Cellular diversity of the regenerating caudal fin

Zebrafish faithfully regenerate their caudal fin after amputation. During this process, both differentiated cells and resident progenitors migrate to the wound site and undergo lineage-restricted, programmed cellular state transitions to populate the new regenerate. Until now, systematic characterizations of cells comprising the new regenerate and molecular definitions of their state transitions have been lacking. We hereby characterize the dynamics of gene regulatory programs during fin regeneration by creating single-cell transcriptome maps of both preinjury and regenerating fin tissues at 1/2/4 days post-amputation. We consistently identified epithelial, mesenchymal, and hematopoietic populations across all stages. We found common and cell type–specific cell cycle programs associated with proliferation. In addition to defining the processes of epithelial replenishment and mesenchymal differentiation, we also identified molecular signatures that could better distinguish epithelial and mesenchymal subpopulations in fish. The insights for natural cell state transitions during regeneration point to new directions for studying this regeneration model.

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Two Different Transgenes to Study Gene Silencing and Re-Expression During Zebrafish Caudal Fin and Retinal Regeneration

The Scientific World JOURNAL ◽

10.1100/tsw.2006.328 ◽

2006 ◽

Vol 6 ◽

pp. 65-81 ◽

Cited By ~ 34

Author(s):

Ryan Thummel ◽

Christopher T. Burket ◽

David R. Hyde

Keyword(s):

Tissue Regeneration ◽

Transgene Expression ◽

Egfp Expression ◽

Transgenic Zebrafish ◽

Retinal Regeneration ◽

Caudal Fin ◽

Fin Regeneration ◽

Differentiated Cells ◽

Neuronal Progenitors ◽

Wound Epithelium

We used the 500-bpXenopusef1-α promoter and the 2-kb zebrafish histone2A.F/Zpromoter to generate several independent transgenic zebrafish lines expressing EGFP. While both promoters drive ubiquitous EGFP expression in early zebrafish development, they are systematically silenced in several adult tissues, including the retina and caudal fin. However, EGFP expression is temporarily renewed in the adult during either caudal fin or retinal regeneration. In the Tg(H2A.F/Z:EGFP)ntline, EGFP is moderately expressed in both the wound epithelium and blastema of the regenerating caudal fin. In the Tg(ef1-α:EGFP)ntline, EGFP expression is reinitiated and restricted to the blastema of the regenerating caudal fin and colabels with BrdU, PCNA, andmsxc-positive cells. Thus, these two ubiquitous promoters drive EGFP transgene expression in different cell populations during caudal fin regeneration. We further analyzed the ability of theef1-α:EGFPtransgene to label nonterminally differentiated cells during adult tissue regeneration. First, we demonstrated that the transgene is highly methylated in adult zebrafish caudal fin tissue, but not during fin regeneration, implicating methylation as a potential means of transgene silencing in this line. Next, we determined that theef1-α:EGFPtransgene is also re-expressed during adult retinal regeneration. Specifically, theef1-α:EGFPtransgene colabels with PCNA in the Müglia, a specialized cell that is the source of neuronal progenitors during zebrafish retinal regeneration. Thus, we concluded that Tg(ef1-α:EGFP)nt line visually marks nonterminally differentiated cells in multiple adult regeneration environments and may prove to be a useful marker in tissue regeneration studies in zebrafish.

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Single-cell Transcriptome Mapping Identifies Common and Cell-type Specific Genes Affected by Acute Delta9-tetrahydrocannabinol in Humans

Scientific Reports ◽

10.1038/s41598-020-59827-1 ◽

2020 ◽

Vol 10 (1) ◽

Cited By ~ 3

Author(s):

Ying Hu ◽

Mohini Ranganathan ◽

Chang Shu ◽

Xiaoyu Liang ◽

Suhas Ganesh ◽

...

Keyword(s):

Single Cell ◽

Cell Type ◽

Cell Type Specific ◽

Cell Transcriptome ◽

Single Cell Transcriptome

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Single-cell transcriptomes of pancreatic preinvasive lesions and cancer reveal acinar metaplastic cells’ heterogeneity

Nature Communications ◽

10.1038/s41467-020-18207-z ◽

2020 ◽

Vol 11 (1) ◽

Cited By ~ 1

Author(s):

Yehuda Schlesinger ◽

Oshri Yosefov-Levi ◽

Dror Kolodkin-Gal ◽

Roy Zvi Granit ◽

Luriano Peters ◽

...

