A human ESC-based screen identifies a role for the translated lncRNA LINC00261 in pancreatic endocrine differentiation
- University of California, San Diego, United States
- Max-Delbruck-Center for Molecular Medicine, Germany
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.
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The role of long noncoding RNAs during pancreas developmentNCBI Gene Expression Omnibus, GSE144682.
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Illumina BodyMap 2.0NCBI Gene Expression Omnibus, GSE30611.
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RNA-seq from ENCODE/CaltechNCBI Gene Expression Omnibus, GSE33480.
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polyA mRNA RNA-seq from BE2C (ENCSR000BYK)NCBI Gene Expression Omnibus, GSE93448.
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polyA mRNA RNA-seq from HepG2 (ENCSR329MHM)NCBI Gene Expression Omnibus, GSE90322.
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polyA mRNA RNA-seq from Jurkat clone E61 (ENCSR000BXX)NCBI Gene Expression Omnibus, GSE93435.
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polyA mRNA RNA-seq from Panc1 (ENCSR000BYM)NCBI Gene Expression Omnibus, GSE93450.
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polyA mRNA RNA-seq from PFSK-1 (ENCSR000BYN)NCBI Gene Expression Omnibus, GSE93451.
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polyA mRNA RNA-seq from U-87 MG (ENCSR000BYO)NCBI Gene Expression Omnibus, GSE90176.
Article and author information
Author details
Sebastiaan van Heesch
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.
Reviewing Editor
- Lori Sussel
Version history
- Received: May 7, 2020
- Accepted: August 1, 2020
- Accepted Manuscript published: August 3, 2020 (version 1)
- Version of Record published: August 12, 2020 (version 2)
Copyright
© 2020, Gaertner et al.
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.
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A human ESC-based screen identifies a role for the translated lncRNA LINC00261 in pancreatic endocrine differentiation
eLife 9:e58659.
https://doi.org/10.7554/eLife.58659
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