B.A. Columbia Univ. (2014)
6th Year MSTP
4th Year Grad Student
Christopher Vakoc, MD-PhD Professor at CSHL
While tRNAs and the genetic code have been known for over half a century, only recently have
tRNAs been implicated in pathways outside protein synthesis. An emerging area of research
involves the study of tRNA fragments (tRFs), their biogenesis, and function. Although previously
thought to be the result of degradation, tRFs are abundant in many tissues and have important
biological functions. We found that fragments derived from the 3’-end of mature tRNAs (3’-tRFs)
are highly abundant in the early embryo when cells undergo epigenetic reprogramming and
inhibit long terminal repeat (LTR)-retroelements released from repressive chromatin. However,
3-tRF biogenesis is still poorly understood and has yet to be examined in context of tRNA
expression. To this end, we have optimized a hydrolysis-based sequencing approach to profile
both tRNA and sRNA populations from human cell lines. RNA is initially size selected for either
tRNAs (60-80 nt) or sRNAs (11-40 nt). Previous studies have shown partial alkaline hydrolysis
to reduce secondary structure and nucleotide modifications, allowing for sRNA library
preparation and greatly improving read coverage of tRNAs. Our preliminary data suggests a
correlation between parent tRNA abundance and the resulting 3’-tRF. We are currently
examining this relationship in context of cell cycle regulation.
Lama, L., Adura, C., Xie, W., Tomita, D., Kamei, T., Kuryavyi, V., Gogakos, T., Steinberg, J. I.,
Miller, M., Ramos-Espiritu, L., Asano, Y., Hashizume, S., Aida, J., Imaeda, T., Okamoto, R.,
Jennings, A. J., Michino, M., Kuroita, T., Stamford, A., Gao, P., Meinke, P., Glickman, F. J.,
Patel, D. J. & Tuschl, T. Development of human cGAS-specific small-molecule inhibitors for
repression of dsDNA-triggered interferon expression. Nat Commun 10, 2261 (2019).
Vincent, J., Adura, C., Gao, P., Luz, A., Lama, L., Asano, Y., Okamoto, R., Imaeda, T., Aida, J.,
Rothamel, K., Gogakos, T., Steinberg, J., Reasoner, S., Aso, K., Tuschl, T., Patel, D. J.,
Glickman, F. J. & Ascano, M. Small molecule inhibition of cGAS reduces interferon expression
in primary macrophages from autoimmune mice. Nat Commun 8, 750 (2017).
Wu, J. W., Herman, M., Liu, L., Simoes, S., Acker, C. M., Figueroa, H., Steinberg, J. I.,
Margittai, M., Kayed, R., Zurzolo, C., Paolo, G. & Duff, K. E. Small Misfolded Tau Species Are
Internalized via Bulk Endocytosis and Anterogradely and Retrogradely Transported in Neurons.
J Biol Chem 288, 1856–1870 (2013).
Flores, G. E., Campbell, J. H., Kirshtein, J. D., Meneghin, J., Podar, M., Steinberg, J. I.,
Seewald, J. S., Tivey, M., Voytek, M. A., Yang, Z. K. & Reysenbach, A. Microbial community
structure of hydrothermal deposits from geochemically different vent fields along the
Mid‐Atlantic Ridge. Environ Microbiol 13, 2158–2171 (2011).