1. The document describes research on genetic instability in the rDNA regions of Schizosaccharomyces pombe (S. pombe) mutant strains called T7. Pulsed-Field Gel Electrophoresis shows expansion of rDNA on chromosome III in T7. 2. Whole genome sequencing identified 11 point mutations in T7, including in genes abp1, gcn5, and cdc22 that genetically interact with proteins important for stability of Replication Fork Barriers in rDNA. Dysfunction of these barriers could lead to double-stranded breaks and recombination events driving rDNA expansion. 3. Further experiments on T7 cultures aim to characterize rDNA size changes over time and

1. Nicholas DiBenedetto
Determining the Dynamics of Genomic Instability in
T7 Schizosaccharomyces pombe Mutants
Nicholas DiBenedetto and Daniel Broek, Ph.D.
Abstract
Genetic instability has been shown in many different types of human
cancers, consisting of alterations to nucleic acid sequence or
rearrangement of chromosomal material. Ribosomal DNA (rDNA) in
eukaryotic genomes are repeating regions that are responsible for
ribosome structure and function. Due to their highly transcribed nature,
rDNA sites are very fragile and prone to breakage, and subsequent fusion
or recombination of rDNA has been suggested in cancer and other genetic
disorders such as Robertsonion translocations, hematologic malignancies,
and neurodegenerative disorders (1,2,3). In an effort to prevent double
stranded breakages, rDNA is replicated unidirectionally (in the same
direction as transcription), so as to prevent collision of replication and
transcription machinery. Unidirectional replication is achieved via
replication fork barriers (RFBs) which are found in each rDNA repeat. In our
lab, strains of Schizosaccharomyces pombe (S. pombe) named the T series
were found to have expansion of rDNA material. Pulsed-Field Gel
Electorphoresis (PFGE) was done to show the expansion of rDNA on
chromosome III. The current hypothesis is that T7 (a strain of T series)
harbors mutations that affect the stability of rDNA. The two theories that
explain the mechanism by which expansion of rDNA occurs are as follows;
(1) double stranded breaks and recombination occur on two different
chromosome IIIs (diploid) and are ligated together via non-homologous end
joining (NHEJ), or (2) double stranded breaks at rDNA repeat sites causes
unequal crossover between sister chromatids. In support of these
hypotheses, certain genes that were found to have point mutations in the T
series, such as CENP-B homolog apb1 and gcn5, genetically interact with
proteins sap1 and reb1 which are important to the stability of RFBs in S.
pombe (4,5).
ScaI Restriction Enzyme
ScaI restriction enzyme digests DNA on chromosomes I, II, and III in S. pombe into very
small fragments, leaving just the rDNA from chromosome III. This allows us to visualize
the rDNA via PFGE and asses whether or not expansion of rDNA material is occurring.
Point Mutations in T Series Affecting Genetic Instability
Gene Protein Function
Abp1 CenP-B centromere binding protein Genetic interaction with reb1 and
pnk1 (kinase involved in DNA
repair)
Gcn5 SAGA complex histone deacetylase Genetic interaction with sap1, reb1
(RFB stability proteins), rad51, and
pnk1
Cdc22 Ribonucleotide reductase Mutants exhibit depleted dNTP
pool resulting in RFB collapse and
DS breaks
Whole genome sequencing revealed 11 point mutations (3 show here) that may
affect the stability of RFBs in rDNA.
T7 Banding Patterns
PFGE of T7 ScaI RE Digests
Models of rDNA Expansion and Contraction
Replication Fork Barriers
S. pombe contain 100s of rDNA repeats at the ends of chr III. Replication occurs bidirectionally at
autonomous replication sites (ars), however RFBs ensure that replication only proceeds in a unidirectional
manner. RFBs ensure that replication and transcription occur in the same direction so that they do not
collide and cause DSB. Sap1 and reb1 proteins interact with the RFB and help to stabilize it. If the mutant
genes identified in the T series interact with sap1 and reb1, then it could cause RFB collapse and
subsequent DSBs.
