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

Kutsche, Lisa K.; Gysi, Deisy M.; Fallmann, Joerg; Lenk, Kerstin; Petri, Rebecca LU ; Swiersy, Anka; Klapper, Simon D.; Pircs, Karolina LU ; Khattak, Shahryar and Stadler, Peter F., et al. (2018) In Cell systems 7(4). p.438-452
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... (More)

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.

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@article{31619e9f-1802-48fe-a92a-96f6270f66ab,
  abstract     = {<p>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.</p>},
  author       = {Kutsche, Lisa K. and Gysi, Deisy M. and Fallmann, Joerg and Lenk, Kerstin and Petri, Rebecca and Swiersy, Anka and Klapper, Simon D. and Pircs, Karolina and Khattak, Shahryar and Stadler, Peter F. and Jakobsson, Johan and Nowick, Katja and Busskamp, Volker},
  issn         = {2405-4712},
  keyword      = {AGO2-RIP-seq,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,ZNF787},
  language     = {eng},
  number       = {4},
  pages        = {438--452},
  publisher    = {Cell Press},
  series       = {Cell systems},
  title        = {Combined Experimental and System-Level Analyses Reveal the Complex Regulatory Network of miR-124 during Human Neurogenesis},
  url          = {http://dx.doi.org/10.1016/j.cels.2018.08.011},
  volume       = {7},
  year         = {2018},
}