Microarray and cDNA sequence analysis of transcription during nerve-dependent limb regeneration.

BMC Biology
James R MonaghanS Randal Voss

Abstract

Microarray analysis and 454 cDNA sequencing were used to investigate a centuries-old problem in regenerative biology: the basis of nerve-dependent limb regeneration in salamanders. Innervated (NR) and denervated (DL) forelimbs of Mexican axolotls were amputated and transcripts were sampled after 0, 5, and 14 days of regeneration. Considerable similarity was observed between NR and DL transcriptional programs at 5 and 14 days post amputation (dpa). Genes with extracellular functions that are critical to wound healing were upregulated while muscle-specific genes were downregulated. Thus, many processes that are regulated during early limb regeneration do not depend upon nerve-derived factors. The majority of the transcriptional differences between NR and DL limbs were correlated with blastema formation; cell numbers increased in NR limbs after 5 dpa and this yielded distinct transcriptional signatures of cell proliferation in NR limbs at 14 dpa. These transcriptional signatures were not observed in DL limbs. Instead, gene expression changes within DL limbs suggest more diverse and protracted wound-healing responses. 454 cDNA sequencing complemented the microarray analysis by providing deeper sampling of transcriptional programs a...Continue Reading

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Datasets Mentioned

BETA
SRA004195.2

Methods Mentioned

BETA
amputation
454 cDNA sequencing
454 sequencing
PCR
454

Software Mentioned

psat
BLASTx
PaCE
Bioconductor
limma
BLAST
R
Genesis
Affy Bioconductor
stats

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