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Open Access Highly Accessed Research article

Microarrays and RNA-Seq identify molecular mechanisms driving the end of nephron production

Eric W Brunskill1, Hsiao L Lai2, D Curtis Jamison3, S Steven Potter1 and Larry T Patterson2*

Author Affiliations

1 Division of Developmental Biology, Cincinnati Children's Hospital Medical Center and the University of Cincinnati School of Medicine, 3333 Burnet Avenue, Cincinnati, Ohio 45229 USA

2 Division of Nephrology and Hypertension, Cincinnati Children's Hospital Medical Center and the University of Cincinnati School of Medicine, 3333 Burnet Avenue, Cincinnati, Ohio 45229 USA

3 Division of Biomedical Informatics, Cincinnati Children's Hospital Medical Center and the University of Cincinnati School of Medicine, 3333 Burnet Avenue, Cincinnati, Ohio 45229 USA

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BMC Developmental Biology 2011, 11:15  doi:10.1186/1471-213X-11-15

Published: 12 March 2011

Abstract

Background

The production of nephrons suddenly ends in mice shortly after birth when the remaining cells of the multi-potent progenitor mesenchyme begin to differentiate into nephrons. We exploited this terminal wave of nephron production using both microarrays and RNA-Seq to serially evaluate gene transcript levels in the progenitors. This strategy allowed us to define the changing gene expression states following induction and the onset of differentiation after birth.

Results

Microarray and RNA-Seq studies of the progenitors detected a change in the expression profiles of several classes of genes early after birth. One functional class, a class of genes associated with cellular proliferation, was activated. Analysis of proliferation with a nucleotide analog demonstrated in vivo that entry into the S-phase of the cell cycle preceded increases in transcript levels of genetic markers of differentiation. Microarrays and RNA-Seq also detected the onset of expression of markers of differentiation within the population of progenitors prior to detectable Six2 repression. Validation by in situ hybridization demonstrated that the markers were expressed in a subset of Six2 expressing progenitors. Finally, the studies identified a third set of genes that provide indirect evidence of an altered cellular microenvironment of the multi-potential progenitors after birth.

Conclusions

These results demonstrate that Six2 expression is not sufficient to suppress activation of genes associated with growth and differentiation of nephrons. They also better define the sequence of events after induction and suggest mechanisms contributing to the rapid end of nephron production after birth in mice.