Bio

Honors & Awards


  • K99/R00 Pathway to Independence Award, National Institutes of Health (2013 - 2018)
  • Katharine McCormick Advanced Postdoctoral Fellowship, Stanford School of Medicine (2012 - 2013)
  • Postdoctoral Fellowship, Helen Hay Whitney Foundation (2009 - 2012)
  • Dean's Postdoctoral Fellowship, Stanford University (2009)
  • Illick Graduate Fellowship, Albert J. Ryan Foundation (2006 - 2008)
  • Graduate Fellowship, National Science Foundation (2003 - 2006)

Education & Certifications


  • Ph.D., Harvard University, Genetics (2008)
  • B.Sc., Univ of California, Los Angeles, Molecular, Cell & Dev. Biology (2003)

Professional

Professional Interests


My long-term goal is to understand how specific chromosome interactions maintain genomic integrity. Although double strand DNA breaks (DSBs) damage the genome and their improper repair can drive genomic instability, DSBs are intentionally formed and then repaired with specific chromosome templates to promote proper chromosome segregation during meiosis, the specialized cell division used by sexually reproducing organisms to produce haploid gametes. Meiotic errors in chromosome segregation contribute to miscarriages, stillbirths, and birth defects. Furthermore, inaccurate DSB repair contributes to the development and progression of cancer. While repair of DSBs with the appropriate chromosome template is necessary for genomic integrity, very little is known as to how germ cells achieve this in the presence of other potential templates (sister chromatids vs. homologs).

The C. elegans model system has genetic, genomic, and cytological features that are ideal for analyzing meiotic DSB repair events. As DSB repair partner preference is not well-studied due to few assays available to detect intersister repair events during the specific stages of meiotic prophase, I have developed several tools in C. elegans that I utilize to detect and study the temporal, mechanistic, and dynamic features of these events.

ASSAYS FOR INTERSISTER REPAIR EVENTS. As the study of recombination pathway and partner preferences has been limited by few assays to assess sister chromatid repair outcomes, I am currently engineering and validating a set of sister chromatid repair assays to understand the relative utilization of both interhomolog and intersister recombination pathways during meiotic prophase progression. This assay system allows me to directly test for the presence of a switch in DSB repair partner preferences. In addition, the system enables the assessment of chromosome position and the roles of several meiotic chromosome structures and recombination proteins in promoting specific DSB repair outcomes and partner preferences.

LIVE IMAGING OF EARLY DSB REPAIR STAGES IN GERM CELLS. The relationships between cytologically observed foci indicating early DSB repair stages and different classes of repair events (crossovers vs. noncrossovers; interhomolog vs. intersister) are not well understood. I am investigating these relationships with a system I have developed to visualize the live dynamics of early DSBR stages in live germ cells. This live imaging assay system for early DSBR stages will be used to assess the dynamics of early DSB repair stages during different phases of meiotic prophase and to establish the roles of specific chromosome structures in regulating DSB formation and repair. Overall, these studies will reveal relationships in early DSB repair dynamics with changes in partner preference.

Publications

Journal Articles


  • Meiotic chromosome structures constrain and respond to designation of crossover sites. Nature Libuda, D. E., Uzawa, S., Meyer, B. J., Villeneuve, A. M. 2013; 502 (7473): 703-706

    Abstract

    Crossover recombination events between homologous chromosomes are required to form chiasmata, temporary connections between homologues that ensure their proper segregation at meiosis I. Despite this requirement for crossovers and an excess of the double-strand DNA breaks that are the initiating events for meiotic recombination, most organisms make very few crossovers per chromosome pair. Moreover, crossovers tend to inhibit the formation of other crossovers nearby on the same chromosome pair, a poorly understood phenomenon known as crossover interference. Here we show that the synaptonemal complex, a meiosis-specific structure that assembles between aligned homologous chromosomes, both constrains and is altered by crossover recombination events. Using a cytological marker of crossover sites in Caenorhabditis elegans, we show that partial depletion of the synaptonemal complex central region proteins attenuates crossover interference, increasing crossovers and reducing the effective distance over which interference operates, indicating that synaptonemal complex proteins limit crossovers. Moreover, we show that crossovers are associated with a local 0.4-0.5-micrometre increase in chromosome axis length. We propose that meiotic crossover regulation operates as a self-limiting system in which meiotic chromosome structures establish an environment that promotes crossover formation, which in turn alters chromosome structure to inhibit other crossovers at additional sites.

