Single-cell-resolved dynamics of chromatin architecture delineate cell and regulatory states in zebrafish embryos

McGarvey, Alison C.; Kopp, Wolfgang; Vučićević, Dubravka; Mattonet, Kenny; Kempfer, Rieke; Hirsekorn, Antje; Bilić, Ilija; Gil, Marine; Trinks, Alexandra; Merks, Anne M.; Panàkovà, Daniela; Pombo, Ana; Akalin, Altuna; Junker, Jan Philipp; Stainier, Didier Y. R.; Garfield, David; Ohler, Uwe; Lacadie, Scott A.

doi:10.1016/j.xgen.2021.100083

Cited by 14 publications

(19 citation statements)

References 117 publications

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“…The DCC and the functional annotation track hub will thus serve as a foundation for future single-cell studies of transcriptomes 66 – 68 , open chromatin 30 and others, as demonstrated with single-cell ATAC-seq data here. The functional annotations presented will also aid in targeted manipulation of genomic elements.…”

Section: Discussionmentioning

confidence: 87%

“…The tracks further include annotation of approximately 140,000 predicted ATAC-seq-supported developmental regulatory elements (PADRE) annotated by ChromHMM categories. The bulk sample-based predictions for regulatory elements are complemented with annotations of cell-type specificity of candidate regulatory elements provided by single-cell ATAC-seq 30 (Supplementary Videos 3 – 5 ).…”

Section: Resultsmentioning

confidence: 99%

“…To assign cell-type specificity to PADREs we integrated them with Prim-5 single-cell ATAC-seq 30 data (Extended Data Fig. 7a ).…”

Section: Resultsmentioning

confidence: 99%

“…The state number in the name corresponds to those defined in McGarvey et al . 30 . b , Overlap of matches between the cell-type assignment and activity tissue determined by transgenic assay.…”

Section: Extended Datamentioning

confidence: 99%

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Multiomic atlas with functional stratification and developmental dynamics of zebrafish cis-regulatory elements

et al. 2022

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Zebrafish, a popular organism for studying embryonic development and for modeling human diseases, has so far lacked a systematic functional annotation program akin to those in other animal models. To address this, we formed the international DANIO-CODE consortium and created a central repository to store and process zebrafish developmental functional genomic data. Our data coordination center (https://danio-code.zfin.org) combines a total of 1,802 sets of unpublished and re-analyzed published genomic data, which we used to improve existing annotations and show its utility in experimental design. We identified over 140,000 cis-regulatory elements throughout development, including classes with distinct features dependent on their activity in time and space. We delineated the distinct distance topology and chromatin features between regulatory elements active during zygotic genome activation and those active during organogenesis. Finally, we matched regulatory elements and epigenomic landscapes between zebrafish and mouse and predicted functional relationships between them beyond sequence similarity, thus extending the utility of zebrafish developmental genomics to mammals.

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Section: Discussionmentioning

confidence: 87%

Section: Resultsmentioning

confidence: 99%

“…To assign cell-type specificity to PADREs we integrated them with Prim-5 single-cell ATAC-seq 30 data (Extended Data Fig. 7a ).…”

Section: Resultsmentioning

confidence: 99%

Section: Extended Datamentioning

confidence: 99%

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Multiomic atlas with functional stratification and developmental dynamics of zebrafish cis-regulatory elements

et al. 2022

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“…Recent work in zebrafish has applied this technology to hematopoietic stem and progenitor cells (HSPCs) ( Avagyan et al, 2021 ). Works from McGarvey et al (2022) investigated changes in chromatin modification on a single cell level between the cloche mutant and wild-type cells. cloche mutants carry a mutation in the transcription factor Npas4l ( Reischauer et al, 2016 ) and display a complete absence of vasculature, blood cells, and endocardium ( Stainier et al, 1995 ).…”

Section: Defining the Chromatin State Of Endothelial Cellsmentioning

confidence: 99%

Epigenetic Regulation of Endothelial Cell Lineages During Zebrafish Development—New Insights From Technical Advances

Panara

Monteiro

Koltowska

2022

Front. Cell Dev. Biol.

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Epigenetic regulation is integral in orchestrating the spatiotemporal regulation of gene expression which underlies tissue development. The emergence of new tools to assess genome-wide epigenetic modifications has enabled significant advances in the field of vascular biology in zebrafish. Zebrafish represents a powerful model to investigate the activity of cis-regulatory elements in vivo by combining technologies such as ATAC-seq, ChIP-seq and CUT&Tag with the generation of transgenic lines and live imaging to validate the activity of these regulatory elements. Recently, this approach led to the identification and characterization of key enhancers of important vascular genes, such as gata2a, notch1b and dll4. In this review we will discuss how the latest technologies in epigenetics are being used in the zebrafish to determine chromatin states and assess the function of the cis-regulatory sequences that shape the zebrafish vascular network.

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Singling out how genes are regulated during development

Burgess¹

2022

Cell Genomics

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Single-cell-resolved dynamics of chromatin architecture delineate cell and regulatory states in zebrafish embryos

Cited by 14 publications

References 117 publications

Multiomic atlas with functional stratification and developmental dynamics of zebrafish cis-regulatory elements

Multiomic atlas with functional stratification and developmental dynamics of zebrafish cis-regulatory elements

Epigenetic Regulation of Endothelial Cell Lineages During Zebrafish Development—New Insights From Technical Advances

Singling out how genes are regulated during development

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