Johnson, Steven

Microbiology & Molecular Biology

Email: 6yzk|ktpFh{4kj{  (Email Form)

Website: http://stevenjohnsonlab.byu.edu

3132  LSB
Provo, UT 84602
(801) 422-9170

Associate Professor

Curriculum Vitae

 Biography
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.
 Education
  • Postdoctoral Fellowship, , Stanford University School of Medicine, 2009
  • Ph.D., Molecular Biology, Yale University, 2004
  • M.Phil., Molecular Biology, Yale University, 2001
  • M.S., Molecular Biology, San Diego State Univerity, 1999
  • B.S., Molecular Biology, Brigham Young University, 1994
 Experience

Academic - Post-Secondary
  • Associate Professor, Department of Microbiology and Molecular Biology, Brigham Young University, 2015-Present

Professional
  • Assistant Professor, Department of Microbiology and Molecular Biology, Brigham Young University, 2009-2015

 Memberships
  • Phi Kappa Phi, 2013-Present
  • The Genetics Society of America, 2011-Present
 Courses Taught

Summer 2017
  • MMBIO 494R: Mentored Research Section 010
Spring 2017
  • MMBIO 699R: Master's Thesis Section 010
  • MMBIO 799R: Dissertation Section 010
Winter 2017
  • MMBIO 468: Genomics Section 001
  • MMBIO 494R: Mentored Research Section 011
  • MMBIO 551R: Current Topics in MMBio Section 003
  • MMBIO 665: Geonomics Section 001
  • MMBIO 695R: Research Section 010
  • MMBIO 699R: Master's Thesis Section 011
  • MMBIO 799R: Dissertation Section 010
Fall 2016
  • MMBIO 441: Adv Molecular Biology Section 001
  • MMBIO 442: Adv Molecular Biology Lab Section 001
  • MMBIO 494R: Mentored Research Section 011
  • MMBIO 551R: Current Topics in MMBio Section 004
  • MMBIO 695R: Research Section 011
  • MMBIO 699R: Master's Thesis Section 011
  • MMBIO 799R: Dissertation Section 011

Selected Publications

Journal Articles

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. <website>

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). <website> doi:10.1128/jmbe.v18i1.1230

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. <website> doi:10.137/journal.pone.0133486

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. <website> doi:10.1371/journal.pone.0103752

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

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. <website>

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. <website>

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

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. <website>

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. <website>

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. <website>

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. <website>

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. <website>

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. <website>

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. <website>

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. <website>

Database

Snyder M, Raha D, Johnson SM, Winters EE, Sidow A, Weng Z, Smith C, Lacroute P, Cayting P, Kundaje A. 2011. Nucleosome Position by MNase-seq from ENCODE/Stanford/BYU. <website>

Presentations

Johnson SM. Nucleosome Positioning. Invited lecture, Department of Microbiology and Biochemistry, Rutgers University. Piscataway, New Jersey. 2015 .

Johnson SM. Nucleosome Positioning, Meta-Shapes and Transgene Expression. Invited seminar, Department of Molecular Biology and Biochemistry, Rutgers University. Piscataway, New Jersey. 2015 .

Johnson SM. Chromatin Architecture, Meta-Shapes and Transgene Expression. Invited seminar, MCDB Genetics Training Grant Seminar, Yale University. New Haven, CT. 2014 .

Johnson SM. Chromatin Patterns, Meta-Shapes and Transgene Expression. Invited Seminar: Biology Department Summer Seminar, San Diego State University. San Diego, CA. 2013 .

Johnson SM. Evaluating, Defining and Applying Sequence-Directed Nucleosome Positioning. Invited Seminar: Center for NanoBiotechnology and Life Sciences Research, Alabama State University. Montgomery, Alabama. 2013 .

Johnson SM. Unraveling The Patterns That Turn On Genes. Research Revolution '13. Orem, UT. 2013 .

Johnson SM. Nucleosome Organization and Positioning: From human Cells to C. elegans. The 2013 Southwest Regional Meeting of the Society for Developmental Biology. University of Utah, Salt Lake City, UT. 2013 .

Johnson SM. Nucleosome Organization and Positioning in Human Cells. 5th Annual GeneExpression Systems-Epigenomics, Sequencing & SNiPomics 2012 meeting. Harvard Medical School, Boston, Massachusetts. 2012 .

Johnson SM. Keynote Address: Chromatin Architecture-Turning On and Off Genes. 6th Annual Biotechnology Symposium. Mesa, Arizona. 2012 .

Johnson SM. Gene Therapy-Turning On and Off Genes. Research Revolution '12. Orem, Utah. 2012 .

Johnson SM. Chromatin Architecture, Nucleosome Positioning and Gene Regulation. Invited Seminar: Department of Physics and Biophysics Graduate Program Symposium, The Ohio State University. Columbus, Ohio. 2012 .

Johnson SM. Nucleosome Organization in Primary Human Cells. Keystone Symposia/Histone Code: Fact or Fiction?. Midway, UT. 2011 .

Johnson SM. Chromatin Architecture and Nucleosome Organization in Primary Human Cells. CTE Seminar Series. Mesa, Arizona. 2010 .

Johnson SM. Epigenetics, Chromatin Architecture and Nucleosome Positioning. Current Topics in Molecular Life Sciences Seminar. Provo, UT. 2010 .

Johnson SM, Valouev A, Boyd S, Smith C, Sidow A, Fire A. Genome-wide Mapping and Analysis of Nucleosome Positions in Multiple Human Tissues. Albany 2009: 16th Conversation, SUNY Albany. Albany, NY. 2009 .

Johnson SM. Contrasting methods of gene regulation: from small RNAs to the chromatin landscape. Invited Nobel Week Seminar: Department of Oncology. Stockholm, Sweden. 2006 .

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