Systematic identification of mammalian regulatory motifs' target genes and functions

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Abstract

We developed an algorithm, Lever, that systematically maps metazoan DNA regulatory motifs or motif combinations to sets of genes. Lever assesses whether the motifs are enriched in cis-regulatory modules (CRMs), predicted by our PhylCRM algorithm, in the noncoding sequences surrounding the genes. Lever analysis allows unbiased inference of functional annotations to regulatory motifs and candidate CRMs. We used human myogenic differentiation as a model system to statistically assess greater than 25,000 pairings of gene sets and motifs or motif combinations. We assigned functional annotations to candidate regulatory motifs predicted previously and identified gene sets that are likely to be co-regulated via shared regulatory motifs. Lever allows moving beyond the identification of putative regulatory motifs in mammalian genomes, toward understanding their biological roles. This approach is general and can be applied readily to any cell type, gene expression pattern or organism of interest.

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Figure 1: Lever schema.
Figure 2: Analysis of the time course of human skeletal muscle differentiation.
Figure 3: Lever screen of 101 myogenic gene sets using a dictionary of 174 motifs.
Figure 4: Experimental validation of computationally predicted CRMs.

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Acknowledgements

We thank E. Margulies and the ENCODE Multiple Sequence Alignment working group for generously allowing use of their phylogenetic tree before its publication; S. Asthana, S. Sunyaev, G. Kryukov, M. Berger, T. Siggers and A. Aboukhalil for helpful discussions; J. Chee, E. Mathewson and T. Sierra for technical assistance; S. Elledge, A. Friedman, T. Siggers, M. Berger and F. De Masi for critical reading of the manuscript; A. Donner (Brigham & Women's Hospital) for the generous gift of human lens epithelial cells; and K. Cichowski (Brigham & Women's Hospital) for kindly providing lentiviral reagents. This work was funded in part by a PhRMA Foundation Informatics Research Starter Grant (M.L.B.), a William F. Milton Fund Award (M.L.B.), a Harvard-MIT Division of Health Sciences & Technology (HST) Taplin Award (M.L.B.) and US National Institutes of Health (NIH) National Human Genome Research Institute (R01 HG002966 to M.L.B.). J.B.W. was supported in part by an NIH Training Grant T32 HL07627 and NIH Individual National Research Service Award F32 AR051287. A.A.P. was supported in part by a National Defense Science and Engineering Graduate Fellowship from the Department of Defense and an Athinoula Martinos Fellowship from HST. S.A.J. was supported in part by a US National Science Foundation Postdoctoral Research Fellowship in Biological Informatics.

Author information

J.B.W. participated in the experimental design, performed the experiments and participated in analysis of the results and drafting of the manuscript. A.A.P. conceived of the PhylCRM scoring algorithm, participated in programming PhylCRM and running PhylCRM analyses, the development of Lever, programming Lever, running Lever analyses and analyzing the results and drafting of the manuscript. S.A.J. optimized the performance and participated in programming PhylCRM, running PhylCRM analyses, development of Lever, programming Lever and running Lever analyses and in analysis of the results and drafting of the manuscript. F.S.H. assisted with programming PhylCRM and running PhylCRM analyses. J.L. assisted with the experiments. M.L.B. conceived of the study and participated in the study design, analysis of the results and drafting of the manuscript.

Correspondence to Martha L Bulyk.

Supplementary information

Supplementary Text and Figures

Supplementary figures 1–12, Supplementary Tables 1, 2, 4, Supplementary Methods, Supplementary Results (PDF 7182 kb)

Supplementary Table 3

Statistically significant GM pairs from Lever analyses. (XLS 3676 kb)

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