References
1) Stimpson, K. M., Sullivan, L. L., Kuo, M. E., & Sullivan, B. A. (2014). Nucleolar Organization, Ribosomal DNA Array Stability, and Acrocentric Chromosome Integrity Are Linked to Telomere Function. PLoS
ONE, 9
2) Kobayashi, S., Taki, T., Nagoshi, H., Chinen, Y., Yokokawa, Y., Kanegane, H. ... Taniwaki, M. (2014). Identification of novel fusion genes with 28S ribosomal DNA in hematologic malignancies. International
Journal of Oncology, 44, 1193-1198.
3) Qiao, Y., Mondal, K., Trapani, V., Wen, J., Carpenter, G., Wildin, R., Price, E. M., Gibbons, R. J., Eichmeyer, J., Jiang, R., DuPont, B., Martell, S., Lewis, S. M. E., Robinson, W. P., O'Driscoll, M., Wolf, F. I.,
Zwick, M. E. and Rajcan-Separovic, E. (2014), Variant ATRX Syndrome with Dysfunction of ATRX and MAGT1 Genes. Hum. Mutat., 35: 58–62.
4) Zaratiegui, M., Vaughn, M. W., Irvine, D. V., Goto, D., Watt, S., Bähler, J., … Martienssen, R. A. (2011). CENP-B preserves genome integrity at replication forks paused by Retrotransposon LTR. Nature,
469(7328), 112–115. doi:10.1038/nature09608
5) Ryan, C. J., Roguev, A., Patrick, K., Xu, J., Jahari, H., Tong, Z., … Krogan, N. J. (2012). Hierarchical modularity and the evolution of genetic interactomes across species. Molecular Cell, 46(5), 691–704. 8
Conclusions and Future Directions
2200
1600
1125
1020
945
825
785
750
680
610
585
450
365
285
225
2200
1600
1125
1020
945
825
785
750
680
610
585
450
365
285
225
T7 cultures were grown as shown to the right
to allow possible expansion/contraction of
rDNA repeats. DNA plugs were made from two
individual colonies and from the whole plate
(labeled A, B, and Plate) and assessed via PFGE
as shown above. The different banding
patterns of rDNA in T7 clearly indicate changes
of rDNA sizes. Different banding patterns
should be noted especially within the same
revertant strain, such as T7R3 and T7R5 (gel on
the right). In lanes where there are no clear
bands present, it is possible that there are
great amounts of heterogeneity, which would
result in a smear rather than a band. These
results support the hypothesis that T7 harbors
a mutation that affects rDNA stability.
1. Point mutations have been identified within the T series, some of which have been shown to
interact with proteins sap1 and reb1.
2. RFBs play a very important role in the stability of rDNA repeats during replication and transcription.
Collapse of the RFB leads to DSB and recombination of chromosome III in various different ways.
3. If genetic interactions occur between the mutant genes discovered in the T7 and sap1 and reb1,
then RFB collapse is much more probable, thus leading to abnormal rearrangement of rDNA.
4. Continuation of PFGE will be done to further analyze rDNA content in T7.
5. Hydroxyurea (HU) assays deplete cells of dNTPs, which causes a stall of replication machinery and
subsequent DSB. Cells with faulty RFBs would likely be sensitive to HU and therefore assays will be
done in the future.
Grow T7 12 days
Plate
Select 5 colonies
Grow 24 hours
Plate
Select 2 colonies and
pool of remaining
colonies from one plate
Prepare plugs and assess
via PFGE
T7R1
Single A
T7R2
Single A
T7R2
Plate
T7R3
Single A
T7R3
Single B
T7R4
Single B
T7R5
Single B
T7R5
Plate
Upper
Band
780 800 750 610 660 700 810 790
Lower
Band
390 395 380 370 370 385 410 425
The table above quantifies the different sizes of the bands in T7. Note that
lanes on the gel that did not show banding were omitted from the table.