PROJECT ID: PRJNA605021


Data source SRA: PRJNA605021
Description This dataset consists of single-cell RNA-seq (10X) data of neuromast cells from zebrafish larvae. Posterior lateral-line neuromast cells were isolated by fluorescence activated cell sorting (FACS) from the dissociated trunks of Tg[myo6b:actb1-EGFP] transgenic zebrafish larvae expressing the green fluorescent protein (EGFP) in hair cells and unipotent hair-cell progenitors (UHCPs), and from Tg[Et(krt4:EGFP)sqgw57A] larvae expressing EGFP in supporting cells.
Key word hair-cell regeneration; gene-expression; myosin-vi; pol arity
Publication Kozak EL, Palit S, Miranda-Rodríguez JR, Janjic A et al. Epithelial Planar Bipolarity Emerges from Notch-Mediated Asymmetric Inhibition of Emx2. Curr Biol 2020 Mar 23;30(6):1142-1151.e6. PMID: 32109392
Abstract Most plane-polarized tissues are formed by identically oriented cells [1, 2]. A notable exception occurs in the vertebrate vestibular system and lateral-line neuromasts, where mechanosensory hair cells orient along a single axis but in opposite directions to generate bipolar epithelia [3-5]. In zebrafish neuromasts, pairs of hair cells arise from the division of a non-sensory progenitor [6, 7] and acquire opposing planar polarity via the asymmetric expression of the polarity-determinant transcription factor Emx2 [8-11]. Here, we reveal the initial symmetry-breaking step by decrypting the developmental trajectory of hair cells using single-cell RNA sequencing (scRNA-seq), diffusion pseudotime analysis, lineage tracing, and mutagenesis. We show that Emx2 is absent in non-sensory epithelial cells, begins expression in hair-cell progenitors, and is downregulated in one of the sibling hair cells via signaling through the Notch1a receptor. Analysis of Emx2-deficient specimens, in which every hair cell adopts an identical direction, indicates that Emx2 asymmetry does not result from auto-regulatory feedback. These data reveal a two-tiered mechanism by which the symmetric monodirectional ground state of the epithelium is inverted by deterministic initiation of Emx2 expression in hair-cell progenitors and a subsequent stochastic repression of Emx2 in one of the sibling hair cells breaks directional symmetry to establish planar bipolarity.


Dataset Information


Dataset ID Species Tissue / Organ Experiment type Sample Source dataset ID
1. PRJNA605021 (supporting cells) Danio rerio neuromast baseline 7dpf, posterior lateral-line neuromast cells were isolated from the dissociated trunks of Tg[Et(krt4:EGFP)sqgw57A] transgenic zebrafish larvae SRA: SRR11031289
2. PRJNA605021 (hair cells) Danio rerio neuromast baseline 7dpf, posterior lateral-line neuromast cells were isolated from the dissociated trunks of Tg[myo6b:actb1-EGFP] transgenic zebrafish larvae SRA: SRR11031290

Clustering Result


Cluster Cell type Gene id (symbol) Marker class Evidence
1 Epidermal cells ENSDARG00000088711 (lgals1l1) marker DOI:10.1016/j.cub.2020.01.027
2 Support cells ENSDARG00000089368 (hopx) marker DOI:10.1016/j.cub.2020.01.027
2 Support cells ENSDARG00000043128 (cldne) marker DOI:10.1016/j.cub.2020.01.027
3 Support cells ENSDARG00000104431 (slc1a3a) marker DOI:10.1016/j.stem.2015.07.002
4 Epidermal cells ENSDARG00000088711 (lgals1l1) marker DOI:10.1016/j.cub.2020.01.027
6 Epidermal cells ENSDARG00000088711 (lgals1l1) marker DOI:10.1016/j.cub.2020.01.027
7 Support cells ENSDARG00000035694 (stm) marker DOI:10.1016/j.cub.2020.01.027
7 Support cells ENSDARG00000089368 (hopx) marker DOI:10.1016/j.cub.2020.01.027
8 Support cells ENSDARG00000073978 (crabp2a) marker DOI:10.7554/eLife.44431
11 Support cells ENSDARG00000089368 (hopx) marker DOI:10.1016/j.cub.2020.01.027
12 HSPCs ENSDARG00000004392 (hdr) marker DOI:10.1016/j.cub.2020.01.027
12 HSPCs ENSDARG00000019930 (tal1) marker DOI:10.1016/j.cub.2020.01.027

Cluster Cell type Gene id (symbol) Marker class Evidence
1 Hair cells ENSDARG00000045038 (tekt3) marker DOI:10.1016/j.cub.2020.01.027
1 Hair cells ENSDARG00000042141 (myo6b) marker DOI:10.1016/j.cub.2020.01.027
2 Epidermal cells ENSDARG00000088711 (lgals1l1) marker DOI:10.1016/j.cub.2020.01.027
4 Support cells ENSDARG00000089368 (hopx) marker DOI:10.1016/j.cub.2020.01.027
5 Hair cells ENSDARG00000045038 (tekt3) marker DOI:10.1016/j.cub.2020.01.027
5 Hair cells ENSDARG00000042141 (myo6b) marker DOI:10.1016/j.cub.2020.01.027
6 Epidermal cells ENSDARG00000088514 (and1) marker DOI:10.1016/j.cub.2020.01.027
7 Epidermal cells ENSDARG00000088514 (and1) marker DOI:10.1016/j.cub.2020.01.027
8 Support cells ENSDARG00000035694 (stm) marker DOI:10.1016/j.cub.2020.01.027
10 Support cells ENSDARG00000061259 (sost) marker DOI:10.1016/j.cub.2020.01.027