Noncoding RNA (ncRNA) constitutes a significant portion of the mammalian transcriptome. Emerging evidence suggests that it regulates gene expression in cis or trans by modulating the chromatin structure. To uncover the functional role of ncRNA in chromatin organization, we deep sequenced chromatin-associated RNAs (CARs) from human fibroblast (HF) cells. This resulted in the identification of 141 intronic regions and 74 intergenic regions harboring CARs. The intronic and intergenic CARs show significant conservation across 44 species of placental mammals. Functional characterization of one of the intergenic CARs, Intergenic10, revealed that it regulates gene expression of neighboring genes through modulating the chromatin structure in cis. Our data suggest that ncRNA is an integral component of chromatin and that it may regulate various biological functions through fine-tuning of the chromatin architecture.

We describe a bioinformatic tool, Tumor Aberration Prediction Suite (TAPS), for the identification of allele-specific copy numbers in tumor samples using data from Affymetrix SNP arrays. It includes detailed visualization of genomic segment characteristics and iterative pattern recognition for copy number identification, and does not require patient-matched normal samples. TAPS can be used to identify chromosomal aberrations with high sensitivity even when the proportion of tumor cells is as low as 30%. Analysis of cancer samples indicates that TAPS is well suited to investigate samples with aneuploidy and tumor heterogeneity, which is commonly found in many types of solid tumors.

This study was undertaken to characterize the current feeding situation and nutritional status of moderately or severely disabled children with cerebral palsy (CP). Thirty-five children with CP (17 with diplegia, 11 with dystonia, 6 with tetraplegia and one child with ataxia) were investigated at a median age of 8 years. Information was obtained from parental interviews, medical records and clinical and anthropometric examinations. Twenty-one of the 35 children (60%), most of whom were severely disabled, were reported by the parents to have current feeding problems. Anthropometric indicators of undernutrition were found in 15 children (43%) and of overnutrition in 3 children (9%), compared with reference values of healthy children. Severely disabled children in the youngest age group were most at risk for poor nutritional status. Early identification of children at nutritional risk requires regular assessments of feeding skills and nutritional status.