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Gene expression profile of the regeneration epithelium during axolotl limb regeneration.

ABSTRACT: Urodele amphibians are unique among adult vertebrates in their ability to regenerate missing limbs. The process of limb regeneration requires several key tissues including a regeneration-competent wound epidermis called the regeneration epithelium (RE). We used microarray analysis to profile gene expression of the RE in the axolotl, a Mexican salamander. A list of 125 genes and expressed sequence tags (ESTs) showed a ?1.5-fold expression in the RE than in a wound epidermis covering a lateral cuff wound. A subset of the RE ESTs and genes were further characterized for expression level changes over the time-course of regeneration. This study provides the first large scale identification of specific gene expression in the RE.

SUBMITTER: Campbell LJ

PROVIDER: S-EPMC3297817 | biostudies-literature | 2011 Jul

REPOSITORIES: biostudies-literature

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Gene expression profile of the regeneration epithelium during axolotl limb regeneration.

Campbell Leah J LJ Suárez-Castillo Edna C EC Ortiz-Zuazaga Humberto H Knapp Dunja D Tanaka Elly M EM Crews Craig M CM

Developmental dynamics : an official publication of the American Association of Anatomists 20110603 7

Urodele amphibians are unique among adult vertebrates in their ability to regenerate missing limbs. The process of limb regeneration requires several key tissues including a regeneration-competent wound epidermis called the regeneration epithelium (RE). We used microarray analysis to profile gene expression of the RE in the axolotl, a Mexican salamander. A list of 125 genes and expressed sequence tags (ESTs) showed a ≥1.5-fold expression in the RE than in a wound epidermis covering a lateral cuf ...[more]

PMID: 21648017

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Dynamic expression of two thrombospondins during axolotl limb regeneration.

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Microarray analysis of microRNA expression during axolotl limb regeneration.

Project description:Among vertebrates, salamanders stand out for their remarkable capacity to quickly regrow a myriad of tissues and organs after injury or amputation. The limb regeneration process in axolotls (Ambystoma mexicanum) has been well studied for decades at the cell-tissue level. While several developmental genes are known to be reactivated during this epimorphic process, less is known about the role of microRNAs in urodele amphibian limb regeneration. Given the compelling evidence that many microRNAs tightly regulate cell fate and morphogenetic processes through development and adulthood by modulating the expression (or re-expression) of developmental genes, we investigated the possibility that microRNA levels change during limb regeneration. Using two different microarray platforms to compare the axolotl microRNA expression between mid-bud limb regenerating blastemas and non-regenerating stump tissues, we found that miR-21 was overexpressed in mid-bud blastemas compared to stump tissue. Mature A. mexicanum ("Amex") miR-21 was detected in axolotl RNA by Northern blot and differential expression of Amex-miR-21 in blastema versus stump was confirmed by quantitative RT-PCR. We identified the Amex Jagged1 as a putative target gene for miR-21 during salamander limb regeneration. We cloned the full length 3'UTR of Amex-Jag1, and our in vitro assays demonstrated that its single miR-21 target recognition site is functional and essential for the response of the Jagged1 gene to miR-21 levels. Our findings pave the road for advanced in vivo functional assays aimed to clarify how microRNAs such as miR-21, often linked to pathogenic cell growth, might be modulating the redeployment of developmental genes such as Jagged1 during regenerative processes.

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Comparative Analysis of Cartilage Marker Gene Expression Patterns during Axolotl and Xenopus Limb Regeneration.

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Gene expression during the first 28 days of axolotl limb regeneration I: Experimental design and global analysis of gene expression.

Project description:While it is appreciated that global gene expression analyses can provide novel insights about complex biological processes, experiments are generally insufficiently powered to achieve this goal. Here we report the results of a robust microarray experiment of axolotl forelimb regeneration. At each of 20 post-amputation time points, we estimated gene expression for 10 replicate RNA samples that were isolated from 1 mm of heterogeneous tissue collected from the distal limb tip. We show that the limb transcription program diverges progressively with time from the non-injured state, and divergence among time adjacent samples is mostly gradual. However, punctuated episodes of transcription were identified for five intervals of time, with four of these coinciding with well-described stages of limb regeneration-amputation, early bud, late bud, and pallet. The results suggest that regeneration is highly temporally structured and regulated by mechanisms that function within narrow windows of time to coordinate transcription within and across cell types of the regenerating limb. Our results provide an integrative framework for hypothesis generation using this complex and highly informative data set.