Keyword(s):

Single Cell ◽

Malignant Lesion ◽

Tumor Development ◽

Initial Step ◽

Cell Types ◽

Tumor Formation ◽

Specific Cell ◽

Preinvasive Lesions ◽

Cell Transcriptome ◽

Single Cell Transcriptome

Abstract Acinar metaplasia is an initial step in a series of events that can lead to pancreatic cancer. Here we perform single-cell RNA-sequencing of mouse pancreas during the progression from preinvasive stages to tumor formation. Using a reporter gene, we identify metaplastic cells that originated from acinar cells and express two transcription factors, Onecut2 and Foxq1. Further analyses of metaplastic acinar cell heterogeneity define six acinar metaplastic cell types and states, including stomach-specific cell types. Localization of metaplastic cell types and mixture of different metaplastic cell types in the same pre-malignant lesion is shown. Finally, single-cell transcriptome analyses of tumor-associated stromal, immune, endothelial and fibroblast cells identify signals that may support tumor development, as well as the recruitment and education of immune cells. Our findings are consistent with the early, premalignant formation of an immunosuppressive environment mediated by interactions between acinar metaplastic cells and other cells in the microenvironment.

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Deep sequencing reveals cell-type-specific patterns of single-cell transcriptome variation

Genome Biology ◽

10.1186/s13059-015-0683-4 ◽

2015 ◽

Vol 16 (1) ◽

Cited By ~ 66

Author(s):

Hannah Dueck ◽

Mugdha Khaladkar ◽

Tae Kyung Kim ◽

Jennifer M. Spaethling ◽

Chantal Francis ◽

...

Keyword(s):

Single Cell ◽

Deep Sequencing ◽

Cell Type ◽

Transcriptome Variation ◽

Cell Type Specific ◽

Cell Transcriptome ◽

Single Cell Transcriptome

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Lifelong single-cell profiling of cranial neural crest diversification

10.1101/2021.08.19.456710 ◽

2021 ◽

Author(s):

Peter Fabian ◽

Kuo-Chang Tseng ◽

Mathi Thiruppathy ◽

Claire Arata ◽

Hung-Jhen Chen ◽

...

Keyword(s):

Neural Crest ◽

Single Cell ◽

Cell Fate ◽

Intrinsic Property ◽

Chromatin Accessibility ◽

Specific Cell ◽

List Type ◽

Cranial Neural Crest ◽

Cell Transcriptome ◽

Single Cell Transcriptome

AbstractThe cranial neural crest generates a huge diversity of derivatives, including the bulk of connective and skeletal tissues of the vertebrate head. How neural crest cells acquire such extraordinary lineage potential remains unresolved. By integrating single-cell transcriptome and chromatin accessibility profiles of cranial neural crest-derived cells across the zebrafish lifetime, we observe region-specific establishment of enhancer accessibility for distinct fates. Neural crest-derived cells rapidly diversify into specialized progenitors, including multipotent skeletal progenitors, stromal cells with a regenerative signature, fibroblasts with a unique metabolic signature linked to skeletal integrity, and gill-specific progenitors generating cell types for respiration. By retrogradely mapping the emergence of lineage-specific chromatin accessibility, we identify a wealth of candidate lineage-priming factors, including a Gata3 regulatory circuit for respiratory cell fates. Rather than multilineage potential being an intrinsic property of cranial neural crest, our findings support progressive and region-specific chromatin remodeling underlying acquisition of diverse neural crest lineage potential.HighlightsSingle-cell transcriptome and chromatin atlas of cranial neural crestProgressive emergence of region-specific cell fate competencyChromatin accessibility mapping identifies candidate lineage regulatorsGata3 function linked to gill-specific respiratory programGraphical Abstract

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Single-cell transcriptome profiling of thyroid hormone effectors in the human fetal neocortex: expression of SLCO1C1, DIO2, and THRB in specific cell types

Thyroid ◽

10.1089/thy.2021.0057 ◽

2021 ◽

Author(s):

