David Zappulla

Assistant Professor

16A Biology East
410-516-8749 | Lab 410-516-7316

Lab Members

Dr. Zappulla's research focuses on telomerase, chromosomes, and long noncoding RNAs and their roles in senescence. David Zappulla earned his PhD at Stony Brook University, and did his postdoctoral work at the Howard Hughes Medical Institute (HHMI), University of Colorado at Boulder.

Telomerase, the chromosome-lengthening RNA-protein enzyme

Eukaryotic nuclear chromosomes are linear and therefore each have two ends, called telomeres. The enzyme telomerase synthesizes telomeric DNA by reverse transcription of an intrinsic RNA subunit and is required for completion of chromosome replication and genome stability. Telomerase is not normally expressed at appreciable levels in human tissues after early stages of development, and telomeres shorten with aging. However, in 90% of cancers, abnormal overproduction of telomerase permits unlimited cell proliferation. A major aim of our research is to understand the functions and coordination of the telomerase ribonucleoprotein (RNP) enzyme complex subunits as well as how telomerase activity at the ends of chromosomes is regulated.

Our previous research has shown that the budding yeast Saccharomyces telomerase RNA, TLC1, is evolving very rapidly – perhaps even more so than in other evolutionary lineages, and much faster than other essential ncRNAs in yeast. Why is this the case? Some insight into this question has also come from deletion analysis that has shown that two-thirds of S. cerevisiae telomerase RNA is dispensable for function in vivo and that protein-binding sites in the RNA (including essential ones) can even be repositioned to very unnatural locations in TLC1 with retention of function. The sum of the evidence has lead us to conclude that the large yeast telomerase RNA functions as a flexible scaffold or tether for protein subunits, thus defining a new class of RNPs.



Using phylogenetic information gleaned from alignments of Saccharomyces species' TLC1 genes and secondary structure software prediction algorithms, we determined the a model for yeast telomerase RNA (shown to right). The global folding of the RNA and its large size relative to the protein subunits begins to more clearly illustrate how TLC1 tethers, or scaffolds, telomerase protein subunits – note how the proteins decorate the three long arms in the figure above where subunits are drawn roughly to scale. Furthermore, it is satisfying to see how the core of the "Y" shaped structure brings the template nucleotides in close proximity to the binding site for telomerase reverse transcriptase (TERT, also called Est2p in yeast); see Zappulla and Cech, 2004, for the detailed model.

The most convincing evidence to date for the flexible scaffolding model for TLC1 is that the essential Est1p binding site can be repositioned to wildly different locations in the RNA with retention of function in vivo. Three of three positions tested (at nucleotide 220, 450 or 1033) all led to functional telomerase.

We also generated a miniaturized TLC1 where all of the rapidly evolving bulk of the three long arms in TLC1 were deleted and found that all of them can complement a tlc1 mutant in vivo. These "Mini-T" RNAs range in size from 500 to only 384 nts. However, the large size of wild-type TLC1 provides greater fitness in competitive growth experiments where wild-type cells are mixed with a strain expressing a miniaturized telomerase RNA called “Mini-T.” We are now determining the limits of flexible scaffolding of protein subunits by TLC1, as well as other major aspects of telomerase architecture.

The compact Mini-T RNA has afforded us the ability to reconstitute yeast telomerase activity in vitro, which has never been possible using the wild-type 1157-nt TLC1 (apparently because the big RNA misfolds in vitro, getting trapped in “alternate conformer hell”). Using this reconstituted yeast mini-telomerase in parallel with wild-type telomerase from yeast extracts and in-vivo experiments, we are investigating yeast telomerase activity. We have shown that the yeast core enzyme, comprised of the RNA and the telomerase reverse transcriptase subunit (TERT; Est2 in yeast), is intrinsically nonprocessive. However, like the human enzyme, yeast telomerase has been shown to readily add multiple telomeric repeats in vivo to a single telomere. Thus, we aim to understand what is required for significant repeat addition by yeast telomerase. One approach is to add proteins purified from heterologous expression systems into the reconstituted yeast telomerase system to test for functions of individual components. However, in addition to this "bottom-up" reductionist approach, we continue to employ "top-down" strategies by studying telomerase in yeast cells using genetic, molecular and cell biological techniques, as well as purifying telomerase regulatory factors from yeast directly.

Senescence and aging

With our knowledge of telomerase, we are now beginning to explore the relationship between telomerase, senescence and aging. Budding yeast is an excellent model to examine such relationships because of its tractability and because many of the basic factors involved have been identified. We are developing experimental conditions that allow us to ask new questions about the role of telomerase in both senescence and aging. These studies will certainly also teach us a great deal about the molecular biological contributions of these conserved processes to human cancer.

Chen, H., Xue, J., Hass, E.P., Churikov, D., Lemon, L.D., Luciano, P., Bertuch, A.A., Zappulla, D.C., Geli, V., Wu, J. and Lei, M. Structural insights into yeast telomerase recruitment to telomeres. (Under revision for Cell)

Hass, E.P. and Zappulla, D.C. (2017) Repositioning the Sm-binding site in S. cerevisiae telomerase RNA reveals RNP organizational flexibility and Sm-directed 3'-end formation. bioRxiv doi: https://doi.org/10.1101/167361. (Manuscript under revision at RNA)

Hass, E.P. and Zappulla, D.C. (2017) A yeast two-hybrid system based on CRISPR-dCas9 for investigating RNA-protein interactions. bioRxiv doi: https://doi.org/10.1101/139600

Niederer, R.O., Hass, E.P., and Zappulla, D.C. (2017) Long non-coding RNAs in the yeast S. cerevisiae in Long non-coding RNA in Biology. M.R.S. Rao, Editor. Switzerland: Springer Nature.

