Whole organism lineage tracing by combinatorial and cumulative genome editing

Details

• Alternative Title:
  Science
• Personal Author:
  McKenna, Aaron ; Findlay, Gregory M. ; Gagnon, James A. ; Horwitz, Marshall S. ; Schier, Alexander F. ; Shendure, Jay
• Description:
  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.
• Subjects:
  Animals Bacterial Proteins Cell Division Cell Lineage Cell Tracking CRISPR-Cas Systems DNA Barcoding, Taxonomic Endonucleases Genetic Engineering Mutation Single-Cell Analysis Stem Cells Zebrafish Zygote

  More +
• Source:
  Science. 353(6298):aaf7907.
• Pubmed ID:
  27229144
• Pubmed Central ID:
  PMC4967023
• Document Type:
  Journal Article
• Funding:
  MH105960/MH/NIMH NIH HHS/United States ; T32HL007312/HL/NHLBI NIH HHS/United States ; GM056211/GM/NIGMS NIH HHS/United States ; T32 HL007312/HL/NHLBI NIH HHS/United States ; R37 GM056211/GM/NIGMS NIH HHS/United States ; DP1HG007811/DP/NCCDPHP CDC HHS/United States ; U01 MH105960/MH/NIMH NIH HHS/United States ; R01 HD085905/HD/NICHD NIH HHS/United States ; R01 GM056211/GM/NIGMS NIH HHS/United States ; Howard Hughes Medical Institute/United States ; HD085905/HD/NICHD NIH HHS/United States ; T32 GM007266/GM/NIGMS NIH HHS/United States ; DP1 HG007811/HG/NHGRI NIH HHS/United States
• Volume:
  353
• Issue:
  6298
• Collection(s):
  CDC Public Access
• Main Document Checksum:
  urn:sha256:60445fbce47709d3d610dc90ad810c4d9d278e15f4a1b64c9236408067ccf82f
• Download URL:
  https://stacks.cdc.gov/view/cdc/40556/cdc_40556_DS1.pdf
• File Type:
  [PDF - 1.38 MB ]