R-loops as a major modulator of transcription-associated recombination and chromatin dynamics

Publications

A new interaction between BRCA2 and DDX5 promotes the repair of DNA breaks at transcribed chromatin

Author(s): Belen Gómez-González, Gaetana Sessa, Aura Carreira, Andrés Aguilera
Published in: Molecular & Cellular Oncology, Issue 8/3, 2021, Page(s) 1910474, ISSN 2372-3556
Publisher: Taylor & Francis
DOI: 10.1080/23723556.2021.1910474

BRCA2 promotes DNA‐RNA hybrid resolution by DDX5 helicase at DNA breaks to facilitate their repair‡

Author(s): Gaetana Sessa, Belén Gómez‐González, Sonia Silva, Carmen Pérez‐Calero, Romane Beaurepere, Sonia Barroso, Sylvain Martineau, Charlotte Martin, Åsa Ehlén, Juan S Martínez, Bérangère Lombard, Damarys Loew, Stephan Vagner, Andrés Aguilera, Aura Carreira
Published in: The EMBO Journal, Issue 40/7, 2021, Page(s) e106018, ISSN 0261-4189
Publisher: Nature Publishing Group
DOI: 10.15252/embj.2020106018

The SWI/SNF chromatin remodeling complex helps resolve R-loop-mediated transcription–replication conflicts

Author(s): Aleix Bayona-Feliu, Sonia Barroso, Sergio Muñoz, Andrés Aguilera
Published in: Nature Genetics, Issue 53(7), 2021, Page(s) 1050-1063, ISSN 1061-4036
Publisher: Nature Publishing Group
DOI: 10.1038/s41588-021-00867-2

The SWI/SNF complex, transcription-replication conflicts and cancer: a connection with high therapeutic potential

Author(s): Aleix Bayona-Feliu, Andrés Aguilera
Published in: Molecular & Cellular Oncology, Issue 8/4, 2021, Page(s) 1976582, ISSN 2372-3556
Publisher: Taylor & Francis Ltd
DOI: 10.1080/23723556.2021.1976582

Harmful R-loops are prevented via different cell cycle-specific mechanisms

Author(s): Marta San Martin-Alonso, María E. Soler-Oliva, María García-Rubio, Tatiana García-Muse, Andrés Aguilera
Published in: Nature Communications, Issue 12/1, 2021, Page(s) 4451, ISSN 2041-1723
Publisher: Nature Publishing Group
DOI: 10.1038/s41467-021-24737-x

The role of chromatin at transcription-replication conflicts as a genome safeguard

Author(s): Aleix Bayona-Feliu, Andrés Aguilera
Published in: Biochemical Society Transactions, 2021, ISSN 0300-5127
Publisher: Portland Press, Ltd.
DOI: 10.1042/bst20210691

Histone H3E73Q and H4E53A mutations cause recombinogenic DNA damage

Author(s): Pedro Ortega, Desiré García-Pichardo, Marta San Martin-Alonso, Ana G. Rondón, Belén Gómez-González, Andrés Aguilera
Published in: Microbial Cell, Issue 7/7, 2020, Page(s) 190-198, ISSN 2311-2638
Publisher: Shared Science Publishers
DOI: 10.15698/mic2020.07.723

ADAR-mediated RNA editing of DNA:RNA hybrids is required for DNA double strand break repair

Author(s): Sonia Jimeno, Rosario Prados-Carvajal, María Jesús Fernández-Ávila, Sonia Silva, Domenico Alessandro Silvestris, Martín Endara-Coll, Guillermo Rodríguez-Real, Judit Domingo-Prim, Fernando Mejías-Navarro, Amador Romero-Franco, Silvia Jimeno-González, Sonia Barroso, Valeriana Cesarini, Andrés Aguilera, Angela Gallo, Neus Visa, Pablo Huertas
Published in: Nature Communications, Issue 12/1, 2021, Page(s) 5512, ISSN 2041-1723
Publisher: Nature Publishing Group
DOI: 10.1038/s41467-021-25790-2

