Pivots of pluripotency: The roles of non-coding RNA in regulating embryonic and induced pluripotent stem cells

Institute for Cell Engineering, The Johns Hopkins University School of Medicine
Biochimica et Biophysica Acta (Impact Factor: 4.66). 10/2012; 1830(2). DOI: 10.1016/j.bbagen.2012.10.014
Source: PubMed


Induced pluripotent stem cells (iPSC) derived from reprogrammed patient somatic cells possess enormous therapeutic potential. However, unlocking the full capabilities of iPSC will require an improved understanding of the molecular mechanisms which govern the induction and maintenance of pluripotency, as well as directed differentiation to clinically relevant lineages. Induced pluripotency of a differentiated cell is mediated by sequential cascades of genetic and epigenetic reprogramming of somatic histone and DNA CpG methylation marks. These genome-wide changes are mediated by a coordinated activity of transcription factors and epigenetic modifying enzymes. Non-coding RNAs (ncRNAs), including microRNAs (miRNAs) and long non-coding RNAs (lncRNAs), are now recognized as an important third class of regulators of the pluripotent state.

Scope of review:
This review surveys the currently known roles and mechanisms of ncRNAs in regulating the embryonic and induced pluripotent states.

Major conclusions:
Through a variety of mechanisms, ncRNAs regulate constellations of key pluripotency genes and epigenetic regulators, and thus critically determine induction and maintenance of the pluripotent state.

General significance:
A further understanding of the roles of ncRNAs in regulating pluripotency may help assess the quality of human iPSC reprogramming. Additionally, ncRNA biology may help decipher potential transcriptional and epigenetic commonalities between the self renewal processes that govern both ESC and tumor initiating cancer stem cells (CSC). This article is part of a Special Issue entitled Biochemistry of Stem Cells.

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    • "LncRNAs play critical roles in epigenetic modulation of chromatin structure by regulating key genes in specific cancerous cells [186,187]. Distinct chromatin signatures are associated with lncRNAs encoding genes, and these signatures are demonstrably different in cancer cells, such as in colorectal carcinoma [188]. It found that the expression of elncRNA, instead of plncRNA, was associated with enhanced expression of neighboring protein-coding genes during erythropoiesis [157]. "
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    ABSTRACT: Long non-coding RNAs (lncRNAs) are non-protein coding transcripts longer than 200 nucleotides. The post-transcriptional regulation is influenced by these lncRNAs by interfering with the microRNA pathways, involving in diverse cellular processes. The regulation of gene expression by lncRNAs at the epigenetic level, transcriptional and post-transcriptional level have been well known and widely studied. Recent recognition that lncRNAs make effects in many biological and pathological processes such as stem cell pluripotency, neurogenesis, oncogenesis and etc. This review will focus on the functional roles of lncRNAs in epigenetics and related research progress will be summarized.
    Full-text · Article · Sep 2014 · Biological Procedures Online
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    • "However, the method for generating iPS cells involves complex genetic manipulation and it is beset by low efficiency of conversion and yield ( Liao et al., 2008). Currently, great strides are being made to improve the efficiency of iPS cell production by incorporating small molecules, vitamin C, valporic acid, microRNAs and different combinations of transcriptional factors into the protocols (reviewed by Huo & Zambidis, 2013; Jung et al., 2014). Two recent sets of groundbreaking studies reported in Nature appear to overcome most of these problems ( Obokata et al., 2014a; Obokata et al., 2014b). "
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    ABSTRACT: Currently, there are genetic- and chemical-based methods for producing pluripotent stem cells from somatic cells, but all of them are extremely inefficient. However, a simple and efficient technique has recently been reported by Obokata et al (2014a, b) that creates pluripotent stem cells through acid-based treatment of somatic cells. These cells were named stimulus-triggered acquisition of pluripotency (STAP) stem cells. This would be a major game changer in regenerative medicine if the results could be independently replicated. Hence, we isolated CD45 + splenocytes from five-day-old Oct4-GFP mice and treated the cells with acidified (pH 5.7) Hank’s Balanced Salt Solution (HBSS) for 25 min, using the methods described by Obokata et al 2014c. However, we found that this method did not induce the splenocytes to express the stem cell marker Oct4-GFP when observed under a confocal microscope three to six days after acid treatment. qPCR analysis also confirmed that acid treatment did not induce the splenocytes to express the stemness markers Oct4, Sox2 and Nanog. In addition, we obtained similar results from acid-treated Oct4-GFP lung fibroblasts. In summary, we have not been able to produce STAP stem cells from neonatal splenocytes or lung fibroblasts using the acid-based treatment reported by Obokata et al (2014a, b, c).
    Full-text · Article · May 2014 · F1000 Research
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    • "Unexpectedly, miR-302a, whose forced expression was also shown to enhance iPSC generation in the context of the Yamanaka factors (Subramanyam and Blelloch, 2011), exhibited transient activation specifically in Oct4-GFP+ cells at day 12 but remained otherwise unchanged (Figures S3G and S3H). Mir-302a is normally expressed in mouse epiblast stem cells (Huo and Zambidis, 2012) but barely detectable in mouse ESCs, suggesting that iPSC induction might entail a transient passage through an epiblast-like state before reaching naive pluripotency. In agreement with this idea, we detected transient downregulation of a number of putative mir-302a targets in Oct4- GFP+ cells such as Rbl2, Rab11fip5, Rbbp6, and transient, albeit modest, upregulation of epiblast stem cell-associated markers including Brachyury (T), Cer1, Foxa2, Eomes, and Fgf5 (Figures S3G and S3I). "
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    ABSTRACT: Factor-induced reprogramming of somatic cells into induced pluripotent stem cells (iPSCs) is inefficient, complicating mechanistic studies. Here, we examined defined intermediate cell populations poised to becoming iPSCs by genome-wide analyses. We show that induced pluripotency elicits two transcriptional waves, which are driven by c-Myc/Klf4 (first wave) and Oct4/Sox2/Klf4 (second wave). Cells that become refractory to reprogramming activate the first but fail to initiate the second transcriptional wave and can be rescued by elevated expression of all four factors. The establishment of bivalent domains occurs gradually after the first wave, whereas changes in DNA methylation take place after the second wave when cells acquire stable pluripotency. This integrative analysis allowed us to identify genes that act as roadblocks during reprogramming and surface markers that further enrich for cells prone to forming iPSCs. Collectively, our data offer new mechanistic insights into the nature and sequence of molecular events inherent to cellular reprogramming.
    Full-text · Article · Dec 2012 · Cell
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