Whole-organism lineage tracing by combinatorial and cumulative genome editing.

Science
Authors
Keywords
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.

Year of Publication
2016
Journal
Science
Volume
353
Issue
6298
Pages
aaf7907
Date Published
2016 Jul 29
ISSN
1095-9203
URL
DOI
10.1126/science.aaf7907
PubMed ID
27229144
PubMed Central ID
PMC4967023
Links
Grant list
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