Genome-wide expression profile of the response to spinal cord injury in Xenopus laevis reveals extensive differences between regenerative and non-regenerative stages
Xenopus laevis has regenerative and non-regenerative stages. As a tadpole, it is fully capable of functional recovery after a spinal cord injury, while its juvenile form (froglet) loses this capability during metamorphosis. We envision that comparative studies between regenerative and non-regenerati...
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| Veröffentlicht in: | Neural development 2014-05, Vol.9 (1), p.12-12, Article 12 |
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| creator | Lee-Liu, Dasfne Moreno, Mauricio Almonacid, Leonardo I Tapia, Víctor S Muñoz, Rosana von Marées, Javier Gaete, Marcia Melo, Francisco Larraín, Juan |
| description | Xenopus laevis has regenerative and non-regenerative stages. As a tadpole, it is fully capable of functional recovery after a spinal cord injury, while its juvenile form (froglet) loses this capability during metamorphosis. We envision that comparative studies between regenerative and non-regenerative stages in Xenopus could aid in understanding why spinal cord regeneration fails in human beings.
To identify the mechanisms that allow the tadpole to regenerate and inhibit regeneration in the froglet, we obtained a transcriptome-wide profile of the response to spinal cord injury in Xenopus regenerative and non-regenerative stages. We found extensive transcriptome changes in regenerative tadpoles at 1 day after injury, while this was only observed by 6 days after injury in non-regenerative froglets. In addition, when comparing both stages, we found that they deployed a very different repertoire of transcripts, with more than 80% of them regulated in only one stage, including previously unannotated transcripts. This was supported by gene ontology enrichment analysis and validated by RT-qPCR, which showed that transcripts involved in metabolism, response to stress, cell cycle, development, immune response and inflammation, neurogenesis, and axonal regeneration were regulated differentially between regenerative and non-regenerative stages.
We identified differences in the timing of the transcriptional response and in the inventory of regulated transcripts and biological processes activated in response to spinal cord injury when comparing regenerative and non-regenerative stages. These genes and biological processes provide an entry point to understand why regeneration fails in mammals. Furthermore, our results introduce Xenopus laevis as a genetic model organism to study spinal cord regeneration. |
| doi_str_mv | 10.1186/1749-8104-9-12 |
| format | Article |
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To identify the mechanisms that allow the tadpole to regenerate and inhibit regeneration in the froglet, we obtained a transcriptome-wide profile of the response to spinal cord injury in Xenopus regenerative and non-regenerative stages. We found extensive transcriptome changes in regenerative tadpoles at 1 day after injury, while this was only observed by 6 days after injury in non-regenerative froglets. In addition, when comparing both stages, we found that they deployed a very different repertoire of transcripts, with more than 80% of them regulated in only one stage, including previously unannotated transcripts. This was supported by gene ontology enrichment analysis and validated by RT-qPCR, which showed that transcripts involved in metabolism, response to stress, cell cycle, development, immune response and inflammation, neurogenesis, and axonal regeneration were regulated differentially between regenerative and non-regenerative stages.
We identified differences in the timing of the transcriptional response and in the inventory of regulated transcripts and biological processes activated in response to spinal cord injury when comparing regenerative and non-regenerative stages. These genes and biological processes provide an entry point to understand why regeneration fails in mammals. Furthermore, our results introduce Xenopus laevis as a genetic model organism to study spinal cord regeneration.</description><identifier>ISSN: 1749-8104</identifier><identifier>EISSN: 1749-8104</identifier><identifier>DOI: 10.1186/1749-8104-9-12</identifier><identifier>PMID: 24885550</identifier><language>eng</language><publisher>England: BioMed Central Ltd</publisher><subject>Amputation ; Animals ; Cell cycle ; Comparative analysis ; Experiments ; Neurogenesis ; Neurogenesis - genetics ; Physiological aspects ; RNA sequencing ; Rodents ; Spinal cord injuries ; Spinal Cord Injuries - genetics ; Spinal Cord Regeneration - genetics ; Transcriptome ; Xenopus laevis</subject><ispartof>Neural development, 2014-05, Vol.9 (1), p.12-12, Article 12</ispartof><rights>COPYRIGHT 2014 BioMed Central Ltd.