Physical proximity of chromatin to nuclear pores prevents harmful R loop accumulation contributing to maintain genome stability

Author(s): Francisco García-Benítez, Hélène Gaillard, Andrés Aguilera
Published in: Proceedings of the National Academy of Sciences, Issue 114/41, 2017, Page(s) 10942-10947, ISSN 0027-8424
Publisher: National Academy of Sciences
DOI: 10.1073/pnas.1707845114

Human THO–Sin3A interaction reveals new mechanisms to prevent R‐loops that cause genome instability

Author(s): Irene Salas‐Armenteros, Carmen Pérez‐Calero, Aleix Bayona‐Feliu, Emanuela Tumini, Rosa Luna, Andrés Aguilera
Published in: The EMBO Journal, Issue 36/23, 2017, Page(s) 3532-3547, ISSN 0261-4189
Publisher: Nature Publishing Group
DOI: 10.15252/embj.201797208

The Role of Replication-Associated Repair Factors on R-Loops

Author(s): Vaibhav Bhatia, Emilia Herrera-Moyano, Andres Aguilera, Belen Gomez-Gonzalez
Published in: Genes, Issue 8/7, 2017, Page(s) 171, ISSN 2073-4425
Publisher: Multidisciplinary Digital Publishing Institute (MDPI)
DOI: 10.3390/genes8070171

Multiple signaling kinases target Mrc1 to prevent genomic instability triggered by transcription-replication conflicts

Author(s): Alba Duch, Berta Canal, Sonia I. Barroso, María García-Rubio, Gerhard Seisenbacher, Andrés Aguilera, Eulàlia de Nadal, Francesc Posas
Published in: Nature Communications, Issue 9/1, 2018, Page(s) 379, ISSN 2041-1723
Publisher: Nature Publishing Group
DOI: 10.1038/s41467-017-02756-x

Gene gating at nuclear pores prevents the formation of R loops

Author(s): Hélène Gaillard, Francisco García-Benítez, Andrés Aguilera
Published in: Molecular & Cellular Oncology, Issue 5/1, 2017, Page(s) e1405140, ISSN 2372-3556
Publisher: Taylor & Francis
DOI: 10.1080/23723556.2017.1405140

Epigenetic features of human telomeres

Author(s): María D Cubiles, Sonia Barroso, María I Vaquero-Sedas, Alicia Enguix, Andrés Aguilera, Miguel A Vega-Palas
Published in: Nucleic Acids Research, Issue 46/5, 2018, Page(s) 2347-2355, ISSN 0305-1048
Publisher: Oxford University Press
DOI: 10.1093/nar/gky006

The Smc5/6 complex regulates the yeast Mph1 helicase at RNA-DNA hybrid-mediated DNA damage

Author(s): Juan Lafuente-Barquero, Sarah Luke-Glaser, Marco Graf, Sonia Silva, Belén Gómez-González, Arianna Lockhart, Michael Lisby, Andrés Aguilera, Brian Luke
Published in: PLOS Genetics, Issue 13/12, 2017, Page(s) e1007136, ISSN 1553-7404
Publisher: San Francisco, CA : Public Library of Science, c2005-
DOI: 10.1371/journal.pgen.1007136

The need to regulate replication fork speed

Author(s): Belén Gómez-González, Andrés Aguilera
Published in: Science, Issue 358/6364, 2017, Page(s) 722-723, ISSN 0036-8075
Publisher: American Association for the Advancement of Science
DOI: 10.1126/science.aaq0678

Yra1-bound RNA–DNA hybrids cause orientation-independent transcription–replication collisions and telomere instability

Author(s): María García-Rubio, Paula Aguilera, Juan Lafuente-Barquero, José F. Ruiz, Marie-Noelle Simon, Vincent Geli, Ana G. Rondón, Andrés Aguilera
Published in: Genes & Development, Issue 32/13-14, 2018, Page(s) 965-977, ISSN 0890-9369
Publisher: Cold Spring Harbor Laboratory Press
DOI: 10.1101/gad.311274.117

