title: Transcribed-ultra conserved region expression profiling from low-input total RNA.
abstract: BACKGROUND
  Ultra Conserved Regions (UCRs) are a class of 481 noncoding sequences located in both intra- and inter-genic regions of the genome. The recent findings that they are significantly altered in adult chronic lymphocytic leukemias, carcinomas, and pediatric neuroblastomas lead to the hypothesis that UCRs may play a role in tumorigenesis.
  
  
  RESULTS
  We present a novel application of Ribo-SPIA isothermal linear amplification of minute RNA quantities for quantifying Transcribed-UCR (T-UCR) expression by quantitative PCR. Direct comparison of non-amplified with amplified cDNA in two neuroblastoma cell lines showed that the amplification approach increases sensitivity and repeatability in T-UCR quantification. It is noteworthy that the Ribo-SPIA step allowed us to analyze all 481 T-UCRs by using 150 ng of RNA, while introducing a minimal bias and preserving the magnitude of relative expression. Only the less abundant T-UCRs have high intra-assay variability, consistently with the Poisson distribution statistics and stochastic effects on PCR repeatability.
  
  
  CONCLUSIONS
  We demonstrated that the quantification procedure shown here is an accurate and reliable technique for genome-wide non coding gene (i.e., UCRs) profiling using small amounts of RNA. This issue is particularly important because studies of transcription regulation are increasingly conducted in small homogeneous samples, such as laser capture microdissected or sorted cell populations.
authors.affiliation: Translational Paediatric Oncology, National Cancer Research Institute (IST), Largo R Benzi 10, Genoa, 16132, Italy. paola.scaruffi@istge.it
authors.forename: Paola
authors.initials: P
authors.lastname: Scaruffi
authors.forename: Sara
authors.initials: S
authors.lastname: Stigliani
authors.forename: Simona
authors.initials: S
authors.lastname: Coco
authors.forename: Franscesca
authors.initials: F
authors.lastname: Valdora
authors.forename: Carla
authors.initials: C
authors.lastname: De Vecchi
authors.forename: Stefano
authors.initials: S
authors.lastname: Bonassi
authors.forename: Gian Paolo
authors.initials: GP
authors.lastname: Tonini
mesh_terms: D002460:Cell Line; D017124:Conserved Sequence; D020869:Gene Expression Profiling / Q000379:methods*; D006801:Humans; D022661:RNA, Untranslated / Q000032:analysis*; D015203:Reproducibility of Results; D020133:Reverse Transcriptase Polymerase Chain Reaction; D018401:Sample Size; D012680:Sensitivity and Specificity; D017423:Sequence Analysis, RNA / Q000379:methods*
chemical_list: D022661:RNA, Untranslated