Patent applications

Aguilar, R., Moreno, M., Cepeda, M. "LNA-modified 10-23 DNAzyme that silences human MALAT1". PCT Patent Application PCT/CL2026/050056. Filed: April 6, 2026.

Aguilar, R., Moreno, M., Cepeda, M. "LNA-modified 10-23 DNAzyme with 12-nucleotide arms that silences human MALAT1". PCT Patent Application PCT/CL2026/050055. Filed: April 6, 2026.

Publications

2026

Singhal A, Mrozowich T, Rivera C, Chaudhury SN, Xu L, Aguilar R, Badmalia M, Lee JT, Patel TR, Sanbonmatsu KY.  Cleavage region organizes the structural architecture of the SINE-derived B2 repressive ribozyme. Commun Biol. 2026 Mar 23;9(1). doi: 10.1038/s42003-026-09819-0. PubMed PMID: 41872304; PubMed Central PMCID: PMC13172522.

Preprint: Aramis Cortes-Arias, Valeria Valdes, Marcelo Muñoz-González, Diego Leiva, Andrew Acevedo, Michelle Tobar-Lara, Nicole Farfán, Lilly Oni, Veronica A. Burzio, Adriana Rojas, Roberto Munita, Srinivas Somarowthu, Fernando J. Bustos, Rodrigo Aguilar. Deletion of the MALAT1 RNA 3’ end Promotes Transcript Decay, TALAM1 downregulation, and Inhibits Proliferation in Gastric and Breast Cancer Cells. bioRxiv 2026.05.20.726613

Preprint: Michelle Tobar-Lara, Andrea Matamoros, Marcelo Muñoz-González, Diego Leiva, Gunther Redenz, Gino Nardocci, Patricio Cabané, Alvaro A. Elorza, Rodrigo Aguilar. Increased MALAT1 Levels in Thyroid Cancer are Linked to Metabolic Reprogramming and Lymphatic Infiltration in Chilean population. bioRxiv 2025.12.23.696116

2025

Aguilar R, Rosenberg M, Levy V, Lee JT.  An evolving landscape of PRC2-RNA interactions in chromatin regulation. Nat Rev Mol Cell Biol. 2025 Aug;26(8):631-642. doi: 10.1038/s41580-025-00850-3. Epub 2025 Apr 30. Review. PubMed PMID: 40307460.

Muñoz-González M, Aguilar R, Moreno AA, Cepeda-Plaza M.  Influence of LNA modifications on the activity of the 10-23 DNAzyme. RSC Adv. 2025 Apr 22;15(17):13031-13040. doi: 10.1039/d5ra00161g. eCollection 2025 Apr 22. PubMed PMID: 40271416; PubMed Central PMCID: PMC12016023.

Muñoz-González M, Silva-Galleguillos V, Parra-Meneses V, Aguilar R, Cepeda-Plaza M.  Catalytic mechanisms of the 8-17 and 10-23 DNAzymes: shared mechanistic strategies. Org Biomol Chem. 2025 May 14;23(19):4564-4577. doi: 10.1039/d5ob00387c. Review. PubMed PMID: 40243498.

2024

Aguilar R, Mardones C, Moreno AA, Cepeda-Plaza M.  A guide to RNA structure analysis and RNA-targeting methods. FEBS J. 2025 Jun;292(11):2751-2766. doi: 10.1111/febs.17368. Epub 2024 Dec 24. Review. PubMed PMID: 39718192.

Cabané P, Correa C, Bode I, Aguilar R (*), Elorza AA (*). Biomarkers in Thyroid Cancer: Emerging Opportunities from Non-Coding RNAs and Mitochondrial Space. Int J Mol Sci. 2024 Jun 18;25(12). doi: 10.3390/ijms25126719. Review. PubMed PMID: 38928426; PubMed Central PMCID: PMC11204084. 

