Genome wide expression profiling during spinal cord regeneration identifies comprehensive cellular responses in zebrafish.
BACKGROUND
Among the vertebrates, teleost and urodele amphibians are capable of regenerating their central nervous system. We have used zebrafish as a model to study spinal cord injury and regeneration. Relatively little is known about the molecular mechanisms underlying spinal cord regeneration and information based on high density oligonucleotide microarray was not available. We have used a high density microarray to profile the temporal transcriptome dynamics during the entire phenomenon.


RESULTS
A total of 3842 genes expressed differentially with significant fold changes during spinal cord regeneration. Cluster analysis revealed event specific dynamic expression of genes related to inflammation, cell death, cell migration, cell proliferation, neurogenesis, neural patterning and axonal regrowth. Spatio-temporal analysis of stat3 expression suggested its possible function in controlling inflammation and cell proliferation. Genes involved in neurogenesis and their dorso-ventral patterning (sox2 and dbx2) are differentially expressed. Injury induced cell proliferation is controlled by many cell cycle regulators and some are commonly expressed in regenerating fin, heart and retina. Expression pattern of certain pathway genes are identified for the first time during regeneration of spinal cord. Several genes involved in PNS regeneration in mammals like stat3, socs3, atf3, mmp9 and sox11 are upregulated in zebrafish SCI thus creating PNS like environment after injury.


CONCLUSIONS
Our study provides a comprehensive genetic blue print of diverse cellular response(s) during regeneration of zebrafish spinal cord. The data highlights the importance of different event specific gene expression that could be better understood and manipulated further to induce successful regeneration in mammals.
Department of Biophysics, Molecular Biology and Bioinformatics, University of Calcutta, Kolkata, India.
Subhra Prakash
SP
Hui
Department of Biophysics, Molecular Biology and Bioinformatics, University of Calcutta, Kolkata, India.
Dhriti
D
Sengupta
Genome Institute of Singapore, Singapore, Singapore.
Serene Gek Ping
SG
Lee
Chittaranjan National Cancer Research Institute, Kolkata, India.
Triparna
T
Sen
Department of Biophysics, Molecular Biology and Bioinformatics, University of Calcutta, Kolkata, India.
Sudip
S
Kundu
Genome Institute of Singapore, Singapore, Singapore.
Sinnakaruppan
S
Mathavan
Department of Biophysics, Molecular Biology and Bioinformatics, University of Calcutta, Kolkata, India.
Sukla
S
Ghosh
D000818:Animals; D055106:Genome-Wide Association Study / Q000379:methods*; D062211:Spatio-Temporal Analysis; D013119:Spinal Cord Injuries / Q000378:metabolism / Q000503:physiopathology; D058630:Spinal Cord Regeneration / Q000235:genetics / Q000502:physiology*; D015027:Zebrafish; D029961:Zebrafish Proteins / Q000235:genetics / Q000378:metabolism
D029961:Zebrafish Proteins