Our group is interested in developing quantitative methods to understand chromosome structure, nuclear
architecture and the formation of chromosome aberrations.
We work closely with experimental groups and use a wide variety of
mathematical methods (knot theory, geometry, probability and stochastic processes), biophysical methods
(statistical physics of polymers and diffusion models) and statistics methods.
Our current main topic of interests are:
- The relative position of chromosomes during interphase and the topology of the interface between chromosomes.
- The formation of chromosome aberrations after exposure to DNA damaging agents
- The role of chromatin
in the recruitment of DNA repair proteins.
Our research is funded by the NIH and by the SFSU Center for Computing in the Life Sciences (CCLS)
The relative position of chromosomes during interphase and the topology of the interface between chromosomes
During interphase chromosomes are confined to sub-nuclear regions called chromosome territories. The position of these territories has been associated with a number of biological processes such as cell differentiation and are believed to have a very important role in cancer and other human diseases.
We are developing statistical methods that interrogate mFISH or SKY data for chromosome clustering (i.e. for deviations from randomness in the relative positions of chromosomes).
Our approach is based on the hypothesis that chromosomes that are in close
proximity form radiation induced chromosome aberrations more often than those that are far apart (known as the proximity effect hypothesis). When applying these methods to human lymphocytes we find two sets of chromosomes that are on average closer to each other than what randomness would predict these are: {1,16,17,19,22}and {13,14,15,21,22} (Cornforth et al. 2002, Arsuaga et al. 2004, Vives et al. 2005).
We are currently characterizing features of
nuclear organization that
different types of radiations (high LET vs low LET) can detect. We are also extending our studies to human fibroblasts for which we are developing data mining methods.
Radiogenic chromosome aberrations are an important, much studied, form of ionizing radiation damage. They can be
used to study nuclear architecture and DNA repair/misrepair pathways. Radiation induced chromosome aberrations are
very important in major applications of radiobiology with significant societal implications. Large (>1Mb)
rearranged chromosome fragments between non-homologous human chromosomes can be identified using mFISH or SKY.
ii) Pathways of aberration formation
There exist two main pathways of aberration formation in G0/G1: Breakage and Reunion and Recombinational
Misrepair. The breakage and Reunion model is mechanistically similar to the molecular mechanism of
Non-Homologous End Joining and requires at least to DSBs to form an aberration. Recombinational
Misrepair on the other hand, is similar to the Homologous recombination repair pathway and introduces aberrations
due to an error in the resolution of the Holliday junction.
We developed a new graph theory framework based on cycles and similar to that used in
comparative genomics to characterize these processes of aberration formation. We concluded that Breakage and
Reunion is the predominant mechanism of aberration formation during G0/G1 in human lymphocytes (Vazquez et al.
2002, Levy et al. 2004).
During interphase chromosomes are confined to sub-nuclear regions called chromosome territories. Position of these
territories are determined at mitosis and do not change drastically during G0/G1. We have developed a statistical
method that
tests for chromosome clustering (i.e. for deviations from randomness in the relative positions of chromosomes).
This phenomenom is believed to play an important role in a number of biological processes and
has important implications for human disease and cancer.
Our approach is based on the fact that chromosomes that are in close
proximity form
radiation induced chromosome aberrations more often than those that are far apart. We have found two sets of
chromosomes that are on average closer to each other than what randomness would predict these are: {1,16,17,19,22}
and {13,14,15,21,22} (Cornforth et al. 2002, Arsuaga et al. 2004, Vives et al. 2005). We are currently developing
data mining techniques to search for other chromosome clusters and cluster related to different types of lymphomas
we are also investigating correlations between chromosome positioning and gene expression.
Analysis of FRAP/FLIP experiments in DNA repair
One of the most deleterious effects that DNA damaging agents have in the cell is the induction of double stranded-breaks (DSBs).
Faithful repair of DSBs is essential for the cell viability and errors in the repair may cause chromosome aberrations (i.e. rearrangements, amplifications and deletions of the genome).
One of the first responses to DNA DSBs is the phosphorylation of the histone H2AX (forming the so-called gamma-H2AX). Phosphorylation of H2AX is believed to recruit repair factors to the place of damage and to trigger a long cascade of reactions with the objective of repairing the DSB.
We are currently developing computational tools that help study how gamma-H2AX may help recruit some repair factors to the site of damage.
DNA
topology and chromosome organization
i) Knotting in confined volumes: DNA packing in bacteriophages
We have done experimental work and computer
simulations to study the organization of dsDNA inside bacteriophage capsids.
In the 1980's Liu et al. observed that DNA molecules extracted from P4 bacteriophages were knotted
with very high probability. The question of why these structures were formed, or whether they
contained any information about the packing of DNA inside the viral capsid was an open question
for a number of years. In collaboration with Prof. D. W. Sumners and Dr. J. Roca, we developed
experimental protocols (Trigueros et al. 2001) as well as Markov-Chain Monte-Carlo methods to analyze these knot
distributions. We showed that the formation of knots inside the viral capsids is driven mainly by
the effects of the confinement (Arsuaga et al 2002). In later studies we found that knot distributions observed
experimentally could be mimicked by imposing chirality on the simulated molecules (Arsuaga et al. 2002, Arsuaga et al. 2005).
i)Linking in confined volumes: Intermingling of chromosomes during interphase