Gene expression during newt lens regeneration and cephalopod eye evolution

Date of Award


Degree Name

Ph.D. in Biology


Department of Biology


Advisor: Panagiotis A. Tsonis


Newts are known for their ability to regenerate lost body parts. In contrast to many other organ systems, lens regeneration has many advantages. The eye lens can be removed as a whole and regeneration can occur through transdifferentiation of dorsal iris cells while ventral iris can be used as natural non-regenerating control. We have used microarrays, RNA-sequencing and mass spectrometry in dorsal and ventral iris samples during early phases of lens regeneration. The selected time points cover the undamaged control at 0 days post-lentecomy (dpl), the reentry of the cell cycle at 4 dpl and the beginning of transdifferentiation at 8 dpl. The newly assembled newt transcriptome was used to obtain annotation and gene expression measurements on newt genes in our samples. Functional analysis revealed genes related to redox balance, DNA repair, regulation of gene expression, cytoskeleton, immune response, metabolic processes, and cell cycle to be enriched in dorsal iris during regeneration time points. These events were associated with the transdifferentiation initiated in the dorsal iris. In addition, comparative transcriptomic and proteomic analyses using high-throughput gene expression data from other amphibian regeneration systems implicated response to stress, proliferation and migration, and cellular reprogramming to be a common program required for regeneration. Gene expression data from newt lens regeneration were extensively validated with quantitative real time polymerase chain reaction. Furthermore, microarrays in young and old axolotls, another amphibian model that was found capable of lens regeneration from the iris for a short window of two week after hatching, were used. Functional annotation indicated that young regeneration-competent axolotls expressed genes related to regulation of gene expression, electron transport chain, cell cycle, DNA repair and metabolic process -- gene groups belonging to the common regeneration program. In addition, we implicated immune response and cell differentiation in repression of lens regeneration in old axolotl iris. Cephalopods are protostome animals that exhibit an impressive vertebrate-like camera-type eye that facilitates high quality vision. Nautilus, however, has a pinhole eye that lacks cornea and lens. We used RNA-sequencing in developing Nautilus and pigmy squid embryos in order to gain more insights into cephalopod eye evolution. Pathway analysis of genes expressed only in Nautilus or pigmy squid developing eyes revealed that SIX3/6 gene is not expressed in the Nautilus. In addition, expression of all the genes regulated by this transcriptional factor was absent. Since, SIX3/6 is necessary for lens development in vertebrates and the gene network between vertebrates and invertebrates is highly conserved we argued that the absence of SIX3/6 in Nautilus leads to the pinhole eye. Functional and molecular evolution analyses of the Nautilus and pigmy squid transcriptomes revealed gene selections, and a gene duplication which might be associated with cephalopod eye evolution as well as in developing a vertebrate-like camera-type eye with invertebrate rhabdomere photoreceptors. The use of high-throughput methods in studying gene expression during newt lens regeneration and cephalopod eye evolution provided us with valuable insights into the underlying mechanisms in these systems.


Gene expression, Regeneration (Biology), Newts Genetics, Eye Regeneration, Biology, Bioinformatics, Molecular Biology, regeneration, lens, newts, eye evolution, cephalopods, gene expression

Rights Statement

Copyright 2014, author