCs.

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Small RNA-Guided Transcriptional Gene Activation (RNAa) in Mammalian Cells

2017

RNA Activation

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Small RNA partnering with Argonaute (Ago) proteins plays important roles in diverse biological processes mainly by suppressing the expression of cognate target sequences. Mounting evidence reveals that the small RNA-Ago pathway can also positively regulate gene expression, a phenomenon termed as RNA activation (RNAa), which is evolutionarily conserved from Caenorhabditis elegans to human. In this chapter, I provide a general overview of mammalian RNAa phenomena and their basic characteristics and discuss recent advances toward understanding the nature of the molecular machinery responsible for RNAa and the development of RNAa-based research tools and therapeutics.

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Identification of Small Activating RNAs that Enhance Endogenous OCT4 Expression in Human Mesenchymal Stem Cells

Cited by 17 publications

References 40 publications

Inducing gene expression by targeting promoter sequences using small activating RNAs

Inducing gene expression by targeting promoter sequences using small activating RNAs

Regulation of Oct4 in stem cells and neural crest cells

Small RNA-Guided Transcriptional Gene Activation (RNAa) in Mammalian Cells

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