Selection of reliable reference genes for quantitative real-time PCR in human T cells and neutrophils

<p>Abstract</p> <p>Background</p> <p>The choice of reliable reference genes is a prerequisite for valid results when analyzing gene expression with real-time quantitative PCR (qPCR). This method is frequently applied to study gene expression patterns in immune cells, yet a thorough validation of potential reference genes is still lacking for most leukocyte subtypes and most models of their in vitro stimulation. In the current study, we evaluated the expression stability of common reference genes in two widely used cell culture models-anti-CD3/CD28 activated T cells and lipopolysaccharide stimulated neutrophils-as well as in unselected untreated leukocytes.</p> <p>Results</p> <p>The mRNA expression of 17 (T cells), 7 (neutrophils) or 8 (unselected leukocytes) potential reference genes was quantified by reverse transcription qPCR, and a ranking of the preselected candidate genes according to their expression stability was calculated using the programs NormFinder, geNorm and BestKeeper. <it>IPO8</it>, <it>RPL13A</it>, <it>TBP </it>and <it>SDHA </it>were identified as suitable reference genes in T cells. <it>TBP</it>, <it>ACTB </it>and <it>SDHA </it>were stably expressed in neutrophils. <it>TBP </it>and <it>SDHA </it>were also the most stable genes in untreated total blood leukocytes. The critical impact of reference gene selection on the estimated target gene expression is demonstrated for <it>IL-2 </it>and <it>FIH </it>expression in T cells.</p> <p>Conclusions</p> <p>The study provides a shortlist of suitable reference genes for normalization of gene expression data in unstimulated and stimulated T cells, unstimulated and stimulated neutrophils and in unselected leukocytes.</p

Alternative polyadenylation allows differential negative feedback of human miRNA miR-579 on its host gene ZFR.

About half of the known miRNA genes are located within protein-coding host genes, and are thus subject to co-transcription. Accumulating data indicate that this coupling may be an intrinsic mechanism to directly regulate the host gene's expression, constituting a negative feedback loop. Inevitably, the cell requires a yet largely unknown repertoire of methods to regulate this control mechanism. We propose APA as one possible mechanism by which negative feedback of intronic miRNA on their host genes might be regulated. Using in-silico analyses, we found that host genes that contain seed matching sites for their intronic miRNAs yield longer 32UTRs with more polyadenylation sites. Additionally, the distribution of polyadenylation signals differed significantly between these host genes and host genes of miRNAs that do not contain potential miRNA binding sites. We then transferred these in-silico results to a biological example and investigated the relationship between ZFR and its intronic miRNA miR-579 in a U87 cell line model. We found that ZFR is targeted by its intronic miRNA miR-579 and that alternative polyadenylation allows differential targeting. We additionally used bioinformatics analyses and RNA-Seq to evaluate a potential cross-talk between intronic miRNAs and alternative polyadenylation. CPSF2, a gene previously associated with alternative polyadenylation signal recognition, might be linked to intronic miRNA negative feedback by altering polyadenylation signal utilization

Bioinformatics and biomolecular analyses indicate a role for APA in regulation of negative feedback.

<p>A) Comparison of APA-sites for HT miRNA host genes and NT miRNA host genes. B) After CPSF2 silencing HT miRNA host gene UTRs display a different poly(A)-site usage pattern compared to NT miRNA host gene UTRs and regular protein-coding genes’ UTRs. C) The motif discovered in upregulated APA regions after CPSF2 silencing resembles the two canonical polyadenylation sites. D) Distribution of canonical poly(A) signals across the 32UTR of HT miRNA host genes and E) NT miRNA host genes.</p

Model of intronic negative feedback regulation.

<p>After coexpression of miRNA and host gene, the miRNA directly regulates its host gene as well as CPSF2. After removal of CPSF2 the polyadenylation-complex is biased towards recognition of canonical sites. In the next transcription cycle, the canonical site that precedes the miRNA binding site is utilized. Hence, regulation of the host gene by its intronic miRNA is disabled.</p

miR-579 targets its host, ZFR, and the APA associated gene CPSF2.

<p>A) Schematic diagram of the <i>ZFR</i> gene. B) Schematic diagram of the ZFR 32UTR including polyadenylation sites and the seed matching site for miR-579. C) U87 cells were co-transfected with reporter constructs containing wildtype ZFR-32UTR or ZFR-32UTR lacking the miR-579 binding site (mut 32UTR) along with pre-miR-579 or negative control (NC). Results are expressed as Rluc/Fluc ratio relative to NC (mean ± 95% CI; n = 6; *, p < 0.05). D) In U87 cells transiently transfected with scrambled control or pre-miR-579, ZFR and CPSF2 mRNA expression was analyzed by quantitative RT-PCR. Values are mean ± 95% CI; n = 5; *, p < 0.05. E) Western blot analysis of the same samples using specific antibodies as indicated (β-Actin served as loading control; one representative experiment of three is shown). F) In U87 cells, expression changes of the long (miRNA binding site containing; red) and short (without miRNA binding site; blue) alternatively polyadenylated UTRs after transfection with pre-miR-579 or with scrambled control was determined by quantitative RT-PCR. Values are shown as miR-579 transfection relative to scrambled control (n = 5; *, p < 0.05).</p

HT miRNA host genes with significant 3´UTR changes after CPSF2-silencing.

<p>HT miRNA host genes with significant 3´UTR changes after CPSF2-silencing.</p