An improved zebrafish transcriptome annotation for sensitive and comprehensive detection of cell type-specific genes
- University of Massachusetts Medical School, United States
- University of Oxford, United Kingdom
Abstract
The zebrafish is ideal for studying embryogenesis and is increasingly applied to model human disease. In these contexts, RNA-sequencing (RNA-seq) provides mechanistic insights by identifying transcriptome changes between experimental conditions. Application of RNA-seq relies on accurate transcript annotation for a genome of interest. Here, we find discrepancies in analysis from RNA-seq datasets quantified using Ensembl and RefSeq zebrafish annotations. These issues were due, in part, to variably annotated 3' untranslated regions and thousands of gene models missing from each annotation. Since these discrepancies could compromise downstream analyses and biological reproducibility, we built a more comprehensive zebrafish transcriptome annotation that addresses these deficiencies. Our annotation improves detection of cell type-specific genes in both bulk and single cell RNA-seq datasets, where it also improves resolution of cell clustering. Thus, we demonstrate that our new transcriptome annotation can outperform existing annotations, providing an important resource for zebrafish researchers.
Data availability
All data generated in this study are available in accompanying source data files. Transcriptome annotation files described in this study are available for download at zf-transcriptome.umassmed.edu. Raw and processed RNA-seq data generated in this study are available at GEO (GSE152759).
-
Bulk RNA-seq data to assess an improved zebrafish transcriptome annotationNCBI Gene Expression Omnibus, GSE152759.
-
Morphogenesis and differentiation of embryonic vascular smooth muscle cells in zebrafishNCBI Gene Expression Omnibus, GSE119718.
-
Comprehensive identification of long non-coding RNAs expressed during zebrafish embryogenesisNCBI Gene Expression Omnibus, GSE32900.
-
Extensive alternative polyadenylation during zebrafish developmentNCBI Gene Expression Omnibus, GSE37453.
Article and author information
Author details
Funding
National Heart, Lung, and Blood Institute (R35HL140017)
- Nathan D Lawson
National Human Genome Research Institute (U01HG007910)
- Onur Yukselen
- Alper Kucukural
National Center for Advancing Translational Sciences (UL1TR001453)
- Onur Yukselen
- Alper Kucukural
National Institute of Neurological Disorders and Stroke (R21NS105654)
- Nathan D Lawson
The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.
Reviewing Editor
- Elisabeth Busch-Nentwich, University of Cambridge
Ethics
Animal experimentation: Zebrafish studies were performed in accordance with protocols #A2613 and #A2632 approved by the University of Massachusetts institutional animal care and use committee (IACUC).
Version history
- Received: February 6, 2020
- Accepted: August 21, 2020
- Accepted Manuscript published: August 24, 2020 (version 1)
- Version of Record published: September 11, 2020 (version 2)
Copyright
© 2020, Lawson 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
-
- 9,490
- Page views
-
- 824
- Downloads
-
- 40
- Citations
Article citation count generated by polling the highest count across the following sources: Crossref, Scopus, PubMed Central.
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)
An improved zebrafish transcriptome annotation for sensitive and comprehensive detection of cell type-specific genes
eLife 9:e55792.
https://doi.org/10.7554/eLife.55792
Further reading
-
- Developmental Biology
- Neuroscience
Human fetal development has been associated with brain health at later stages. It is unknown whether growth in utero, as indexed by birth weight (BW), relates consistently to lifespan brain characteristics and changes, and to what extent these influences are of a genetic or environmental nature. Here we show remarkably stable and lifelong positive associations between BW and cortical surface area and volume across and within developmental, aging and lifespan longitudinal samples (N = 5794, 4–82 y of age, w/386 monozygotic twins, followed for up to 8.3 y w/12,088 brain MRIs). In contrast, no consistent effect of BW on brain changes was observed. Partly environmental effects were indicated by analysis of twin BW discordance. In conclusion, the influence of prenatal growth on cortical topography is stable and reliable through the lifespan. This early-life factor appears to influence the brain by association of brain reserve, rather than brain maintenance. Thus, fetal influences appear omnipresent in the spacetime of the human brain throughout the human lifespan. Optimizing fetal growth may increase brain reserve for life, also in aging.
-
- Developmental Biology
- Immunology and Inflammation
During embryogenesis, the fetal liver becomes the main hematopoietic organ, where stem and progenitor cells as well as immature and mature immune cells form an intricate cellular network. Hematopoietic stem cells (HSCs) reside in a specialized niche, which is essential for their proliferation and differentiation. However, the cellular and molecular determinants contributing to this fetal HSC niche remain largely unknown. Macrophages are the first differentiated hematopoietic cells found in the developing liver, where they are important for fetal erythropoiesis by promoting erythrocyte maturation and phagocytosing expelled nuclei. Yet, whether macrophages play a role in fetal hematopoiesis beyond serving as a niche for maturing erythroblasts remains elusive. Here, we investigate the heterogeneity of macrophage populations in the murine fetal liver to define their specific roles during hematopoiesis. Using a single-cell omics approach combined with spatial proteomics and genetic fate-mapping models, we found that fetal liver macrophages cluster into distinct yolk sac-derived subpopulations and that long-term HSCs are interacting preferentially with one of the macrophage subpopulations. Fetal livers lacking macrophages show a delay in erythropoiesis and have an increased number of granulocytes, which can be attributed to transcriptional reprogramming and altered differentiation potential of long-term HSCs. Together, our data provide a detailed map of fetal liver macrophage subpopulations and implicate macrophages as part of the fetal HSC niche.
