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...
| Main Authors: | , , , , , , , , , , , , , , , , , , , , , |
|---|---|
| Other Authors: | |
| Format: | Article |
| Language: | en_US |
| Published: |
Elsevier
2017
|
| Online Access: | http://hdl.handle.net/1721.1/109834 https://orcid.org/0000-0001-8567-2049 |
| _version_ | 1826188988889694208 |
|---|---|
| author | Bryant, Donald M. Johnson, Kimberly DiTommaso, Tia Tickle, Timothy Couger, Matthew Brian Payzin-Dogru, Duygu Lee, Tae J. Leigh, Nicholas D. Kuo, Tzu-Hsing Davis, Francis G. Bateman, Joel Bryant, Sevara Guzikowski, Anna R. Tsai, Stephanie L. Coyne, Steven Ye, William W. Freeman, Robert M. Peshkin, Leonid Tabin, Clifford J. Whited, Jessica L. Regev, Aviv Haas, Brian |
| author2 | Broad Institute of MIT and Harvard |
| author_facet | Broad Institute of MIT and Harvard Bryant, Donald M. Johnson, Kimberly DiTommaso, Tia Tickle, Timothy Couger, Matthew Brian Payzin-Dogru, Duygu Lee, Tae J. Leigh, Nicholas D. Kuo, Tzu-Hsing Davis, Francis G. Bateman, Joel Bryant, Sevara Guzikowski, Anna R. Tsai, Stephanie L. Coyne, Steven Ye, William W. Freeman, Robert M. Peshkin, Leonid Tabin, Clifford J. Whited, Jessica L. Regev, Aviv Haas, Brian |
| author_sort | Bryant, Donald M. |
| collection | MIT |
| 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. |
| first_indexed | 2024-09-23T08:08:06Z |
| format | Article |
| id | mit-1721.1/109834 |
| institution | Massachusetts Institute of Technology |
| language | en_US |
| last_indexed | 2024-09-23T08:08:06Z |
| publishDate | 2017 |
| publisher | Elsevier |
| record_format | dspace |
| spelling | mit-1721.1/1098342022-09-30T07:47:41Z 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. Kuo, Tzu-Hsing Davis, Francis G. Bateman, Joel Bryant, Sevara Guzikowski, Anna R. Tsai, Stephanie L. Coyne, Steven Ye, William W. Freeman, Robert M. Peshkin, Leonid Tabin, Clifford J. Whited, Jessica L. Regev, Aviv Haas, Brian Broad Institute of MIT and Harvard Regev, Aviv Haas, Brian 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. United States. National Institutes of Health (1U24CA180922-01) 2017-06-13T19:04:14Z 2017-06-13T19:04:14Z 2017-01 2016-10 Article http://purl.org/eprint/type/JournalArticle 2211-1247 http://hdl.handle.net/1721.1/109834 Bryant, Donald M.; Johnson, Kimberly; DiTommaso, Tia; Tickle, Timothy; Couger, Matthew Brian; Payzin-Dogru, Duygu; Lee, Tae J. et al. “A Tissue-Mapped Axolotl De Novo Transcriptome Enables Identification of Limb Regeneration Factors.” Cell Reports 18, no. 3 (January 2017): 762–776 © 2016 The Author(s) https://orcid.org/0000-0001-8567-2049 en_US http://dx.doi.org/10.1016/j.celrep.2016.12.063 Cell Reports Creative Commons Attribution-NonCommercial-NoDerivs License http://creativecommons.org/licenses/by-nc-nd/4.0/ application/pdf Elsevier Elsevier |
| spellingShingle | Bryant, Donald M. Johnson, Kimberly DiTommaso, Tia Tickle, Timothy Couger, Matthew Brian Payzin-Dogru, Duygu Lee, Tae J. Leigh, Nicholas D. Kuo, Tzu-Hsing Davis, Francis G. Bateman, Joel Bryant, Sevara Guzikowski, Anna R. Tsai, Stephanie L. Coyne, Steven Ye, William W. Freeman, Robert M. Peshkin, Leonid Tabin, Clifford J. Whited, Jessica L. Regev, Aviv Haas, Brian A Tissue-Mapped Axolotl De Novo Transcriptome Enables Identification of Limb Regeneration Factors |
| title | 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_short | 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 |
| url | http://hdl.handle.net/1721.1/109834 https://orcid.org/0000-0001-8567-2049 |
