Genome Instability / mRNP Biogenesis

Home departments Molecular Biology Genome Instability / mRNP Biogenesis

Research areas:

Our laboratory investigates two different biological problems:

    1. Genome Instability
    2. mRNP biogenesis

Our studies are performed with the model eukaryotic organisms S. cerevisiae and C. elegans and with mouse and human cell cultures.



Genome Instability.

Cell proliferation involves a number of processes that need to be tightly coordinated to ensure preservation of genome integrity and to promote faithful genome propagation. Genome instability can take place in the form of mutations, recombination and DNA rearrangements as well as of chromosome loss. Although such events may be harmful for the cell and the organism, they also are the molecular motors of evolution and generators of genetic variation. Genome instability, however, is usually associated with pathological disorders, and in humans is often associated with premature aging, various cancer predispositions and hereditary diseases.

Coordination of DNA replication with DNA-damage surveillance mechanisms (termed checkpoints), repair and cell cycle progression ensures genome integrity during cell divisions. Failures during replication and repair may lead to either mutation or to replication fork stalling and DNA breaks that would need to be repaired via recombination and that can lead to chromosomal rearrangements. Two types of elements play a key role in instability leading to rearrangements: those that act in trans to prevent instability – among them are replication, repair and S-phase checkpoint factors - and those that act in cis - chromosomal hotspots of instability such as Fragile sites and highly-transcribed DNA sequences.

The relationship between mechanisms responsible for genome stability is also evident during meiosis, where cells undergo a single round of replication followed by two consecutive rounds of division. During these two divisions, replicated chromosomes must segregate properly ensuring that each haploid cell has the correct number and type of chromosomes. Correct meiosis relies on the coordination of DNA repair and checkpoint pathways. In humans, this is particularly relevant because meiotic genome instability, such as chromosome missegregation, results in miscarriages and birth defects due to aneuploid embryos that survive like Down syndrome.

Along these lines, our main research interests are to identify and understand the causes and mechanisms of genome instability in eukaryotes, including mitotic instability associated with transcription and defective mRNP biogenesis and export, mitotic instability derived from replication and DNA-damage checkpoint failures, and meiotic instability related to checkpoint and repair defects. We try to understand how RNA polymerases and other obstacles, such as DNA lesions, R-loops and particular DNA structures, affect the progression of replication forks leading to recombination and chromosome rearrangements, as well as how aberrant replication intermediates signal the DNA-damage and S-phase checkpoints. For a comprehensive view of the whole process we are investigating the factors and mechanisms governing sister-chromatid recombination as a major pathway of repair of both single and double-stranded DNA breaks occurring during replication. In meiosis, our main focus is on genome instability associated with mRNP biogenesis and export and the checkpoint regulation via posttranscriptional modifications.

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mRNP biogenesis.

Transcription is a key cellular process, which occurs in the nucleus of eukaryotic cells in a tightly coordinated manner with RNA processing, packaging an export. Interestingly, transcription and mRNP biogenesis may play a critical role in genome stability. One of our major research interests is to understand the coupling between transcription elongation and mRNP formation and export and its connection with genome instability. In this line of research we have identified a number of factors, like the THO complex, Thp1-Sac3, Tho1, etc. in the yeast S. cerevisiae that have contributed to establish a connection between transcription elongation and RNA export. We are trying to decipher the function of these and other related factors in mRNP biogenesis and how they can modulate genome integrity. For these objectives we are trying to define the structure and function of the THO complex and the Thp1-Sac3 complex, and we are investigating new factors involved in the connection of transcription elongation with mRNP biogenesis and export.

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Funding

Research funded by

    Spanish Ministry of Science of Education
    Junta de Andalucía (Consejeria de Innovacion, Ciencia y Empresa)
    European Science Foundation
    European Union (FEDER)

Postdocs and PhD students supported by

    EMBO
    Spanish Ministry of Science and Education
    Spanish Ministry of Health (Instituto de Salud Carlos III)
    Junta de Andalucía (Consejeria de Innovacion, Ciencia y Empresa)
    Spanish National Research Council (CSIC)
    Swiss National Foundation
    European Union (FEDER)

Selected Publications:

Books

A. Aguilera y R. Rothstein (Eds.) 2007. Molecular Genetics of Recombination. Topics in Current Genetics vol. 17 (Springer Verlag, Heidelberg)

Reviews

A. Aguilera, 2001. Double-strand break repair: are Rad51/RecA-DNA joints barriers to DNA replication? Trends Genet. 17: 318-321

A. Aguilera, 2002. The connection between transcription and genetic instability. EMBO J. 21:195-201

A. Aguilera. 2005. Cotranscriptional mRNP assembly: from the DNA to the nuclear pore. Curr. Opin. Cell Biol. 17: 242-250

A. Aguilera, 2005. mRNA processing and genomic instability. Nature Struct. Mol. Biol. 12: 737-738

A. Aguilera y B. Gómez-González, 2008. Genomic Instability: A mechanistic view of its causes and consequences. Nature Rev. Genet. 9: 204-217

R. Luna, H. Gaillard, C. Gonzalez-Aguilera, A. Aguilera.  2008. Biogénesis of mRNPs: Integrating different processes in the eukaryotic nucleus.  Chromosoma117: 319-331


Recent Articles

S. Jimeno, A.G. Rondón, R. Luna, A. Aguilera. 2002. The yeast THO complex and mRNA export factors link mRNA metabolism with transcription and genome instability. EMBO J. .21: 3526-3535

