Researh & development

Epigenetics and Chromatin


In eukaryotes, DNA is compacted into chromatin, of which the basic unit is the nucleosome. Nucleosomes are comprised of two copies of each of four histones proteins wrapped by 147 base pairs of DNA. Compacting DNA allows the molecule to fit into cells in an orderly fashion but makes DNA less accessible to cellular machinery such as transcription factors. To overcome this difficulty, histone post-translational modifications and histone variants, among others, maintain chromatin in a dynamic state regulating its accessibility. Thus, genes that are required for cellular processes can be expressed or repressed at the appropriate time. Our research focuses on understanding the mechanisms by which chromatin and its modifications regulate cellular processes. We have two main areas of investigation: the analysis of post-translational modifications of newly synthesized histones and its impact on cellular processes, and the role of the viral chromatin in the replication of the Hepatitis B Virus.

  • Research Head: Alejandra Loyola
  • Undergraduate students: Constanza Ortiz  •  Scarleth Larrain
  • PhD Students: Patricio Zapata
  • Internship PhD Student: Blanca Llanquilef
  • Research Assistants: Perla Cruz
  • Research Associates: Rodrigo Villanueva

  • Juan Hormazábal (Former Ph.D. student, 2016-2020)
  • Pilar Castillo (Former undergraduate student, 2015-2019)
  • Rodrigo Flores (Former post-doctoral fellow, 2018-2019)
  • Francisca Álvarez Astudillo (Former undergraduate student and Ph.D. student, 2009-2019)
    Post-doctoral fellow at Universidad San Sebastian, Chile
  • Pía Vidal (Former post-doctoral fellow, 2018-2019)
    Assistant professor at Universidad Catolica de la Santisima Concepcion
  • Francisca Muñoz Garrido (Former undergraduate student and Ph.D. student, 2009-2018)
  • Sebastián Marty Lombardi (Former undergraduate student, 2015-2017)
    AG Siemens, Pharmakologisches Institut. Universität Heidelberg
  • Daniel Garrido Norambuena (Former Master degree student 2014-2017)
    Biochemist at Laboratorio Quimica Clínica Especializada.
  • Sergio Hernández Tapia (Former Ph.D. student, 2013-2017)
    Post-doctoral fellow at University of Marseille
  • Jocelyn Neira (Former Ph.D. student 2013-2017)
    Head of the Flow Cytometer Facility at UNAB
  • Cristian Doñas Cuadra (Former undergraduate student and Ph.D. student, 2012-2017)
    Post-doctoral fellow at Karolinska Institutet, Sweden
  • Lorena Rubio Quiroz (Former Master degree student 2013-2016)
  • Paola Merino (Former post-doctoral fellow, 2015)
    Post-doctoral fellow at Emory University
  • Yvo Flores León (Former Master degree student 2013-2015)
    Research assistant at INIA
  • Carlos Rivera Alvarez (Former Master degree student 2013-2015)
    Ph.D. student at Pontificia Universidad Católica de Chile/Massachusetts General Hospital, Harvard Medical School
  • Germán Púas Villega (Former undergraduate student, 2012-2014)
    Master of Philosophy, Universidad Santiago de Chile
  • Macarena Fritz Kelly (Former Ph.D. student, 2009-2013)
  • César Díaz Célis (Former post-doctoral fellow, 2012)
    Post-doctoral fellow at HHMI/University of California
  • Valentina Ugalde Tagle (Former Master degree student 2009-2011)
    Research assistant at Fundacion Ciencia & Vida
  • Francisco Saavedra (former PhD student and post-doctoral fellow, 2012-2021). Post-doctoral fellow at Washington University, Seattle, USA.
  • Tatiana Cruzes (former undergraduate student, 2019-2020)

National Collaborations:
• Dr. Iván Alfaro (Universidad del Desarrollo)
• Dra. Andrea Calixto (Universidad Mayor)
• Dr. Rodrigo Pacheco (Fundación Ciencia & Vida)
• Dra. Raquel Quatrini (Fundación Ciencia & Vida)
• Dr. Mario Rosemblatt (Fundación Ciencia & Vida)
• Dr. Rodrigo Villanueva (Fundación Ciencia & Vida)

International Collaborations:
• Dr. Genevieve Almouzni (Institut Curie, Paris, France)
• Dr. Eric Campos (University of Toronto, Toronto, Canada)
• Dra. Thelma Escobar (Washington University)
• Dr. Axel Imhof (Ludwig-Maximilians Universität München, Munich, Germany)
• Dr. Danny Reinberg (Howard Hughes Medical Institute / NYU Langone School of Medicine, New York, USA)


Hernández, S.; Álvarez-Astudillo, F.; Garrido, D.; Prieto, C.; Loyola, A.; Villanueva, R.A. (2021) “Canonical and Divergent N-Terminal HBx Isoform Proteins Unveiled: Characteristics and Roles during HBV Replication”. Biomedicines. 9, 1701.