    View details for DOI 10.1038/nature12577

    View details for PubMedID 24107990

  • The C. elegans DSB-2 Protein Reveals a Regulatory Network that Controls Competence for Meiotic DSB Formation and Promotes Crossover Assurance. PLoS genetics Rosu, S., Zawadzki, K. A., Stamper, E. L., Libuda, D. E., Reese, A. L., Dernburg, A. F., Villeneuve, A. M. 2013; 9 (8)

    Abstract

    For most organisms, chromosome segregation during meiosis relies on deliberate induction of DNA double-strand breaks (DSBs) and repair of a subset of these DSBs as inter-homolog crossovers (COs). However, timing and levels of DSB formation must be tightly controlled to avoid jeopardizing genome integrity. Here we identify the DSB-2 protein, which is required for efficient DSB formation during C. elegans meiosis but is dispensable for later steps of meiotic recombination. DSB-2 localizes to chromatin during the time of DSB formation, and its disappearance coincides with a decline in RAD-51 foci marking early recombination intermediates and precedes appearance of COSA-1 foci marking CO-designated sites. These and other data suggest that DSB-2 and its paralog DSB-1 promote competence for DSB formation. Further, immunofluorescence analyses of wild-type gonads and various meiotic mutants reveal that association of DSB-2 with chromatin is coordinated with multiple distinct aspects of the meiotic program, including the phosphorylation state of nuclear envelope protein SUN-1 and dependence on RAD-50 to load the RAD-51 recombinase at DSB sites. Moreover, association of DSB-2 with chromatin is prolonged in mutants impaired for either DSB formation or formation of downstream CO intermediates. These and other data suggest that association of DSB-2 with chromatin is an indicator of competence for DSB formation, and that cells respond to a deficit of CO-competent recombination intermediates by prolonging the DSB-competent state. In the context of this model, we propose that formation of sufficient CO-competent intermediates engages a negative feedback response that leads to cessation of DSB formation as part of a major coordinated transition in meiotic prophase progression. The proposed negative feedback regulation of DSB formation simultaneously (1) ensures that sufficient DSBs are made to guarantee CO formation and (2) prevents excessive DSB levels that could have deleterious effects.

    View details for DOI 10.1371/journal.pgen.1003674

    View details for PubMedID 23950729

  • Robust Crossover Assurance and Regulated Interhomolog Access Maintain Meiotic Crossover Number SCIENCE Rosu, S., Libuda, D. E., Villeneuve, A. M. 2011; 334 (6060): 1286-1289

    Abstract

    Most organisms rely on interhomolog crossovers (COs) to ensure proper meiotic chromosome segregation but make few COs per chromosome pair. By monitoring repair events at a defined double-strand break (DSB) site during Caenorhabditis elegans meiosis, we reveal mechanisms that ensure formation of the obligate CO while limiting CO number. We find that CO is the preferred DSB repair outcome in the absence of inhibitory effects of other (nascent) recombination events. Thus, a single DSB per chromosome pair is largely sufficient to ensure CO formation. Further, we show that access to the homolog as a repair template is regulated, shutting down simultaneously for both CO and noncrossover (NCO) pathways. We propose that regulation of interhomolog access limits CO number and contributes to CO interference.

    View details for DOI 10.1126/science.1212424

    View details for Web of Science ID 000297553600053

    View details for PubMedID 22144627

  • Alterations in DNA Replication and Histone Levels Promote Histone Gene Amplification in Saccharomyces cerevisiae GENETICS Libuda, D. E., Winston, F. 2010; 184 (4): 985-U161

    Abstract

    Gene amplification, a process that increases the copy number of a gene or a genomic region to two or more, is utilized by many organisms in response to environmental stress or decreased levels of a gene product. Our previous studies in Saccharomyces cerevisiae identified the amplification of a histone H2A-H2B gene pair, HTA2-HTB2, in response to the deletion of the other H2A-H2B gene pair, HTA1-HTB1. This amplification arises from a recombination event between two flanking Ty1 elements to form a new, stable circular chromosome and occurs at a frequency higher than has been observed for other Ty1-Ty1 recombination events. To understand the regulation of this amplification event, we screened the S. cerevisiae nonessential deletion set for mutations that alter the amplification frequency. Among the deletions that increase HTA2-HTB2 amplification frequency, we identified those that either decrease DNA replication fork progression (rrm3Delta, dpb3Delta, dpb4Delta, and clb5Delta) or that reduce histone H3-H4 levels (hht2-hhf2Delta). These two classes are related because reduced histone H3-H4 levels increase replication fork pauses, and impaired replication forks cause a reduction in histone levels. Consistent with our mutant screen, we found that the introduction of DNA replication stress by hydroxyurea induces the HTA2-HTB2 amplification event. Taken together, our results suggest that either reduced histone levels or slowed replication forks stimulate the HTA2-HTB2 amplification event, contributing to the restoration of normal chromatin structure.

