RTPrimerDB: the portal for real-time PCR primers and probes

Lefever, Steve; Vandesompele, Jo; Speleman, Franki; Pattyn, Filip

doi:10.1093/nar/gkn777

Cited by 131 publications

(107 citation statements)

References 11 publications

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“…T-UCR primer design RT-qPCR primers for 481 T-UCRs were designed using Primer3 (stand alone or implemented in Beacondesigner) (Rozen and Skaletsky, 2000) and validated through an in silico primer analysis pipeline (Lefever et al, 2009). Designs were selected according to four different criteria: absence of stable secondary structures in the primer-annealing regions, specificity, absence of SNPs in the primer-annealing regions and 3 0 GC content.…”

Section: Patient Samplesmentioning

confidence: 99%

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An integrative genomics screen uncovers ncRNA T-UCR functions in neuroblastoma tumours

et al. 2010

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Different classes of non-coding RNAs, including microRNAs, have recently been implicated in the process of tumourigenesis. In this study, we examined the expression and putative functions of a novel class of non-coding RNAs known as transcribed ultraconserved regions (T-UCRs) in neuroblastoma. Genome-wide expression pro. ling revealed correlations between specific T-UCR expression levels and important clinicogenetic parameters such as MYCN amplification status. A functional genomics approach based on the integration of multi-level transcriptome data was adapted to gain insights into T-UCR functions. Assignments of T-UCRs to cellular processes such as TP53 response, differentiation and proliferation were verified using various cellular model systems. For the first time, our results de. ne a T-UCR expression landscape in neuroblastoma and suggest widespread T-UCR involvement in diverse cellular processes that are deregulated in the process of tumourigenesis

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Section: Patient Samplesmentioning

confidence: 99%

“…For the independent validation cohort of 366 tumours, RT-qPCR data were normalized using qbasePLUS v1.2 as described previously (Vermeulen et al, 2009). T-UCR RT-qPCR data are available in rdml format (Lefever et al, 2009) …”

Section: Rt-qpcrmentioning

confidence: 99%

An integrative genomics screen uncovers ncRNA T-UCR functions in neuroblastoma tumours

et al. 2010

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“…In brief, a qPCR assay was designed for FOXR1 and five reference sequences (HMBS, HPRT1, SDHA, UBC and Alu) and validated using our in silico analysis pipeline (Lefever et al, 2009). Real-time qPCR was performed in a 384-well plate instrument (LC480, Roche, Germany) and data analyzed using qbasePLUS 1.4 (http://www.qbaseplus.com; Hellemans et al, 2007).…”

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confidence: 99%

Oncogenic activation of FOXR1 by 11q23 intrachromosomal deletion-fusions in neuroblastoma

et al. 2011

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Neuroblastoma tumors frequently show loss of heterozygosity of chromosome 11q with a shortest region of overlap in the 11q23 region. These deletions are thought to cause inactivation of tumor suppressor genes leading to haploinsufficiency. Alternatively, micro-deletions could lead to gene fusion products that are tumor driving. To identify such events we analyzed a series of neuroblastomas by comparative genomic hybridization and single-nucleotide polymorphism arrays and integrated these data with Affymetrix mRNA profiling data with the bioinformatic tool R2 (http://r2.amc.nl). We identified three neuroblastoma samples with small interstitial deletions at 11q23, upstream of the forkhead-box R1 transcription factor (FOXR1). Genes at the proximal side of the deletion were fused to FOXR1, resulting in fusion transcripts of MLL-FOXR1 and PAFAH1B2-FOXR1. FOXR1 expression has only been detected in early embryogenesis. Affymetrix microarray analysis showed high FOXR1 mRNA expression exclusively in the neuroblastomas with micro-deletions and rare cases of other tumor types, including osteosarcoma cell line HOS. RNAi silencing of FOXR1 strongly inhibited proliferation of HOS cells and triggered apoptosis. Expression profiling of these cells and reporter assays suggested that FOXR1 is a negative regulator of fork-head box factormediated transcription. The neural crest stem cell line JoMa1 proliferates in culture conditional to activity of a MYC-ER transgene. Over-expression of the wild-type FOXR1 could functionally replace MYC and drive proliferation of JoMa1. We conclude that FOXR1 is recurrently activated in neuroblastoma by intrachromosomal deletion/fusion events, resulting in overexpression of fusion transcripts. Forkhead-box transcription factors have not been previously implicated in neuroblastoma pathogenesis. Furthermore, this is the first identification of intrachromosomal fusion genes in neuroblastoma.

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“…5. The HBV cccDNA levels were then normalized to cellular DNA using b-globin DNA levels measured using real-time PCR with appropriate primers (Lefever et al, 2009); normalized cccDNA levels were used for all subsequent analyses. Standard curves were generated for all real-time PCR assays using serial dilutions of the appropriate clones to facilitate absolute quantification.…”

Section: Methodsmentioning

confidence: 99%

Enhanced hepatitis B virus (HBV) pre-genomic RNA levels and higher transcription efficiency of defective HBV genomes

Kandpal

Samal

Biswas

et al. 2015

Journal of General Virology

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Defective hepatitis B virus (dHBV) particles contain genomes corresponding to singly spliced HBV RNA. A limited number of studies show that dHBV is present in all chronically HBVinfected patients. Clinical studies have linked dHBV and dHBV gene products to high virus loads and liver damage. The replication characteristics of dHBV genomes remain poorly understood. We found that the splice donor/acceptor sites critical for the formation of dHBV genomes are conserved across HBV genotypes. We report a novel method to create dHBV constructs from corresponding wild-type (WT) HBV constructs. We assessed the transcriptional characteristics of the dHBV constructs with those of the corresponding WT construct using a cell culture model. Interestingly, dHBV constructs had higher pre-genomic RNA levels, transcription efficiency, HBV e antigen levels and intracellular HBV core antigen levels compared with the corresponding WT HBV constructs. Our findings highlight previously unrecognized fundamental molecular characteristics of dHBV genomes and their potential role in the pathogenesis of HBV infection.

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RTPrimerDB: the portal for real-time PCR primers and probes

Cited by 131 publications

References 11 publications

An integrative genomics screen uncovers ncRNA T-UCR functions in neuroblastoma tumours

An integrative genomics screen uncovers ncRNA T-UCR functions in neuroblastoma tumours

Oncogenic activation of FOXR1 by 11q23 intrachromosomal deletion-fusions in neuroblastoma

Enhanced hepatitis B virus (HBV) pre-genomic RNA levels and higher transcription efficiency of defective HBV genomes

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