Associate Professor of Biology
B.A., Grinnell College;
Ph.D., University of Iowa
Member of: Institute of Molecular Biology
Office: Streisinger Hall Room 312
Lab: Streisinger Hall Room 315
The Johnson lab works on new applications for next-generation sequencing and studying the regulatory network controlling the response to low oxygen. When possible, we combine these interests in genomics and gene regulation.
We develop new molecular and computational methods to harness the rapidly-increasing power of next-generation sequencing. Our lab developed Restriction-site Associated DNA (RAD) sequencing, which is being used for trait mapping, creation of genetic maps, phylogeography, association and population structure studies. A variant called RAD paired-end contig sequencing is used to create high-quality genome assemblies by partitioning the sequence reads into manageable groups. We have also developed new methods for rapidly screening populations for mutations, an update to TILLING, and genome-wide methods for assaying enhancer activity.
RAD paired-end contigs are assembled from the randomly sheared fragment ends that sample the region around a restriction site. Sequences sharing a restriction site sequence are assembled into a contig that forgoes many of the problems of whole-genome assembly.
The response to low oxygen, or hypoxia, involves the regulation of many cellular pathways that shut down low priority cellular activity and increase stress responses. We carry out genome-wide studies to identify genetic targets of hypoxic regulation and how the regulatory network is organized. Using the fruit fly Drosophila as a model system, we have shown that HIF-1, the key transcription factor regulating the response to low oxygen, has connections to many other key signaling pathways in the cell that allow it to orchestrate the cellular response. Hypoxia is an important aspect of the pathology of heart attack and stroke, so understanding the regulatory network gives insight into potential therapeutic targets.
Drosophila tissue culture cells carrying a fluorescent reporter driven by a HIF-1 enhancer from the Heat shock factor gene is turned on by low oxygen stress and requires HIF-1.
A list of all Johnson lab publications can be found here.
Baird NA, Etter PD, Atwood TS, Currey MC, Shiver AL, Lewis ZA, Selker EU,Cresko WA, Johnson EA. Rapid SNP discovery and genetic mapping using sequenced RAD markers. PLoS ONE. 2008;3(10):e3376. Epub 2008 Oct 13.
Lewis ZA, Shiver AL, Stiffler N, Miller MR, Johnson EA, Selker EU. High-density detection of restriction-site-associated DNA markers for rapidmapping of mutated loci in Neurospora. Genetics. 2007 Oct;177(2):1163-71. Epub 2007 Jul 29.
Miller MR, Atwood TS, Eames BF, Eberhart JK, Yan YL, Postlethwait JH, Johnson EA. RAD marker microarrays enable rapid mapping of zebrafish mutations. Genome Biol. 2007;8(6):R105.
Miller MR, Dunham JP, Amores A, Cresko WA, Johnson EA. Rapid and cost-effective polymorphism identification and genotyping using restriction site associated DNA (RAD) markers. Genome Res. 2007 Feb;17(2):240-8.
Baird NA, Turnbull DW, Johnson EA. Induction of the heat shock pathway during hypoxia requires regulation of heatshock factor by hypoxia-inducible factor-1. J Biol Chem. 2006 Dec 15;281(50):38675-81.
Liu G, Roy J, Johnson EA. Identification and function of hypoxia-response genes in Drosophila melanogaster. Physiol Genomics. 2006 Mar 13;25(1):134-41.
Johnson, E., Estes, P., Crews, S., and Krasnow, M.A.. Conservation and function of the HIF-1 hypoxia response pathway in living Drosophila. Manuscript in preparation.
Hollich V, Johnson E, Furlong E, Beckmann B, Carlson J., Celniker S, Hoheisel J. (2004) Arraying the Drosophila genome; provision of a resource. Biotechniques, 2004 Aug;37(2):282-4.
Freeman MR, Delrow J, Kim J, Johnson E, Doe CQ. (2003) Unwrapping glial biology: Gcm target genes regulating glial development, diversification, and function. Neuron. 2003 May 22;38(4):567-80.
Cho N.K., L. Keyes, E. Johnson, J. Heller, L. Ryner, F. Karim, and M.A. Krasnow. (2002) Developmental control of blood cell migration by the Drosophila VEGF pathway. Cell 108:865-76.
Arbeitman, M., E. Furlong, F. Imam, E. Johnson, B. Null, B. Baker, M.A. Krasnow, M. Scott, R. Davis, and K. White. (2002) Gene Expression During the Life Cycle of Drosophila melanogaster. Science 297: 2270-5.
Johnson, E., J. Jarecki, and M.A. Krasnow. (1999) Oxygen regulation of airway branching in Drosophila is mediated by Branchless FGF. Cell 99:211-20.