Genomic Resolution of DLX-Orchestrated Transcriptional Circuits Driving Development of Forebrain GABAergic Neurons

S. Lindtner, Rinaldo Catta-Preta, Hua Tian, L. Su-Feher, James D. Price, Diane E. Dickel, Vanille Greiner, Shanni N. Silberberg, Gabriel L. McKinsey, Michael T. McManus, L. A. Pennacchio, Axel Visel, Alexander Nord, John L.R. Rubenstein

Research output: Contribution to journalArticle

Abstract

DLX transcription factors (TFs) are master regulators of the developing vertebrate brain, driving forebrain GABAergic neuronal differentiation. Ablation of Dlx1&2 alters expression of genes that are critical for forebrain GABAergic development. We integrated epigenomic and transcriptomic analyses, complemented with in situ hybridization (ISH), and in vivo and in vitro studies of regulatory element (RE) function. This revealed the DLX-organized gene regulatory network at genomic, cellular, and spatial levels in mouse embryonic basal ganglia. DLX TFs perform dual activating and repressing functions; the consequences of their binding were determined by the sequence and genomic context of target loci. Our results reveal and, in part, explain the paradox of widespread DLX binding contrasted with a limited subset of target loci that are sensitive at the epigenomic and transcriptomic level to Dlx1&2 ablation. The regulatory properties identified here for DLX TFs suggest general mechanisms by which TFs orchestrate dynamic expression programs underlying neurodevelopment. Lindtner et al. reveal the regulatory wiring organized by DLX transcription factors in forebrain GABAergic neuronal specification, by integrating functional genomic, epigenomic, and genetic data on a transgenic mouse model. This network determines key sequence-encoded regulatory elements and implicates a combination of histone modifications and biophysical interactions.

Original languageEnglish (US)
JournalCell Reports
DOIs
StateAccepted/In press - Jan 1 2019

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GABAergic Neurons
Prosencephalon
Neurons
Transcription Factors
Epigenomics
Networks (circuits)
Ablation
Histone Code
Genes
General Transcription Factors
Gene Regulatory Networks
Electric wiring
Basal Ganglia
Histones
Transgenic Mice
In Situ Hybridization
Vertebrates
Brain
Specifications
Gene Expression

Keywords

  • basal ganglia
  • ChIP-seq
  • chromatin
  • development
  • DLX
  • enhancers
  • GABA neuron
  • ganglionic eminence
  • genome
  • histone
  • regulatory element
  • telencephalon
  • transcription factor
  • transcriptional circuits

ASJC Scopus subject areas

  • Biochemistry, Genetics and Molecular Biology(all)

Cite this

Lindtner, S., Catta-Preta, R., Tian, H., Su-Feher, L., Price, J. D., Dickel, D. E., ... Rubenstein, J. L. R. (Accepted/In press). Genomic Resolution of DLX-Orchestrated Transcriptional Circuits Driving Development of Forebrain GABAergic Neurons. Cell Reports. https://doi.org/10.1016/j.celrep.2019.07.022

Genomic Resolution of DLX-Orchestrated Transcriptional Circuits Driving Development of Forebrain GABAergic Neurons. / Lindtner, S.; Catta-Preta, Rinaldo; Tian, Hua; Su-Feher, L.; Price, James D.; Dickel, Diane E.; Greiner, Vanille; Silberberg, Shanni N.; McKinsey, Gabriel L.; McManus, Michael T.; Pennacchio, L. A.; Visel, Axel; Nord, Alexander; Rubenstein, John L.R.

In: Cell Reports, 01.01.2019.

Research output: Contribution to journalArticle

Lindtner, S, Catta-Preta, R, Tian, H, Su-Feher, L, Price, JD, Dickel, DE, Greiner, V, Silberberg, SN, McKinsey, GL, McManus, MT, Pennacchio, LA, Visel, A, Nord, A & Rubenstein, JLR 2019, 'Genomic Resolution of DLX-Orchestrated Transcriptional Circuits Driving Development of Forebrain GABAergic Neurons', Cell Reports. https://doi.org/10.1016/j.celrep.2019.07.022
Lindtner, S. ; Catta-Preta, Rinaldo ; Tian, Hua ; Su-Feher, L. ; Price, James D. ; Dickel, Diane E. ; Greiner, Vanille ; Silberberg, Shanni N. ; McKinsey, Gabriel L. ; McManus, Michael T. ; Pennacchio, L. A. ; Visel, Axel ; Nord, Alexander ; Rubenstein, John L.R. / Genomic Resolution of DLX-Orchestrated Transcriptional Circuits Driving Development of Forebrain GABAergic Neurons. In: Cell Reports. 2019.
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