THE BLOOM LAB
OUR MISSION
The lab is dedicated to uncovering the fundamental biophysical and molecular principles governing genome organization, chromosomal mechanics, and nuclear architecture, with an emphasis on how mechanical forces, structural transitions, and spatial organization contribute to genome stability and cellular function.
OUR FOCUS
Centromere biology and chromosome fragility, especially under mechanical stress and genomic perturbation.
Kinetochore and spindle mechanics, including how force and chromatin structure contribute to chromosome segregation.
Pericentromeric and nucleolar compartmentalization, including the role of DNA-protein and RNA-mediated phase separation.
Polymer physics of chromatin, including how transient crosslinking and chromatin network properties drive nuclear organization and condensate formation.
These studies combine live-cell imaging, molecular genetics, and statistical physics modeling to reveal how chromatin behaves as a responsive and mechanically active material in space and time.
WHY IT MATTERS
This research redefines how we understand genome regulation—not merely as a biochemical code, but as a dynamic, physical system responsive to force, topology, and emergent material properties. Insights into centromere fragility, condensate formation, and chromatin mechanics help explain:
- How cells maintain genomic stability under stress.
- Why certain genome regions (like centromeres and rDNA) are hotspots for fragility and repair.
- How nuclear architecture adapts in development, disease, and evolution.
- Fundamental mechanisms behind diseases such as cancer, where chromosomal instability and altered nuclear mechanics play critical roles.
By integrating molecular cell biology with polymer physics and systems modeling, the lab contributes to a paradigm shift in how we conceptualize the genome—not just as information, but as matter governed by the laws of physics.
Current Projects:
(Undergraduate authors in bold)
– Discovery that centromeres are stress-induced chromosome fragile sites.
Chromosomes with two centromeres provide a unique opportunity to study chromosome breakage and DNA repair using completely endogenous cellular machinery. We found that the rate of appearance of DNA repair products resulting from homology-based mechanisms exceeds the expected rate based on their limited centromere homology (340 bp) and distance from one another (up to 46.3 kb). To identify whether DNA breaks originate in the centromere, we introduced 12 single-nucleotide polymorphisms (SNPs) into one of the centromeres. Analysis of the distribution of SNPs in the recombinant centromeres reveals that recombination was initiated with about equal frequency within the conserved centromere DNA elements CDEII and CDEIII of the two centromeres. The conversion tracts range from about 50 bp to the full length of the homology between the two centromeres (340 bp). Breakage and repair events within and between the centromeres can account for the efficiency and distribution of DNA repair products. We proposed that in addition to providing a site for kinetochore assembly, the centromere may be a point of stress relief in the face of genomic perturbations.
The centromere has been reported to be wrapped in a non-canonical right-handed turn around a histone core containing the centromere specific histone H3. The reduced number of negative turns of centromere DNA around the centromere-specific histone core is based on comparison to the number of turns observed in plasmids containing function-inactivating point mutations in the centromere. We discovered that the difference between plasmids with mutant vs. wildtype centromeres reflects the propensity of the mutant centromere DNA to unwind. The energy from supercoiling drives the AT-rich mutant centromere into a locally unwound state. Supercoiling energy is not sufficient to drive the wtCEN into an unwound state due to the binding of kinetochore proteins. In situations such as dicentric chromosomes where tension exceeds the threshold for nucleosome binding, nucleosome release at the centromere renders the AT-rich centromere susceptible to rapid unwinding and nucleolytic attack.
Cook, D., Kozmin, S.G., Yeh, E., Petes, T.D., and Bloom K., (2024) Dicentric chromosomes are resolved through breakage and repair at their centromeres. In Chromosoma doi: 10.1007/s00412-023-00814-6.
Kolbin D., Locatelli, M., Stanton J., Kesselman, K., Kokkanti A., Li, J., Yeh, E. and Bloom, K. (2025) Centromeres are stress-induced fragile sites Current Biology 2025 Mar 24;35(6):1197-1210.e4. doi: 10.1016/j.cub.2025.01.055.
– Discovery that centromeres are stress-induced chromosome fragile sites.
The pericentric bottlebrush exerts force on the kinetochore. The pericentric bottlebrush provides a mechanism for building tension between sister kinetochores. Several aspects of the spatial distribution of kinetochore proteins and their response to perturbation lack a mechanistic understanding. Changes in physical parameters of bottlebrush, DNA stiffness, and DNA loops directly impact the architecture of the inner kinetochore. The Lawrimore et al. (2022) study reveals that the bottlebrush is an active participant in building tension between sister kinetochores and proposes a mechanism for chromatin feedback directly to the kinetochore.
The centromeres on 16 chromosomes that comprise the haploid karyotype of Saccharomyces cerevisiae contribute to organization of the bottlebrush. In cells with a two chromosome karyotype, both the spindle microtubules and chromatin bottlebrush are disorganized and exhibit greater variation in form relative to the 16-Chromosome cells. The kinetochore is re-organized, such that inner centromere components (Cse4 and Ame1) are disproportionally expanded relative to the number of chromosomes and relative to the outer kinetochore. Furthermore, coordination of kinetochore and pole separation representing Anaphase A and B is lost in the two-chromosome strain. The Kolbin et al. (2025) studies reveal the plasticity of kinetochore organization and mitotic spindle function, a feature observed in centromere DNA organization and kinetochores throughout phylogeny.
Lawrimore, J., de Larminat, S., Cook, D., Friedman, B., Doshi, A.,Yeh, E., and Bloom K. (2022) Polymer models reveal how chromatin modification can modulate force at the kinetochore. Molecular Biology of the Cell 10.1091/mbc.E22-02-0041.
Kolbin, D., Stanton, J., Kokkanti, A., Yeh, E. and Bloom, K. The centromere bottlebrush requires a multi-microtubule attachment In Molecular Biology of the Cell 2025 (in press).
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– The rDNA is Biomolecular Condensate Formed by Polymer-Polymer Phase Separation and is Sequestered in the Nucleolus by Transcription and R-loops.
RNA cross-linking keeps the rDNA polymer-polymer phase miscible with the proteinaceous liquid-liquid phase. In budding yeast, the rDNA behaves like a condensate formed by polymer-polymer phase separation, while ribonucleoproteins behave like a condensate formed by liquid-liquid phase separation. Upon repression of transcription, ribonucleoproteins form a single, stable droplet that excludes rDNA from its center. Degradation of RNA-DNA hybrid structures, known as R-loops, by overexpression of RNase H1 also results in the physical exclusion of the rDNA locus from the nucleolar center. These studies reveal RNA as a critical cross-linker that encapsulates rDNA in the nucleolar condensate.
Lawrimore, J., Kolbin, D., Stanton, J., Khan, M., de Larminat, S., Lawrimore, C., Yeh, E., Bloom, K. (2021) The rDNA is Biomolecular Condensate Formed by Polymer-Polymer Phase Separation and is Sequestered in the Nucleolus by Transcription and R-loops. Nucl. Acids Res. 49(8):4586-4598. doi: 10.1093/nar/gkab229.
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