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

Lucia Lorenzi; Hua-Sheng Chiu; Francisco Avila Cobos; Stephen Gross; Pieter-Jan Volders; Robrecht Cannoodt; Justine Nuytens; Katrien Vanderheyden; Jasper Anckaert; Steve Lefever; Aidan P. Tay; Eric J. de Bony; Wim Trypsteen; Fien Gysens; Marieke Vromman; Tine Goovaerts; Thomas Birkballe Hansen; Scott Kuersten; Nele Nijs; Tom Taghon; Karim Vermaelen; Ken R. Bracke; Yvan Saeys; Tim de Meyer; Nandan P. Deshpande; Govardhan Anande; Ting-Wen Chen; Marc R. Wilkins; Ashwin Unnikrishnan; Katleen de Preter; J. rgen Kjems; Jan Koster; Gary P. Schroth; Jo Vandesompele; Pavel Sumazin; Pieter Mestdagh

doi:https://doi.org/10.1038/s41587-021-00936-1

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

Lucia Lorenzi, Hua-Sheng Chiu, Francisco Avila Cobos, Stephen Gross, Pieter-Jan Volders, Robrecht Cannoodt, Justine Nuytens, Katrien Vanderheyden, Jasper Anckaert, Steve Lefever, Aidan P. Tay, Eric J. de Bony, Wim Trypsteen, Fien Gysens, Marieke Vromman, Tine Goovaerts, Thomas Birkballe Hansen, Scott Kuersten, Nele Nijs, Tom TaghonKarim Vermaelen, Ken R. Bracke, Yvan Saeys, Tim de Meyer, Nandan P. Deshpande, Govardhan Anande, Ting-Wen Chen, Marc R. Wilkins, Ashwin Unnikrishnan, Katleen de Preter, J. rgen Kjems, Jan Koster, Gary P. Schroth, Jo Vandesompele, Pavel Sumazin, Pieter Mestdagh

Research output: Contribution to journal › Article › Academic › peer-review

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Abstract

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.

Original language	English
Pages (from-to)	1453-1465
Number of pages	13
Journal	Nature biotechnology
Volume	39
Issue number	11
Early online date	2021
DOIs	https://doi.org/10.1038/s41587-021-00936-1
Publication status	Published - Nov 2021

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Lorenzi, L., Chiu, H.-S., Avila Cobos, F., Gross, S., Volders, P.-J., Cannoodt, R., Nuytens, J., Vanderheyden, K., Anckaert, J., Lefever, S., Tay, A. P., de Bony, E. J., Trypsteen, W., Gysens, F., Vromman, M., Goovaerts, T., Hansen, T. B., Kuersten, S., Nijs, N., ... Mestdagh, P. (2021). The RNA Atlas expands the catalog of human non-coding RNAs. Nature biotechnology, 39(11), 1453-1465. https://doi.org/10.1038/s41587-021-00936-1

@article{4e9913226cb44bf6b178b8b07857b601,

title = "The RNA Atlas expands the catalog of human non-coding RNAs",

abstract = "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.",

author = "Lucia Lorenzi and Hua-Sheng Chiu and {Avila Cobos}, Francisco and Stephen Gross and Pieter-Jan Volders and Robrecht Cannoodt and Justine Nuytens and Katrien Vanderheyden and Jasper Anckaert and Steve Lefever and Tay, {Aidan P.} and {de Bony}, {Eric J.} and Wim Trypsteen and Fien Gysens and Marieke Vromman and Tine Goovaerts and Hansen, {Thomas Birkballe} and Scott Kuersten and Nele Nijs and Tom Taghon and Karim Vermaelen and Bracke, {Ken R.} and Yvan Saeys and {de Meyer}, Tim and Deshpande, {Nandan P.} and Govardhan Anande and Ting-Wen Chen and Wilkins, {Marc R.} and Ashwin Unnikrishnan and {de Preter}, Katleen and Kjems, {J. rgen} and Jan Koster and Schroth, {Gary P.} and Jo Vandesompele and Pavel Sumazin and Pieter Mestdagh",

note = "Funding Information: 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{\textquoteright}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. Publisher Copyright: {\textcopyright} 2021, The Author(s), under exclusive licence to Springer Nature America, Inc.",

year = "2021",

month = nov,

doi = "https://doi.org/10.1038/s41587-021-00936-1",

language = "English",

volume = "39",

pages = "1453--1465",

journal = "Nature biotechnology",

issn = "1087-0156",

publisher = "Nature Publishing Group",

number = "11",

}

Lorenzi, L, Chiu, H-S, Avila Cobos, F, Gross, S, Volders, P-J, Cannoodt, R, Nuytens, J, Vanderheyden, K, Anckaert, J, Lefever, S, Tay, AP, de Bony, EJ, Trypsteen, W, Gysens, F, Vromman, M, Goovaerts, T, Hansen, TB, Kuersten, S, Nijs, N, Taghon, T, Vermaelen, K, Bracke, KR, Saeys, Y, de Meyer, T, Deshpande, NP, Anande, G, Chen, T-W, Wilkins, MR, Unnikrishnan, A, de Preter, K, Kjems, JR, Koster, J, Schroth, GP, Vandesompele, J, Sumazin, P & Mestdagh, P 2021, 'The RNA Atlas expands the catalog of human non-coding RNAs', Nature biotechnology, vol. 39, no. 11, pp. 1453-1465. https://doi.org/10.1038/s41587-021-00936-1

TY - JOUR

T1 - The RNA Atlas expands the catalog of human non-coding RNAs

AU - Lorenzi, Lucia

AU - Chiu, Hua-Sheng

AU - Avila Cobos, Francisco

AU - Gross, Stephen

AU - Volders, Pieter-Jan

AU - Cannoodt, Robrecht

AU - Nuytens, Justine

AU - Vanderheyden, Katrien

AU - Anckaert, Jasper

AU - Lefever, Steve

AU - Tay, Aidan P.

AU - de Bony, Eric J.

AU - Trypsteen, Wim

AU - Gysens, Fien

AU - Vromman, Marieke

AU - Goovaerts, Tine

AU - Hansen, Thomas Birkballe

AU - Kuersten, Scott

AU - Nijs, Nele

AU - Taghon, Tom

AU - Vermaelen, Karim

AU - Bracke, Ken R.

AU - Saeys, Yvan

AU - de Meyer, Tim

AU - Deshpande, Nandan P.

AU - Anande, Govardhan

AU - Chen, Ting-Wen

AU - Wilkins, Marc R.

AU - Unnikrishnan, Ashwin

AU - de Preter, Katleen

AU - Kjems, J. rgen

AU - Koster, Jan

AU - Schroth, Gary P.

AU - Vandesompele, Jo

AU - Sumazin, Pavel

AU - Mestdagh, Pieter

N1 - Funding Information: 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. Publisher Copyright: © 2021, The Author(s), under exclusive licence to Springer Nature America, Inc.

PY - 2021/11

Y1 - 2021/11

N2 - 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.

AB - 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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U2 - https://doi.org/10.1038/s41587-021-00936-1

DO - https://doi.org/10.1038/s41587-021-00936-1

M3 - Article

C2 - 34140680

SN - 1087-0156

VL - 39

SP - 1453

EP - 1465

JO - Nature biotechnology

JF - Nature biotechnology

IS - 11

ER -

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

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