Human mitochondrial degradosome prevents harmful mitochondrial R loops and mitochondrial genome instability

Author(s): Sonia Silva, Lola P. Camino, Andrés Aguilera
Published in: Proceedings of the National Academy of Sciences, Issue 115/43, 2018, Page(s) 11024-11029, ISSN 0027-8424
Publisher: National Academy of Sciences
DOI: 10.1073/pnas.1807258115

The Antitumor Drugs Trabectedin and Lurbinectedin Induce Transcription-Dependent Replication Stress and Genome Instability

Author(s): Emanuela Tumini, Emilia Herrera-Moyano, Marta San Martín-Alonso, Sonia Barroso, Carlos M. Galmarini, Andrés Aguilera
Published in: Molecular Cancer Research, Issue 17/3, 2019, Page(s) 773-782, ISSN 1541-7786
Publisher: American Association for Cancer Research
DOI: 10.1158/1541-7786.mcr-18-0575

A Meiotic Checkpoint Alters Repair Partner Bias to Permit Inter-sister Repair of Persistent DSBs

Author(s): Tatiana Garcia-Muse, U. Galindo-Diaz, M. Garcia-Rubio, J.S. Martin, J. Polanowska, N. O’Reilly, A. Aguilera, Simon J. Boulton
Published in: Cell Reports, Issue 26/3, 2019, Page(s) 775-787.e5, ISSN 2211-1247
Publisher: Cell Press
DOI: 10.1016/j.celrep.2018.12.074

Guidelines for DNA recombination and repair studies: Cellular assays of DNA repair pathways

Author(s): Hannah L. Klein, Giedrė Bačinskaja, Jun Che, Anais Cheblal, Rajula Elango, Anastasiya Epshtein, Devon M. Fitzgerald, Belén Gómez-González, Sharik R. Khan, Sandeep Kumar, Bryan A. Leland, Léa Marie, Qian Mei, Judith Miné-Hattab, Alicja Piotrowska, Erica J. Polleys, Christopher D. Putnam, Elina A. Radchenko, Anissia Ait Saada, Cynthia J. Sakofsky, Eun Yong Shim, Mathew Stracy, Jun Xia, Zhenxi
Published in: Microbial Cell, Issue 6/1, 2019, Page(s) 1-64, ISSN 2311-2638
Publisher: Shared Science Publishers OG
DOI: 10.15698/mic2019.01.664

The Nup84 complex coordinates the DNA damage response to warrant genome integrity

Author(s): Hélène Gaillard, José M Santos-Pereira, Andrés Aguilera
Published in: Nucleic Acids Research, Issue 47/8, 2019, Page(s) 4054-4067, ISSN 0305-1048
Publisher: Oxford University Press
DOI: 10.1093/nar/gkz066

The DNA damage response acts as a safeguard against harmful DNA–RNA hybrids of different origins

Author(s): Sonia Barroso, Emilia Herrera‐Moyano, Sergio Muñoz, María García‐Rubio, Belén Gómez‐González, Andrés Aguilera
Published in: EMBO reports, Issue 20/9, 2019, Page(s) e47250, ISSN 1469-221X
Publisher: Nature Publishing Group
DOI: 10.15252/embr.201847250

What causes an RNA-DNA hybrid to compromise genome integrity?

