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miR-124, -128, and -137 Orchestrate Neural Differentiation by Acting on Overlapping Gene Sets Containing a Highly Connected Transcription Factor Network

Santos, Márcia C. T., Tegge, Allison N., Correa, Bruna R., Mahesula, Swetha, Kohnke, Luana Q., Qiao, Mei, Ferreira, Marco A. R., Kokovay, Erzsebet, Penalva, Luiz O. F.·2016·Stem Cells
DOI 10.1002/stem.2204
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Abstract

The ventricular-subventricular zone harbors neural stem cells (NSCs) that can differentiate into neurons, astrocytes, and oligodendrocytes. This process requires loss of stem cell properties and gain of characteristics associated with differentiated cells. miRNAs function as important drivers of this transition; miR-124, -128, and -137 are among the most relevant ones and have been shown to share commonalities and act as proneurogenic regulators. We conducted biological and genomic analyses to dissect their target repertoire during neurogenesis and tested the hypothesis that they act cooperatively to promote differentiation. To map their target genes, we transfected NSCs with antagomiRs and analyzed differences in their mRNA profile throughout differentiation with respect to controls. This strategy led to the identification of 910 targets for miR-124, 216 for miR-128, and 652 for miR-137. The target sets show extensive overlap. Inspection by gene ontology and network analysis indicated that transcription factors are a major component of these miRNAs target sets. Moreover, several of these transcription factors form a highly interconnected network. Sp1 was determined to be the main node of this network and was further investigated. Our data suggest that miR-124, -128, and -137 act synergistically to regulate Sp1 expression. Sp1 levels are dramatically reduced as cells differentiate and silencing of its expression reduced neuronal production and affected NSC viability and proliferation. In summary, our results show that miRNAs can act cooperatively and synergistically to regulate complex biological processes like neurogenesis and that transcription factors are heavily targeted to branch out their regulatory effect.

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Metadata

Authors
Santos, M. C. T., Tegge, A. N., Correa, B. R., Mahesula, S., Kohnke, L. Q., Qiao, M., Ferreira, M. A. R., Kokovay, E., & Penalva, L. O. F.
Affiliations
  • Department of Cellular and Structural Biology, University of Texas Health Science Center at San Antonio, San Antonio, Texas, USA
  • Department of Computer Science, Virginia Tech, Blacksburg, Virginia, USA
  • Children's Cancer Research Institute, University of Texas Health Science Center at San Antonio, San Antonio, Texas, USA
  • Department of Statistics, Virginia Tech, Blacksburg, Virginia, USA
Venue
Stem Cells
Publisher
Oxford University Press (OUP)
Published
2015-09-15
Volume
34
Issue
1
Pages
220-232
ISSN
  • 1066-5099
  • 1549-4918
DOI
10.1002/stem.2204
Cited by
57
References
6
Language
en
Licence
academic.oup.com/journals/pages/open_access/funder_policies/chorus/standard_publication_model (vor)
Funders
  • FAPESP (2011/51588-2, 2012/22950-8, 2013/25483-4)
  • Sam and Ann Barshop Aging Institute
  • Center for Biomedical Neuroscience (UTHSCSA)

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