</rights><rights>2014 Lee-Liu et al.; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License ( http://creativecommons.org/licenses/by/4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited. The Creative Commons Public Domain Dedication waiver ( http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.</rights><rights>Copyright © 2014 Lee-Liu et al.; licensee BioMed Central Ltd. 2014 Lee-Liu et al.; licensee BioMed Central Ltd.</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-b676t-2dc04b0ee162579b65c86c8d011f57ba160462b0f5bf3ae7412574b67cc665183</citedby><cites>FETCH-LOGICAL-b676t-2dc04b0ee162579b65c86c8d011f57ba160462b0f5bf3ae7412574b67cc665183</cites></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC4046850/pdf/$$EPDF$$P50$$Gpubmedcentral$$Hfree_for_read</linktopdf><linktohtml>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC4046850/$$EHTML$$P50$$Gpubmedcentral$$Hfree_for_read</linktohtml><link.rule.ids>230,314,724,777,781,861,882,27905,27906,53772,53774</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/24885550$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Lee-Liu, Dasfne</creatorcontrib><creatorcontrib>Moreno, Mauricio</creatorcontrib><creatorcontrib>Almonacid, Leonardo I</creatorcontrib><creatorcontrib>Tapia, Víctor S</creatorcontrib><creatorcontrib>Muñoz, Rosana</creatorcontrib><creatorcontrib>von Marées, Javier</creatorcontrib><creatorcontrib>Gaete, Marcia</creatorcontrib><creatorcontrib>Melo, Francisco</creatorcontrib><creatorcontrib>Larraín, Juan</creatorcontrib><title>Genome-wide expression profile of the response to spinal cord injury in Xenopus laevis reveals extensive differences between regenerative and non-regenerative stages</title><title>Neural development</title><addtitle>Neural Dev</addtitle><description>Xenopus laevis has regenerative and non-regenerative stages. As a tadpole, it is fully capable of functional recovery after a spinal cord injury, while its juvenile form (froglet) loses this capability during metamorphosis. We envision that comparative studies between regenerative and non-regenerative stages in Xenopus could aid in understanding why spinal cord regeneration fails in human beings.
To identify the mechanisms that allow the tadpole to regenerate and inhibit regeneration in the froglet, we obtained a transcriptome-wide profile of the response to spinal cord injury in Xenopus regenerative and non-regenerative stages. We found extensive transcriptome changes in regenerative tadpoles at 1 day after injury, while this was only observed by 6 days after injury in non-regenerative froglets. In addition, when comparing both stages, we found that they deployed a very different repertoire of transcripts, with more than 80% of them regulated in only one stage, including previously unannotated transcripts. This was supported by gene ontology enrichment analysis and validated by RT-qPCR, which showed that transcripts involved in metabolism, response to stress, cell cycle, development, immune response and inflammation, neurogenesis, and axonal regeneration were regulated differentially between regenerative and non-regenerative stages.
We identified differences in the timing of the transcriptional response and in the inventory of regulated transcripts and biological processes activated in response to spinal cord injury when comparing regenerative and non-regenerative stages. These genes and biological processes provide an entry point to understand why regeneration fails in mammals. Furthermore, our results introduce Xenopus laevis as a genetic model organism to study spinal cord regeneration.</description><subject>Amputation</subject><subject>Animals</subject><subject>Cell cycle</subject><subject>Comparative analysis</subject><subject>Experiments</subject><subject>Neurogenesis</subject><subject>Neurogenesis - genetics</subject><subject>Physiological aspects</subject><subject>RNA sequencing</subject><subject>Rodents</subject><subject>Spinal cord injuries</subject><subject>Spinal Cord Injuries - genetics</subject><subject>Spinal Cord Regeneration - genetics</subject><subject>Transcriptome</subject><subject>Xenopus