title: Comparative RNA-seq analysis in the unsequenced axolotl: the oncogene burst highlights early gene expression in the blastema.
abstract: The salamander has the remarkable ability to regenerate its limb after amputation. Cells at the site of amputation form a blastema and then proliferate and differentiate to regrow the limb. To better understand this process, we performed deep RNA sequencing of the blastema over a time course in the axolotl, a species whose genome has not been sequenced. Using a novel comparative approach to analyzing RNA-seq data, we characterized the transcriptional dynamics of the regenerating axolotl limb with respect to the human gene set. This approach involved de novo assembly of axolotl transcripts, RNA-seq transcript quantification without a reference genome, and transformation of abundances from axolotl contigs to human genes. We found a prominent burst in oncogene expression during the first day and blastemal/limb bud genes peaking at 7 to 14 days. In addition, we found that limb patterning genes, SALL genes, and genes involved in angiogenesis, wound healing, defense/immunity, and bone development are enriched during blastema formation and development. Finally, we identified a category of genes with no prior literature support for limb regeneration that are candidates for further evaluation based on their expression pattern during the regenerative process.
authors.affiliation: Regenerative Biology, Morgridge Institute for Research, Madison, Wisconsin, United States of America. rstewart@morgridgeinstitute.org
authors.forename: Ron
authors.initials: R
authors.lastname: Stewart
authors.forename: Cynthia Alexander
authors.initials: CA
authors.lastname: Rascón
authors.forename: Shulan
authors.initials: S
authors.lastname: Tian
authors.forename: Jeff
authors.initials: J
authors.lastname: Nie
authors.forename: Chris
authors.initials: C
authors.lastname: Barry
authors.forename: Li-Fang
authors.initials: LF
authors.lastname: Chu
authors.forename: Hamisha
authors.initials: H
authors.lastname: Ardalani
authors.forename: Ryan J
authors.initials: RJ
authors.lastname: Wagner
authors.forename: Mitchell D
authors.initials: MD
authors.lastname: Probasco
authors.forename: Jennifer M
authors.initials: JM
authors.lastname: Bolin
authors.forename: Ning
authors.initials: N
authors.lastname: Leng
authors.forename: Srikumar
authors.initials: S
authors.lastname: Sengupta
authors.forename: Michael
authors.initials: M
authors.lastname: Volkmer
authors.forename: Bianca
authors.initials: B
authors.lastname: Habermann
authors.forename: Elly M
authors.initials: EM
authors.lastname: Tanaka
authors.forename: James A
authors.initials: JA
authors.lastname: Thomson
authors.forename: Colin N
authors.initials: CN
authors.lastname: Dewey
mesh_terms: D000558:Ambystoma mexicanum / Q000235:genetics / Q000502:physiology*; D000671:Amputation, Surgical; D000818:Animals; D016000:Cluster Analysis; D005121:Extremities / Q000293:injuries / Q000502:physiology; D020869:Gene Expression Profiling / Q000379:methods*; D005786:Gene Expression Regulation; D009857:Oncogenes; D012038:Regeneration / Q000235:genetics / Q000502:physiology; D017423:Sequence Analysis, RNA / Q000379:methods*; D015854:Up-Regulation; D014945:Wound Healing / Q000235:genetics / Q000502:physiology