Author(s): Ana G. Rondón, Andrés Aguilera
Published in: DNA Repair, Issue 81, 2019, Page(s) 102660, ISSN 1568-7864
Publisher: Elsevier BV
DOI: 10.1016/j.dnarep.2019.102660

Transcription-mediated replication hindrance: a major driver of genome instability

Author(s): Belén Gómez-González, Andrés Aguilera
Published in: Genes & Development, Issue 33/15-16, 2019, Page(s) 1008-1026, ISSN 0890-9369
Publisher: Cold Spring Harbor Laboratory Press
DOI: 10.1101/gad.324517.119

Depletion of the MFAP1/SPP381 Splicing Factor Causes R-Loop-Independent Genome Instability

Author(s): Irene Salas-Armenteros, Sonia I. Barroso, Ana G. Rondón, Mónica Pérez, Eloisa Andújar, Rosa Luna, Andrés Aguilera
Published in: Cell Reports, Issue 28/6, 2019, Page(s) 1551-1563.e7, ISSN 2211-1247
Publisher: Cell Press
DOI: 10.1016/j.celrep.2019.07.010

Elongation Factor TFIIS Prevents Transcription Stress and R-Loop Accumulation to Maintain Genome Stability

Author(s): Diana Zatreanu, Zhong Han, Richard Mitter, Emanuela Tumini, Hannah Williams, Lea Gregersen, A. Barbara Dirac-Svejstrup, Stefania Roma, Aengus Stewart, Andres Aguilera, Jesper Q. Svejstrup
Published in: Molecular Cell, Issue 76/1, 2019, Page(s) 57-69.e9, ISSN 1097-2765
Publisher: Cell Press
DOI: 10.1016/j.molcel.2019.07.037

R Loops: From Physiological to Pathological Roles

Author(s): Tatiana García-Muse, Andrés Aguilera
Published in: Cell, Issue 179/3, 2019, Page(s) 604-618, ISSN 0092-8674
Publisher: Cell Press
DOI: 10.1016/j.cell.2019.08.055

Rpd3L and Hda1 histone deacetylases facilitate repair of broken forks by promoting sister chromatid cohesion

Author(s): Pedro Ortega, Belén Gómez-González, Andrés Aguilera
Published in: Nature Communications, Issue 10/1, 2019, ISSN 2041-1723
Publisher: Nature Publishing Group
DOI: 10.1038/s41467-019-13210-5

Histone deacetylases facilitate the accurate repair of broken forks

Author(s): Belén Gómez-González, Pedro Ortega, Andrés Aguilera
Published in: Molecular & Cellular Oncology, Issue 7/2, 2020, Page(s) 1705731, ISSN 2372-3556
Publisher: Taylor and Francis Ltd
DOI: 10.1080/23723556.2019.1705731

Spontaneous DNA-RNA hybrids: differential impacts throughout the cell cycle

Author(s): Belén Gómez-González, Sonia Barroso, Emilia Herrera-Moyano, Andrés Aguilera
Published in: Cell Cycle, Issue 19/5, 2020, Page(s) 525-531, ISSN 1538-4101
Publisher: Landes Bioscience
DOI: 10.1080/15384101.2020.1728015

UAP56/DDX39B is a major cotranscriptional RNA–DNA helicase that unwinds harmful R loops genome-wide

Author(s): Carmen Pérez-Calero, Aleix Bayona-Feliu, Xiaoyu Xue, Sonia I. Barroso, Sergio Muñoz, Víctor M. González-Basallote, Patrick Sung, Andrés Aguilera
Published in: Genes & Development, 2020, ISSN 0890-9369
Publisher: Cold Spring Harbor Laboratory Press
DOI: 10.1101/gad.336024.119

The THO Complex as a Paradigm for the Prevention of Cotranscriptional R-Loops

Author(s): Rosa Luna, Ana G. Rondón, Carmen Pérez-Calero, Irene Salas-Armenteros, Andrés Aguilera
Published in: Cold Spring Harbor Symposia on Quantitative Biology, 2020, Page(s) 039594, ISSN 0091-7451
Publisher: Cold Spring Harbor Laboratory Press
DOI: 10.1101/sqb.2019.84.039594

Histone Mutants Separate R Loop Formation from Genome Instability Induction

Author(s): Desiré García-Pichardo, Juan C. Cañas, María L. García-Rubio, Belén Gómez-González, Ana G. Rondón, Andrés Aguilera
Published in: Molecular Cell, Issue 66/5, 2017, Page(s) 597-609.e5, ISSN 1097-2765
Publisher: Cell Press
DOI: 10.1016/j.molcel.2017.05.014

