Zebrafish pigment cells develop directly from persistent highly multipotent progenitors
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PROVIDER: PRJNA769741 | ENA |
REPOSITORIES: ENA
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Project description:Neural crest cells (NCCs) are highly multipotent stem cells. A long-standing controversy exists over the mechanism of NCC fate specification, specifically regarding the presence and potency of intermediate progenitors. The direct fate restriction (DFR) model, based on early in vivo clonal studies, hypothesised that intermediates are absent and that migrating cells maintain full multipotency1-6. However, most authors favour progressive fate restriction (PFR) models, with fully multipotent early NCCs (ENCCs) transitioning to partially- restricted intermediates before committing to individual fates7-12. Here, single cell transcriptional profiling of zebrafish pigment cell development leads to us proposing a Cyclical Fate Restriction mechanism of NCC development that reconciles the DFR and PFR models. Our clustering of single NCC Nanostring transcriptional profiles identifies only broadly multipotent intermediate states between ENCCs and differentiated melanocytes and iridophores. Leukocyte tyrosine kinase (Ltk) marks the multipotent progenitor and iridophores, consistent with biphasic ltk expression13-15. Ltk inhibitor and constitutive activation studies support expression at an early multipotent stage, whilst lineage-tracing of ltk-expressing cells reveals their multipotency extends beyond pigment cell-types to neural fates. We conclude that pigment cell development does not involve a conventional PFR mechanism, but instead occurs directly and more dynamically from a broadly multipotent intermediate state.
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Project description:RAG1+ multipotent progenitors emerge directly from hemogenic endothelium of human PSC derived haemopoietic organoids [single cell RNA-Seq]
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Project description:In zebrafish, there are interactions between black pigment cells (melanophores) and yellow pigment cells (xanthophores) for pigment-pattern formation. However, the detailed molecular mechanism of these interactions remains largely unknown. We used microarray for identifying the molecular basis of these interactions by comparing gene expression between melanophores and xanthophores. Zebrafish pigment cells were collected from adult-fish fins by centrifugal separation or using cell sorter. melanophores vs. xanthophores
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Project description:RNA polymerase II (pol II) can backtrack during transcription elongation, exposing the 3’ end of nascent RNA. Nascent RNA sequencing can approximate the location of backtracking events that are quickly resolved; however, the extent and genome wide distribution of more persistent backtracking is unknown. Consequently, we developed a novel method to directly sequence backtracked RNA. Our data shows that pol II slides backwards more than 20 nucleotides in human cells and can persist in this backtracked state. Persistent backtracking mainly occurs where pol II pauses near promoters and intron-exon junctions, and is enriched in genes involved in translation, replication, and development, where gene expression is inhibited if these events are unresolved. Histone genes are highly prone to persistent backtracking, where the accumulation and resolution of such events is required for timely expression during cell division. These results demonstrate that persistent backtracking has the potential to affect diverse gene expression programs.
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Project description:In zebrafish, there are interactions between black pigment cells (melanophores) and yellow pigment cells (xanthophores) for pigment-pattern formation. However, the detailed molecular mechanism of these interactions remains largely unknown. We used microarray for identifying the molecular basis of these interactions by comparing gene expression between melanophores and xanthophores.
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Project description:Pigment cells bear molecules with diverse physiological roles across phylogeny and are often under strict evolutionary selection. Thus, the mechanisms of regulating these cells, and the pigments within them, are of critical importance. Here, we explore the regulation of pigment cells in the purple sea urchin Strongylocentrotus purpuratus, an emerging model for understudied pigments at a molecular level. Sea urchins display a variety of pigments in both embryos and adults, but how the pigment cells form during development has not been resolved, nor has their breadth of biological significance been revealed. Known genes expressed by embryonic pigment cells are the transcriptional factor glial cells missing (gcm), and the enzymes pks1 and fmo1,2 and 3 (polyketide synthase1, flavin-dependent monooxygenase 1, 2, 3 respectively). In this study, we took advantage of single cell RNA-seq technology to interrogate the cell state of emerging pigment cells, and to test their diversity in fate and function.
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