Loss of non-coding RNA expression from the DLK1-DIO3 imprinted locus correlates with reduced neural differentiation potential in human embryonic stem cell lines
Journal
Stem Cell Research and Therapy
Journal Volume
6
Journal Issue
1
Date Issued
2015
Author(s)
Abstract
Introduction: Pluripotent stem cells are increasingly used to build therapeutic models, including the transplantation of neural progenitors derived from human embryonic stem cells (hESCs). Recently, long non-coding RNAs (lncRNAs), including delta-like homolog 1 gene and the type III iodothyronine deiodinase gene (DLK1-DIO3) imprinted locus-derived maternally expressed gene 3 (MEG3), were found to be expressed during neural development. The deregulation of these lncRNAs is associated with various neurological diseases. The imprinted locus DLK1-DIO3 encodes abundant non-coding RNAs (ncRNAs) that are regulated by differential methylation of the locus. We aim to study the correlation between the DLK1-DIO3-derived ncRNAs and the capacity of hESCs to differentiate into neural lineages. Methods: We classified hESC sublines into MEG3-ON and MEG3-OFF based on the expression levels of MEG3 and its downstream microRNAs as detected by quantitative reverse transcription-polymerase chain reaction (qRT-PCR). A cDNA microarray was used to analyze the gene expression profiles of hESCs. To investigate the capacity of neural differentiation in MEG3-ON and MEG3-OFF hESCs, we performed neural lineage differentiation followed by neural lineage marker expression and neurite formation analyses via qRT-PCR and immunocytochemistry, respectively. MEG3-knockdown via small interfering RNA (siRNA) and small hairpin RNA (shRNA) was used to investigate the potential causative effect of MEG3 in regulating neural lineage-related gene expression. Results: DLK1-DIO3-derived ncRNAs were repressed in MEG3-OFF hESCs compared with those in the MEG3-ON hESCs. The transcriptome profile indicated that many genes related to nervous system development and neural-type tumors were differentially expressed in MEG3-OFF hESCs. Three independent MEG3-knockdown assays using different siRNA and shRNA constructs consistently resulted in downregulation of some neural lineage genes. Lower expression levels of stage-specific neural lineage markers and reduced neurite formation were observed in neural lineage-like cells derived from MEG3-OFF-associated hESCs compared with those in the MEG3-ON groups at the same time points after differentiation. Conclusions: Repression of ncRNAs derived from the DLK1-DIO3 imprinted locus is associated with reduced neural lineage differentiation potential in hESCs. ? 2015 Mo et al.; licensee BioMed Central.
SDGs
Other Subjects
long untranslated RNA; short hairpin RNA; small interfering RNA; transcription factor PAX6; transcriptome; eye protein; homeodomain protein; iodide peroxidase; iodothyronine deiodinase type III; long untranslated RNA; MEG3 non-coding RNA, human; microRNA; paired box transcription factor; PAX6 protein, human; repressor protein; transcription factor PAX6; transcriptome; untranslated RNA; Article; controlled study; DIO3 gene; DLK1 gene; embryo; embryonic stem cell; gene; gene control; gene expression; gene locus; genetic correlation; human; human cell; immunocytochemistry; Lentivirinae; MEG3 gene; nerve cell differentiation; nervous system development; neurite; priority journal; protein expression; reverse transcription polymerase chain reaction; RNA methylation; antagonists and inhibitors; cell differentiation; cell line; cell lineage; cytology; DNA microarray; DNA sequence; embryoid body; genetics; genome imprinting; human embryonic stem cell; immunohistochemistry; induced pluripotent stem cell; metabolism; nerve cell; real time polymerase chain reaction; RNA interference; Cell Differentiation; Cell Line; Cell Lineage; Embryoid Bodies; Eye Proteins; Genetic Loci; Genomic Imprinting; Homeodomain Proteins; Human Embryonic Stem Cells; Humans; Immunohistochemistry; Induced Pluripotent Stem Cells; Iodide Peroxidase; MicroRNAs; Neurons; Oligonucleotide Array Sequence Analysis; Paired Box Transcription Factors; PAX6 Transcription Factor; Real-Time Polymerase Chain Reaction; Repressor Proteins; RNA Interference; RNA, Long Noncoding; RNA, Small Interfering; RNA, Untranslated; Sequence Analysis, DNA; Transcriptome
Type
journal article