Roles of human POLD1 and POLD3 in genome stability

Author(s): Emanuela Tumini, Sonia Barroso, Carmen Pérez -Calero, Andrés Aguilera
Published in: Scientific Reports, Issue 6/1, 2016, ISSN 2045-2322
Publisher: Nature Publishing Group
DOI: 10.1038/srep38873

FANCD2 Facilitates Replication through Common Fragile Sites

Author(s): Advaitha Madireddy, Settapong T. Kosiyatrakul, Rebecca A. Boisvert, Emilia Herrera-Moyano, María L. García-Rubio, Jeannine Gerhardt, Elizabeth A. Vuono, Nichole Owen, Zi Yan, Susan Olson, Andrés Aguilera, Niall G. Howlett, Carl L. Schildkraut
Published in: Molecular Cell, Issue 64/2, 2016, Page(s) 388-404, ISSN 1097-2765
Publisher: Cell Press
DOI: 10.1016/j.molcel.2016.09.017

A new role for Rrm3 in repair of replication-born DNA breakage by sister chromatid recombination

Author(s): Sandra Muñoz-Galván, María García-Rubio, Pedro Ortega, Jose F. Ruiz, Sonia Jimeno, Benjamin Pardo, Belén Gómez-González, Andrés Aguilera
Published in: PLOS Genetics, Issue 13/5, 2017, Page(s) e1006781, ISSN 1553-7390
Publisher: Public Library of Science
DOI: 10.1371/journal.pgen.1006781

Transcription as a Threat to Genome Integrity

Author(s): Hélène Gaillard, Andrés Aguilera
Published in: Annual Review of Biochemistry, Issue 85/1, 2016, Page(s) 291-317, ISSN 0066-4154
Publisher: Annual Reviews, Inc.
DOI: 10.1146/annurev-biochem-060815-014908

Transcription–replication conflicts: how they occur and how they are resolved

Author(s): Tatiana García-Muse, Andrés Aguilera
Published in: Nature Reviews Molecular Cell Biology, Issue 17/9, 2016, Page(s) 553-563, ISSN 1471-0072
Publisher: Nature Publishing Group
DOI: 10.1038/nrm.2016.88

DNA–RNA hybrids: the risks of DNA breakage during transcription

Author(s): Andrés Aguilera, Belén Gómez-González
Published in: Nature Structural & Molecular Biology, Issue 24/5, 2017, Page(s) 439-443, ISSN 1545-9993
Publisher: Nature Publishing Group
DOI: 10.1038/nsmb.3395

A transcription-based mechanism for oncogenic β-catenin-induced lethality in BRCA1/2-deficient cells

Author(s): Rebecca A. Dagg, Gijs Zonderland, Emilia Puig Lombardi, Giacomo G. Rossetti, Florian J. Groelly, Sonia Barroso, Eliana M. C. Tacconi, Benjamin Wright, Helen Lockstone, Andrés Aguilera, Thanos D. Halazonetis, Madalena Tarsounas
Published in: Nature Communications, Issue 12/1, 2021, Page(s) 4919, ISSN 2041-1723
Publisher: Nature Publishing Group
DOI: 10.1038/s41467-021-25215-0

C. elegans THSC/TREX-2 deficiency causes replication stress and genome instability

Author(s): Angelina Zheleva, Lola P Camino, Nuria Fernández-Fernández, María García-Rubio, Peter Askjaer, Tatiana García-Muse, Andrés Aguilera
Published in: Journal of Cell Science, 2021, ISSN 0021-9533
Publisher: The Company of Biologists Ltd.
DOI: 10.1242/jcs.258435

