The key role of genome instability in tumorigenesis and a number of rare cancer-prone genetic diseases, as well as its potential risks in stem cell–based therapies, has made it a major subject in basic biological research, cancer biology and biomedicine. Our research goals are to identify and understand the causes and mechanisms of genome instability. They are based on the facts that eukaryotic DNA replication starts at multiple sites throughout the genome and is necessarily coordinated with transcription, sister chromatid cohesion, nucleosome assembly and cell cycle progression. During replication cells need to deal with DNA damage and stalled forks, originated inevitably by the action of exogenous and endogenous agents, the success of this process being crucial to preserve genome integrity. The inability of cells to deal with DNA lesions during replication or to protect or restart stalled forks may lead to DNA breaks, chromosomal rearrangements and mutations that can cause loss of viability and a defect in cell proliferation. As a consequence, errors in DNA replication and repair result in a large number of human syndromes, including premature aging, cancer predispositions and genetic abnormalities.
Our research is focused on the factors and mechanisms responsible for genome instability associated with replication stress and replication-born DNA breaks, including that caused by transcription-replication conflicts and R-loop accumulation. Our ultimate goals are:
1) to identify the main determinants of replication failures that lead to the stalling or collapse of the replication fork and to DNA breaks;
2) to understand how a replication-born DNA break is repaired to allow replication restart and prevent chromosome rearrangements and genome instability; and
3) to evaluate the implication of such determinants and processes in the origin of cancer and its potential use in cancer therapy.
Our research is performed in human cells and the model organism Saccharomyces cerevisiae, with specific incursions in Caenorhabditis elegans.
1. Transcription-associated genome instability: R-loops and chromatin condensation
We are determining the mechanisms by which cells solve transcription-replication conflicts to prevent genome instability. We explore the role of RNA-DNA hybrids in these conflicts and investigate how they form and how can they modulate chromatin structure and remodeling (histone acetylation, methylation, phosphorylation, chromatin condensation, heterochromatin, etc) and how do they lead to chromosome breakage and fragility.
2. mRNP biogenesis and export: The THO complex and other RNA-binding factors
To understand how RNA metabolism and export factors control genome integrity, we are purifying the mRNP particle and performing studies for understanding their mechanisms of action of specific RNA-binding proteins, such as THO, THSC/TREX-2, Sub2/UAP56, Yra/ALY, Npl3, etc. along the transcription cycle in relation to the nuclear structure, the nuclear periphery and gene gating to the nuclear pores.
3. Repair of replication-born DNA breaks and replication restart
We study the mechanism of repair of replication-born double-strand breaks (DSBs) using an in vivo system developed in our lab to determine the role of a number of factors, such as chromatin modifiers (histone acetylases and deacetylases), nucleases (Rad1, Slx4, Yen1 or Mus81) and recombination factors (Rad51, Sgs1), via sister-chromatid recombination or break-induced replication as mechanisms involved in replication resumption.
4. RNA-mediated replication stress and cancer
We are assaying whether co-transcriptional DNA-RNA hybrids and R-loops are a mark of cancer cells and a major source or genome instability and replication stress in tumorigenic cells. We are determining whether specific proteins that prevent or solve R-loops can constitute a new group of tumor suppressors. In this sense, we have shown that BRCA1 and BRCA2 tumor suppressors are key proteins to prevent or resolve R-loops in tumor cells and that different components of the THO/TREX complex have altered levels of gene expression in a significant class of tumor cells.
5. Transcription-coupled DNA repair and disease
We are trying to define the factors and mechanisms of Transcription-Coupled Repair (TCR), which repairs the DNA lesions that are blocking RNA polymerases. We are particularly interested in understanding the different ways by which alterations in TFIIH and related factors causes different diseases like Xeroderma pigmentosum and Cockayne Syndrome, among others.
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