McMurdie, K.E., Mefford, M.A., Box, J.A., Baumann, P. and Zappulla, D.C.
S. pombe telomerase RNA, TER1: secondary structure and flexible-scaffold function. (Submitted)

Niederer, R.O., Papadopoulos, N. and Zappulla, D.C. (2016) Identification of novel noncoding transcripts in telomerase-negative yeast using RNA-seq. Scientific Reports 6, 19376; doi: https://doi.org/10.1038/srep19376

Mefford, M.A. and Zappulla, D.C. (2016) Physical connectivity mapping by circular permutation of human telomerase RNA reveals new regions critical for activity and processivity. Molecular and Cellular Biology 36:251–261.

Hass, E. and Zappulla, D.C. (2015) The Ku subunit of telomerase binds Sir4 to recruit telomerase to lengthen telomeres in S. cerevisiae. eLIFE 2015; 10.7554/eLife.07750 [Cover story] [JHU press release]

Lebo, K.J., Niederer, R.O., and Zappulla, D.C. (2015) A second essential function of the Est1-binding arm of yeast telomerase RNA. RNA 21:862–76.

Niederer, R.O. and Zappulla, D.C. (2015) Refined secondary structure models of the core of yeast and human telomerase RNAs directed by SHAPE. RNA 21:254–261.

Mefford, M.A., Rafiq, Q., and Zappulla, D.C. (2013) RNA connectivity requirements between conserved elements in the core of the yeast telomerase RNP. The EMBO Journal 32:2980-2993.

Lebo, K.J., and Zappulla, D.C. (2012) Stiffened yeast telomerase RNA supports RNP function in vitro and in vivo. RNA 18:1666–78.

Zappulla, D.C. (corresponding author), Goodrich, K.J., Arthur, J.R., Gurski, L.A., Denham, E.M., Stellwagen, A.E. and Cech, T.R. (2011) Ku can contribute to telomere lengthening in yeast at multiple positions in the telomerase RNP. RNA 17:298–311.

Zappulla, D.C.*1, Roberts, J.N.1, Goodrich, K.J., Cech, T.R. and Wuttke, D.S.* (2009) (*corresponding authors, 1first authors) Inhibition of yeast telomerase action by the telomeric ssDNA-binding protein, Cdc13p. Nucleic Acids Research 37:354–367.

Box, J.A., Bunch, J.T., Zappulla, D.C., Glynn, E.F., and Baumann, P. (2008) A flexible template boundary element in the RNA subunit of fission yeast telomerase. Journal of Biological Chemistry 283:24224–33.

Zappulla, D.C. and Cech, T.R. (2006) RNA as a flexible scaffold for proteins: yeast telomerase and beyond. Cold Spring Harbor Symposia on Quantitative Biology 71:217–224.

Zappulla, D.C., Maharaj, A.M., Connelly, J.J., Jockusch, R., and Sternglanz, R. (2006) Rtt107/Esc4 binds silent chromatin and DNA repair proteins using different BRCT motifs. BMC Molecular Biology 4:40–52.

Zappulla, D.C., Goodrich, K., and Cech, T.R. (2005) A miniature yeast telomerase RNA functions in vivo and reconstitutes activity in vitro. Nature Structural and Molecular Biology 12:1072–1077.

Zappulla, D.C. and Cech, T.R. (2004) Yeast telomerase RNA: a flexible scaffold for protein subunits. Proceedings of the National Academy of Sciences 101:10024–10029.

Andrulis, E.D., Zappulla, D.C., Alexieva-Botcheva, K., Evangelista, C. and Sternglanz, R. (2004) One-hybrid screens at the Saccharomyces cerevisiae HMR locus identify novel transcriptional silencing factors. Genetics 166:631–635.

Zappulla, D.C., Sternglanz, R., and Leatherwood, J. (2002) Control of DNA replication timing by a transcriptional silencer. Current Biology 12:869–875.

Andrulis, E.D.*, Zappulla, D.C.*, Ansari, A.*, Perrod, S., Laiosa, C.V., Gartenberg, M.R., and Sternglanz, R. (* equal contribution). (2002) Esc1, a nuclear periphery protein required for Sir4-based plasmid anchoring and partitioning. Molecular and Cellular Biology 22:8292–8301.

Andrulis, E.D., Neiman, A.M., Zappulla, D.C., and Sternglanz, R. (1998) Perinuclear localization of chromatin facilitates transcriptional silencing. Nature 394:592–595.

Tufarelli, C., Fujiwara, Y., Zappulla, D.C., and Neufeld, E.J. (1998) Hair defects and pup loss in mice with targeted deletion of the first cut repeat domain of the Cux/CDP homeoprotein gene. Developmental Biology 200:69–81.

Yandava, C.N., Zappulla, D.C., Korf, B.R., Neufeld, E.J. (1996) ARMS test for diagnosis of factor VLeiden mutation, a common cause of inherited thrombotic tendency. Journal of Clinical Laboratory Analysis 10:414-7.

Graduate Students

Evan P. Hass
Karen E. McMurdie

Undergraduate Students

Timothy Kistner
(Ms.) Alex Rittenhouse
Jenny Yang

Lab Alumni

Dr. Melissa A. Mefford (postdoc — now faculty at Luther College)
Dr. Rachel O. Niederer (PhD student — now postdoc with Wendy Gilbert, Yale)
Dr. Kevin J. Lebo (PhD student — now postdoc with Ron Weiss, MIT)
Erin (Gunter) Kirkby (PhD student — now medical writer/editor at American Urological Association)
Sean Gao (Master’s student — now medical student)