title: MicroRNA dynamics during human embryonic stem cell differentiation to pancreatic endoderm.
abstract: MicroRNAs (miRNAs) are small non-coding RNAs that have emerged as critical regulators of human embryonic stem cell (hESC) pluripotency and differentiation. Despite the wealth of information about the role individual that miRNAs play in these two processes, there has yet to be a large-scale temporal analysis of the dynamics of miRNA expression as hESCs move from pluripotency into defined lineages. In this report, we used Next Generation Sequencing (NGS) to map temporal expression of miRNAs over ten 24-hour intervals as pluripotent cells were differentiated into pancreatic endoderm. Of the 2042 known human miRNAs, 694 had non-zero expression on all 11 days. Of these 694 miRNAs, 494 showed statistically significant changes in expression during differentiation. Clusters of miRNAs were identified, each displaying unique expression profiles distributed over multiple days. Selected miRNAs associated with pluripotency/differentiation (miR-302/367 and miR-371/372/373) and development/growth (miR-21, miR-25, miR-103, miR-9, and miR-92a) were found to have distinct expression profiles correlated with changes in media used to drive the differentiation process. Taken together, the clustering of miRNAs to identify expression dynamics that occur over longer periods of time (days vs. hours) provides unique insight into specific stages of differentiation. Major shifts in defined stages of hESC differentiation appear to be heavily dependent upon changes in external environmental factors, rather than intrinsic conditions in the cells.
authors: Natural Selection, Inc., 9330 Scranton Rd., Suite 150, San Diego CA 92121, USA.
authors: Gary B
authors: GB
authors: Fogel
authors: Pediatric Diabetes Research Center, University of California, San Diego, La Jolla, CA 92121 USA.
authors: Zoya S
authors: ZS
authors: Kai
authors: Pediatric Diabetes Research Center, University of California, San Diego, La Jolla, CA 92121 USA.
authors: Sahar
authors: S
authors: Zargar
authors: Pediatric Diabetes Research Center, University of California, San Diego, La Jolla, CA 92121 USA.
authors: Andrew
authors: A
authors: Hinton
authors: Pediatric Diabetes Research Center, University of California, San Diego, La Jolla, CA 92121 USA.
authors: G Adam
authors: GA
authors: Jones
authors: Pediatric Diabetes Research Center, University of California, San Diego, La Jolla, CA 92121 USA.
authors: Augusta S
authors: AS
authors: Wong
authors: Natural Selection, Inc., 9330 Scranton Rd., Suite 150, San Diego CA 92121, USA.
authors: Sevan G
authors: SG
authors: Ficici
authors: Pediatric Diabetes Research Center, University of California, San Diego, La Jolla, CA 92121 USA.
authors: Ana D
authors: AD
authors: Lopez
authors: Pediatric Diabetes Research Center, University of California, San Diego, La Jolla, CA 92121 USA. Electronic address: chking@ucsd.edu.
authors: Charles C
authors: CC
authors: King
mesh_terms: D002454:Cell Differentiation / Q000235:genetics*; D019070:Cell Lineage / Q000235:genetics; D002478:Cells, Cultured; D004707:Endoderm / Q000196:embryology* / Q000378:metabolism / Q000502:physiology; D020869:Gene Expression Profiling; D018507:Gene Expression Regulation, Developmental; D000066449:Human Embryonic Stem Cells / Q000502:physiology*; D006801:Humans; D035683:MicroRNAs / Q000235:genetics*; D020411:Oligonucleotide Array Sequence Analysis; D038081:Organogenesis / Q000235:genetics; D010179:Pancreas / Q000196:embryology* / Q000378:metabolism
chemical_list: D035683:MicroRNAs
keywords: NGS; Pancreatic endoderm; hESC; miRNA