laevis</subject><issn>1749-8104</issn><issn>1749-8104</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2014</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><sourceid>ABUWG</sourceid><sourceid>AFKRA</sourceid><sourceid>AZQEC</sourceid><sourceid>BENPR</sourceid><sourceid>CCPQU</sourceid><sourceid>DWQXO</sourceid><sourceid>GNUQQ</sourceid><recordid>eNqNkl1r1jAUgIsobk5vvZSAN3rRmaRJmt4IL0PnYCD4Ad6FND3t8tImNWnfuR_k_zR183XVCZKLhJPnPPk4J8ueEnxMiBSvSMmqXBLM8ion9F52uA_cv7U-yB7FuMWYYyrkw-yAMik55_gw-34Kzg-QX9oGEHwbA8RovUNj8K3tAfkWTReAUnj0LgKaPIqjdbpHxocGWbedw1Wa0JfkGeeIeg07G1PCDnQfk3ICF-0OUGPbFgI4AxHVMF0CuER14CDoaQG0a5DzLl8F46Q7iI-zB22ywZOb-Sj7_PbNp5N3-fn707OTzXlei1JMOW0MZjUGIILysqoFN1IY2WBCWl7WmgjMBK1xy-u20FAykjCWco0RghNZHGWvr73jXA_QGHBT0L0agx10uFJeW7XecfZCdX6nWBJLjpNgcy2orf-HYL1j_KCWMqmlTKpShCbHi5tLBP91hjipwUYDfa8d-DkqwhmmRSUr8R9owXBVlXJ52vM_0K2fQyrkT0oyySnFv6lO96Csa326pVmkapOOFbKkmCXq-A4qjQYGa7yDpXXWCS9XCYmZUmd0eo5RnX38cKfcBB9jgHb_ewSrpef__q9nt4u2x381efEDwG3-dg</recordid><startdate>20140522</startdate><enddate>20140522</enddate><creator>Lee-Liu, Dasfne</creator><creator>Moreno, Mauricio</creator><creator>Almonacid, Leonardo I</creator><creator>Tapia, Víctor S</creator><creator>Muñoz, Rosana</creator><creator>von Marées, Javier</creator><creator>Gaete, Marcia</creator><creator>Melo, Francisco</creator><creator>Larraín, Juan</creator><general>BioMed Central Ltd</general><general>BioMed Central</general><scope>CGR</scope><scope>CUY</scope><scope>CVF</scope><scope>ECM</scope><scope>EIF</scope><scope>NPM</scope><scope>AAYXX</scope><scope>CITATION</scope><scope>ISR</scope><scope>3V.</scope><scope>7TK</scope><scope>7X7</scope><scope>7XB</scope><scope>88E</scope><scope>88G</scope><scope>8FI</scope><scope>8FJ</scope><scope>8FK</scope><scope>ABUWG</scope><scope>AFKRA</scope><scope>AZQEC</scope><scope>BENPR</scope><scope>CCPQU</scope><scope>DWQXO</scope><scope>FYUFA</scope><scope>GHDGH</scope><scope>GNUQQ</scope><scope>K9.</scope><scope>M0S</scope><scope>M1P</scope><scope>M2M</scope><scope>PIMPY</scope><scope>PQEST</scope><scope>PQQKQ</scope><scope>PQUKI</scope><scope>PRINS</scope><scope>PSYQQ</scope><scope>Q9U</scope><scope>7X8</scope><scope>5PM</scope></search><sort><creationdate>20140522</creationdate><title>Genome-wide expression profile of the response to spinal cord injury in Xenopus laevis reveals extensive differences between regenerative and non-regenerative stages</title><author>Lee-Liu, Dasfne ; 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As a tadpole, it is fully capable of functional recovery after a spinal cord injury, while its juvenile form (froglet) loses this capability during metamorphosis. We envision that comparative studies between regenerative and non-regenerative stages in Xenopus could aid in understanding why spinal cord regeneration fails in human beings.
To identify the mechanisms that allow the tadpole to regenerate and inhibit regeneration in the froglet, we obtained a transcriptome-wide profile of the response to spinal cord injury in Xenopus regenerative and non-regenerative stages. We found extensive transcriptome changes in regenerative tadpoles at 1 day after injury, while this was only observed by 6 days after injury in non-regenerative froglets. In addition, when comparing both stages, we found that they deployed a very different repertoire of transcripts, with more than 80% of them regulated in only one stage, including previously unannotated transcripts. This was supported by gene ontology enrichment analysis and validated by RT-qPCR, which showed that transcripts involved in metabolism, response to stress, cell cycle, development, immune response and inflammation, neurogenesis, and axonal regeneration were regulated differentially between regenerative and non-regenerative stages.
We identified differences in the timing of the transcriptional response and in the inventory of regulated transcripts and biological processes activated in response to spinal cord injury when comparing regenerative and non-regenerative stages. These genes and biological processes provide an entry point to understand why regeneration fails in mammals. Furthermore, our results introduce Xenopus laevis as a genetic model organism to study spinal cord regeneration.</abstract><cop>England</cop><pub>BioMed Central Ltd</pub><pmid>24885550</pmid><doi>10.1186/1749-8104-9-12</doi><tpages>1</tpages><oa>free_for_read</oa></addata></record> |
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| subjects | Amputation Animals Cell cycle Comparative analysis Experiments Neurogenesis Neurogenesis - genetics Physiological aspects RNA sequencing Rodents Spinal cord injuries Spinal Cord Injuries - genetics Spinal Cord Regeneration - genetics Transcriptome Xenopus laevis |
| title | Genome-wide expression profile of the response to spinal cord injury in Xenopus laevis reveals extensive differences between regenerative and non-regenerative stages |
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