A Tissue-Mapped Axolotl De Novo Transcriptome Enables Identification of Limb Regeneration Factors
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 stu...
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| Format: | Article |
| Language: | English |
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Elsevier
2017-01-01
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| Series: | Cell Reports |
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| Online Access: | http://www.sciencedirect.com/science/article/pii/S2211124716317703 |
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Article |
| collection |
DOAJ |
| language |
English |
| format |
Article |
| sources |
DOAJ |
| author |
Donald M. Bryant Kimberly Johnson Tia DiTommaso Timothy Tickle Matthew Brian Couger Duygu Payzin-Dogru Tae J. Lee Nicholas D. Leigh Tzu-Hsing Kuo Francis G. Davis Joel Bateman Sevara Bryant Anna R. Guzikowski Stephanie L. Tsai Steven Coyne William W. Ye Robert M. Freeman Jr. Leonid Peshkin Clifford J. Tabin Aviv Regev Brian J. Haas Jessica L. Whited |
| spellingShingle |
Donald M. Bryant Kimberly Johnson Tia DiTommaso Timothy Tickle Matthew Brian Couger Duygu Payzin-Dogru Tae J. Lee Nicholas D. Leigh Tzu-Hsing Kuo Francis G. Davis Joel Bateman Sevara Bryant Anna R. Guzikowski Stephanie L. Tsai Steven Coyne William W. Ye Robert M. Freeman Jr. Leonid Peshkin Clifford J. Tabin Aviv Regev Brian J. Haas Jessica L. Whited A Tissue-Mapped Axolotl De Novo Transcriptome Enables Identification of Limb Regeneration Factors Cell Reports axolotl transcriptome Trinity Trinotate limb regeneration blastema expression analysis cirbp kazald1 |
| author_facet |
Donald M. Bryant Kimberly Johnson Tia DiTommaso Timothy Tickle Matthew Brian Couger Duygu Payzin-Dogru Tae J. Lee Nicholas D. Leigh Tzu-Hsing Kuo Francis G. Davis Joel Bateman Sevara Bryant Anna R. Guzikowski Stephanie L. Tsai Steven Coyne William W. Ye Robert M. Freeman Jr. Leonid Peshkin Clifford J. Tabin Aviv Regev Brian J. Haas Jessica L. Whited |
| author_sort |
Donald M. Bryant |
| title |
A Tissue-Mapped Axolotl De Novo Transcriptome Enables Identification of Limb Regeneration Factors |
| title_short |
A Tissue-Mapped Axolotl De Novo Transcriptome Enables Identification of Limb Regeneration Factors |
| title_full |
A Tissue-Mapped Axolotl De Novo Transcriptome Enables Identification of Limb Regeneration Factors |
| title_fullStr |
A Tissue-Mapped Axolotl De Novo Transcriptome Enables Identification of Limb Regeneration Factors |
| title_full_unstemmed |
A Tissue-Mapped Axolotl De Novo Transcriptome Enables Identification of Limb Regeneration Factors |
| title_sort |
tissue-mapped axolotl de novo transcriptome enables identification of limb regeneration factors |
| publisher |
Elsevier |
| series |
Cell Reports |
| issn |
2211-1247 |
| publishDate |
2017-01-01 |
| description |
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. |
| topic |
axolotl transcriptome Trinity Trinotate limb regeneration blastema expression analysis cirbp kazald1 |
| url |
http://www.sciencedirect.com/science/article/pii/S2211124716317703 |
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1725081790204346368 |
