title: A Tissue-Mapped Axolotl De Novo Transcriptome Enables Identification of Limb Regeneration Factors.
abstract: Mammals have extremely limited regenerative capabilities; however, axolotls are profoundly regenerative and can replace entire limbs. The mechanisms underlying limb regeneration remain poorly understood, partly because the enormous and incompletely sequenced genomes of axolotls have hindered the study of genes facilitating regeneration. We assembled and annotated a de novo transcriptome using RNA-sequencing profiles for a broad spectrum of tissues that is estimated to have near-complete sequence information for 88% of axolotl genes. We devised expression analyses that identified the axolotl orthologs of cirbp and kazald1 as highly expressed and enriched in blastemas. Using morpholino anti-sense oligonucleotides, we find evidence that cirbp plays a cytoprotective role during limb regeneration whereas manipulation of kazald1 expression disrupts regeneration. Our transcriptome and annotation resources greatly complement previous transcriptomic studies and will be a valuable resource for future research in regenerative biology.
authors.affiliation: Harvard Medical School, Harvard Stem Cell Institute, and Department of Orthopedic Surgery, Brigham & Women's Hospital, 65 Landsdowne St., Cambridge, MA 02139, USA.
authors.forename: Donald M
authors.initials: DM
authors.lastname: Bryant
authors.affiliation: Harvard Medical School, Harvard Stem Cell Institute, and Department of Orthopedic Surgery, Brigham & Women's Hospital, 65 Landsdowne St., Cambridge, MA 02139, USA.
authors.forename: Kimberly
authors.initials: K
authors.lastname: Johnson
authors.affiliation: Harvard Medical School, Harvard Stem Cell Institute, and Department of Orthopedic Surgery, Brigham & Women's Hospital, 65 Landsdowne St., Cambridge, MA 02139, USA.
authors.forename: Tia
authors.initials: T
authors.lastname: DiTommaso
authors.affiliation: Broad Institute of MIT and Harvard and Klarman Cell Observatory, 7 Cambridge Center, Cambridge, MA 02142, USA.
authors.forename: Timothy
authors.initials: T
authors.lastname: Tickle
authors.affiliation: Department of Microbiology and Molecular Genetics, Oklahoma State University, 307 Life Sciences East, Stillwater, OK 74078, USA.
authors.forename: Matthew Brian
authors.initials: MB
authors.lastname: Couger
authors.affiliation: Harvard Medical School, Harvard Stem Cell Institute, and Department of Orthopedic Surgery, Brigham & Women's Hospital, 65 Landsdowne St., Cambridge, MA 02139, USA.
authors.forename: Duygu
authors.initials: D
authors.lastname: Payzin-Dogru
authors.affiliation: Harvard Medical School, Harvard Stem Cell Institute, and Department of Orthopedic Surgery, Brigham & Women's Hospital, 65 Landsdowne St., Cambridge, MA 02139, USA.
authors.forename: Tae J
authors.initials: TJ
authors.lastname: Lee
authors.affiliation: Harvard Medical School, Harvard Stem Cell Institute, and Department of Orthopedic Surgery, Brigham & Women's Hospital, 65 Landsdowne St., Cambridge, MA 02139, USA.
authors.forename: Nicholas D
authors.initials: ND
authors.lastname: Leigh
authors.affiliation: Harvard Medical School, Harvard Stem Cell Institute, and Department of Orthopedic Surgery, Brigham & Women's Hospital, 65 Landsdowne St., Cambridge, MA 02139, USA.
authors.forename: Tzu-Hsing
authors.initials: TH
authors.lastname: Kuo
authors.affiliation: Harvard Medical School, Harvard Stem Cell Institute, and Department of Orthopedic Surgery, Brigham & Women's Hospital, 65 Landsdowne St., Cambridge, MA 02139, USA.
authors.forename: Francis G
authors.initials: FG
authors.lastname: Davis
authors.affiliation: Harvard Medical School, Harvard Stem Cell Institute, and Department of Orthopedic Surgery, Brigham & Women's Hospital, 65 Landsdowne St., Cambridge, MA 02139, USA.
