MicroRNA Discovery and Profiling in Human Embryonic Stem Cells by Deep Sequencing of Small RNA Libraries

摘要: 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 isogenic differentiating cultures yielded a total 425,505 high-quality sequence reads. A custom data analysis pipeline delineated expression profiles for 191 previously annotated miRNAs, 13 novel miRNAs 56 candidate miRNAs. Further characterization subset the Dicer-knockdown demonstrated Dicer-dependent expression, providing additional validation our results. set 14 (9 known 5 novel) were noted be then strongly down-regulated with differentiation. Functional annotation predicted targets these comparison null model using non-hESC-expressed identified statistically enriched functional categories, including chromatin remodeling lineage-specific differentiation annotations. Finally, integration genome-wide immunoprecipitation on OCT4, SOX2 NANOG binding sites implicates transcription factors regulation nine novel/candidate here. Comparison results those recent deep sequencing studies mouse ESC show that most found here not other studies. The indicate express larger complement than appreciated, provide resource further miRNA physiology.