title: Staged miRNA re-regulation patterns during reprogramming.
abstract: BACKGROUND
  MiRNAs often operate in feedback loops with transcription factors and represent a key mechanism for fine-tuning gene expression. In transcription factor-induced reprogramming, miRNAs play a critical role; however, detailed analyses of miRNA expression changes during reprogramming at the level of deep sequencing have not been previously reported.
  
  
  RESULTS
  We use four factor reprogramming to induce pluripotent stem cells from mouse fibroblasts and isolate FACS-sorted Thy1- and SSEA1+ intermediates and Oct4-GFP+ induced pluripotent stem cells (iPSCs). Small RNAs from these cells, and two partial-iPSC lines, another iPSC line, and mouse embryonic stem cells (mES cells) were deep sequenced. A comprehensive resetting of the miRNA profile occurs during reprogramming; however, analysis of miRNA co-expression patterns yields only a few patterns of change. Dlk1-Dio3 region miRNAs dominate the large pool of miRNAs experiencing small but significant fold changes early in reprogramming. Overexpression of Dlk1-Dio3 miRNAs early in reprogramming reduces reprogramming efficiency, suggesting the observed downregulation of these miRNAs may contribute to reprogramming. As reprogramming progresses, fewer miRNAs show changes in expression, but those changes are generally of greater magnitude.
  
  
  CONCLUSIONS
  The broad resetting of the miRNA profile during reprogramming that we observe is due to small changes in gene expression in many miRNAs early in the process, and large changes in only a few miRNAs late in reprogramming. This corresponds with a previously observed transition from a stochastic to a more deterministic signal.
authors.forename: Christine M
authors.initials: CM
authors.lastname: Henzler
authors.forename: Zhonghan
authors.initials: Z
authors.lastname: Li
authors.forename: Jason
authors.initials: J
authors.lastname: Dang
authors.forename: Mary Luz
authors.initials: ML
authors.lastname: Arcila
authors.forename: Hongjun
authors.initials: H
authors.lastname: Zhou
authors.forename: Jingya
authors.initials: J
authors.lastname: Liu
authors.forename: Kung-Yen
authors.initials: KY
authors.lastname: Chang
authors.forename: Danielle S
authors.initials: DS
authors.lastname: Bassett
authors.forename: Tariq M
authors.initials: TM
authors.lastname: Rana
authors.forename: Kenneth S
authors.initials: KS
authors.lastname: Kosik
mesh_terms: D000818:Animals; D002135:Calcium-Binding Proteins; D002478:Cells, Cultured; D065150:Cellular Reprogramming; D005347:Fibroblasts / Q000166:cytology / Q000378:metabolism; D005786:Gene Expression Regulation; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods; D057026:Induced Pluripotent Stem Cells / Q000378:metabolism*; D036341:Intercellular Signaling Peptides and Proteins / Q000235:genetics; D007453:Iodide Peroxidase / Q000235:genetics; D051379:Mice; D035683:MicroRNAs / Q000235:genetics*; D014157:Transcription Factors / Q000378:metabolism
chemical_list: D002135:Calcium-Binding Proteins; C512925:Dlk1 protein, mouse; D036341:Intercellular Signaling Peptides and Proteins; D035683:MicroRNAs; D014157:Transcription Factors; C117274:iodothyronine deiodinase type III; D007453:Iodide Peroxidase