(1) Generate ATAC-seq data on Xenopus embryonic ectoderm organoids induced to form placodal tissue.
(2) Use bioinformatics to analyse the data and compare it to the neural crest data. Differential analysis will uncover specific neural crest and placodal enhancers.
(3) Test and validate potential enhancers using transgenic and CRISPR/Cas9 technologies.
References
Alice M. Godden, Nicole J. Ward, Michael van der Lee, Anita Abu-Daya, Matthew Guille, Grant N. Wheeler (2021). An efficient miRNA knockout approach using CRISPR-Cas9 in Xenopus. BiorXiv, 10.1101/2021.08.05.454468
Gi Fay Mok, Leighton Folkes, Shannon Weldon, Eirini Maniou, Victor Martinez-Heredia, Alice Godden, Ruth Williams, Grant N. Wheeler, Simon Moxon, Andrea E. Münsterberg (2020). Characterising open chromatin identifies novel cis-regulatory elements important for paraxial mesoderm formation and axis extension. Nature Communications. 12(1):1157. doi: 10.1038/s41467-021-21426-7
Victoria L. Hatch, Marta Marin-Barba, Simon Moxon, Christopher T. Ford, Nicole J. Ward, Matthew L. Tomlinson, Ines Desanlis, Adam E. Hendry, Saartje Hontelez, Ila van Kruijsbergen, Gert Jan C. Veenstra, Andrea E. Münsterberg and Grant N. Wheeler (2016). The Positive Transcriptional Elongation Factor (P-TEFb) is required for Neural Crest Specification. Developmental Biology, 416: 361-372
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