2023

Rojas F(*), Aguilar R(*), Almeida S, Fritz E, Corvalán D, Ampuero E, Abarzúa S, Garcés P, Amaro A, Diaz I, Arredondo C, Cortes N, Sanchez M, Mercado C, Varela-Nallar L, Gao FB, Montecino M, van Zundert B.  Mature iPSC-derived astrocytes of an ALS/FTD patient carrying the TDP43(A90V) mutation display a mild reactive state and release polyP toxic to motoneurons. Front Cell Dev Biol. 2023;11:1226604. doi: 10.3389/fcell.2023.1226604. eCollection 2023. PubMed PMID: 37645251; PubMed Central PMCID: PMC10461635.

Arratia F, Fierro C, Blanco A, Fuentes S, Nahuelquen D, Montecino M, Rojas A, Aguilar R.  Selective Concurrence of the Long Non-Coding RNA MALAT1 and the Polycomb Repressive Complex 2 to Promoter Regions of Active Genes in MCF7 Breast Cancer Cells. Curr Issues Mol Biol. 2023 May 30;45(6):4735-4748. doi: 10.3390/cimb45060301. PubMed PMID: 37367050; PubMed Central PMCID: PMC10297253.

Lee HG, Imaichi S, Kraeutler E, Aguilar R, Lee YW, Sheridan SD, Lee JT.  Site-specific R-loops induce CGG repeat contraction and fragile X gene reactivation. Cell. 2023 Jun 8;186(12):2593-2609.e18. doi: 10.1016/j.cell.2023.04.035. Epub 2023 May 19. PubMed PMID: 37209683. 

2022

Aguilar R, Spencer KB, Kesner B, Rizvi NF, Badmalia MD, Mrozowich T, Mortison JD, Rivera C, Smith GF, Burchard J, Dandliker PJ, Patel TR, Nickbarg EB, Lee JT.  Targeting Xist with compounds that disrupt RNA structure and X inactivation. Nature. 2022 Apr;604(7904):160-166. doi: 10.1038/s41586-022-04537-z. Epub 2022 Mar 30. PubMed PMID: 35355011.

Arredondo C, Cefaliello C, Dyrda A, Jury N, Martinez P, Díaz I, Amaro A, Tran H, Morales D, Pertusa M, Stoica L, Fritz E, Corvalán D, Abarzúa S, Méndez-Ruette M, Fernández P, Rojas F, Kumar MS, Aguilar R, Almeida S, Weiss A, Bustos FJ, González-Nilo F, Otero C, Tevy MF, Bosco DA, Sáez JC, Kähne T, Gao FB, Berry JD, Nicholson K, Sena-Esteves M, Madrid R, Varela D, Montecino M, Brown RH, van Zundert B.  Excessive release of inorganic polyphosphate by ALS/FTD astrocytes causes non-cell-autonomous toxicity to motoneurons. Neuron. 2022 May 18;110(10):1656-1670.e12. doi: 10.1016/j.neuron.2022.02.010. Epub 2022 Mar 10. PubMed PMID: 35276083; PubMed Central PMCID: PMC9119918.  

2021

Oh HJ, Aguilar R, Kesner B, Lee HG, Kriz AJ, Chu HP, Lee JT.  Jpx RNA regulates CTCF anchor site selection and formation of chromosome loops. Cell. 2021 Dec 9;184(25):6157-6173.e24. doi: 10.1016/j.cell.2021.11.012. Epub 2021 Dec 1. PubMed PMID: 34856126; PubMed Central PMCID: PMC8671370. 

Szanto A, Aguilar R, Kesner B, Blum R, Wang D, Cifuentes-Rojas C, Del Rosario BC, Kis-Toth K, Lee JT.  A disproportionate impact of G9a methyltransferase deficiency on the X chromosome. Genes Dev. 2021 Jul 1;35(13-14):1035-1054. doi: 10.1101/gad.337592.120. Epub 2021 Jun 24. PubMed PMID: 34168040; PubMed Central PMCID: PMC8247598. 