Diego Diez ◽

Beatriz Morte ◽

Juan Bernal

Keyword(s):

Thyroid Hormone ◽

Single Cell ◽

Transcriptome Profiling ◽

Cell Types ◽

Specific Cell ◽

Cell Transcriptome ◽

Single Cell Transcriptome

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Single-cell transcriptome profiling of the Ciona larval brain

10.1101/319327 ◽

2018 ◽

Cited By ~ 1

Author(s):

Sarthak Sharma ◽

Wei Wang ◽

Alberto Stolfi

Keyword(s):

Single Cell ◽

Single Cells ◽

Expression Patterns ◽

Transcriptome Profiling ◽

Specific Gene ◽

Larval Brain ◽

Rnaseq Data ◽

Cell Type Specific ◽

Cell Transcriptome ◽

Single Cell Transcriptome

AbstractThe tadpole-type larva of Ciona has emerged as an intriguing model system for the study of neurodevelopment. The Ciona intestinalis connectome has been recently mapped, revealing the smallest central nervous system (CNS) known in any chordate, with only 177 neurons. This minimal CNS is highly reminiscent of larger CNS of vertebrates, sharing many conserved developmental processes, anatomical compartments, neuron subtypes, and even specific neural circuits. Thus, the Ciona tadpole offers a unique opportunity to understand the development and wiring of a chordate CNS at single-cell resolution. Here we report the use of single-cell RNAseq to profile the transcriptomes of single cells isolated by fluorescence-activated cell sorting (FACS) from the whole brain of Ciona robusta (formerly intestinalis Type A) larvae. We have also compared these profiles to bulk RNAseq data from specific subsets of brain cells isolated by FACS using cell type-specific reporter plasmid expression. Taken together, these datasets have begun to reveal the compartment- and cell-specific gene expression patterns that define the organization of the Ciona larval brain.

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Cell-type specialization in the brain is encoded by specific long-range chromatin topologies

10.1101/2020.04.02.020990 ◽

2020 ◽

Author(s):

Warren Winick-Ng ◽

Alexander Kukalev ◽

Izabela Harabula ◽

Luna Zea Redondo ◽

Mandy Meijer ◽

...

Keyword(s):

Gene Expression ◽

Genome Architecture ◽

Specific Cell ◽

Genome Organisation ◽

Cell Type ◽

Topological Domains ◽

3D Genome ◽

Differentiated Cells ◽

Cell Type Specific ◽

The Brain

AbstractNeurons and oligodendrocytes are terminally differentiated cells that perform highly specialized functions, which depend on cascades of gene activation and repression to retain homeostatic control over a lifespan. Gene expression is regulated by three-dimensional (3D) genome organisation, from local levels of chromatin compaction to the organisation of topological domains and chromosome compartments. Whereas our understanding of 3D genome architecture has vastly increased in the past decade, it remains difficult to study specialized cells in their native environment without disturbing their activity. To develop the application of Genome Architecture Mapping (GAM) in small numbers of specialized cells in complex tissues, we combined GAM with immunoselection. We applied immunoGAM to map the genome architecture of specific cell populations in the juvenile/adult mouse brain: dopaminergic neurons (DNs) from the midbrain, pyramidal glutamatergic neurons (PGNs) from the hippocampus, and oligodendrocyte lineage cells (OLGs) from the cortex. We integrate 3D genome organisation with single-cell transcriptomics data, and find specific chromatin structures that relate with cell-type specific patterns of gene expression. We discover abundant changes in compartment organisation, especially a strengthening of heterochromatin compartments which establish strong contacts spanning tens of megabases, especially in brain cells. These compartments contain olfactory and taste receptor genes, which are de-repressed in a subpopulation of PGNs with molecular signatures of long-term potentiation (LTP). We also show extensive reorganisation of topological domains where activation of neuronal or oligodendrocyte genes coincides with formation of new TAD borders. Finally, we discover loss of TAD organisation, or ‘TAD melting’, at long (>1Mb) neuronal genes when they are most highly expressed. Our work shows that the 3D organisation of the genome is highly cell-type specific in terminally differentiated cells of the brain, and essential to better understand brain-specific mechanisms of gene regulation.

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