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Eric Johnson

Eric Johnson

Associate Professor, Biology
Member, IMB

Ph.D., University of Iowa
B.A., Grinnell College

Email
Office: Streisinger Hall Room 312
Office Phone: 541-346-5183
Lab: Streisinger Hall Room 315
Lab Phone: 541-346-5994

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Research Interests

Genomics

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.

johnson research 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.

Gene regulation

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.

johnson research 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.

Recent publications

(pulled from pubmed)

Recent publications

(pulled from pubmed)

Rapid identification and recovery of ENU-induced mutations with next-generation sequencing and Paired-End Low-Error analysis.
Pan L, Shah AN, Phelps IG, Doherty D, Johnson EA, Moens CB
BMC Genomics 2015 Feb 14;16:83
Massively parallel characterization of restriction endonucleases.
Kamps-Hughes N, Quimby A, Zhu Z, Johnson EA
Nucleic Acids Res 2013 Jun;41(11):e119
Sgt1 acts via an LKB1/AMPK pathway to establish cortical polarity in larval neuroblasts.
Andersen RO, Turnbull DW, Johnson EA, Doe CQ
Dev Biol 2012 Mar 1;363(1):258-65
Construction and application for QTL analysis of a Restriction Site Associated DNA (RAD) linkage map in barley.
Chutimanitsakun Y, Nipper RW, Cuesta-Marcos A, Cistué L, Corey A, Filichkina T, Johnson EA, Hayes PM
BMC Genomics 2011 Jan 4;12:4
Mapping with RAD (restriction-site associated DNA) markers to rapidly identify QTL for stem rust resistance in Lolium perenne.
Pfender WF, Saha MC, Johnson EA, Slabaugh MB
Theor Appl Genet 2011 May;122(8):1467-80
A survey of new temperature-sensitive, embryonic-lethal mutations in C. elegans: 24 alleles of thirteen genes.
O'Rourke SM, Carter C, Carter L, Christensen SN, Jones MP, Nash B, Price MH, Turnbull DW, Garner AR, Hamill DR, Osterberg VR, Lyczak R, Madison EE, Nguyen MH, Sandberg NA, Sedghi N, Willis JH, Yochem J, Johnson EA, Bowerman B
PLoS One 2011 Mar 1;6(3):e16644
Local de novo assembly of RAD paired-end contigs using short sequencing reads.
Etter PD, Preston JL, Bassham S, Cresko WA, Johnson EA
PLoS One 2011 Apr 13;6(4):e18561
HIF takes it up a notch.
Johnson EA
Sci Signal 2011 Jul 12;4(181):pe33
Rapid mapping and identification of mutations in Caenorhabditis elegans by restriction site-associated DNA mapping and genomic interval pull-down sequencing.
O'Rourke SM, Yochem J, Connolly AA, Price MH, Carter L, Lowry JB, Turnbull DW, Kamps-Hughes N, Stiffler N, Miller MR, Johnson EA, Bowerman B
Genetics 2011 Nov;189(3):767-78
SNP discovery and genotyping for evolutionary genetics using RAD sequencing.
Etter PD, Bassham S, Hohenlohe PA, Johnson EA, Cresko WA
Methods Mol Biol 2011;772:157-78
Population genomics of parallel adaptation in threespine stickleback using sequenced RAD tags.
Hohenlohe PA, Bassham S, Etter PD, Stiffler N, Johnson EA, Cresko WA
PLoS Genet 2010 Feb 26;6(2):e1000862
Expression profiling of zebrafish sox9 mutants reveals that Sox9 is required for retinal differentiation.
Yokoi H, Yan YL, Miller MR, BreMiller RA, Catchen JM, Johnson EA, Postlethwait JH
Dev Biol 2009 May 1;329(1):1-15
Rapid SNP discovery and genetic mapping using sequenced RAD markers.
Baird NA, Etter PD, Atwood TS, Currey MC, Shiver AL, Lewis ZA, Selker EU, Cresko WA, Johnson EA
PLoS One 2008;3(10):e3376
Recent advances in crustacean genomics.
Stillman JH, Colbourne JK, Lee CE, Patel NH, Phillips MR, Towle DW, Eads BD, Gelembuik GW, Henry RP, Johnson EA, Pfrender ME, Terwilliger NB
Integr Comp Biol 2008 Dec;48(6):852-68
Rapid and cost-effective polymorphism identification and genotyping using restriction site associated DNA (RAD) markers.
Miller MR, Dunham JP, Amores A, Cresko WA, Johnson EA
Genome Res 2007 Feb;17(2):240-8
RAD marker microarrays enable rapid mapping of zebrafish mutations.
Miller MR, Atwood TS, Eames BF, Eberhart JK, Yan YL, Postlethwait JH, Johnson EA
Genome Biol 2007;8(6):R105
High-density detection of restriction-site-associated DNA markers for rapid mapping of mutated loci in Neurospora.
Lewis ZA, Shiver AL, Stiffler N, Miller MR, Johnson EA, Selker EU
Genetics 2007 Oct;177(2):1163-71
Identification and function of hypoxia-response genes in Drosophila melanogaster.
Liu G, Roy J, Johnson EA
Physiol Genomics 2006 Mar 13;25(1):134-41