Open AccessIdentification and Validation of Suitable Housekeeping Genes for Normalizing Quantitative Real-Time PCR Assays in Injured Peripheral Nerves
Author(s) -
Giovanna Gambarotta,
Giulia Ronchi,
Olivier Friard,
Galletta Pantaleo,
Isabelle Perroteau,
Stefano Geuna
Publication year - 2014
Publication title -
plos one
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.99
H-Index - 332
ISSN - 1932-6203
DOI - 10.1371/journal.pone.0105601
Subject(s) - housekeeping gene , gene , reference genes , biology , microarray analysis techniques , real time polymerase chain reaction , peripheral nerve injury , computational biology , microarray , housekeeping , peripheral , gene expression , bioinformatics , regeneration (biology) , medicine , microbiology and biotechnology , genetics
Injury to the peripheral nerve induces dramatic changes in terms of cellular composition that are reflected on RNA quality and quantity, making messenger RNA expression analysis very complex. Several commonly used housekeeping genes are regulated following peripheral nerve injury and are thus not suitable for quantitative real-time PCR normalization; moreover, the presence of pseudogenes in some of them impairs their use. To deal with this problem, we have developed a new method to identify new stable housekeeping genes based on publicly available microarray data on normal and injured nerves. Four new candidate stable genes were identified and validated by quantitative real-time PCR analysis on nerves during the different phases after nerve injury: nerve degeneration, regeneration and remyelination. The stability measure of these genes was calculated with both NormFinder and geNorm algorithms and compared with six commonly used housekeeping genes. This procedure allowed us to identify two new and highly stable genes that can be employed for normalizing injured peripheral nerve data: ANKRD27 and RICTOR . Besides providing a tool for peripheral nerve research, our study also describes a simple and cheap procedure that can be used to identify suitable housekeeping genes in other tissues and organs.