Cell Identification and Cell Lineage Analysis - Caenorhabditis Elegans: Molecular Genetics and Development - page 324

There has been rapid recent progress in automation of cell identification and
lineage analysis. Cell lineage analysis in embryos can be partly automated as
discussed in detail below. Automatic cell lineage analysis in larval stages has so
far not been possible, largely due to the difficulty in immobilizing larvae in a
way that allows normal development. However, digital atlases of cell positions
at defined stages can be generated, allowing gene expression patterns to be
mapped semiautomatically ( Long et al., 2009 ). At present such atlases represent
65% of the nuclei in the L1 stage. However, many neuronal nuclei are too
closely spaced to be reliably identified by automated analysis. Thus, to identify
specific neuronal expression patterns a knowledge of the anatomy remains
indispensable.
II. Rationale
A. Analysis of Mutant Phenotypes
One of the most frequent goals in cell-lineage analysis is to address the develop-
mental basis of a specific phenotype, whether caused by mutation, RNAi, or some
other perturbation. For example, using cell type specific GFP reporters it is straight-
forward to screen for mutants affecting the number of cells that express a given
reporter ( Doitsidou et al., 2008; Kanamori et al., 2008 ). A change in the number of
expressing cells could have a number of causes and lineage analysis can resolve
these possibilities. For example, do excess GFP-expressing cells arise from ectopic
expression of the reporter or from an overproliferation of specific precursors? Does
failure to generate a given cell type reflect a cell fate transformation or an earlier
defect in the lineage?
B. Cell Division Pattern as the Focus of Interest
In some cases, the pattern of cell divisions itself is the focus of interest, especially
where no other molecular markers are available. For example, the role of the Wnt
ligand LIN-44 in cell polarity was deduced from its effects on the polarity of certain
cell divisions in the male tail ( Herman and Horvitz, 1994 ). The stage specificity of
cell-division patterns was critical in inferring the genetic control of developmental
timing in larval development ( Ambros and Horvitz, 1984 ). The regulative ability of
certain tissues to undergo compensatory growth after damage was studied using cell-
lineage analysis ( Sulston and White, 1980 ).
Stem-cell-like division is inherently polarized. The stem-cell-like behavior of
larval seam cells has been extensively analyzed by direct lineage analysis (e.g.
Nimmo et al., 2005 ). Analysis of cell-lineage mutants has also been important in
understanding the genetic basis of cell cycle control (e.g. Kostic and Roy, 2002;
Fukuyama et al., 2003 ).