Hormazabal, J.; Saavedra, F.; Espinoza-A, C.; Martinez, N.W.; Cruces, T.; Alfaro, I.E.; Loyola A. (2022) “Chaperone mediated autophagy contributes to the newly synthesized histones H3 and H4 quality control”. Nucleic Acids Research 50(4):1875-1887. https://doi: 10.1093/nar/gkab1296.

LeRoy G., Loyola A., Lane W. S., Reinberg D. Purification and characterization of a human factor that assembles and remodels chromatin. J. Biol. Chem. 275(20): 14787–14790 (2000) | PDF | Abstract

Loyola A., LeRoy G., Wang Y-H., Reinberg D. Reconstitution of recombinant chromatin establishes a requirement for histone-tail modifications during chromatin assembly and transcription. Genes Dev. 15(21): 2837–2851 (2001) | PDF | Abstract

He S., Bauman D., Davis J. S., Loyola A., Nishioka K., Gronlund J. L., Reinberg D., Meng F., Kelleher N., McCafferty D. G. Facile synthesis of site-specifically acetylated and methylated histone proteins: Reagents for evaluation of the histone code hypothesis. PNAS 100(21): 12033-12038 (2003) | PDF | Abstract

Loyola A., Reinberg D. Histone deposition and chromatin assembly by RSF. Methods, vol 31: 96–103 (2003) | PDF | Abstract

Loyola A., Huang J. Y., LeRoy G., Hu S., Wang Y-H., Donnelly R. J., Lane W. S., Lee S-C., Reinberg D. Functional analysis of the subunits of the chromatin assembly factor RSF. Mol. Cell. Biol. 23(19): 6759–6768 (2003) | PDF | Abstract

Vaquero A., Loyola A., Reinberg D. The constantly changing face of chromatin. Sci. Aging Knowl. Environ. 2003(14): 01-16 (2003) | PDF | Abstract

Loyola A., Almouzni G.Bromodomains in living cells participate in deciphering the histone code. Trends Cell Biol. 14(6): 279-281 (2004) | PDF | Abstract

Loyola A., Almouzni G.Histone chaperones, a supporting role in the limelight. Institut Curie/Section de Recherche 1677, 03-11 (2004) | PDF | Abstract

Loyola, A., He S., Oh S., McCafferty D. G., Reinberg D. Techniques used to study transcription on chromatin templates. Methods Enzymol., vol. 377, pp 474-499 (2004)

Loyola L., Bonaldi T., Roche D., Imhof A., Almouzni G. PTMs on H3 variants before chromatin assembly potentiate their final epigenetic state. Mol. Cell. 24, 309–316 (2006) | PDF | Abstract

Loyola A., Almouzni G. Marking histone H3 variants: How, when and why?. Trends Biochem. Sci. 32(09): 425-433 (2007) | PDF | Abstract

Loyola A., Tagami H., Bonaldi T., Roche D., Quivy J. P., Imhof A., Nakatani Y., Dent S. Y. R., Almouzni G. The HP1α -CAF1-SetDB1-containing complex provides H3K9me1 for Suv39-mediated K9me3 in pericentric heterochromatin. EMBO Rep. 10(7): 769-775 (2009) | PDF | Abstract

Alvarez F., Muñoz F., Schilcher P., Imhof A., Almouzni G., Loyola A. Sequential establishment of marks on soluble histones H3 and H4. J. Biol. Chem. 20(286): 17714-17721 (2011) | PDF | Abstract

Doñas C., Fritz M., Manríquez V., Tejón G., Bono M. R., Loyola A., Rosemblatt M.Trichostatin A promotes the generation and suppressive functions of regulatory T cells. Clin. Dev. Immunol 2013, 679804 (2013) | PDF | Abstract

Rivera C., Gurard-Levin Z. A., Almouzni G., Loyola A. Histone lysine methylation and chromatin replication. Biochim. Biophys. Acta 1839(12):1433-1439 (2014)

Ugarte G. D., Vargas M. F., Medina M. A., León P., Necuñir D., Elorza A. A., Gutiérrez S. E., Moon R. T., Loyola A., De Ferrari G. V. Wnt signaling induces transcription, spatial proximity and translocation of fusion gene partners in human hematopoietic cells. Blood 126(15): 1785 (2015)