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doaj-1952cf1abfac437ca3a57a2785b1e5782020-11-25T01:32:29ZengElsevierCell Reports2211-12472017-01-0118376277610.1016/j.celrep.2016.12.063A Tissue-Mapped Axolotl De Novo Transcriptome Enables Identification of Limb Regeneration FactorsDonald M. Bryant0Kimberly Johnson1Tia DiTommaso2Timothy Tickle3Matthew Brian Couger4Duygu Payzin-Dogru5Tae J. Lee6Nicholas D. Leigh7Tzu-Hsing Kuo8Francis G. Davis9Joel Bateman10Sevara Bryant11Anna R. Guzikowski12Stephanie L. Tsai13Steven Coyne14William W. Ye15Robert M. Freeman Jr.16Leonid Peshkin17Clifford J. Tabin18Aviv Regev19Brian J. Haas20Jessica L. Whited21Harvard Medical School, Harvard Stem Cell Institute, and Department of Orthopedic Surgery, Brigham & Women’s Hospital, 65 Landsdowne St., Cambridge, MA 02139, USAHarvard Medical School, Harvard Stem Cell Institute, and Department of Orthopedic Surgery, Brigham & Women’s Hospital, 65 Landsdowne St., Cambridge, MA 02139, USAHarvard Medical School, Harvard Stem Cell Institute, and Department of Orthopedic Surgery, Brigham & Women’s Hospital, 65 Landsdowne St., Cambridge, MA 02139, USABroad Institute of MIT and Harvard and Klarman Cell Observatory, 7 Cambridge Center, Cambridge, MA 02142, USADepartment of Microbiology and Molecular Genetics, Oklahoma State University, 307 Life Sciences East, Stillwater, OK 74078, USAHarvard Medical School, Harvard Stem Cell Institute, and Department of Orthopedic Surgery, Brigham & Women’s Hospital, 65 Landsdowne St., Cambridge, MA 02139, USAHarvard Medical School, Harvard Stem Cell Institute, and Department of Orthopedic Surgery, Brigham & Women’s Hospital, 65 Landsdowne St., Cambridge, MA 02139, USAHarvard Medical School, Harvard Stem Cell Institute, and Department of Orthopedic Surgery, Brigham & Women’s Hospital, 65 Landsdowne St., Cambridge, MA 02139, USAHarvard Medical School, Harvard Stem Cell Institute, and Department of Orthopedic Surgery, Brigham & Women’s Hospital, 65 Landsdowne St., Cambridge, MA 02139, USAHarvard Medical School, Harvard Stem Cell Institute, and Department of Orthopedic Surgery, Brigham & Women’s Hospital, 65 Landsdowne St., Cambridge, MA 02139, USAHarvard Medical School, Harvard Stem Cell Institute, and Department of Orthopedic Surgery, Brigham & Women’s Hospital, 65 Landsdowne St., Cambridge, MA 02139, USAHarvard Medical School, Harvard Stem Cell Institute, and Department of Orthopedic Surgery, Brigham & Women’s Hospital, 65 Landsdowne St., Cambridge, MA 02139, USAHarvard Medical School, Harvard Stem Cell Institute, and Department of Orthopedic Surgery, Brigham & Women’s Hospital, 65 Landsdowne St., Cambridge, MA 02139, USADepartment of Genetics, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA 02115, USAHarvard Medical School, Harvard Stem Cell Institute, and Department of Orthopedic Surgery, Brigham & Women’s Hospital, 65 Landsdowne St., Cambridge, MA 02139, USAHarvard Medical School, Harvard Stem Cell Institute, and Department of Orthopedic Surgery, Brigham & Women’s Hospital, 65 Landsdowne St., Cambridge, MA 02139, USADepartment of Systems Biology, Harvard Medical School, 200 Longwood Avenue, Boston, MA 02115, USADepartment of Systems Biology, Harvard Medical School, 200 Longwood Avenue, Boston, MA 02115, USADepartment of Genetics, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA 02115, USABroad Institute of MIT and Harvard and Klarman Cell Observatory, 7 Cambridge Center, Cambridge, MA 02142, USABroad Institute of MIT and Harvard and Klarman Cell Observatory, 7 Cambridge Center, Cambridge, MA 02142, USAHarvard Medical School, Harvard Stem Cell Institute, and Department of Orthopedic Surgery, Brigham & Women’s Hospital, 65 Landsdowne St., Cambridge, MA 02139, USAMammals 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.http://www.sciencedirect.com/science/article/pii/S2211124716317703axolotltranscriptomeTrinityTrinotatelimbregenerationblastemaexpression analysiscirbpkazald1 |