Abstract
While it is appreciated that global gene expression analyses can provide novel insights about complex biological processes, experiments are generally insufficiently powered to achieve this goal. Here we report the results of a robust microarray experiment of axolotl forelimb regeneration. At each of 20 post‐amputation time points, we estimated gene expression for 10 replicate RNA samples that were isolated from 1 mm of heterogeneous tissue collected from the distal limb tip. We show that the limb transcription program diverges progressively with time from the non‐injured state, and divergence among time adjacent samples is mostly gradual. However, punctuated episodes of transcription were identified for five intervals of time, with four of these coinciding with well‐described stages of limb regeneration—amputation, early bud, late bud, and pallet. The results suggest that regeneration is highly temporally structured and regulated by mechanisms that function within narrow windows of time to coordinate transcription within and across cell types of the regenerating limb. Our results provide an integrative framework for hypothesis generation using this complex and highly informative data set.
Highlights
Among tetrapod vertebrates, only salamanders maintain potential throughout life to regenerate limbs after injury
An important objective of our work is to develop informational resources that show how changes in gene expression correlate with morphological, developmental, physiological, and molecular events that are well documented to occur during limb regeneration
We call the period extending from limb amputation to the early bud stage as the pre-bud (PB) phase of limb regeneration, and use subsequent developmental stages defined by Tank et al (1976) as a working model to integrate transcriptional data and results
Summary
Only salamanders maintain potential throughout life to regenerate limbs after injury. Microarray and RNASeq methodologies offer the potential to detail regeneration globally and in its entirety, as a dynamic continuous process that involves thousands of expression differences and hundreds of biological processes To date, these powerful approaches have been used in experiments with sparse tissue sampling and no or few biological replicates. A unique wound epidermis covers an amputated limb; it differs structurally and functionally from the type of epidermis that covers a superficial skin wound (reviewed in Stocum 1995). Another key difference between epidermal wound healing and regeneration is that the latter encompasses repair of a greater diversity of tissues. We call the period extending from limb amputation to the early bud stage as the pre-bud (PB) phase of limb regeneration, and use subsequent developmental stages defined by Tank et al (1976) as a working model to integrate transcriptional data and results
Sign-in/Register to view highlights & summary Sign-in/Register to access full text options 
Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have
Schedule a call
