Existing compendia of non-coding RNA (ncRNA) are incomplete, in part because they are derived almost exclusively from small and polyadenylated RNAs. Here we present a more comprehensive atlas of the human transcriptome, which includes small and polyA RNA as well as total RNA from 300 human tissues and cell lines. We report thousands of previously uncharacterized RNAs, increasing the number of documented ncRNAs by approximately 8%. To infer functional regulation by known and newly characterized ncRNAs, we exploited pre-mRNA abundance estimates from total RNA sequencing, revealing 316 microRNAs and 3,310 long non-coding RNAs with multiple lines of evidence for roles in regulating protein-coding genes and pathways. Our study both refines and expands the current catalog of human ncRNAs and their regulatory interactions. All data, analyses and results are available for download and interrogation in the R2 web portal, serving as a basis for future exploration of RNA biology and function.
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All types of RNA entities can be readily explored via the online R2: Genomics Analysis and Visualization Platform (http://r2.amc.nl) and via a dedicated accessible portal (http://r2platform.com/rna_atlas). This portal includes genome browser profiles for the total RNA as well as polyA tracks for all samples. All samples can also be used for correlations, differential signals and many more analyses. In addition, the LongHorn results, described in this manuscript, can be explored.
The raw data (FASTQ files) and processed expression measurement tables from all RNA biotypes across samples have been deposited in the National Center for Biotechnology Information’s Gene Expression Omnibus (GEO) and are accessible through GEO series accession number GSE138734.
Computer code used to generate the results presented in this manuscript is available at https://github.com/llorenzi90/RNA_Atlas.
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F.A.C. is supported by a Special Research Fund (BOF) scholarship of Ghent University (BOF.DOC.2017.0026.01). R.C. is supported by the Fonds Wetenschappelijk Onderzoek (11Y6218N). T.-W.C. is supported by grants from the Ministry of Science and Technology, Taiwan (MOST-109-2311-B-009 −002). A.U. is supported by research funding from the National Health and Medical Research Council (Australia) and the Leukemia & Lymphoma Society, the Leukemia Foundation and the Snowdome Foundation. G.A. is supported by a postgraduate scholarship from the Translational Cancer Research Network. M.R.W. and N.P.D. acknowledge support from the National Collaborative Research Infrastructure Strategy program, administered by Bioplatforms Australia. We thank N. Yigit, A. Barr, S. Pathak, L. Way and A. Mai for their contributions in library preparation and A. Yunghans, E. Jaeger and A. Moshrefi for their assistance in library organization and sequencing/tracking/data management. This project was funded by the European Union’s Horizon 2020 Research and Innovation Programme under grant agreements 668858 and 826121 to P.M., P.S. and J. Koster and the Concerted Research Action of Ghent University (BOF/GOA 01G00819) to P.M. and K.B.
The authors declare no competing interests.
Peer review information Nature Biotechnology thanks Steven Salzberg and the other, anonymous, reviewer(s) for their contribution to the peer review of this work.
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