Chromatin states at homeoprotein loci distinguish axolotl limb segments prior to regeneration [ATAC-seq]

The salamander limb regenerates only the missing portion. Each limb segment can only form segments equivalent to- or more distal to their own identity, relying on a property termed “positional information”. How positional information is encoded in limb cells has been unknown. By cell-type-specific chromatin profiling of upper arm, lower arm, and hand, we found segment-specific levels of histone H3K27me3 at limb homeoprotein gene loci but not their upstream regulators, constituting an intrinsic segment information code. During regeneration, regeneration-specific regulatory elements became active prior to the re-appearance of developmental regulatory elements. This means that, in the hand segment, the permissive chromatin state of the hand homeoprotein gene HoxA13 engages with regeneration regulatory elements, bypassing the upper limb program. Profiling chromatin accessibility (ACRs) of Axoltol limb connective tissue cells, and compare among developmental limb buds, and mature limb at different segments and regeneration time points. Overall design: We performed ACR profiling analysis using data obtained from ATAC-seq libraries of developmental limb buds (stage 40/41, stage 46 proximal and distal parts), and mature limb at different segments (mature UA vs LA vs hand). Therefore, we also performed libraries from the mature arm and 5, 9, 13 dpa (13 dpa blastema data have two different positions like proximal and distal parts) regenerating arm blastema.