Phylogenetic fate mapping

Abstract

Cell fate maps describe how the sequence of cell division, migration, and apoptosis transform a zygote into an adult. Yet, it is only in Caenorhabditis elegans where microscopic observation of each cell division has allowed for construction of a complete fate map. More complex, and opaque, animals prove less yielding. DNA replication, however, generates somatic mutations. Consequently, multicellular organisms comprise mosaics where most cells acquire unique genomes that are potentially capable of delineating their ancestry. Here we take a phylogenetic approach to passively retrace embryonic relationships by deducing the order in which mutations have arisen during development. We show that polyguanine repeat DNA sequences are particularly useful genetic markers, because they frequently change length during mitosis. To demonstrate feasibility, we phylogenetically reconstruct the lineage of cultured mouse NIH 3T3 cells based on mutations affecting the length of polyguanine markers. We then employ whole genome amplification to genotype polyguanine markers in single cells taken from a mouse and use phylogenetics to infer the developmental relationships of the sampled tissues. The result is consistent with the present understanding of embryogenesis and demonstrates the large scale potential of this method for producing a complete mammalian cell fate at the resolution of a single cell.

Fig. 1.

Known and reconstructed phylogeny of cultured NIH 3T3 cells, shown as rooted, rectangular phylograms. (A) Known phylogeny. (B) Phylogeny inferred from somatic mutation by using Bayesian method. Posterior probabilities indicated alongside corresponding nodes. (C) Simplified known tree, in which all but the root and terminal nodes are deleted. (D) Bayesian reconstruction from data set limited to sampling of the root and terminal nodes. Scale bar, in mitotic divisions, is applicable to all trees in the horizontal axis.

Fig. 2.

Examples of polyguanine marker genotype variation. Electropherograms of the root isolate of NIH 3T3 cell phylogeny aligned with derivatives obtained from various descendants. Allele lengths are indicated. Blue and green traces designate labeling with 6-FAM and HEX, respectively.

Fig. 3.

Cell fate map showing lineage relationships between different types of cells sampled from different anatomic regions of an adult mouse, depicted as an unrooted, rectangular, Bayesian-derived phylogram. Each terminal node is a single cell. Cells taken from the same site are denoted by a dash followed by a number. Cells from the kidney are colored in pink, heart in red, neurons in gray, parotid in yellow, and liver in green. The shading corresponds to laterality and subdivisions within each organ. Confidence values are indicated alongside their corresponding nodes. Scale bar records mitotic divisions along the horizontal axis. R., right; L., left.