MicroRNA Discovery and Profiling in Human Embryonic Stem Cells by Deep Sequencing of Small RNA Libraries
| العنوان: | MicroRNA Discovery and Profiling in Human Embryonic Stem Cells by Deep Sequencing of Small RNA Libraries |
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| المؤلفون: | Junlin Qi, Evan M. Kroh, Rachael K. Parkin, Brian R. Fritz, Merav Bar, Carol B. Ware, Angelique M. Nelson, Walter L. Ruzzo, Hannele Ruohola-Baker, Muneesh Tewari, Patrick S. Mitchell, Ausra Bendoraite, Robert Gentleman, Stacia K. Wyman, Kavita Garg, Jerald P. Radich |
| المصدر: | Stem Cells. 26:2496-2505 |
| بيانات النشر: | Oxford University Press (OUP), 2008. |
| سنة النشر: | 2008 |
| مصطلحات موضوعية: | Pluripotent Stem Cells, Ribonuclease III, Homeobox protein NANOG, Small RNA, Molecular Sequence Data, Computational biology, Biology, Article, Deep sequencing, Cell Line, SOX2, Databases, Genetic, microRNA, Humans, RNA, Small Interfering, Induced pluripotent stem cell, reproductive and urinary physiology, Embryonic Stem Cells, Gene Library, Expressed Sequence Tags, Genetics, Expressed sequence tag, Base Sequence, Reverse Transcriptase Polymerase Chain Reaction, Sequence Analysis, RNA, Gene Expression Profiling, Multipotent Stem Cells, Gene Expression Regulation, Developmental, Reproducibility of Results, Cell Differentiation, Cell Biology, Gene expression profiling, MicroRNAs, embryonic structures, Nucleic Acid Conformation, Molecular Medicine, biological phenomena, cell phenomena, and immunity, Transcription Factors, Developmental Biology |
| الوصف: | We used massively parallel pyrosequencing to discover and characterize microRNAs (miRNAs) expressed in human embryonic stem cells (hESC). Sequencing of small RNA cDNA libraries derived from undifferentiated hESC and from isogenic differentiating cultures yielded a total of 425,505 high-quality sequence reads. A custom data analysis pipeline delineated expression profiles for 191 previously annotated miRNAs, 13 novel miRNAs, and 56 candidate miRNAs. Further characterization of a subset of the novel miRNAs in Dicer-knockdown hESC demonstrated Dicer-dependent expression, providing additional validation of our results. A set of 14 miRNAs (9 known and 5 novel) was noted to be expressed in undifferentiated hESC and then strongly downregulated with differentiation. Functional annotation analysis of predicted targets of these miRNAs and comparison with a null model using non-hESC-expressed miRNAs identified statistically enriched functional categories, including chromatin remodeling and lineage-specific differentiation annotations. Finally, integration of our data with genome-wide chromatin immunoprecipitation data on OCT4, SOX2, and NANOG binding sites implicates these transcription factors in the regulation of nine of the novel/candidate miRNAs identified here. Comparison of our results with those of recent deep sequencing studies in mouse and human ESC shows that most of the novel/candidate miRNAs found here were not identified in the other studies. The data indicate that hESC express a larger complement of miRNAs than previously appreciated, and they provide a resource for additional studies of miRNA regulation of hESC physiology. Disclosure of potential conflicts of interest is found at the end of this article. |
| تدمد: | 1549-4918 1066-5099 |
| URL الوصول: | https://explore.openaire.eu/search/publication?articleId=doi_dedup___::005b727b51c27f5d3215793477906055 https://doi.org/10.1634/stemcells.2008-0356 |
| حقوق: | OPEN |
| رقم الأكسشن: | edsair.doi.dedup.....005b727b51c27f5d3215793477906055 |
| قاعدة البيانات: | OpenAIRE |
| تدمد: | 15494918 10665099 |
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