Nuclear Architecture and Chromatin Dynamics in Development and Regeneration

Abstract

The nucleus and its contents are not just static entities which offer a location and template for transcription. In both development and disease alterations in nuclear structure and/or chromatin architecture can contribute to normal or impaired function. In this study I used Xenopus tropicalis to study two processes that alter nuclear structure or chromatin architecture. Fist, to study the impact of nuclear compartment shape I characterized cells with branched nuclei in the tail fin. We found that despite an extreme nuclear shape, cell with branched nuclei had active cell cycles, and marks of active transcription, as well as transcriptional repression. Our characterization also determined that actin and laminb1 were necessary for maintaining branched nuclear structure. Second, I studied how dynamic changes in chromatin structure facilitated by epigenetic modifications enabled tail regeneration. Using ATAC-seq (An Assay for Transposase Accessible Chromatin) we queried changes in chromatin accessibility upon inhibition of Histone deacetylases (HDACs), and the enzymatic component of the polycomb repressive 2 complex, enhancer of zeste 2 (EZH2), both of which serve to close chromatin. We found that HDACs and EZH2 had distinct targets in the first 24 hours post amputation (hpa). Early inhibition of HDAC activity impairs tail regeneration and promoter regions are particularly sensitive. Our analysis uncovered a role for HDAC activity in regulation of neural regeneration. EZH2 inhibition during the first 24 hpa also impairs regeneration, however gene bodies were much more susceptible to be more accessible upon EZH2 inhibition. We also uncovered a role in early EZH2 activity in regulating the immune response that occurs after injury. Overall, we leveraged the powerful model system Xenopus tropicalis to establish a new model for extreme nuclear morphology and identify alterations in chromatin structure that regulate regenerative processes.