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Comparison of Protein Expression During Early Phases of Limb Regeneration Between Regeneration-permissive and Regeneration-deficient Axolotl

Project description:In this project, we studied the proteomic profiles of the early stages of blastema formation of neotenic and metamorphic axolotls after limb amputation by means of LC-MS/MS technology. We quantified a total of 714 proteins having an adjusted p < 0.01 with FC greater or equal to 2 between two conditions. Principal component analysis revealed a conspicuous clustering between neotenic and metamorphic samples at 7 days post-amputation. Different set of proteins was identified as differentially expressed at all of the time points (1, 4, and 7 days post-amputations against day0) for neotenic and metamorphic stages. Although functional enrichment analyses underline the presence of common pathways between regenerative and non-regenerative stages, cell proliferation and its regulation associated pathways, immune system related pathways and muscle tissue and ECM remodeling and degradation pathways were represented at different rate between both stages.

2019-11-25 | PXD014806 | Pride

Gene Expression During the First 28 Days of Axolotl Limb Regeneration

Project description:Here we report the results of a robust microarray experiment that examined the first 28 days of axolotl forelimb regeneration. At each of 20 post-amputation time points, we estimated gene expression for 10 replicate RNA samples that were isolated from 1m of heterogeneous tissue collected from the distal limb tip. The distal 1.0mm of heterogeneous tissue from regenerating limb tip were removed and used for RNA extraction. 10 samples were collected for each of 20 time points.

2015-04-20 | E-GEOD-67118 | biostudies-arrayexpress

Microarray Analysis of microRNA Expression during Axolotl Limb Regeneration

Project description:The salamander microRNA expression between mid-bud limb regenerating blastemas (17 days post amputation) and non-regenerating stump tissues was compared by microarray analysis. LC Sciences arrays: Six paired samples were analyzed: three mid-bud 17dpa blastemas (bl), and three non-regenerating stumps (st). Three arrays were hybridized comparing two paired samples each time. Biological dye-swaps were made by labeling bl samples once with Cy3 and twice with Cy5; st samples were labeled accordingly twice with Cy5 and once with Cy3. Multiple arrays averaged into a single Sample record. Supplementary files: GSE29727_LC_MultiArray_SimpleNormalizedData.txt.gz GSE29727_LC_signal_ratio_mean_SD.txt.gz GSE29727_LC_t-Test_st-vs-bl.txt.gz Exiqon arrays: Six paired samples were analyzed: three mid-bud 17dpa blastemas (bl), and three non-regenerating stumps (st). Six arrays were hybridized comparing each sample labeled with Hy3 against a common reference sample made by pooling all the samples and labeling it with Hy5. Multiple arrays not averaged, represented as multiple Sample records. Supplementary file: GSE29727_Exiqon_matrix_complete.txt

2012-11-06 | E-GEOD-29727 | biostudies-arrayexpress

The Meis homeoprotein regulates the axolotl Prod 1 promoter during limb regeneration.

Project description:During limb regeneration in salamanders the blastemal cells give rise only to structures distal to the level of amputation. This proximodistal identity can be regulated by ectopic expression of Meis homeoproteins or the three finger protein Prod 1 which acts at the cell surface. It has been suggested that Meis acts by regulating the transcription of Prod 1. We have sequenced the axolotl Prod 1 promoter and selected two candidate sites for binding Meis homeoproteins. The sites were mutated in various combinations in promoters expressing a luciferase reporter gene. The promoter activity was assayed by nucleofecting AL1 cells, a cultured axolotl limb cell line that expresses both Prod 1 and Meis 1 and 2. The activity of the promoter was inhibited by 60% after mutation at Meis site 1, but not at Meis site 2. The promoter constructs were electroporated into axolotl limb blastemas and the wild type promoter was more active in a proximal blastema than in a contralateral distal blastema. The wild type promoter was significantly more active than a (site 1+site 2) mutant promoter in contralateral proximal blastemas, but the promoters were equivalent in contralateral distal blastemas. The separate site 1 or site 2 mutants were not significantly different from wild type in contralateral proximal blastemas, thus contrasting with the site 1 results in AL1 cells. These data provide strong support for the hypotheses that the Prod 1 promoter is regulated on the proximodistal axis, and that Meis homeoproteins directly regulate the promoter on this axis during limb regeneration in addition to cultured cells.

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Project description: Not available

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Single-cell analysis uncovers convergence of cell identities during axolotl limb regeneration.

Project description:Amputation of the axolotl forelimb results in the formation of a blastema, a transient tissue where progenitor cells accumulate prior to limb regeneration. However, the molecular understanding of blastema formation had previously been hampered by the inability to identify and isolate blastema precursor cells in the adult tissue. We have used a combination of Cre-loxP reporter lineage tracking and single-cell messenger RNA sequencing (scRNA-seq) to molecularly track mature connective tissue (CT) cell heterogeneity and its transition to a limb blastema state. We have uncovered a multiphasic molecular program where CT cell types found in the uninjured adult limb revert to a relatively homogenous progenitor state that recapitulates an embryonic limb bud-like phenotype including multipotency within the CT lineage. Together, our data illuminate molecular and cellular reprogramming during complex organ regeneration in a vertebrate.

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