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

View ORCID ProfileLucia Lorenzi, Hua-Sheng Chiu, View ORCID ProfileFrancisco Avila Cobos, View ORCID ProfileStephen Gross, View ORCID ProfilePieter-Jan Volders, View ORCID ProfileRobrecht Cannoodt, Justine Nuytens, Katrien Vanderheyden, View ORCID ProfileJasper Anckaert, View ORCID ProfileSteve Lefever, Tine Goovaerts, View ORCID ProfileThomas Birkballe Hansen, Scott Kuersten, Nele Nijs, Tom Taghon, Karim Vermaelen, Ken R. Bracke, Yvan Saeys, Tim De Meyer, Nandan Deshpande, Govardhan Anande, Ting-Wen Chen, Marc R. Wilkins, Ashwin Unnikrishnan, Katleen De Preter, Jørgen Kjems, View ORCID ProfileJan Koster, Gary P. Schroth, View ORCID ProfileJo Vandesompele, View ORCID ProfilePavel Sumazin, View ORCID ProfilePieter Mestdagh
doi: https://doi.org/10.1101/807529
Lucia Lorenzi
Center for Medical Genetics, Ghent University, BelgiumCancer Research Institute Ghent (CRIG), Ghent, Belgium
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Hua-Sheng Chiu
Texas Children’s Cancer Center, Baylor College of Medicine, Houston, USA
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Francisco Avila Cobos
Center for Medical Genetics, Ghent University, BelgiumCancer Research Institute Ghent (CRIG), Ghent, Belgium
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Stephen Gross
Illumina, San Diego, California, USA
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Pieter-Jan Volders
Center for Medical Genetics, Ghent University, BelgiumCancer Research Institute Ghent (CRIG), Ghent, Belgium
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Robrecht Cannoodt
Center for Medical Genetics, Ghent University, BelgiumCancer Research Institute Ghent (CRIG), Ghent, BelgiumData Mining and Modelling for Biomedicine group, VIB Center for Inflammation Research, Ghent, BelgiumDepartment of Applied Mathematics, Computer Science, and Statistics, Ghent University, Ghent, Belgium
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Justine Nuytens
Center for Medical Genetics, Ghent University, BelgiumCancer Research Institute Ghent (CRIG), Ghent, Belgium
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Katrien Vanderheyden
Center for Medical Genetics, Ghent University, BelgiumCancer Research Institute Ghent (CRIG), Ghent, Belgium
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Jasper Anckaert
Center for Medical Genetics, Ghent University, BelgiumCancer Research Institute Ghent (CRIG), Ghent, Belgium
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Steve Lefever
Center for Medical Genetics, Ghent University, BelgiumCancer Research Institute Ghent (CRIG), Ghent, Belgium
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Tine Goovaerts
Department of Data Analysis and Mathematical Modelling, Ghent University, Belgium
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Thomas Birkballe Hansen
Department of Molecular Biology and Genetics, Aarhus University, Denmark
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Scott Kuersten
Illumina, San Diego, California, USA
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Nele Nijs
Biogazelle, Zwijnaarde, Belgium
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Tom Taghon
Department of Diagnostic Sciences, Ghent University, Belgium
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Karim Vermaelen
Department of Pulmonary Medicine, Ghent University, Belgium
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Ken R. Bracke
Department of Respiratory Medicine, Ghent University, Belgium
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Yvan Saeys
Data Mining and Modelling for Biomedicine group, VIB Center for Inflammation Research, Ghent, BelgiumDepartment of Applied Mathematics, Computer Science, and Statistics, Ghent University, Ghent, Belgium
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Tim De Meyer
Department of Data Analysis and Mathematical Modelling, Ghent University, Belgium
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Nandan Deshpande
University Systems Biology Initiative, School of Biotechnology and Biomolecular Sciences, UNSW Sydney, Sydney, NSW, 2052, Australia
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Govardhan Anande
Adult Cancer Program, Lowy Cancer Research Centre, UNSW Sydney, NSW 2052, AustraliaPrince of Wales Clinical School, UNSW Sydney, NSW 2052, Australia
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Ting-Wen Chen
Institute of Bioinformatics and Systems Biology, National Chiao Tung University, Taiwan
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Marc R. Wilkins
University Systems Biology Initiative, School of Biotechnology and Biomolecular Sciences, UNSW Sydney, Sydney, NSW, 2052, Australia
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Ashwin Unnikrishnan
Adult Cancer Program, Lowy Cancer Research Centre, UNSW Sydney, NSW 2052, AustraliaPrince of Wales Clinical School, UNSW Sydney, NSW 2052, Australia
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Katleen De Preter
Center for Medical Genetics, Ghent University, BelgiumCancer Research Institute Ghent (CRIG), Ghent, Belgium
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Jørgen Kjems
Department of Molecular Biology and Genetics, Aarhus University, Denmark
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Jan Koster
Academisch Medisch Centrum (AMC), University of Amsterdam, The Netherlands
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Gary P. Schroth
Illumina, San Diego, California, USA
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Jo Vandesompele
Center for Medical Genetics, Ghent University, BelgiumCancer Research Institute Ghent (CRIG), Ghent, Belgium
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Pavel Sumazin
Texas Children’s Cancer Center, Baylor College of Medicine, Houston, USA
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Pieter Mestdagh
Center for Medical Genetics, Ghent University, BelgiumCancer Research Institute Ghent (CRIG), Ghent, Belgium
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  • ORCID record for Pieter Mestdagh
  • For correspondence: pieter.mestdagh@ugent.be
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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.

Footnotes

  • ↵* Shared first authors

  • https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE138734

  • http://r2platform.com/rna_atlas

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC-ND 4.0 International license.
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Posted October 17, 2019.
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The RNA Atlas, a single nucleotide resolution map of the human transcriptome
Lucia Lorenzi, Hua-Sheng Chiu, Francisco Avila Cobos, Stephen Gross, Pieter-Jan Volders, Robrecht Cannoodt, Justine Nuytens, Katrien Vanderheyden, Jasper Anckaert, Steve Lefever, Tine Goovaerts, Thomas Birkballe Hansen, Scott Kuersten, Nele Nijs, Tom Taghon, Karim Vermaelen, Ken R. Bracke, Yvan Saeys, Tim De Meyer, Nandan Deshpande, Govardhan Anande, Ting-Wen Chen, Marc R. Wilkins, Ashwin Unnikrishnan, Katleen De Preter, Jørgen Kjems, Jan Koster, Gary P. Schroth, Jo Vandesompele, Pavel Sumazin, Pieter Mestdagh
bioRxiv 807529; doi: https://doi.org/10.1101/807529
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The RNA Atlas, a single nucleotide resolution map of the human transcriptome
Lucia Lorenzi, Hua-Sheng Chiu, Francisco Avila Cobos, Stephen Gross, Pieter-Jan Volders, Robrecht Cannoodt, Justine Nuytens, Katrien Vanderheyden, Jasper Anckaert, Steve Lefever, Tine Goovaerts, Thomas Birkballe Hansen, Scott Kuersten, Nele Nijs, Tom Taghon, Karim Vermaelen, Ken R. Bracke, Yvan Saeys, Tim De Meyer, Nandan Deshpande, Govardhan Anande, Ting-Wen Chen, Marc R. Wilkins, Ashwin Unnikrishnan, Katleen De Preter, Jørgen Kjems, Jan Koster, Gary P. Schroth, Jo Vandesompele, Pavel Sumazin, Pieter Mestdagh
bioRxiv 807529; doi: https://doi.org/10.1101/807529

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