Open Access Research

Staged miRNA re-regulation patterns during reprogramming

Christine M Henzler15, Zhonghan Li2, Jason Dang2, Mary Luz Arcila1, Hongjun Zhou1, Jingya Liu2, Kung-Yen Chang2, Danielle S Bassett346, Tariq M Rana2* and Kenneth S Kosik1*

Author Affiliations

1 Neuroscience Research Institute and Department of Cellular, Molecular and Developmental Biology, University of California, Santa Barbara, CA 93106, USA

2 Program for RNA Biology, Sanford-Burnham Medical Research Institute, La Jolla, CA 92037, USA

3 Department of Physics, University of California, Santa Barbara, CA 93106, USA

4 Sage Center for the Study of the Mind, University of California, Santa Barbara, CA 93106, USA

5 Current address: Minnesota Supercomputing Institute, University of Minnesota, Minneapolis, MN 55455, USA

6 Current address: Department of Bioengineering, University of Pennsylvania, Philadelphia, PA 19104, USA

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Genome Biology 2013, 14:R149  doi:10.1186/gb-2013-14-12-r149

Published: 31 December 2013

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+‚ÄČinduced 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.