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| Status |
Public on Oct 09, 2019 |
| Title |
Reconstruction of the global neural crest gene regulatory network in vivo [CRISPR_RNA-seq] |
| Organism |
Gallus gallus |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
Precise control of developmental processes is encoded in the genome in the form of gene regulatory networks (GRNs). Such multi-factorial systems are difficult to decode in vertebrates owing to their complex gene hierarchies and transient dynamic molecular interactions. Here we present a genome-wide in vivo reconstruction of the GRN underlying development of neural crest (NC), an emblematic embryonic multipotent cell population. By coupling NC-specific epigenomic and single-cell transcriptome profiling with genome/epigenome engineering in vivo, we identify multiple regulatory layers governing NC ontogeny, including NC-specific enhancers and super-enhancers, novel trans-factors and cis-signatures. Assembling the NC regulome has allowed the comprehensive reverse engineering of the NC-GRN at unprecedented resolution. Furthermore, identification and dissection of divergent upstream combinatorial regulatory codes has afforded new insights into opposing gene circuits t hat define canonical and neural NC fates. Our integrated approach, allowing dissection of cell-type-specific regulatory circuits in vivo, has broad implications for GRN discovery and investigation.
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| Overall design |
Bulk RNA-seq was performed on neural crest cells dissected from the developing chick embryo to determine the effect of CRISPR/Cas9 knock down and its downstream effects on a set of putative core transcription factors.
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| Contributor(s) |
Williams RM, Candido-Ferreira I, Repapi E, Gavriouchkina D, Senanayake U, Telenius J, Ling I, Taylor S, Hughes J, Sauka-Spengler T |
| Citation(s) |
31639368 |
| |
| Submission date |
Oct 16, 2018 |
| Last update date |
Jan 27, 2020 |
| Contact name |
Tatjana Sauka-Spengler |
| E-mail(s) |
[email protected]
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| Organization name |
MRC Weatherall Institute of Molecular Medicine
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| Department |
University of Oxford
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| Lab |
Sauka-Spengler lab
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| Street address |
Radcliffe Department of Medicine
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| City |
Oxford |
| State/province |
Oxfordshire |
| ZIP/Postal code |
OX3 9DS |
| Country |
United Kingdom |
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| Platforms (1) |
| GPL19787 |
Illumina NextSeq 500 (Gallus gallus) |
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| Samples (6)
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| This SubSeries is part of SuperSeries: |
| GSE121527 |
Reconstruction of the global neural crest gene regulatory network in vivo |
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| Relations |
| BioProject |
PRJNA497072 |
| SRA |
SRP165873 |
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