Abstract
Unlike adult mammals, adult frogs regrow their optic nerve following a crush injury, making . Xenopus laevis a compelling model for studying the molecular mechanisms that underlie neuronal regeneration. Using Translational Ribosome Affinity Purification (TRAP), a method to isolate ribosome-associated mRNAs from a target cell population, we have generated a transcriptional profile by RNA-Seq for retinal ganglion cells (RGC) during the period of recovery following an optic nerve injury. Based on bioinformatic analysis using the . Xenopus laevis 9.1 genome assembly, our results reveal a profound shift in the composition of ribosome-associated mRNAs during the early stages of RGC regeneration. As factors involved in cell signaling are rapidly down-regulated, those involved in protein biosynthesis are up-regulated alongside key initiators of axon development. Using the new genome assembly, we were also able to analyze gene expression profiles of homeologous gene pairs arising from a whole-genome duplication in the . Xenopus lineage. Here we see evidence of divergence in regulatory control among a significant proportion of pairs. Our data should provide a valuable resource for identifying genes involved in the regeneration process to target for future functional studies, in both naturally regenerative and non-regenerative vertebrates.
| Original language | English (US) |
|---|---|
| Journal | Developmental Biology |
| DOIs | |
| State | Accepted/In press - Feb 12 2016 |
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Keywords
- Expression profile
- Optic nerve crush injury
- TRAP
ASJC Scopus subject areas
- Molecular Biology
- Developmental Biology
- Cell Biology
Cite this
Translational profiling of retinal ganglion cell optic nerve regeneration in Xenopus laevis. / Whitworth, G. B.; Misaghi, B. C.; Rosenthal, D. M.; Mills, E. A.; Heinen, D. J.; Watson, A. H.; Ives, C. W.; Ali, S. H.; Bezold, K.; Marsh-Armstrong, N.; Watson, F. L.
In: Developmental Biology, 12.02.2016.Research output: Contribution to journal › Article
}
TY - JOUR
T1 - Translational profiling of retinal ganglion cell optic nerve regeneration in Xenopus laevis
AU - Whitworth, G. B.
AU - Misaghi, B. C.
AU - Rosenthal, D. M.
AU - Mills, E. A.
AU - Heinen, D. J.
AU - Watson, A. H.
AU - Ives, C. W.
AU - Ali, S. H.
AU - Bezold, K.
AU - Marsh-Armstrong, N.
AU - Watson, F. L.
PY - 2016/2/12
Y1 - 2016/2/12
N2 - Unlike adult mammals, adult frogs regrow their optic nerve following a crush injury, making . Xenopus laevis a compelling model for studying the molecular mechanisms that underlie neuronal regeneration. Using Translational Ribosome Affinity Purification (TRAP), a method to isolate ribosome-associated mRNAs from a target cell population, we have generated a transcriptional profile by RNA-Seq for retinal ganglion cells (RGC) during the period of recovery following an optic nerve injury. Based on bioinformatic analysis using the . Xenopus laevis 9.1 genome assembly, our results reveal a profound shift in the composition of ribosome-associated mRNAs during the early stages of RGC regeneration. As factors involved in cell signaling are rapidly down-regulated, those involved in protein biosynthesis are up-regulated alongside key initiators of axon development. Using the new genome assembly, we were also able to analyze gene expression profiles of homeologous gene pairs arising from a whole-genome duplication in the . Xenopus lineage. Here we see evidence of divergence in regulatory control among a significant proportion of pairs. Our data should provide a valuable resource for identifying genes involved in the regeneration process to target for future functional studies, in both naturally regenerative and non-regenerative vertebrates.
AB - Unlike adult mammals, adult frogs regrow their optic nerve following a crush injury, making . Xenopus laevis a compelling model for studying the molecular mechanisms that underlie neuronal regeneration. Using Translational Ribosome Affinity Purification (TRAP), a method to isolate ribosome-associated mRNAs from a target cell population, we have generated a transcriptional profile by RNA-Seq for retinal ganglion cells (RGC) during the period of recovery following an optic nerve injury. Based on bioinformatic analysis using the . Xenopus laevis 9.1 genome assembly, our results reveal a profound shift in the composition of ribosome-associated mRNAs during the early stages of RGC regeneration. As factors involved in cell signaling are rapidly down-regulated, those involved in protein biosynthesis are up-regulated alongside key initiators of axon development. Using the new genome assembly, we were also able to analyze gene expression profiles of homeologous gene pairs arising from a whole-genome duplication in the . Xenopus lineage. Here we see evidence of divergence in regulatory control among a significant proportion of pairs. Our data should provide a valuable resource for identifying genes involved in the regeneration process to target for future functional studies, in both naturally regenerative and non-regenerative vertebrates.
KW - Expression profile
KW - Optic nerve crush injury
KW - TRAP
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UR - http://www.scopus.com/inward/citedby.url?scp=84996615292&partnerID=8YFLogxK
U2 - 10.1016/j.ydbio.2016.06.003
DO - 10.1016/j.ydbio.2016.06.003
M3 - Article
C2 - 27471010
AN - SCOPUS:84996615292
JO - Developmental Biology
JF - Developmental Biology
SN - 0012-1606
ER -