Transcriptional network orchestrating regional patterning of cortical progenitors

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

doi:10.1073/pnas.2024795118

Title: Transcriptional network orchestrating regional patterning of cortical progenitors

Journal Article · 16 December 2021 · Proceedings of the National Academy of Sciences of the United States of America

DOI: https://doi.org/10.1073/pnas.2024795118 · OSTI ID:1860335

^[1];

^[2]; Golonzhka, Olga ^[1]; Lindtner, Susan ^[1];

^[3]; Jones, Ian R. ^[1]; Abnousi, Armen ^[4]; Juric, Ivan ^[4];

^[4]; Shen, Yin ^[1]; Dickel, Diane E. ^[5]; Visel, Axel ^[6]; Pennacchio, Len A. ^[7]; Hawrylycz, Michael ^[8];

^[8];

^[9];

^[2];

^[1]

Univ. of California, San Francisco, CA (United States)
Univ. of California, Davis, CA (United States)
Guangzhou Univ. (China)
Cleveland Clinic Foundation, Cleveland, OH (United States)
Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States); Univ. of California, Merced, CA (United States); USDOE Joint Genome Institute (JGI), Berkeley, CA (United States)
Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States); Univ. of California, Berkeley, CA (United States); USDOE Joint Genome Institute (JGI), Berkeley, CA (United States)
Allen Institute for Brain Science, Seattle, WA (United States)
Imperial College, London (United Kingdom)

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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Research Organization:: Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)

Sponsoring Organization:: Imperial College Research Fellowship; National Cancer Institute; National Institute of General Medical Sciences; National Institute of Health; National Institute of Mental Health; National Institute of Neurological Disorders and Stroke; National Institutes of Health (NIH); USDOE

Grant/Contract Number:: AC02-05CH11231

OSTI ID:: 1860335

Journal Information:: Proceedings of the National Academy of Sciences of the United States of America, Journal Name: Proceedings of the National Academy of Sciences of the United States of America Journal Issue: 51 Vol. 118; ISSN 0027-8424

Publisher:: National Academy of SciencesCopyright Statement

Country of Publication:: United States

Language:: English

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transcription factors

Title: Transcriptional network orchestrating regional patterning of cortical progenitors

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