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Steve Johnson

Associate Professor
Microbiology & Molecular Biology

3132 LSB
Provo, UT 84602

Dr. Steven M. Johnson joined the faculty of the Microbiology and Molecular Biology Department at Brigham Young University as an assistant professor in 2009, the same department from which he received his B.S. in Molecular Biology in 1994. After working for Dr. Raoul Nelson as a laboratory technician at the University of Utah’s Eccles Institute of Human Genetics from 1995 to 1997, Dr. Johnson discovered his love of teaching while pursuing a M.S. (’99) in molecular biology in the lab of Dr. Michael Breindl at San Diego State University. Having decided to stay in academia and become a professor, Dr. Johnson left San Diego for Yale where he worked with Dr. Frank Slack to earn his M.Phil. (’01) and Ph.D (’04) by studying microRNAs and discovering the regulation of the oncogene RAS by let-7 family microRNAs, providing evidence that microRNAs could act as tumor suppressors (Johnson et al, Cell 2005). In 2004, Dr. Johnson joined the lab of Dr. Andrew Fire at Stanford University School of Medicine where as a Fellow of the American Cancer Society (’05-’08) he studied the relationship between DNA sequence, nucleosome positioning, and gene expression; the same topic he and his group are currently researching in his own lab at BYU.

Research Interests
In my lab we study chromatin architecture by looking at nucleosome positioning and its relation to the underlying DNA sequence in the genome, with the goal of learning how to modulate chromatin architecture by subtly manipulating the underlying DNA sequence to regulate gene expression. We are using both in vivo (in live animals) and in vitro (in the test tube) approaches in our studies coupled with ultra-high-throughput DNA sequencing technologies. For these studies we use the nematode worm C. elegans (a common model organism for human genetics and disease). We are also using in vitro nucleosome reconstitution assays to define and test putative nucleosome attractive or repulsive sequences. These sequences can then be tested in vivo in the worm for their potential to regulate genic expression both temporally and spatially in C. elegans.

Because of the highly conserved nature of histone proteins within the domain Eukaryotae and the absolute conservation of the chemical structure of DNA between all forms of life, what we learn from these basic studies in the worm may enable us to subtly manipulate gene expression in human cells and tissues with the potential to overcome the universal problem of gene silencing which occurs with DNA-based disease treatments such as those seen in current applications of gene-therapy.

Stanford University School of Medicine, Postdoctoral Fellowship (2009)
Yale University, Molecular Biology, Ph.D. (2004)
Yale University, Molecular Biology, M.Phil. (2001)
San Diego State University, Molecular Biology, M.S. (1999)
Brigham Young University, Molecular Biology, B.Sc. (1994)

Honors and Awards
Brigham Young University: Phi Kappa Phi Faculty Initiate, ΦΚΦ Chapter 58
BYU Department of Microbiology and Molecular Biology: Teaching Award (Highest Students Ratings in a 500-level Course)
BYU Department of Microbiology and Molecular Biology: Research Award (Highest Impact Factor Journal Publication).
Karolinska Institutet, Stockholm, Sweden: Invited Nobel week seminar
Yale University: Exceptionally clear and effective poster presentation Award, MCDB Retreat
SDSU Biology Department: Outstanding Teaching Associate of 1999
American Society of Nephrology Annual Meeting: Blue Ribbon Protocol Award
Brigham Young University: Trustees’ Scholar and Scholarship
Arizona State University: Regents’ Scholarship, gratefully declined


Carter JL, Morales R, Johnson SM. 2018. Chemotaxis based enrichment for transgenic animals containing the rol-6 marker. microPublication Biology. 3.

Weber KS, Bridgewater LC, Jensen JL, Breakwell DP, Nielsen B, Johnson SM. 2018. Personal microbiome analysis improves student engagement and interest in Immunology, Molecular Biology, and Genomics undergraduate courses. PLoS One. 13(4):20 pages.