authors.forename: Joel
authors.initials: J
authors.lastname: Bateman
authors.affiliation: Harvard Medical School, Harvard Stem Cell Institute, and Department of Orthopedic Surgery, Brigham & Women's Hospital, 65 Landsdowne St., Cambridge, MA 02139, USA.
authors.forename: Sevara
authors.initials: S
authors.lastname: Bryant
authors.affiliation: Harvard Medical School, Harvard Stem Cell Institute, and Department of Orthopedic Surgery, Brigham & Women's Hospital, 65 Landsdowne St., Cambridge, MA 02139, USA.
authors.forename: Anna R
authors.initials: AR
authors.lastname: Guzikowski
authors.affiliation: Department of Genetics, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA 02115, USA.
authors.forename: Stephanie L
authors.initials: SL
authors.lastname: Tsai
authors.affiliation: Harvard Medical School, Harvard Stem Cell Institute, and Department of Orthopedic Surgery, Brigham & Women's Hospital, 65 Landsdowne St., Cambridge, MA 02139, USA.
authors.forename: Steven
authors.initials: S
authors.lastname: Coyne
authors.affiliation: Harvard Medical School, Harvard Stem Cell Institute, and Department of Orthopedic Surgery, Brigham & Women's Hospital, 65 Landsdowne St., Cambridge, MA 02139, USA.
authors.forename: William W
authors.initials: WW
authors.lastname: Ye
authors.affiliation: Department of Systems Biology, Harvard Medical School, 200 Longwood Avenue, Boston, MA 02115, USA.
authors.forename: Robert M
authors.initials: RM
authors.lastname: Freeman
authors.affiliation: Department of Systems Biology, Harvard Medical School, 200 Longwood Avenue, Boston, MA 02115, USA.
authors.forename: Leonid
authors.initials: L
authors.lastname: Peshkin
authors.affiliation: Department of Genetics, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA 02115, USA.
authors.forename: Clifford J
authors.initials: CJ
authors.lastname: Tabin
authors.affiliation: Broad Institute of MIT and Harvard and Klarman Cell Observatory, 7 Cambridge Center, Cambridge, MA 02142, USA.
authors.forename: Aviv
authors.initials: A
authors.lastname: Regev
authors.affiliation: Broad Institute of MIT and Harvard and Klarman Cell Observatory, 7 Cambridge Center, Cambridge, MA 02142, USA. Electronic address: bhaas@broadinstitute.org.
authors.forename: Brian J
authors.initials: BJ
authors.lastname: Haas
authors.affiliation: Harvard Medical School, Harvard Stem Cell Institute, and Department of Orthopedic Surgery, Brigham & Women's Hospital, 65 Landsdowne St., Cambridge, MA 02139, USA. Electronic address: jwhited@bwh.harvard.edu.
authors.forename: Jessica L
authors.initials: JL
authors.lastname: Whited
mesh_terms: D000558:Ambystoma mexicanum; D000818:Animals; D005121:Extremities / Q000502:physiology*; D017403:In Situ Hybridization; D018969:Insulin-Like Growth Factor Binding Proteins / Q000037:antagonists & inhibitors / Q000235:genetics / Q000378:metabolism; D012313:RNA / Q000737:chemistry / Q000378:metabolism; D034622:RNA Interference; D012326:RNA Splicing; D034741:RNA, Small Interfering / Q000378:metabolism; D016601:RNA-Binding Proteins / Q000235:genetics / Q000378:metabolism; D012038:Regeneration; D017423:Sequence Analysis, RNA; D059467:Transcriptome
chemical_list: D018969:Insulin-Like Growth Factor Binding Proteins; D034741:RNA, Small Interfering; D016601:RNA-Binding Proteins; D012313:RNA
keywords: Trinity; Trinotate; axolotl; blastema; cirbp; expression analysis; kazald1; limb; regeneration; transcriptome