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.
-
The role of long noncoding RNAs during pancreas developmentNCBI Gene Expression Omnibus, GSE144682.
-
Illumina BodyMap 2.0NCBI Gene Expression Omnibus, GSE30611.
-
RNA-seq from ENCODE/CaltechNCBI Gene Expression Omnibus, GSE33480.
-
polyA mRNA RNA-seq from BE2C (ENCSR000BYK)NCBI Gene Expression Omnibus, GSE93448.
-
polyA mRNA RNA-seq from HepG2 (ENCSR329MHM)NCBI Gene Expression Omnibus, GSE90322.
-
polyA mRNA RNA-seq from Jurkat clone E61 (ENCSR000BXX)NCBI Gene Expression Omnibus, GSE93435.
-
polyA mRNA RNA-seq from Panc1 (ENCSR000BYM)NCBI Gene Expression Omnibus, GSE93450.
-
polyA mRNA RNA-seq from PFSK-1 (ENCSR000BYN)NCBI Gene Expression Omnibus, GSE93451.
-
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.
Metrics
-
- 2,584
- views
-
- 354
- downloads
-
- 27
- citations
Views, downloads and citations are aggregated across all versions of this paper published by eLife.
Download links
A two-part list of links to download the article, or parts of the article, in various formats.
Downloads (link to download the article as PDF)
Open citations (links to open the citations from this article in various online reference manager services)
Cite this article (links to download the citations from this article in formats compatible with various reference manager tools)
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
Further reading
-
- Computational and Systems Biology
- Medicine
Background:
Preterm birth is the leading cause of neonatal morbidity and mortality worldwide. Most cases of preterm birth occur spontaneously and result from preterm labor with intact (spontaneous preterm labor [sPTL]) or ruptured (preterm prelabor rupture of membranes [PPROM]) membranes. The prediction of spontaneous preterm birth (sPTB) remains underpowered due to its syndromic nature and the dearth of independent analyses of the vaginal host immune response. Thus, we conducted the largest longitudinal investigation targeting vaginal immune mediators, referred to herein as the immunoproteome, in a population at high risk for sPTB.
Methods:
Vaginal swabs were collected across gestation from pregnant women who ultimately underwent term birth, sPTL, or PPROM. Cytokines, chemokines, growth factors, and antimicrobial peptides in the samples were quantified via specific and sensitive immunoassays. Predictive models were constructed from immune mediator concentrations.
Results:
Throughout uncomplicated gestation, the vaginal immunoproteome harbors a cytokine network with a homeostatic profile. Yet, the vaginal immunoproteome is skewed toward a pro-inflammatory state in pregnant women who ultimately experience sPTL and PPROM. Such an inflammatory profile includes increased monocyte chemoattractants, cytokines indicative of macrophage and T-cell activation, and reduced antimicrobial proteins/peptides. The vaginal immunoproteome has improved predictive value over maternal characteristics alone for identifying women at risk for early (<34 weeks) sPTB.
Conclusions:
The vaginal immunoproteome undergoes homeostatic changes throughout gestation and deviations from this shift are associated with sPTB. Furthermore, the vaginal immunoproteome can be leveraged as a potential biomarker for early sPTB, a subset of sPTB associated with extremely adverse neonatal outcomes.
Funding:
This research was conducted by the Perinatology Research Branch, Division of Obstetrics and Maternal-Fetal Medicine, Division of Intramural Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, U.S. Department of Health and Human Services (NICHD/NIH/DHHS) under contract HHSN275201300006C. ALT, KRT, and NGL were supported by the Wayne State University Perinatal Initiative in Maternal, Perinatal and Child Health.
-
- Computational and Systems Biology
- Genetics and Genomics
Runs of homozygosity (ROH) segments, contiguous homozygous regions in a genome were traditionally linked to families and inbred populations. However, a growing literature suggests that ROHs are ubiquitous in outbred populations. Still, most existing genetic studies of ROH in populations are limited to aggregated ROH content across the genome, which does not offer the resolution for mapping causal loci. This limitation is mainly due to a lack of methods for the efficient identification of shared ROH diplotypes. Here, we present a new method, ROH-DICE, to find large ROH diplotype clusters, sufficiently long ROHs shared by a sufficient number of individuals, in large cohorts. ROH-DICE identified over 1 million ROH diplotypes that span over 100 SNPs and are shared by more than 100 UK Biobank participants. Moreover, we found significant associations of clustered ROH diplotypes across the genome with various self-reported diseases, with the strongest associations found between the extended HLA region and autoimmune disorders. We found an association between a diplotype covering the HFE gene and hemochromatosis, even though the well-known causal SNP was not directly genotyped or imputed. Using a genome-wide scan, we identified a putative association between carriers of an ROH diplotype in chromosome 4 and an increase in mortality among COVID-19 patients (P-value=1.82×10-11). In summary, our ROH-DICE method, by calling out large ROH diplotypes in a large outbred population, enables further population genetics into the demographic history of large populations. More importantly, our method enables a new genome-wide mapping approach for finding disease-causing loci with multi-marker recessive effects at a population scale.
