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C. Elegans Exhibits Coordinated Oscillation in Gene Expression During Development

32 Pages Posted: 8 Apr 2018 Publication Status: Under Review

See all articles by Luke A. D. Hutchison

Luke A. D. Hutchison

Massachusetts Institute of Technology (MIT)

Bonnie Berger

Massachusetts Institute of Technology (MIT)

Isaac Kohane

Harvard Children's Hospital

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Abstract

The advent of automated cell lineaging and the ability to track gene expression at single‐cell resolution in vivo in C. elegans has yielded a dramatically more complete view into developmental processes. We present a novel meta‐analysis of the EPIC single‐cell‐resolution gene expression dataset of Bao, Murray, Waterston et al., and show that a linear combination of the expression levels of the developmental genes in that dataset is strongly correlated with the wall‐ clock developmental age of the organism during early development, irrespective of the cell division rate of different cell lineages. We uncover a pattern of collective sinusoidal oscillation in gene expression, with multiple dominant sinusoidal frequencies, pointing to the existence of a global coordinated mechanism governing the timing of gene expression during development. We furthermore present a new method derived from Fisher's Discriminant Analysis that can be used to produce sinusoidal oscillations of any frequency and phase using just a linear weighting of the expression patterns of the genes in this dataset, strengthening the view that oscillatory timing mechanisms play an important role in development. The Fisher's Discriminant Analysis method also constitutes a generally useful tool for identifying the differential gene expression patterns that most strongly separate two distinct phenotypic or developmental traits.

Suggested Citation

Hutchison, Luke A. D. and Berger, Bonnie and Kohane, Isaac, C. Elegans Exhibits Coordinated Oscillation in Gene Expression During Development (2018). Available at SSRN: https://ssrn.com/abstract=3155649 or http://dx.doi.org/10.2139/ssrn.3155649
This version of the paper has not been formally peer reviewed.

Luke A. D. Hutchison

Massachusetts Institute of Technology (MIT)

77 Massachusetts Avenue
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Bonnie Berger (Contact Author)

Massachusetts Institute of Technology (MIT) ( email )

77 Massachusetts Avenue
50 Memorial Drive
Cambridge, MA 02139-4307
United States

Isaac Kohane

Harvard Children's Hospital

300 Longwood Avenue, Enders-6
Boston, MA 02115
United States

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