    View details for DOI 10.1534/genetics.109.113662

    View details for Web of Science ID 000281889000009

    View details for PubMedID 20139344

  • Amplification of histone genes by circular chromosome formation in Saccharomyces cerevisiae NATURE Libuda, D. E., Winston, F. 2006; 443 (7114): 1003-1007

    Abstract

    Proper histone levels are critical for transcription, chromosome segregation, and other chromatin-mediated processes(1-7). In Saccharomyces cerevisiae, the histones H2A and H2B are encoded by two gene pairs, named HTA1-HTB1 and HTA2-HTB2 (ref. 8). Previous studies have demonstrated that when HTA2-HTB2 is deleted, HTA1-HTB1 dosage compensates at the transcriptional level(4,9). Here we show that a different mechanism of dosage compensation, at the level of gene copy number, can occur when HTA1-HTB1 is deleted. In this case, HTA2-HTB2 amplifies via creation of a new, small, circular chromosome. This duplication, which contains 39 kb of chromosome II, includes HTA2-HTB2, the histone H3-H4 locus HHT1-HHF1, a centromere and origins of replication. Formation of the new chromosome occurs by recombination between two Ty1 retrotransposon elements that flank this region. Following meiosis, recombination between these two particular Ty1 elements occurs at a greatly elevated level in hta1-htb1Delta mutants, suggesting that a decreased level of histones H2A and H2B specifically stimulates this amplification of histone genes. Our results demonstrate another mechanism by which histone gene dosage is controlled to maintain genomic integrity.

    View details for DOI 10.1038/nature05205

    View details for Web of Science ID 000241523400057

    View details for PubMedID 17066037

  • Connective tissue growth factor coordinates chondrogenesis and angiogenesis during skeletal development DEVELOPMENT Ivkovic, S., Yoon, B. S., Popoff, S. N., Safadi, F. F., Libuda, D. E., Stephenson, R. C., Daluiski, A., Lyons, K. M. 2003; 130 (12): 2779-2791

    Abstract

    Coordinated production and remodeling of the extracellular matrix is essential during development. It is of particular importance for skeletogenesis, as the ability of cartilage and bone to provide structural support is determined by the composition and organization of the extracellular matrix. Connective tissue growth factor (CTGF, CCN2) is a secreted protein containing several domains that mediate interactions with growth factors, integrins and extracellular matrix components. A role for CTGF in extracellular matrix production is suggested by its ability to mediate collagen deposition during wound healing. CTGF also induces neovascularization in vitro, suggesting a role in angiogenesis in vivo. To test whether CTGF is required for extracellular matrix remodeling and/or angiogenesis during development, we examined the pattern of Ctgf expression and generated Ctgf-deficient mice. Ctgf is expressed in a variety of tissues in midgestation embryos, with highest levels in vascular tissues and maturing chondrocytes. We confirmed that CTGF is a crucial regulator of cartilage extracellular matrix remodeling by generating Ctgf(-/-) mice. Ctgf deficiency leads to skeletal dysmorphisms as a result of impaired chondrocyte proliferation and extracellular matrix composition within the hypertrophic zone. Decreased expression of specific extracellular matrix components and matrix metalloproteinases suggests that matrix remodeling within the hypertrophic zones in Ctgf mutants is defective. The mutant phenotype also revealed a role for Ctgf in growth plate angiogenesis. Hypertrophic zones of Ctgf mutant growth plates are expanded, and endochondral ossification is impaired. These defects are linked to decreased expression of vascular endothelial growth factor (VEGF) in the hypertrophic zones of Ctgf mutants. These results demonstrate that CTGF is important for cell proliferation and matrix remodeling during chondrogenesis, and is a key regulator coupling extracellular matrix remodeling to angiogenesis at the growth plate.

    View details for DOI 10.1242/dev.00505

    View details for Web of Science ID 000183759600020

    View details for PubMedID 12736220

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