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

Research output: Contribution to journalArticle

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.

Details

Authors
  • Lisa K. Kutsche
  • Deisy M. Gysi
  • Joerg Fallmann
  • Kerstin Lenk
  • Rebecca Petri
  • Anka Swiersy
  • Simon D. Klapper
  • Karolina Pircs
  • Shahryar Khattak
  • Peter F. Stadler
  • Johan Jakobsson
  • Katja Nowick
  • Volker Busskamp
Organisations
External organisations
  • Dresden University of Technology
  • Leipzig University
  • Santa Fe Institute
  • Free University of Berlin
  • Max Planck Institute for Mathematics in the Sciences
Research areas and keywords

Subject classification (UKÄ) – MANDATORY

  • Neurosciences
  • Cell and Molecular Biology

Keywords

  • 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
Original languageEnglish
Pages (from-to)438-452
Number of pages15
JournalCell systems
Volume7
Issue number4
Publication statusPublished - 2018 Oct
Publication categoryResearch
Peer-reviewedYes