Abstract
Neurogenins are proneural transcription factors required to specify neuronal identity. Their overexpression in human pluripotent stem cells rapidly produces cortical-like neurons with spiking activity and, because of this, they have been widely adopted for human neuron disease models. However, we do not fully understand the key downstream regulatory effectors responsible for driving neural differentiation. Here, using inducible expression of NEUROG1 and NEUROG2, we identify transcription factors (TFs) required for directed neuronal differentiation by combining expression and chromatin accessibility analyses with a pooled in vitro CRISPR-Cas9 screen targeting all ~1900 TFs in the human genome. The loss of one of these essential TFs (ZBTB18) yields few MAP2-positive neurons. Differentiated ZBTB18-null cells have radically altered gene expression, leading to cytoskeletal defects and stunted neurites and spines. In addition to identifying key downstream TFs for neuronal differentiation, our work develops an integrative multi-omics and TFome-wide perturbation platform to rapidly characterize essential TFs for the differentiation of any human cell type.
| Original language | English |
|---|---|
| Article number | 8362 |
| Journal | Nature Communications |
| Volume | 14 |
| Issue number | 1 |
| DOIs | |
| State | Published - 15 Dec 2023 |
| Externally published | Yes |
Bibliographical note
Publisher Copyright:© 2023, The Author(s).
Funding
We thank the entire Sanjana and Mazzoni laboratories for support and advice and N. Dahmane for helpful feedback. We thank the NYU Biology Genomics Core for sequencing and flow cytometry resources. This work was supported by the NICHD (R01HD079682) to E.O.M. N.E.S. is supported by New York University and New York Genome Center startup funds, National Institutes of Health (NIH)/National Human Genome Research Institute (grant nos. R00HG008171, DP2HG010099, R01HG012790), NIH/National Cancer Institute (grant no. R01CA218668, R01CA279135), the NIH/National Institute of General Medical Sciences (R01GM138635), the NIH/National Institute of Allergy and Infectious Diseases (R01AI176601), the NIH/National Institute of Neurological Disorders and Stroke (R01NS124920), the MacMillan Center for the Study of the Noncoding Cancer Genome at the New York Genome Center, Defense Advanced Research Projects Agency (grant no. D18AP00053), the Simons Foundation for Autism Research (Genomics of ASD 896724), and the Brain and Behavior Foundation.
| Funders | Funder number |
|---|---|
| MacMillan Center for the Study | |
| Simons Foundation for Autism Research | ASD 896724 |
| National Institutes of Health | |
| National Human Genome Research Institute | R00HG008171, DP2HG010099, R01HG012790 |
| National Cancer Institute | R01CA218668, R01CA279135 |
| National Institute of General Medical Sciences | R01GM138635 |
| National Institute of Allergy and Infectious Diseases | R01AI176601 |
| National Institute of Neurological Disorders and Stroke | R01NS124920 |
| Defense Advanced Research Projects Agency | D18AP00053 |
| Brain and Behavior Research Foundation | |
| New York University | |
| Eunice Kennedy Shriver National Institute of Child Health and Human Development | R01HD079682 |
| New York Genome Center |