| work_keys_str_mv | AT bryantdonaldm atissuemappedaxolotldenovotranscriptomeenablesidentificationoflimbregenerationfactors AT johnsonkimberly atissuemappedaxolotldenovotranscriptomeenablesidentificationoflimbregenerationfactors AT ditommasotia atissuemappedaxolotldenovotranscriptomeenablesidentificationoflimbregenerationfactors AT tickletimothy atissuemappedaxolotldenovotranscriptomeenablesidentificationoflimbregenerationfactors AT cougermatthewbrian atissuemappedaxolotldenovotranscriptomeenablesidentificationoflimbregenerationfactors AT payzindogruduygu atissuemappedaxolotldenovotranscriptomeenablesidentificationoflimbregenerationfactors AT leetaej atissuemappedaxolotldenovotranscriptomeenablesidentificationoflimbregenerationfactors AT leighnicholasd atissuemappedaxolotldenovotranscriptomeenablesidentificationoflimbregenerationfactors AT kuotzuhsing atissuemappedaxolotldenovotranscriptomeenablesidentificationoflimbregenerationfactors AT davisfrancisg atissuemappedaxolotldenovotranscriptomeenablesidentificationoflimbregenerationfactors AT batemanjoel atissuemappedaxolotldenovotranscriptomeenablesidentificationoflimbregenerationfactors AT bryantsevara atissuemappedaxolotldenovotranscriptomeenablesidentificationoflimbregenerationfactors AT guzikowskiannar atissuemappedaxolotldenovotranscriptomeenablesidentificationoflimbregenerationfactors AT tsaistephaniel atissuemappedaxolotldenovotranscriptomeenablesidentificationoflimbregenerationfactors AT coynesteven atissuemappedaxolotldenovotranscriptomeenablesidentificationoflimbregenerationfactors AT yewilliamw atissuemappedaxolotldenovotranscriptomeenablesidentificationoflimbregenerationfactors AT freemanrobertm atissuemappedaxolotldenovotranscriptomeenablesidentificationoflimbregenerationfactors AT peshkinleonid atissuemappedaxolotldenovotranscriptomeenablesidentificationoflimbregenerationfactors AT tabincliffordj atissuemappedaxolotldenovotranscriptomeenablesidentificationoflimbregenerationfactors AT whitedjessical atissuemappedaxolotldenovotranscriptomeenablesidentificationoflimbregenerationfactors AT regevaviv atissuemappedaxolotldenovotranscriptomeenablesidentificationoflimbregenerationfactors AT haasbrian atissuemappedaxolotldenovotranscriptomeenablesidentificationoflimbregenerationfactors AT bryantdonaldm tissuemappedaxolotldenovotranscriptomeenablesidentificationoflimbregenerationfactors AT johnsonkimberly tissuemappedaxolotldenovotranscriptomeenablesidentificationoflimbregenerationfactors AT ditommasotia tissuemappedaxolotldenovotranscriptomeenablesidentificationoflimbregenerationfactors AT tickletimothy tissuemappedaxolotldenovotranscriptomeenablesidentificationoflimbregenerationfactors AT cougermatthewbrian tissuemappedaxolotldenovotranscriptomeenablesidentificationoflimbregenerationfactors AT payzindogruduygu tissuemappedaxolotldenovotranscriptomeenablesidentificationoflimbregenerationfactors AT leetaej tissuemappedaxolotldenovotranscriptomeenablesidentificationoflimbregenerationfactors AT leighnicholasd tissuemappedaxolotldenovotranscriptomeenablesidentificationoflimbregenerationfactors AT kuotzuhsing tissuemappedaxolotldenovotranscriptomeenablesidentificationoflimbregenerationfactors AT davisfrancisg tissuemappedaxolotldenovotranscriptomeenablesidentificationoflimbregenerationfactors AT batemanjoel tissuemappedaxolotldenovotranscriptomeenablesidentificationoflimbregenerationfactors AT bryantsevara tissuemappedaxolotldenovotranscriptomeenablesidentificationoflimbregenerationfactors AT guzikowskiannar tissuemappedaxolotldenovotranscriptomeenablesidentificationoflimbregenerationfactors AT tsaistephaniel tissuemappedaxolotldenovotranscriptomeenablesidentificationoflimbregenerationfactors AT coynesteven tissuemappedaxolotldenovotranscriptomeenablesidentificationoflimbregenerationfactors AT yewilliamw tissuemappedaxolotldenovotranscriptomeenablesidentificationoflimbregenerationfactors AT freemanrobertm tissuemappedaxolotldenovotranscriptomeenablesidentificationoflimbregenerationfactors AT peshkinleonid tissuemappedaxolotldenovotranscriptomeenablesidentificationoflimbregenerationfactors AT tabincliffordj tissuemappedaxolotldenovotranscriptomeenablesidentificationoflimbregenerationfactors AT whitedjessical tissuemappedaxolotldenovotranscriptomeenablesidentificationoflimbregenerationfactors AT regevaviv tissuemappedaxolotldenovotranscriptomeenablesidentificationoflimbregenerationfactors AT haasbrian tissuemappedaxolotldenovotranscriptomeenablesidentificationoflimbregenerationfactors |