PMC:3091645 / 19693-22167
Annnotations
{"target":"http://pubannotation.org/docs/sourcedb/PMC/sourceid/3091645","sourcedb":"PMC","sourceid":"3091645","source_url":"https://www.ncbi.nlm.nih.gov/pmc/3091645","text":"The microarray data were confirmed for 5 out of 9 analyzed genes (Table 5). Among the non-confirmed genes is the above mentioned AV451297.1 putative gene. This gene, located in mouse chromosome 17 and/or mouse chromosome 6, encodes for a hypothetical protein, and its transcription was only reported as an EST in ES cells. The non-confirmation of the differential expression of this gene was surprising since its estimated log ratio was relatively high. Blast alignment of the microarray oligonucleotide corresponding to this gene allowed us to design primers that recognized a family of mouse ESTs that encompass this sequence (Table 6). However, this oligonucleotide aligns with various regions of the mouse genome (data not shown), located on several chromosomes, and we therefore cannot exclude that a transcript, originating from one of these regions, that will not be amplified by our set of primers is responsible for the observed differential expression. Although showing a down-regulated expression in Tg37+/- NFH-Cre+/- mice in both the micro-array analysis and the QPCR experiment, the ratio observed by QPCR was relatively lower than could be expected for the ifitm3 gene. The primers used for the QPCR were chosen in order not to amplify the other ifitm gene family mRNAs (see Table 6 for the QPCR primer sequences). However, they share some homology with the ankyrin repeat domain 12 (data not shown) which might interfere with the obtained results. The other non-confirmed genes correspond to differentially expressed genes showing very low log2 ratios on the microarray results, between -0.8 and + 0.8. Overall the qPCR obtained data for these genes strengthen the relative transcriptomic stability of the Prnp knockout brain. The microarray and QPCR data were consistent for the Erf1 transcriptional deregulation (Table 5). We further analyzed the expression level of this gene in the brain of Prnp-knockout mice expressing or not the NFH-Cre transgene. No difference was observed (data not shown), demonstrating that the Cre expression does not significantly influence the expression profile of this locus and thus that its observed deregulation in our experiment results from the Prnp invalidation. Although we cannot formally exclude that some of the other deregulated genes listed in Tables 3 and 4 results from the Cre expression, this data strongly suggest that the neuronal PrP depletion is responsible for the observed transcriptional modifications.","tracks":[]}