2015 March | Matthew K. Iyer, Yashar S. Niknafs, Rohit Malik, Udit Singhal, Anirban Sahu, Yasuyuki Hosono, Terrence R. Barrette, John R. Premsner, Joseph R. Evans, Shuang Zhao, Anton Poliakov, Xuhong Cao, Saravana M. Dhanasekaran, Yi-Mi Wu, Dan R. Robinson, David G. Beer, Felix Y. Feng, Hariharan K. Iyer, and Arul M. Chinnaiyan
The study by Iyer et al. aims to delineate the genome-wide landscape of long non-coding RNAs (lncRNAs) in the human transcriptome. The researchers curated 7,256 RNA-Seq libraries from various tissues, normal samples, and cell lines, totaling over 43 terabases of sequence from 25 independent studies. They applied *ab initio* assembly methodology to this dataset, resulting in a consensus human transcriptome of 91,013 expressed genes, of which 58,648 were classified as lncRNAs, with 79% being previously unannotated. The lncRNA landscape identified includes 1% harboring ultraconserved elements and 7% overlapping disease-associated single nucleotide polymorphisms (SNPs). To prioritize lineage-specific and disease-associated lncRNA expression, the researchers employed non-parametric differential expression testing, identifying 7,942 lineage- or cancer-associated lncRNA genes. The study highlights the importance of lncRNAs in normal biology and cancer pathogenesis and provides a valuable resource for future biomarker development.The study by Iyer et al. aims to delineate the genome-wide landscape of long non-coding RNAs (lncRNAs) in the human transcriptome. The researchers curated 7,256 RNA-Seq libraries from various tissues, normal samples, and cell lines, totaling over 43 terabases of sequence from 25 independent studies. They applied *ab initio* assembly methodology to this dataset, resulting in a consensus human transcriptome of 91,013 expressed genes, of which 58,648 were classified as lncRNAs, with 79% being previously unannotated. The lncRNA landscape identified includes 1% harboring ultraconserved elements and 7% overlapping disease-associated single nucleotide polymorphisms (SNPs). To prioritize lineage-specific and disease-associated lncRNA expression, the researchers employed non-parametric differential expression testing, identifying 7,942 lineage- or cancer-associated lncRNA genes. The study highlights the importance of lncRNAs in normal biology and cancer pathogenesis and provides a valuable resource for future biomarker development.