Kieffer-Kwon KR, Nimura K, Rao SS, Xu J, Jung S, Pekowska A, Dose M, Stevens E, Mathe E, Dong P, et al. 2017. Myc Regulates Chromatin Decompaction and Nuclear Architecture during B Cell Activation. Molecular Cell. 67(4):566-578.

Kempton CE, Weber KS, Johnson SM. 2017. Method to increase undergraduate laboratory student confidence in performing independent research. Journal of Microbiology & Biology Eudcation. 18(1).

Weber KS, Jensen JL, Johnson SM. 2015. Anticipation of personal genomics data enhances interest and learning environment in genomics and molecular biology undergraduate courses. PLoS One. 10(8):e0133486.

Kempton CE, Heninger JR, Johnson SM. 2014. Reproducibility and Consistency of In Vitro Nucleosome Reconstitutions Demonstrated by Invitrosome Isolation and Sequencing. PLoS One. 9(8):e103752.

Locke G, Haberman D, Johnson SM, Morozov AV. 2013. Global remodeling of nucleosome positions in C. elegans. BMC Genomics. 14:284.

Kundaje A, Kyriazopoulou-Panagiotopoulou S, Libbrecht M, Smith CL, Raha D, Winters EE, Johnson SM, Snyder MP, Batzoglou S, Sidow A. 2012. Ubiquitous heterogeneity and asymmetry of the chromatin environment at regulatory elements. Genome Research. 22:1735-1747.

Valouev A, Johnson SM, Boyd SD, Smith CL, Fire AZ, Sidow A. 2011. Determinants of nucleosome organization in primary human cells. Nature. 474:516-520.

Johnson SM. 2010. Painting a perspective on the landscape of nucleosome positioning. Journal of Biomolecular Structure and Dynamics. 27(6):795-802.

Valouev A, Ichikawa J, Tonthat T, Stuart J, Ranade S, Peckham H, Zeng K, Malek JA, Costa G, McKernan K, et al. 2008. A high-resolution, nucleosome position map of C. elegans reveals a lack of universal sequence-dictated positioning. Genome Research. 18:1051-1063.

Johnson SM, Tan FJ, McCullough HL, Riordan DP, Fire AZ. 2006. Flexibility and constraint in the nucleosome core landscape of Caenorhabditis elegans chromatin. Genome Research. 16:1505-1516.

Moreno-Herrero F, Seidel R, Johnson SM, Fire A, Dekker NH. 2006. Structural analysis of hyperperiodic DNA from Caenorhabditis elegans. Nucleic Acids Research. 34:3057-3066.

Esquela-Kerscher A, Johnson SM, Bai L, Saito K, Partridge J, Reinert KL, Slack FJ. 2005. Post-embryonic expression of C. elegans microRNAs belonging to the lin-4 and let-7 families in the hypodermis and the reproductive system. Developmental Dynamics. 234:868-877.

Johnson SM, Grosshans H, Shingara J, Byrom M, Jarvis R, Cheng A, Labourier E, Reinert KL, Brown D, Slack FJ. 2005. RAS is regulated by the let-7 microRNA family. Cell. 120:635-647.

Lin S, Johnson SM, Abraham M, Vella MC, Pasquinelli A, Gamberi C, Gottlieb E, Slack FJ. 2003. The C. elegans hunchback homolog, hbl-1 controls temporal patterning and is a probable microRNA target. Developmental Cell. 4:639-650.

Johnson SM, Lin S, Slack FJ. 2003. The time of appearance of the C. elegans let-7 microRNA is transcriptionally controlled utilizing a temporal regulatory element in its promoter. Developmental Biology. 259:364-379.

Ma X, Husain T, Peng H, Lin S, Mironenko O, Maun N, Johnson SM, Tuck D, Berliner N, Krause DS, et al. 2002. Development of a murine hematopoietic progenitor complementary DNA microarray using a subtracted complementary DNA library. Blood. 100:833-844.

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