Aguilar R, Bustos FJ, Nardocci G, van Zundert B, Montecino M.  Epigenetic silencing of the osteoblast-lineage gene program during hippocampal maturation. J Cell Biochem. 2021 Apr;122(3-4):367-384. doi: 10.1002/jcb.29865. Epub 2020 Nov 2. PubMed PMID: 33135214. 

2020

Guajardo L, Aguilar R, Bustos FJ, Nardocci G, Gutiérrez RA, van Zundert B, Montecino M.  Downregulation of the Polycomb-Associated Methyltransferase Ezh2 during Maturation of Hippocampal Neurons Is Mediated by MicroRNAs Let-7 and miR-124. Int J Mol Sci. 2020 Nov 11;21(22). doi: 10.3390/ijms21228472. PubMed PMID: 33187138; PubMed Central PMCID: PMC7697002. 

Rizvi NF, Santa Maria JP Jr, Nahvi A, Klappenbach J, Klein DJ, Curran PJ, Richards MP, Chamberlin C, Saradjian P, Burchard J, Aguilar R, Lee JT, Dandliker PJ, Smith GF, Kutchukian P, Nickbarg EB.  Targeting RNA with Small Molecules: Identification of Selective, RNA-Binding Small Molecules Occupying Drug-Like Chemical Space. SLAS Discov. 2020 Apr;25(4):384-396. doi: 10.1177/2472555219885373. Epub 2019 Nov 8. PubMed PMID: 31701793. 

2019

Rojas A, Sepulveda H, Henriquez B, Aguilar R, Opazo T, Nardocci G, Bustos F, Lian JB, Stein JL, Stein GS, van Zundert B, van Wijnen AJ, Allende ML, Montecino M.  Mll-COMPASS complexes mediate H3K4me3 enrichment and transcription of the osteoblast master gene Runx2/p57 in osteoblasts. J Cell Physiol. 2019 May;234(5):6244-6253. doi: 10.1002/jcp.27355. Epub 2018 Sep 7. PubMed PMID: 30256410; PubMed Central PMCID: PMC7261149. 

López C, Aguilar R, Nardocci G, Cereceda K, Vander Stelt K, Slebe JC, Montecino M, Concha II.  Wnt/β-catenin signaling enhances transcription of the CX43 gene in murine Sertoli cells. J Cell Biochem. 2019 Apr;120(4):6753-6762. doi: 10.1002/jcb.27973. Epub 2018 Nov 11. PubMed PMID: 30417410. 

2017

Bustos FJ, Ampuero E, Jury N, Aguilar R, Falahi F, Toledo J, Ahumada J, Lata J, Cubillos P, Henríquez B, Guerra MV, Stehberg J, Neve RL, Inestrosa NC, Wyneken U, Fuenzalida M, Härtel S, Sena-Esteves M, Varela-Nallar L, Rots MG, Montecino M, van Zundert B.  Epigenetic editing of the Dlg4/PSD95 gene improves cognition in aged and Alzheimer's disease mice. Brain. 2017 Dec 1;140(12):3252-3268. doi: 10.1093/brain/awx272. PubMed PMID: 29155979; PubMed Central PMCID: PMC5841035. 

Sepulveda H(*), Aguilar R(*), Prieto CP, Bustos F, Aedo S, Lattus J, van Zundert B, Palma V, Montecino M.  Epigenetic Signatures at the RUNX2-P1 and Sp7 Gene Promoters Control Osteogenic Lineage Commitment of Umbilical Cord-Derived Mesenchymal Stem Cells. J Cell Physiol. 2017 Sep;232(9):2519-2527. doi: 10.1002/jcp.25627. Epub 2017 Mar 28. PubMed PMID: 27689934. 

2016

Lopez CI, Saud KE, Aguilar R, Berndt FA, Cánovas J, Montecino M, Kukuljan M.  The chromatin modifying complex CoREST/LSD1 negatively regulates notch pathway during cerebral cortex development. Dev Neurobiol. 2016 Dec;76(12):1360-1373. doi: 10.1002/dneu.22397. Epub 2016 May 31. PubMed PMID: 27112428. 

