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; Jørgen Kjems; Jan Koster; Gary P. Schroth; Jo Vandesompele; Pavel Sumazin; Pieter Mestdagh

doi: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, Jørgen Kjems, Jan Koster, Gary P. Schroth, Jo Vandesompele, Pavel Sumazin, Pieter Mestdagh^*

^*Corresponding author for this work

Faculty of Medicine, Health and Human Sciences

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

86 Citations (Scopus)

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	23
Journal	Nature Biotechnology
Volume	39
Issue number	11
DOIs	https://doi.org/10.1038/s41587-021-00936-1
Publication status	Published - Nov 2021

Bibliographical note

A correction exists for this article and can be found at doi: 10.1038/s41587-021-00996-3.
It has been included in the current version of the article.

Access to Document

10.1038/s41587-021-00936-1

Cite this

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{434f726a64ac4ceba61541be88f72c4c,

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 Chiu, {Hua Sheng} and {Avila Cobos}, Francisco and Stephen Gross and Volders, {Pieter Jan} 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 Chen, {Ting Wen} and Wilkins, {Marc R.} and Ashwin Unnikrishnan and {De Preter}, Katleen and J{\o}rgen Kjems and Jan Koster and Schroth, {Gary P.} and Jo Vandesompele and Pavel Sumazin and Pieter Mestdagh",

note = "A correction exists for this article and can be found at doi: 10.1038/s41587-021-00996-3. It has been included in the current version of the article.",

year = "2021",

month = nov,

doi = "10.1038/s41587-021-00936-1",

language = "English",

volume = "39",

pages = "1453--1465",

journal = "Nature Biotechnology",

issn = "1087-0156",

publisher = "Springer, Springer Nature",

number = "11",

}

Lorenzi, L, Chiu, HS, Avila Cobos, F, Gross, S, Volders, PJ, 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, TW, Wilkins, MR, Unnikrishnan, A, De Preter, K, Kjems, J, 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, Jørgen

AU - Koster, Jan

AU - Schroth, Gary P.

AU - Vandesompele, Jo

AU - Sumazin, Pavel

AU - Mestdagh, Pieter

N1 - A correction exists for this article and can be found at doi: 10.1038/s41587-021-00996-3. It has been included in the current version of the article.

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.

UR - http://www.scopus.com/inward/record.url?scp=85108148404&partnerID=8YFLogxK

U2 - 10.1038/s41587-021-00936-1

DO - 10.1038/s41587-021-00936-1

M3 - Article

C2 - 34140680

AN - SCOPUS:85108148404

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

Abstract

Bibliographical note

Access to Document

Other files and links

Fingerprint

Cite this