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Published March 27, 2018 | public
Journal Article Open

Reconstructing a metazoan genetic pathway with transcriptome-wide epistasis measurements


RNA-sequencing (RNA-seq) is commonly used to identify genetic modules that respond to perturbations. In single cells, transcriptomes have been used as phenotypes, but this concept has not been applied to whole-organism RNA-seq. Also, quantifying and interpreting epistatic effects using expression profiles remains a challenge. We developed a single coefficient to quantify transcriptome-wide epistasis that reflects the underlying interactions and which can be interpreted intuitively. To demonstrate our approach, we sequenced four single and two double mutants of Caenorhabditis elegans. From these mutants, we reconstructed the known hypoxia pathway. In addition, we uncovered a class of 56 genes with HIF-1–dependent expression that have opposite changes in expression in mutants of two genes that cooperate to negatively regulate HIF-1 abundance; however, the double mutant of these genes exhibits suppression epistasis. This class violates the classical model of HIF-1 regulation but can be explained by postulating a role of hydroxylated HIF-1 in transcriptional control.

Additional Information

© 2018 National Academy of Sciences. Published under the PNAS license. Contributed by Paul W. Sternberg, February 6, 2018 (sent for review July 13, 2017; reviewed by Erik C. Andersen and Aviv Regev). Published ahead of print March 12, 2018. We thank Hillel Schwartz, Erich Schwarz, Jonathan Liu, Han Wang, and Porfirio Quintero for their advice throughout this project. This work was supported by the Howard Hughes Medical Institute, with whom P.W.S. is an investigator, and by the Millard and Muriel Jacobs Genetics and Genomics Laboratory at Caltech. Strains were provided by the Caenorhabditis Genetics Center, which is funded by the NIH Office of Research Infrastructure Programs (P40 OD010440). Author contributions: D.A.-A., C.P.R., and P.W.S. designed research; D.A.-A., C.P.R., and B.A.W. performed research; D.A.-A., B.A.W., and B.J.W. contributed new reagents/analytic tools; D.A.-A. analyzed data; and D.A.-A., C.P.R., and P.W.S. wrote the paper. Reviewers: E.C.A., Northwestern University; and A.R., Broad Institute. The authors declare no conflict of interest. Data deposition: The data reported in this paper have been deposited in the Gene Expression Omnibus (GEO) database, https://www.ncbi.nlm.nih.gov/geo (accession no. GSE97355). Raw reads were deposited in the Short Read Archive (accession no. SRP100886). All code and processed data are available in the GitHub database, https://github.com/WormLabCaltech/mprsq. Our Jupyter Notebook and interactive graphs for this project can be found at https://wormlabcaltech.github.io/mprsq/, or in SI Appendix. This article contains supporting information online at www.pnas.org/lookup/suppl/doi:10.1073/pnas.1712387115/-/DCSupplemental.

Attached Files

Submitted - 112920.1.full.pdf

Published - E2930.full.pdf

Supplemental Material - pnas.1712387115.sapp.pdf

Supplemental Material - pnas.1712387115.sd01.csv

Supplemental Material - pnas.1712387115.sd01.xlsx


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