Genome-wide target analysis of NEUROD2 provides new insights into regulation of cortical projection neuron migration and differentiation

BMC Genomics
Efil BayamGulayse Ince-Dunn

Abstract

Cellular differentiation programs are controlled, to a large extent, by the combinatorial functioning of specific transcription factors. Cortical projection neurons constitute the major excitatory neuron population within the cortex and mediate long distance communication between the cortex and other brain regions. Our understanding of effector transcription factors and their downstream transcriptional programs that direct the differentiation process of cortical projection neurons is far from complete. In this study, we carried out a ChIP-Seq (chromatin-immunoprecipitation and sequencing) analysis of NEUROD2, an effector transcription factor expressed in lineages of cortical projection neurons during the peak of cortical excitatory neurogenesis. Our results suggest that during cortical development NEUROD2 targets key genes that are required for Reelin signaling, a major pathway that regulates the migration of neurons from germinal zones to their final layers of residence within the cortex. We also find that NEUROD2 binds to a large set of genes with functions in layer-specific differentiation and in axonal pathfinding of cortical projection neurons. Our analysis of in vivo NEUROD2 target genes offers mechanistic insight into si...Continue Reading

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Citations

Mar 1, 2019·Life Science Alliance·Florian NoackFederico Calegari
Oct 9, 2020·BMC Genomics·Michelle M HalsteadPablo J Ross
Jan 12, 2021·Frontiers in Molecular Neuroscience·Karolina Serwach, Joanna Gruszczynska-Biegala
Jun 29, 2021·Frontiers in Molecular Neuroscience·Svetlana TutukovaLuis R Hernandez-Miranda
Jun 29, 2021·Nature Machine Intelligence·Qiao LiuWing Hung Wong

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Datasets Mentioned

BETA
GSE67539

Methods Mentioned

BETA
ChIP-Seq
PCR
ChIP
ChIP-PCR
transfection
laser capture microscopy
immunoprecipitation
dissection

Software Mentioned

custom Perl scripts
MEME
rmdup
MACS ( Model - based analysis of )
- CHIP Suite
Bioperl
NEUROD2
ChIP suite
Ensembl
MFOLD

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