Using ATAC-seq to study placodal development in Xenopus

WHEELER_U23DTP

The Placodes and neural crest are groups of cells found only in vertebrates, specifically in the embryo. They form at the neural border between the ectoderm and neuroectoderm. Once specified the placodes differentiate into major parts of the sensory organs such as the eyes, ears and nose. The Neural Crest on the other hand undergo an epithelial to mesenchymal transition (EMT) and then migrate to various parts of the embryo where they differentiate into tissues such as parts of the heart, the peripheral nervous system, the cartilage of the face and pigment cells.

The Placodes and Neural Crest are of critical importance for normal vertebrate development and errors in their development are the cause of many birth defects. Identifying regulatory elements, such as enhancers, required for specification of the Placodes and Neural Crest is important in order to understand how their specification and induction is regulated during development.

Understanding these processes will help in developing techniques to engineer specific cells and tissues that the placodes and neural crest give rise to and which could be used in stem cell and regenerative therapies. ATAC-seq is a method to identify ‘open’ regions in the chromatin landscape which can correspond to active enhancers and promoters.

We have previously carried out ATAC-seq on Xenopus embryonic tissue induced to form neural crest and neural ectoderm to determine active enhancers and promoters.

In this project the student will:
(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 placodal and neural crest enhancers.
(3) Test and validate potential enhancers using transgenic and CRISPR/Cas9 technologies.

References

1. Alice M. Godden, Marco Antonaci, Nicole J. Ward, Michael van der Lee, Anita Abu-Daya, Matthew Guille, Grant N. Wheeler (2022). An efficient miRNA knockout approach using CRISPR-Cas9 in Xenopus. Developmental Biology. 483, p. 66-75.

2. Gi Fay Mok, Leighton Folkes, Shannon Weldon, Eirini Maniou, Victor Martinez-Heredia, Alice Godden, Ruth Williams, Grant N. Wheeler, Simon Moxon, Andrea E. M√ľnsterberg (2021). 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.

3. 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. M√ľnsterberg and Grant N. Wheeler (2016). The Positive Transcriptional Elongation Factor (P-TEFb) is required for Neural Crest Specification. Developmental Biology, 416: 361-372.

4. Stefan Hoppler and Grant N. Wheeler (2015) It’s about time for neural crest. Science, 348 (6241):1316-1317.