Aguilar R, Bustos FJ, Saez M, Rojas A, Allende ML, van Wijnen AJ, van Zundert B, Montecino M.  Polycomb PRC2 complex mediates epigenetic silencing of a critical osteogenic master regulator in the hippocampus. Biochim Biophys Acta. 2016 Aug;1859(8):1043-55. doi: 10.1016/j.bbagrm.2016.05.009. Epub 2016 May 20. PubMed PMID: 27216774; PubMed Central PMCID: PMC4958507. 

2015

Montecino M, Stein G, Stein J, Zaidi K, Aguilar R.  Multiple levels of epigenetic control for bone biology and pathology. Bone. 2015 Dec;81:733-738. doi: 10.1016/j.bone.2015.03.013. Epub 2015 Apr 10. Review. PubMed PMID: 25865577; PubMed Central PMCID: PMC4600412. 

Rojas A, Aguilar R, Henriquez B, Lian JB, Stein JL, Stein GS, van Wijnen AJ, van Zundert B, Allende ML, Montecino M.  Epigenetic Control of the Bone-master Runx2 Gene during Osteoblast-lineage Commitment by the Histone Demethylase JARID1B/KDM5B. J Biol Chem. 2015 Nov 20;290(47):28329-28342. doi: 10.1074/jbc.M115.657825. Epub 2015 Oct 9. PubMed PMID: 26453309; PubMed Central PMCID: PMC4653688. 

Cánovas J, Berndt FA, Sepúlveda H, Aguilar R, Veloso FA, Montecino M, Oliva C, Maass JC, Sierralta J, Kukuljan M.  The Specification of Cortical Subcerebral Projection Neurons Depends on the Direct Repression of TBR1 by CTIP1/BCL11a. J Neurosci. 2015 May 13;35(19):7552-64. doi: 10.1523/JNEUROSCI.0169-15.2015. PubMed PMID: 25972180; PubMed Central PMCID: PMC6705430. 

2014

Aguilar R(*), Grandy R(*), Meza D, Sepulveda H, Pihan P, van Wijnen AJ, Lian JB, Stein GS, Stein JL, Montecino M.  A functional N-terminal domain in C/EBPβ-LAP* is required for interacting with SWI/SNF and to repress Ric-8B gene transcription in osteoblasts. J Cell Physiol. 2014 Oct;229(10):1521-8. doi: 10.1002/jcp.24595. PubMed PMID: 24585571; PubMed Central PMCID: PMC4135720. 

2013

Henriquez B(*), Bustos FJ(*), Aguilar R, Becerra A, Simon F, Montecino M, van Zundert B.  Ezh1 and Ezh2 differentially regulate PSD-95 gene transcription in developing hippocampal neurons. Mol Cell Neurosci. 2013 Nov;57:130-43. doi: 10.1016/j.mcn.2013.07.012. Epub 2013 Aug 8. PubMed PMID: 23932971. 

2011

Grandy R, Sepulveda H, Aguilar R, Pihan P, Henriquez B, Olate J, Montecino M.  The Ric-8B gene is highly expressed in proliferating preosteoblastic cells and downregulated during osteoblast differentiation in a SWI/SNF- and C/EBPbeta-mediated manner. Mol Cell Biol. 2011 Jul;31(14):2997-3008. doi: 10.1128/MCB.05096-11. Epub 2011 May 23. PubMed PMID: 21606199; PubMed Central PMCID: PMC3133387. 

2010

Puchi M, García-Huidobro J, Cordova C, Aguilar R, Dufey E, Imschenetzky M, Bustos P, Morin V.  A new nuclear protease with cathepsin L properties is present in HeLa and Caco-2 cells. J Cell Biochem. 2010 Dec 1;111(5):1099-106. doi: 10.1002/jcb.22712. PubMed PMID: 20506357.