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| Status |
Public on Mar 04, 2021 |
| Title |
Profiling NSD3-dependent neural crest gene expression reveals known and novel candidate regulatory factors |
| Organism |
Gallus gallus |
| Experiment type |
Expression profiling by high throughput sequencing
|
| Summary |
The lysine methyltransferase NSD3 is required for the expression of key neural crest transcription factors and the migration of neural crest cells. Nevertheless, a complete view of the genes dependent upon NSD3 for expression and the developmental processes impacted by NSD3 in the neural crest was lacking. We used RNA sequencing (RNA-seq) to profile transcripts differentially expressed after NSD3 knockdown in chick premigratory neural crest cells, identifying 674 genes. Gene Ontology and gene set enrichment analyses further support a requirement for NSD3 during neural crest development and show that NSD3 knockdown also upregulates ribosome biogenesis. To validate our results, we selected three genes not previously associated with neural crest development, Astrotactin-1 (Astn1), Dispatched-3 (Disp3), and Tropomyosin-1 (Tpm1). Using whole mount in situ hybridization, we show that premigratory neural crest cells express these genes and that NSD3 knockdown downregulates (Astn1 and Disp3) and upregulates (Tpm1) their expression, consistent with RNA-seq results. Altogether, this study identifies novel putative regulators of neural crest development and provides insight into the transcriptional consequences of NSD3 in the neural crest, with implications for cancer.
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| |
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| Overall design |
NSD3-dependent gene expression in chick neural folds is profiled by RNA-seq with 5 control and 5 knockdown replicates.
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| Web link |
https://github.com/micahgearhart/nsd3
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| |
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| Contributor(s) |
Jacques-Fricke BT, Roffers-Agarwal J, Gearhart MD, Gammill LS, Hussein AO, Yoder KJ |
| Citation(s) |
33705737 |
| |
| Submission date |
Nov 16, 2020 |
| Last update date |
Mar 22, 2021 |
| Contact name |
Micah Gearhart |
| E-mail(s) |
[email protected]
|
| Organization name |
University of Minnesota
|
| Department |
Genetics, Cell Biology and Development
|
| Street address |
6-160 Jackson Hall, 321 Church St.
|
| City |
Minneapolis |
| State/province |
MN |
| ZIP/Postal code |
55455 |
| Country |
USA |
| |
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| Platforms (1) |
| GPL19005 |
Illumina HiSeq 2500 (Gallus gallus) |
|
| Samples (10)
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| Relations |
| BioProject |
PRJNA678725 |
| SRA |
SRP292751 |
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