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A Tissue-Mapped Axolotl De Novo Transcriptome Enables Identification of Limb Regeneration Factors

Bryant, Donald M ; Johnson, Kimberly ; DiTommaso, Tia ; Tickle, Timothy ; Couger, Matthew Brian ; Payzin-Dogru, Duygu ; Lee, Tae J ; Leigh, Nicholas D LU orcid ; Kuo, Tzu-Hsing and Davis, Francis G , et al. (2017) In Cell Reports 18(3). p.762-776
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... (More)

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.

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publishing date
type
Contribution to journal
publication status
published
subject
keywords
Ambystoma mexicanum, Animals, Extremities/physiology, In Situ Hybridization, Insulin-Like Growth Factor Binding Proteins/antagonists & inhibitors, RNA/chemistry, RNA Interference, RNA Splicing, RNA, Small Interfering/metabolism, RNA-Binding Proteins/genetics, Regeneration, Sequence Analysis, RNA, Transcriptome
in
Cell Reports
volume
18
issue
3
pages
762 - 776
publisher
Cell Press
external identifiers
  • scopus:85009782265
  • pmid:28099853
ISSN
2211-1247
DOI
10.1016/j.celrep.2016.12.063
language
English
LU publication?
no
additional info
Copyright © 2017 The Author(s). Published by Elsevier Inc. All rights reserved.
id
b38f553b-8ad9-4daa-af87-403d291e65ac
date added to LUP
2020-04-28 00:02:29
date last changed
2024-05-02 08:43:22
@article{b38f553b-8ad9-4daa-af87-403d291e65ac,
  abstract     = {{<p>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.</p>}},
  author       = {{Bryant, Donald M and Johnson, Kimberly and DiTommaso, Tia and Tickle, Timothy and Couger, Matthew Brian and Payzin-Dogru, Duygu and Lee, Tae J and Leigh, Nicholas D and Kuo, Tzu-Hsing and Davis, Francis G and Bateman, Joel and Bryant, Sevara and Guzikowski, Anna R and Tsai, Stephanie L and Coyne, Steven and Ye, William W and Freeman, Robert M and Peshkin, Leonid and Tabin, Clifford J and Regev, Aviv and Haas, Brian J and Whited, Jessica L}},
  issn         = {{2211-1247}},
  keywords     = {{Ambystoma mexicanum; Animals; Extremities/physiology; In Situ Hybridization; Insulin-Like Growth Factor Binding Proteins/antagonists & inhibitors; RNA/chemistry; RNA Interference; RNA Splicing; RNA, Small Interfering/metabolism; RNA-Binding Proteins/genetics; Regeneration; Sequence Analysis, RNA; Transcriptome}},
  language     = {{eng}},
  month        = {{01}},
  number       = {{3}},
  pages        = {{762--776}},
  publisher    = {{Cell Press}},
  series       = {{Cell Reports}},
  title        = {{A Tissue-Mapped Axolotl De Novo Transcriptome Enables Identification of Limb Regeneration Factors}},
  url          = {{https://lup.lub.lu.se/search/files/78924486/2017_Bryant_CellReports.pdf}},
  doi          = {{10.1016/j.celrep.2016.12.063}},
  volume       = {{18}},
  year         = {{2017}},
}