The human nucleoporin Tpr protects cells from RNA-mediated replication stress

Author(s): Martin Kosar, Michele Giannattasio, Daniele Piccini, Apolinar Maya-Mendoza, Francisco García-Benítez, Jirina Bartkova, Sonia I. Barroso, Hélène Gaillard, Emanuele Martini, Umberto Restuccia, Miguel Angel Ramirez-Otero, Massimiliano Garre, Eleonora Verga, Miguel Andújar-Sánchez, Scott Maynard, Zdenek Hodny, Vincenzo Costanzo, Amit Kumar, Angela Bachi, Andrés Aguilera, Jiri Bartek, Marco Foia
Published in: Nature Communications, Issue 12/1, 2021, Page(s) 3937, ISSN 2041-1723
Publisher: Nature Publishing Group
DOI: 10.1038/s41467-021-24224-3

R-Loop–Mediated ssDNA Breaks Accumulate Following Short-Term Exposure to the HDAC Inhibitor Romidepsin

Author(s): Maryam Safari, Thomas Litman, Robert W. Robey, Andrés Aguilera, Arup R. Chakraborty, William C. Reinhold, Agnes Basseville, Lubov Petrukhin, Luigi Scotto, Owen A. O'Connor, Yves Pommier, Antonio T. Fojo, Susan E. Bates
Published in: Molecular Cancer Research, Issue 19/8, 2021, Page(s) 1361-1374, ISSN 1541-7786
Publisher: American Association for Cancer Research
DOI: 10.1158/1541-7786.mcr-20-0833

DNA-RNA hybrids at DSBs interfere with repair by homologous recombination

Author(s): Pedro Ortega, Jose Antonio Mérida-Cerro, Ana G Rondón, Belén Gómez-González, Andrés Aguilera
Published in: eLife, Issue 10, 2021, ISSN 2050-084X
Publisher: eLife Sciences Publications
DOI: 10.7554/elife.69881

Heterogeneity of DNA damage incidence and repair in different chromatin contexts

Author(s): Pedro Ortega, Belén Gómez-González, Andrés Aguilera
Published in: DNA Repair, Issue 107, 2021, Page(s) 103210, ISSN 1568-7864
Publisher: Elsevier BV
DOI: 10.1016/j.dnarep.2021.103210

TDP-43 mutations link Amyotrophic Lateral Sclerosis with R-loop homeostasis and R loop-mediated DNA damage

Author(s): Marta Giannini, Aleix Bayona-Feliu, Daisy Sproviero, Sonia I. Barroso, Cristina Cereda, Andrés Aguilera
Published in: PLOS Genetics, Issue 16/12, 2020, Page(s) e1009260, ISSN 1553-7404
Publisher: Public Library of Science
DOI: 10.1371/journal.pgen.1009260

Detection of DNA-RNA Hybrids In Vivo

Author(s): María García-Rubio, Sonia I. Barroso, Andrés Aguilera
Published in: Methods in Molecular Biology, 2018, Page(s) 347-361, ISBN 978-1-4939-7305-7
Publisher: Springer New York
DOI: 10.1007/978-1-4939-7306-4_24

The Sister-Chromatid Exchange Assay in Human Cells

Author(s): Emanuela Tumini, Andrés Aguilera
Published in: Homologous Recombination - Methods and Protocols, Issue 2153, 2021, Page(s) 383-393, ISBN 978-1-0716-0643-8
Publisher: Springer US
DOI: 10.1007/978-1-0716-0644-5_26

Analysis of repair of replication-born double-strand breaks by sister chromatid recombination in yeast

Author(s): Belén Gómez-González, Pedro Ortega, Andrés Aguilera
Published in: The DNA Replication-Repair Interface, Issue 661, 2021, Page(s) 121-138, ISBN 9780323907330
Publisher: Elsevier
DOI: 10.1016/bs.mie.2021.08.010

Detection of DNA Double-Strand Breaks by γ-H2AX Immunodetection

Author(s): Sonia I. Barroso, Andrés Aguilera
Published in: Homologous Recombination - Methods and Protocols, Issue 2153, 2021, Page(s) 1-8, ISBN 978-1-0716-0643-8
Publisher: Springer US
DOI: 10.1007/978-1-0716-0644-5_1

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