The gene regulatory program of planarian regenerative polarity

Regeneration is one of the greatest remaining mysteries in biology. Planarians are highly regenerative flatworms that have been studied for centuries to understand the mechanisms of this biological feat. However, how positional information instructs regeneration is still largely unknown. For my doctoral thesis, I would like to study
the role of the position-control genes pbx, prep and meis in planarian regeneration.

In other models, pbx is known to form dimers with both prep and meis, which interact further with other homeodomain containing proteins, e.g. Hox proteins, thus regulating the transcription of downstream genes. Therefore, the hypothesis I would like to test is whether pbx-prep and pbx-meis control anterior and posterior specification, respectively. In order to understand their regulatory dynamics, I would like to screen the DNA binding sites with ChIP-seq and look for candidate target genes using RNA-seq both in wildtype animals and in pbx, prep, and meis RNAi knockdown animals. Asit might not be possible to develop antibodies for ChIP-seq, I will also use ATAC-seq to look for changes in chromatin accessibility that reflect the knockdown of these transcription factors after RNAi.