Rivera C., Saavedra F., Alvarez F., Díaz-Celis C., Ugalde V., Li J., Forné I., Gurard-Levin Z. A., Almouzni G., Imhof A., Loyola A. Methylation of histone H3 lysine 9 occurs during translation. Nucleic Acids Res. 43(19): 9097-9106 (2015)

Hernández S., Jiménez G., Alarcón V., Prieto C., Muñoz F., Riquelme C., Venegas M., Brahm J., Loyola A., Villanueva R. A. Replication of a chronic hepatitis B virus genotype F1b construct. Arch. Virol. 161(3): 583 (2016)

Alarcón V., Hernández S., Rubio L., Alvarez F., Flores Y., Varas-Godoy M., De Ferrari G. V., Kann M., Villanueva R. A., Loyola A. The enzymes LSD1 and Set1A cooperate with the viral protein HBx to establish an active hepatitis B viral chromatin state. Sci. Rep. May 13; 6:25901. doi: 10.1038/srep25901 (2016) | PDF

Saavedra F., Rivera C., Rivas E., Merino P., Garrido D., Hernández S., Forné I., Vassias I., Gurard-Levin Z.A., Alfaro I.E., Imhof A., Almouzni G.A., Loyola A. PP32 and SET/TAF-Iβ proteins regulate the acetylation of newly synthesized histone H4. Nucleic Acids Res. 45 (20): 11700-11710. DOI: 10.1093/nar/gkx775 (2017)

Álvarez F., Loyola A.Histone variants: Structure, function and implication in diseases (Chapter 7). In: Gene Regulation, Epigenetics and Hormone Signaling, edited by Dr. S. Mandal. Publishing Editor: Gregor Cicchetti. Wiley-VCH in Weinheim, Germany. Pp: 209-226. DOI: 10.1002/9783527697274.ch7 (2017)

Saavedra F., Marty-Lombardi S., Loyola A. “Characterization of Posttranslational Modifications on Histone Variants”. In: Histone Variants. Methods in Molecular Biology, edited by G. Orsi G and G. Almouzni, vol 1832. Humana Press, New York, NY. DOI: 10.1007/978-1-4939-8663-7_2 (2018) | PDF

Saavedra F., Boyarchuk E., Alvarez F., Almouzni G., Loyola A. Metabolic deregulations affecting chromatin architecture: One-carbon metabolism and Krebs cycle impact histone methylation. In: The DNA, RNA, and Histone Methylomes, edited by S. Jurga and J. Barciszewski., vol 9. RNA TECHNOLOGIES, Springer Series (2019) | PDF

Hernández S., Díaz A., Loyola A., Villanueva RA. Recombinant HCV NS3 and NS5b enzymes exhibit multiple posttranslational modifications for potential regulation. Virus Genes. 55 (2): 227-232. DOI: 10.1007/s11262-019-01638-2 (2019) | PDF

Flores-Rios R., Quatrini R., Loyola A. Endogenous and Foreign Nucleoid-Associated Proteins of Bacteria: occurrence, interactions and effects on Mobile Genetic Elements and host ́s biology. Computational and Structural Biotechnology Journal. 17: 746-756. DOI: (2019) | PDF

Saavedra F., Gurard-Levin ZA., Rojas-Villalobos C., Vassias I., Quatrini R., Almouzni G., Loyola A. JMJD1B, a novel player in histone H3 and H4 processing to ensure genome stability. Epigenetics & Chromatin. 13:6. DOI: 10.1186/s13072-020-00331-1 (2020) | PDF

Prieto, C.; Montecinos, J.; Jim, G.; Riquelme, C.; Garrido, D.; Hern, S.; Loyola, A.; Villanueva, R.A. “Phosphorylation of phylogenetically conserved amino acid residues confines HBx within different cell compartments of human hepatocarcinoma cells”. Molecules, 26, 1254.

Escobar T., *Loyola A. and Reinberg D.“Parental nucleosome segregation and the inheritance of cellular identity”. (2021) Nature Reviews Genetics. *equal contribution

Doñas C., Neira J., Osorio-Barrios F., Carrasco M., Prado C., Loyola A., Pacheco R. and Rosemblatt M. (2021)“The demethylase inhibitor GSK-J4 limits inflammatory colitis by promoting de novo synthesis of retinoic acid in dendritic cells”. Scientific Reports. 11(1):1342. DOI: 10.1038/s41598-020-79122-3

Alvarez F., Garrido D., Varas-Godoy M., Gutiérrez JL., Villanueva RA. and Loyola A. (2021) “The Histone Variant H3.3 Regulates the Transcription of the Hepatitis B Virus”. Annals of Hepatolgy. 21:100261. DOI: 10.1016/j.aohep.2020.09.005

Principal investigator

Alejandra Loyola, PhD