In eukaryotic cells the genetic material is packaged into chromatin and the basic subunit is the nucleosome. Nucleosomes represent physical barriers for cellular processes that use DNA as a template. Chromatin is a dynamic structure and cells count on ATP dependent Chromatin Remodelling Complexes (SNF2 family) and with histone modifiers. The first group is responsible for making conformational changes on nucleosome organization and positioning and the second group has enzymatic activities capable of introducing post translacional modifications into histones building a code that allows the recruitment of specific complexes.
Many of these mechanisms are very well conserved from yeast to human. In our lab, we have experience in the Saccharomyces cerevisiae model, and we are interested in studying nucleosome positioning, remodelling complexes and histone modifiers in biologically relevant organisms. Currently, in a collaboration with Dr. Guillermo D. Alonso (http://ingebi-conicet.gov.ar/es_senalizacion-y-mecanismos-adaptativos-en-tripanosomatidos) we are studying chromatin structure and function in trypanosomatid parasites, very early branching eukaryotes. These organisms are of great interest, not only they are clinically relevant, they present unusual histones and post translational modifications, and their gene expression is punctuated by special histone variants. To approach these studies, we use genomics and bioinformatic techniques as well as molecular biology and biochemistry.
Group members
Sofía Balestra
Undergraduate student
Lic. Santiago Carena
PhD student
Lic. María del Rosario López
PhD student
Publications
Improving genome-wide mapping of nucleosomes in Trypanosome cruzi
Paula Beati1, Milena Massimino Stepñicka1, Salome C. Vilchez Larrea, Pablo Smircich, Guillermo D. Alonso*, Josefina Ocampo*. Plos ONE 2023 Nov 21;18(11):e0293809. doi: 10.1371/journal.pone.0293809. eCollection 2023.
*co-correspondencia
Interplay among ATP-Dependent Chromatin Remodelers Determines Chromatin Organisation in Yeast
Prajapati HK, Ocampo J*, Clark DJ* (2020)
* co-corresponding authors
doi.org/10.3390/biology9080190
Accessibility of promoter DNA is not the primary determinant of chromatin mediated gene regulation
Chereji RV*, Eriksson PR*, Ocampo J*, Prajapati HK, Clark DJ (2019)
* equal contribution authorship
Genome research, 2019 Dec;29(12):1985-1995 DOI: 10.1101/gr.249326.119
Contrasting roles of the RSC and ISW1/CHD1 chromatin remodelers in RNA polymerase II elongation and termination
Ocampo J, Chereji RV, Eriksson PR, Clark DJ. (2019)
Genome Res. 2019 Jan 25. doi: 10.1101/gr.242032.118
Gcn4 binding in coding regions can activate internal and canonical 5′ promoters in yeast
Rawal Y, Chereji RV, Valabhoju V, Qiu H, Ocampo J, Clark DJ, Hinnebusch AG. (2018)
Molecular Cell 70(2):297-311, Apr 19, 2018
MNase-sensitive Complexes in Yeast: Nucleosomes and Non-histone Barriers
Chereji R*, Ocampo J*, Clark D. (2017)
* Equal contribution
Molecular Cell 65, 578–580, February 2, 2017
The Proto-chromatosome: A Fundamental Subunit of Chromatin?
Ocampo J*, Cui F*, Zhurkin VB, Clark DJ. (2016)
* Equal contribution
Nucleus. 2016 Jul 3;7(4):382-7
The ISW1 and CHD1 ATP-dependent chromatin remodelers compete to set nucleosome spacing in vivo
Ocampo J1, Chereji RV1, Eriksson PR, Clark DJ. (2016)
1 Equal contribution
Nucleic Acid Research. 2016 Jun 2; 44 (10) 4625-35.
A Positive Twist to the Centromeric Nucleosome
Ocampo J and Clark DJ (2015)
Cell Reports. Preview, 2015 Oct 27;13(4):645-6.
Novel Nucleosomal Particles Containing Core Histones and Linker DNA but no Histone H1
Cole HA*, Cui F*, Ocampo J*, Burke TL, Nikitina T, Nagarajavel V, Kotomura N, Zhurkin VB, Clark DJ. (2015)
* Igual contribución de los autores
Nucleic Acids Res. 2015 Sep 22. pii: gkv943
Heavy transcription of yeast genes correlates with differential loss of histone H2B relative to H4 and queued RNA polymerases
Cole HA, Ocampo J, Iben JR, Chereji RV, Clark DJ. (2014)
Nucleic Acids Res. 2014 Nov 10;42(20):12512-22.
Projects
– Chromatin structure in the different stages of Trypanosome cruzi life cycle: impact in differential gene expression
– Characterization of TcDOT1a and TcDOT1b histone methyl transferases
– Role of H3K76me in T. cruzi life cycle
Grants
Proyectos de Investigación Científica y Tecnológica 2018 (PICT 2018). ANPCyT, FONCyT. Nro. 00621
“Caracterización de las isoformas TcDOT1a y TcDOT1b e implicancia de la metilación diferencial de H3K76 en los distintos estadios del ciclo de vida de Trypanosoma cruzi”
Proyectos de Investigación Científica y Tecnológica 2020 (PICT 2020). ANPCyT, FONCyT. Nro. 0047
“Metilación diferencial de H3K76 y del ADN en los distintos estadios del ciclo de vida de Trypanosoma cruzi”
Proyectos de Investigación Bianuales para Investigadoras/es Asistentes y Adjuntas/os de reciente ingreso al CONICET PIBBA 2022-2023.
“Implicancias de la metilación diferencial de H3K76 mediada por las isoformas TcDOT1A y TcDOT1B en los distintos estadios del ciclo de vida de Trypanosoma cruzi”
Former members
Lic. Malena Balestrasse
Lic. Valentina Sol Vela
Lic. Romina Zambrano Siri
- Adjunt Investigator CONICET
- 2002 Biochemist, National University of Rosario
- 2003-2004 Contractor at Parasitology Department of ANLIS “Dr. Carlos G. Malbrán”
- 2010 Dra. de la UBA área Química Biólogica FCEyN UBA
- 2010-2012 Post-doctoral fellow CONICET
- 2012-2018 Post-doctoral (Visiting Fellow) NICHD NIH
- 2015 Fellow Award for Research Excellence (FARE) 2015, NIH
- 2017 Fellow Award for Research Excellence (FARE) 2017, NIH