The RNA Atlas, a single nucleotide resolution map of the human transcriptome

Abstract

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 heterogeneous collection of nearly 300 human tissues and cell lines. We report on 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 test and verify functional regulation by novel non-coding RNAs. Our study represents a substantial expansion of the current catalogue of human ncRNAs and their regulatory interactions. All data, analyses, and results are available in the R2 web portal and serve as a basis to further explore RNA biology and function.

Cell type-specific novel long non-coding RNA and circular RNA in the BLUEPRINT hematopoietic transcriptomes atlas

“…5). Our findings support the notion that some lncRNAs and circRNAs may have roles in determining cell fate and functions in hematopoiesis 53,54 , in line with findings in other tissues and organs 55 . However, further work is needed to understand the underlying mechanisms.…”

“…Our findings support the notion that some lncRNA and circRNA may have roles in determining cell fate and functions in hematopoiesis, 53 , 54 in line with findings in other tissues and organs. 55 However, further work is needed to understand the underlying mechanisms. Finally, to allow a wider access to these data, we created a web-based application ( https://blueprint.haem.cam.ac.uk/bloodatlas/ ).…”

Charting Extracellular Transcriptomes in The Human Biofluid RNA Atlas

“…Assessment of tissue and cell contribution to biofluid exRNA Using total RNA-sequencing data from 27 normal human tissue types and 5 immune cell types from peripheral blood from the RNA Atlas (Lorenzi et al, 2019), we created gene sets containing marker genes for each individual entity (Table S1). We removed redundant tissues and cell types from the original RNA Atlas (e.g., granulocytes and monocytes were present twice; brain was kept and specific brain sub-regions such as cerebellum, frontal cortex, occipital cortex and parietal cortex were removed) and we used genes where at least one tissue or cell type had expression values greater or equal to 1 TPM normalized counts.…”

Exploring the extracellular transcriptome in seminal plasma for non-invasive prostate cancer diagnosis

“…Using total RNA-sequencing data from 27 normal human tissue types and 5 immune cell types from peripheral blood from the RNA Atlas 15 , we created gene sets containing marker genes for each individual entity as described 4 . We removed redundant tissues and cell types from the original RNA Atlas (e.g.…”