Whole-organism lineage tracing by combinatorial and cumulative genome editing
Aaron McKenna,Gregory M. Findlay,James A. Gagnon,Marshall S. Horwitz,Alexander F. Schier,Jay Shendure,Jay Shendure +6 more
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TLDR
It is shown that combinatorial, cumulative genome editing of a compact barcode can be used to record lineage information in multicellular systems and that rich, systematically generated maps of organismal development will advance the understanding of development in both healthy and disease states.Abstract:
Multicellular systems develop from single cells through distinct lineages. However, current lineage-tracing approaches scale poorly to whole, complex organisms. Here, we use genome editing to progressively introduce and accumulate diverse mutations in a DNA barcode over multiple rounds of cell division. The barcode, an array of clustered regularly interspaced short palindromic repeats (CRISPR)/Cas9 target sites, marks cells and enables the elucidation of lineage relationships via the patterns of mutations shared between cells. In cell culture and zebrafish, we show that rates and patterns of editing are tunable and that thousands of lineage-informative barcode alleles can be generated. By sampling hundreds of thousands of cells from individual zebrafish, we find that most cells in adult organs derive from relatively few embryonic progenitors. In future analyses, genome editing of synthetic target arrays for lineage tracing (GESTALT) can be used to generate large-scale maps of cell lineage in multicellular systems for normal development and disease.read more
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The Human Cell Atlas
Aviv Regev,Aviv Regev,Aviv Regev,Sarah A. Teichmann,Sarah A. Teichmann,Sarah A. Teichmann,Eric S. Lander,Eric S. Lander,Eric S. Lander,Ido Amit,Christophe Benoist,Ewan Birney,Bernd Bodenmiller,Bernd Bodenmiller,Peter J. Campbell,Peter J. Campbell,Piero Carninci,Menna R. Clatworthy,Hans Clevers,Bart Deplancke,Ian Dunham,James Eberwine,Roland Eils,Roland Eils,Wolfgang Enard,Andrew Farmer,Lars Fugger,Berthold Göttgens,Nir Hacohen,Nir Hacohen,Muzlifah Haniffa,Martin Hemberg,Seung K. Kim,Paul Klenerman,Paul Klenerman,Arnold R. Kriegstein,Ed S. Lein,Sten Linnarsson,Emma Lundberg,Emma Lundberg,Joakim Lundeberg,Partha P. Majumder,John C. Marioni,John C. Marioni,John C. Marioni,Miriam Merad,Musa M. Mhlanga,Martijn C. Nawijn,Mihai G. Netea,Garry P. Nolan,Dana Pe'er,Anthony Phillipakis,Chris P. Ponting,Stephen R. Quake,Wolf Reik,Wolf Reik,Wolf Reik,Orit Rozenblatt-Rosen,Joshua R. Sanes,Rahul Satija,Ton N. Schumacher,Alex K. Shalek,Alex K. Shalek,Alex K. Shalek,Ehud Shapiro,Padmanee Sharma,Jay W. Shin,Oliver Stegle,Michael R. Stratton,Michael J. T. Stubbington,Fabian J. Theis,Matthias Uhlen,Matthias Uhlen,Alexander van Oudenaarden,Allon Wagner,Fiona M. Watt,Jonathan S. Weissman,Barbara J. Wold,Ramnik J. Xavier,Nir Yosef,Nir Yosef,Human Cell Atlas Meeting Participants +81 more
TL;DR: An open comprehensive reference map of the molecular state of cells in healthy human tissues would propel the systematic study of physiological states, developmental trajectories, regulatory circuitry and interactions of cells, and also provide a framework for understanding cellular dysregulation in human disease.
Journal ArticleDOI
Comprehensive single-cell transcriptional profiling of a multicellular organism
Junyue Cao,Jonathan S. Packer,Vijay Ramani,Darren A. Cusanovich,Chau Huynh,Ray A. M. Daza,Xiaojie Qiu,Choli Lee,Scott N. Furlan,Scott N. Furlan,Scott N. Furlan,Frank J. Steemers,Andrew Adey,Andrew Adey,Robert H. Waterston,Cole Trapnell,Jay Shendure,Jay Shendure +17 more
TL;DR: The authors profiled almost 50,000 single cells from an individual Caenorhabditis elegans larval stage and were able to identify and recover information from different, even rare, cell types and develop combinatorial indexing strategies to profile the transcriptomes of single cells or nuclei.
Journal ArticleDOI
Integrative single-cell analysis
Tim Stuart,Rahul Satija +1 more
TL;DR: Diverse approaches for integrative single-cell analysis are discussed, including experimental methods for profiling multiple omics types from the same cells, analytical approaches for extracting additional layers of information directly from scRNA-seq data and computational integration of omics data collected across different cell samples.
Journal ArticleDOI
CHOPCHOP v3: expanding the CRISPR web toolbox beyond genome editing
Kornel Labun,Tessa G. Montague,Maximilian Krause,Yamila N. Torres Cleuren,Håkon Tjeldnes,Eivind Valen +5 more
TL;DR: This major update of CHOPCHOP introduces functionality for targeting RNA with Cas13, which includes support for alternative transcript isoforms and RNA accessibility predictions, and incorporates new DNA targeting modes, including CRISPR activation/repression, targeted enrichment of loci for long-read sequencing, and prediction of Cas9 repair outcomes.
Journal ArticleDOI
The next generation of CRISPR-Cas technologies and applications.
TL;DR: The CRISPR–Cas toolkit has been expanding to include single-base editing enzymes, targeting RNA and fusing inactive Cas proteins to effectors that regulate various nuclear processes, and the new advances are considerably improving the authors' understanding of biological processes and are propelling CRISpr–Cas-based tools towards clinical use in gene and cell therapies.
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