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Cell Syst. 2018 Oct 24;7(4):438-452.e8. doi: 10.1016/j.cels.2018.08.011. Epub 2018 Oct 3.

Combined Experimental and System-Level Analyses Reveal the Complex Regulatory Network of miR-124 during Human Neurogenesis.

Author information

1
Technische Universität Dresden, DFG Research Center for Regenerative Therapies, Dresden 01307, Germany.
2
Department of Computer Science, Bioinformatics Group, Interdisciplinary Center for Bioinformatics, University of Leipzig, Leipzig 04107, Germany; Faculty of Mathematics and Computer Science, Swarm Intelligence and Complex Systems Group, University of Leipzig, Leipzig 04109, Germany; Faculty for Biology, Chemistry and Pharmacy, Freie Universität Berlin, Institute for Biology, Berlin 14195, Germany.
3
Department of Computer Science, Bioinformatics Group, Interdisciplinary Center for Bioinformatics, University of Leipzig, Leipzig 04107, Germany.
4
Department of Experimental Medical Science, Laboratory of Molecular Neurogenetics, Wallenberg Neuroscience Center and Lund Stem Cell Center, Lunds Universitet, Lund 22184, Sweden.
5
Department of Computer Science, Bioinformatics Group, Interdisciplinary Center for Bioinformatics, University of Leipzig, Leipzig 04107, Germany; Max Planck Institute for Mathematics in the Sciences, Leipzig 04103, Germany; Santa Fe Institute, 1399 Hyde Park Road, Santa Fe, NM 87501, USA.
6
Faculty for Biology, Chemistry and Pharmacy, Freie Universität Berlin, Institute for Biology, Berlin 14195, Germany.
7
Technische Universität Dresden, DFG Research Center for Regenerative Therapies, Dresden 01307, Germany. Electronic address: volker.busskamp@tu-dresden.de.

Abstract

Non-coding RNAs regulate many biological processes including neurogenesis. The brain-enriched miR-124 has been assigned as a key player of neuronal differentiation via its complex but little understood regulation of thousands of annotated targets. To systematically chart its regulatory functions, we used CRISPR/Cas9 gene editing to disrupt all six miR-124 alleles in human induced pluripotent stem cells. Upon neuronal induction, miR-124-deleted cells underwent neurogenesis and became functional neurons, albeit with altered morphology and neurotransmitter specification. Using RNA-induced-silencing-complex precipitation, we identified 98 high-confidence miR-124 targets, of which some directly led to decreased viability. By performing advanced transcription-factor-network analysis, we identified indirect miR-124 effects on apoptosis, neuronal subtype differentiation, and the regulation of previously uncharacterized zinc finger transcription factors. Our data emphasize the need for combined experimental- and system-level analyses to comprehensively disentangle and reveal miRNA functions, including their involvement in the neurogenesis of diverse neuronal cell types found in the human brain.

KEYWORDS:

AGO2-RIP-seq; ZNF787; gene regulatory network analysis; miR-124 targetome; miRNA dynamics; miRNA regulation; miRNA-transcription factor networks; neuronal differentiation from human stem cells; neuronal miRNAs; systems biology

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