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Transcriptional network orchestrating regional patterning of cortical progenitors

by Tang, Ke , Catta-Preta, Rinaldo , Lindtner, Susan , Jones, Ian R. , Juric, Ivan , Golonzhka, Olga , Hawrylycz, Michael , Zeng, Hongkui , Barozzi, Iros , Thompson, Carol L. , Pattabiraman, Kartik , Pennacchio, Len A. , Visel, Axel , Dickel, Diane E. , Rubenstein, John L. , Hu, Ming , Shen, Yin , Ypsilanti, Athena R. , Abnousi, Armen , Nord, Alex S.

in Animals / BASIC BIOLOGICAL SCIENCES / Biological Sciences / Cerebral Cortex - embryology / Cerebral Cortex - metabolism / Chromatin / Conformation / cortical patterning / COUP Transcription Factor I - metabolism / Enhancers / epigenetics / Epigenome / Gene Regulatory Networks / Glial stem cells / Homeodomain Proteins - metabolism / INAUGURAL ARTICLES / LIM-Homeodomain Proteins - metabolism / Mice / Mutants / Neuroscience / Pattern formation / Pax6 protein / PAX6 Transcription Factor - metabolism / Pre-B-Cell Leukemia Transcription Factor 1 - metabolism / Progenitor cells / Regulatory Elements, Transcriptional / Stem cell transplantation / Stem cells / transcription factors / Transcription Factors - genetics / Transcription Factors - metabolism / Ventricle / Ventricular zone

2021

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2021

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2021

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Journal Article

Transcriptional network orchestrating regional patterning of cortical progenitors

Tang, Ke,

Catta-Preta, Rinaldo,

Lindtner, Susan,

Jones, Ian R.,

Juric, Ivan,

Golonzhka, Olga,

Hawrylycz, Michael,

Zeng, Hongkui,

Barozzi, Iros,

Thompson, Carol L.,

Pattabiraman, Kartik,

Pennacchio, Len A.,

Visel, Axel,

Dickel, Diane E.,

Rubenstein, John L.,

Hu, Ming,

Shen, Yin,

Ypsilanti, Athena R.,

Abnousi, Armen,

Nord, Alex S.

2021

Overview

We uncovered a transcription factor (TF) network that regulates cortical regional patterning in radial glial stem cells. Screening the expression of hundreds of TFs in the developing mouse cortex identified 38 TFs that are expressed in gradients in the ventricular zone (VZ). We tested whether their cortical expression was altered in mutant mice with known patterning defects (Emx2, Nr2f1, and Pax6), which enabled us to define a cortical regionalization TF network (CRTFN). To identify genomic programming underlying this network, we performed TF ChIP-seq and chromatin-looping conformation to identify enhancer–gene interactions. To map enhancers involved in regional patterning of cortical progenitors, we performed assays for epigenomic marks and DNA accessibility in VZ cells purified from wild-type and patterning mutant mice. This integrated approach has identified a CRTFN and VZ enhancers involved in cortical regional patterning in the mouse.

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Publisher

National Academy of Sciences

Subject

Animals

/ BASIC BIOLOGICAL SCIENCES

/ Biological Sciences

/ Cerebral Cortex - embryology

/ Cerebral Cortex - metabolism

/ Chromatin

/ Conformation