K. Straesser, S. Masuda, P. Mason, J. Pfannstiel, M. Opizzi, S. Rodríguez-Navarro, A.G. Rondón, A. Aguilera, K. Struhl, R. Reed and E. Hurt, 2002. TREX is a conserved complex coupling transcription with messenger RNA export. Nature 417:304-308

S. González-Barrera, F. Cortés-Ledesma, R.E. Wellinger, A. Aguilera. 2003. Equal sister-chromatid exchange is a major mechanism of double-strand-break repair in yeast. Mol. Cell. 11: 1661-1671

P. Huertas, A. Aguilera, 2003. Co-transcriptionally formed DNA: RNA hybrids mediate transcription elongation impairment and transcription-associated recombination. Mol. Cell. 12: 711-721

F. Prado, F. Cortés-Ledesma, A. Aguilera, 2004. The absence of the yeast chromatin assembly factor Asf1 increases genomic instability and sister chromatid exchange. EMBO Reports. 5: 497-502

R. Luna, S. Jimeno, M. Marín, P. Huertas, M. García-Rubio, A. Aguilera. 2005. Interdependence between Transcription and mRNP Processing and Export. and Its impact on Genetic Stability. Mol. Cell. 8: 711-722

F. Prado, A. Aguilera, 2005. Impairment of replication fork progression mediates RNA polII transcription-associated recombination. EMBO J. 24: 1267-1276

R. Wellinger, F. Prado, A. Aguilera. 2006. Replication fork progression is impaired by transcription in yeast cells lacking a functional THO complex. Mol. Cell. Biol. 26: 3327-3334

P. Huertas, M. Gracía-Rubio, R. Wellinger, R. Luna, A.Aguilera, 2006. A hpr1 point mutation that impairs trancription and mRNP biogenesis without increasing reconbination. Mol. Cell. Biol. 26: 7451-7465

F. Cortés-Ledesma, A. Aguilera, 2006. Double-strand breaks arising by replication through a nick are repaired by cohesin-dependent sister-chromatid exchange. EMBO Reports 7: 919-926

G. De Piccoli, F. Cortés-Ledesma, G. Ira, J. Torres-Rosell, S. Hule, S. Farmer, JY. Hwang, F. Machin, A. Ceschia, B. Leitao, D. Bressan, F. Dotiwala, A. Papusha, X. Zhao, K. Myung, JE. Haber*, A. Aguilera*, L. Aragón*, 2006. Smc5-Smc6 mediate DNA double-strand-break repair by promoting sister-chromatid recombination. Nature Cell Biol. 8: 1032-1034

S. Jimeno, R. Luna, A. Aguilera, 2006. Tho1, a novel hnRNP, and Sub2 provide alternative pathways for mRNP biogenesis in yeast THO mutants. Mol. Cell. Biol. 26: 4387-4398

B. Gómez-González, A. Aguilera, 2007. AID action is strongly stimulated by mutations of the THO complex. Proc. Natl. Acad. Sci. USA. 104: 8409-8414

H.Gaillard, R.E.Wellinger, A.Aguilera, 2007. A new connection of mRNP biogenesis and export with transcription-coupled repair. Nucleic Acids Res. 35: 3893-3906

Cortés-Ledesma F, Tous C y Aguilera A, 2007. Different genetic requirements for repair of replication-born double-strand breaks by sister-chromatid recombination and break-induced replication. Nucleic Acids Res. 35: 6560-6570

P. Huertas, F. Cortes-Ledesma, A.A.  Sartori, A. Aguilera, S.P. Jackson, 2008. CDK Targets Sae2 to Control DNA-end Resection and Homologous Recombination. Nature 455:689-692

C. Gonzalez-Aguilera, C. Tous, B. Gomez-Gonzalez, P. Huertas, R. Luna, A. Aguilera.  2008. The THP1-SAC3-SUS1-CDC31 Complex Works in Transcription Elongation-mRNA Export Preventing RNA-mediated Genome Instability.  Mol. Biol. Cell. 19:4310-4318

H. Gaillard, A. Aguilera  2008. A Novel Class of mRNA Containing Cytoplasmic Granules Are Produced in Response to UV-Irradiation. Mol. Biol. Cell. 19:4980-4992

H. Gaillard, C. Tous, J. Botet, C. Gonzalez-Aguilera, M.J. Quintero, L. Viladevall, M.L. García-Rubio, A. Rodriguez-Gil, A. Marín, J. Ariño, J.L. Revuelta, S. Chávez, A. Aguilera.  2009. Genome-Wide Analysis of Factors Affecting Transcription Elongation and DNA Repair:  a New Role for PAF and Ccr4 Not in Transcription-Coupled Repair PLos Genetics 5:e1000364

M.B. Faza, S. Kemmler, S. Jimeno, C. Gonzalez-Aguilera, A. Aguilera, E. Hurt, V.G. Panse.  2009. Sem 1 is a Functional Component of the Nuclear Pore Complex-Associated Messenger RNA Export Machinery  J. Cell Biol. 184:833-846
       
B. Gomez-Gonzalez, I. Felipe-Abrio, A. Aguilera.  2009. The S-Phase checkpoint is required to respond to R-loops accumulated in THO mutants.  Mol. Cell. Biol 29:5203-5213

J. F. Ruiz, B. Gomez-Gonzalez, A. Aguilera.  2009. Chromosomal Translocations Caused by Either Pol32-Dependant or Independant Triparental Break-Induced Replication. 2009. Mol. Cell. Biol 29:5441-5454

B. Gomez-Gonzalez, A. Aguilera.  2009.  R-loops do not accumulate in transcription-defective hpr1-101 mutants:  implications for the functional role of THO/TREX.  Nucl. Acids Res. 37:4315-4321