A human ESC-based screen identifies a role for the translated lncRNA LINC00261 in pancreatic endocrine differentiation

Abstract
Data availability
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Abstract

Long noncoding RNAs (lncRNAs) are a heterogenous group of RNAs, which can encode small proteins. The extent to which developmentally regulated lncRNAs are translated and whether the produced microproteins are relevant for human development is unknown. Using a human embryonic stem cell (hESC)-based pancreatic differentiation system, we show that many lncRNAs in direct vicinity of lineage-determining transcription factors (TFs) are dynamically regulated, predominantly cytosolic, and highly translated. We genetically ablated ten such lncRNAs, most of them translated, and found that nine are dispensable for pancreatic endocrine cell development. However, deletion of LINC00261 diminishes insulin⁺ cells, in a manner independent of the nearby TF FOXA2. One-by-one deletion of each of LINC00261's open reading frames suggests that the RNA, rather than the produced microproteins, is required for endocrine development. Our work highlights extensive translation of lncRNAs during hESC pancreatic differentiation and provides a blueprint for dissection of their coding and noncoding roles.

Data availability

All mRNA-seq and Ribo-seq datasets generated for this study have been deposited at GEO under the accession number GSE144682.

The following data sets were generated

1. Gaertner B
2. van Heesch S
3. Schneider-Lunitz V
4. Schulz JF
5. Witte F
6. Blachut S
7. Nguyen S
8. Wong R
9. Matta I
10. Hubner N
11. Sander M
(2020) The role of long noncoding RNAs during pancreas development
NCBI Gene Expression Omnibus, GSE144682.

http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE144682

The following previously published data sets were used

1. Khrebtukova I
(2011) Illumina BodyMap 2.0
NCBI Gene Expression Omnibus, GSE30611.

http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE30611
(2012) RNA-seq from ENCODE/Caltech
NCBI Gene Expression Omnibus, GSE33480.

http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE33480
1. ENCODE Project Consortium
(2012) polyA mRNA RNA-seq from BE2C (ENCSR000BYK)
NCBI Gene Expression Omnibus, GSE93448.

http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE93448
1. Huelga SC
2. Vu AQ
3. Arnold JD
4. Liang TY
5. Liu PP
6. Yan BY
7. Donohue JP
8. Shiue L
9. Hoon S
10. Brenner S
11. Ares M
12. Yeo GW
(2012) Integrative genome-wide analysis reveals cooperative regulation of alternative splicing by hnRNP proteins (RNA-Seq)
NCBI Gene Expression Omnibus, GSE34995.

http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE34995
1. ENCODE Project Consortium
(2016) polyA mRNA RNA-seq from HepG2 (ENCSR329MHM)
NCBI Gene Expression Omnibus, GSE90322.

http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE90322
1. ENCODE Project Consortium
(2017) polyA mRNA RNA-seq from Jurkat clone E61 (ENCSR000BXX)
NCBI Gene Expression Omnibus, GSE93435.

http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE93435
1. Sherman MH
2. Yu RT
3. Engle DD
4. Ding N
5. Atkins AR
6. Tiriac H
7. Collisson EA
8. Connor F
9. Van Dyke T
10. Kozlov S
11. Martin P
12. Tseng TW
13. Dawson DW
14. Donahue TR
15. Masamune A
16. Shimosegawa T
17. Apte MV
18. Wilson JS
19. Ng B
20. Lau SL
21. Gunton JE
22. Wahl GM
23. Hunter T
24. Drebin JA
25. O'Dwyer PJ
26. Liddle C
27. Tuveson DA
28. Downes M
29. Evans RM
(2014) Vitamin d receptor-mediated stromal reprogramming suppresses pancreatitis and enhances pancreatic cancer therapy
NCBI Gene Expression Omnibus, GSE43770.

http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE43770
1. ENCODE Project Consortium
(2017) polyA mRNA RNA-seq from Panc1 (ENCSR000BYM)
NCBI Gene Expression Omnibus, GSE93450.

http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE93450
1. ENCODE Project Consortium
(2017) polyA mRNA RNA-seq from PFSK-1 (ENCSR000BYN)
NCBI Gene Expression Omnibus, GSE93451.

http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE93451
1. ENCODE Project Consortium
(2016) polyA mRNA RNA-seq from U-87 MG (ENCSR000BYO)
NCBI Gene Expression Omnibus, GSE90176.

http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE90176
1. Xie R
2. Everett LJ
3. Lim HW
4. Patel NA
5. Schug J
6. Kroon E
7. Kelly OG
8. Wang A
9. D'Amour KA
10. Robins AJ
11. Won KJ
12. Kaestner KH
13. Sander M
(2013) ChIP-seq and RNA-seq of coding RNA of the progression of human embryonic stem cells to beta cells to characterize the epigenetic programs that underlie pancreas differentiation
ArrayExpress, E-MTAB-1086.

https://www.ebi.ac.uk/arrayexpress/experiments/E-MTAB-1086/

Article and author information

Author details

Bjoern Gaertner

Department of Pediatrics, University of California, San Diego, La Jolla, United States

Competing interests
The authors declare that no competing interests exist.
Sebastiaan van Heesch

Cardiovascular Research, Max-Delbruck-Center for Molecular Medicine, Berlin, Germany

Competing interests
The authors declare that no competing interests exist.

"This ORCID iD identifies the author of this article:" 0000-0001-9593-1980
Valentin Schneider-Lunitz

Cardiovascular Research, Max-Delbruck-Center for Molecular Medicine, Berlin, Germany

Competing interests
The authors declare that no competing interests exist.
Jana Felicitas Schulz

Cardiovascular Research, Max-Delbruck-Center for Molecular Medicine, Berlin, Germany

Competing interests
The authors declare that no competing interests exist.
Franziska Witte

Cardiovascular Research, Max-Delbruck-Center for Molecular Medicine, Berlin, Germany

Competing interests
The authors declare that no competing interests exist.
Susanne Blachut

Cardiovascular Research, Max-Delbruck-Center for Molecular Medicine, Berlin, Germany

Competing interests
The authors declare that no competing interests exist.
Steven Nguyen

Department of Pediatrics, University of California, San Diego, La Jolla, United States

Competing interests
The authors declare that no competing interests exist.
Regina Wong

Department of Pediatrics, University of California, San Diego, La Jolla, United States

Competing interests
The authors declare that no competing interests exist.
Ileana Matta

Department of Pediatrics, University of California, San Diego, La Jolla, United States

Competing interests
The authors declare that no competing interests exist.
Norbert Hübner

Cardiovascular Research, Max-Delbruck-Center for Molecular Medicine, Berlin, Germany

Competing interests
The authors declare that no competing interests exist.
Maike Sander

Department of Pediatrics and Cellular and Molecular Medicine, University of California, San Diego, La Jolla, United States

For correspondence
masander@ucsd.edu

Competing interests
The authors declare that no competing interests exist.

"This ORCID iD identifies the author of this article:" 0000-0001-5308-7785

Funding

National Institutes of Health (DK068471 and DK078803)

Maike Sander

Alexander von Humboldt-Stiftung

Maike Sander

Larry L. Hillblom Foundation (2015-D-021-FEL)

Bjoern Gaertner

European Molecular Biology Organization (ALTF 186-2015)

Sebastiaan van Heesch

Horizon 2020 Framework Programme (AdG788970)

Norbert Hübner

The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.

Copyright

This article is distributed under the terms of the Creative Commons Attribution License permitting unrestricted use and redistribution provided that the original author and source are credited.