The RNA Atlas expands the catalog of human non-coding RNAs

The human transcriptome consists of various RNA biotypes including multiple types of non-coding RNAs (ncRNAs). Current ncRNA compendia remain incomplete partially because they are almost exclusively derived from the interrogation of small- and polyadenylated RNAs. Here, we present a more comprehensive atlas of the human transcriptome that is derived from matching polyA-, total-, and small-RNA profiles of a heterogenous collection of nearly 300 human tissues and cell lines. We report thousands of novel RNA species across all major RNA biotypes, including a hitherto poorly-cataloged class of non-polyadenylated single-exon long non-coding RNAs. In addition, we exploit intron abundance estimates from total RNA-sequencing to predict the regulatory potential of various non-coding RNAs. Our study represents a substantial expansion of the current catalogue of human ncRNAs and their regulatory interactions. All data and results are accessible through the R2 webtool and serve as a basis to further explore RNA biology and function. We applied three complementary RNA-seq methods on a heterogeneous collection of 300 human samples, including 45 tissues, 162 cell types, and 93 cell lines. From these samples, we generated strand-specific small RNA (298 samples), polyA (295 samples) and total RNA (296 samples) libraries that were sequenced at a median depth of 13 M, 60 M paired-end, and 125 M paired-end reads respectively, resulting in a total of 125 Billion reads.