{"id":20349,"date":"2026-04-09T07:14:24","date_gmt":"2026-04-09T06:14:24","guid":{"rendered":"https:\/\/cabd.es\/investigation\/departments\/regulacion-genica-y-morfogenesis\/dr-ozren-bogdanovic\/"},"modified":"2026-05-22T08:42:05","modified_gmt":"2026-05-22T07:42:05","slug":"dr-ozren-bogdanovic","status":"publish","type":"page","link":"https:\/\/cabd.es\/en\/investigation\/departments\/genome-dynamics\/dr-ozren-bogdanovic\/","title":{"rendered":"Dr Ozren Bogdanovic"},"content":{"rendered":"

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Genome Dynamics<\/p>\n

Developmental Epigenomics<\/h1>\n

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Dr Ozren Bogdanovic<\/h4>\n

Principal Investigator<\/p>\n

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Summary<\/h2>\n
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How a complex, multicellular organism develops from a single fertilised egg is one of the most intriguing concepts in biology. This phenomenon is further augmented by the fact that metazoan organisms consist of many distinct cell types that largely differ in their morphology, function and gene expression patterns, yet contain identical genomic DNA. Nowadays, we know that such a vast variety of cell types is generated and maintained by mechanisms that in most cases do not involve alterations in the primary DNA sequence. Such epigenetic mechanisms include (but are not limited to): DNA methylation, post-translational modifications of histone tails, long non-coding RNA and nucleosome positioning. The development of massively parallel DNA sequencing technologies has facilitated the generation of precise epigenome maps corresponding to myriad cell-lines, tissues and disease samples with the aim of deciphering the epigenomic component of diverse cellular forms and functions. Through the use of vertebrate and invertebrate models systems, the research in our lab aims to understand the contributions of the epigenome to embryonic development, cell differentiation, evolution, and disease. A more detailed description of specific projects can be found below:<\/div>\n

1. Non-canonical DNA methylation as a regulator of embryonic genome function<\/strong>
We have recently described embryonic reprogramming of non-canonical DNA methylation (mCH, where H = C, T, A) within mosaic satellite repeats (MOSAT mCH), coincident with zygotic genome activation (Ross et al, 2020; Nuc Acids Res). Our CRISPR\/Cas9 functional analyses in zebrafish larvae have unravelled Dnmt3ba as the primary MOSAT mCH methyltransferase enzyme. By using CRISPR\/Cas9 and Cas13d genome editing technology in zebrafish, we are functionally interrogating the contribution of mCH and Dnmt3ba to embryogenesis, to better understand the developmental requirements for proper mCH patterning.<\/p>\n

2. The rogue germline: epigenetic regulation of cancer testis antigens in embryonic development and cancer<\/strong>
A surprisingly small number of genes becomes silenced by promoter DNA hypermethyation during vertebrate embryogenesis. In many cases, these genes are essential regulators of germline development that are frequently found altered in multiple adult cancers. Through a combination of biochemical and zebrafish transgenesis approaches we are trying to understand the mechanisms of this targeting specificity as well as the roles of these genes in embryonic development cancer formation in vivo.<\/p>\n

3. Bluebottle blues: System level characterisation of the siphonophore, Indo-Pacific man o’ war (bluebottle)<\/strong>
The overarching objective of this project is to utilise system level approaches and functional analysis to establish foundation knowledge of the Indo-Pacific man o’ war (bluebottle), a marine animal that is infamous for their painful sting. Bluebottles are not jellyfish, yet are siphonophores, a remarkable group of animals that are made up of colonies of highly modified individuals (zooids). This makes them an exciting species to study at the genome, epigenome and proteome levels to further our understanding of animal multicellularity and toxins.<\/p>\n<\/div>\n<\/div>\n

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Relevant publications<\/a><\/h2>\n
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1. Skvortsova K, Bertrand S, Voronov D, Duckett PE, Ross SE, Magri MS, Maeso I, Weatheritt RJ, G\u00f3mez Skarmeta JL, Arnone MI, Escriva H,\u00a0Bogdanovic O<\/strong>. Active DNA demethylation of developmental cis-regulatory regions predates vertebrate origins.\u00a0bioRxiv<\/a>. 2021.11.07.467601.<\/p>\n

2. Angeloni A, Ferguson J,\u00a0Bogdanovic O<\/strong>. Nanopore Sequencing and Data Analysis for Base-Resolution Genome-Wide 5-Methylcytosine Profiling.\u00a0Methods Mol Biol<\/a>. 2022;2458:75-94.<\/p>\n

3. Skvortsova K,\u00a0Bogdanovic O<\/strong>. TAB-seq and ACE-seq Data Processing for Genome-Wide DNA hydroxymethylation Profiling.\u00a0Methods Mol Biol<\/a>. 2021;2272:163-178.<\/p>\n

4. Ross SE, Hesselson D,\u00a0Bogdanovic O<\/strong>. Developmental Accumulation of Gene Body and Transposon Non-CpG Methylation in the Zebrafish Brain.\u00a0Front Cell Dev Biol<\/a>. 2021 Mar 4;9:643603.<\/p>\n

5. Ross SE, Angeloni A, Geng FS, de Mendoza A,\u00a0Bogdanovic O<\/strong>. Developmental remodelling of non-CG methylation at satellite DNA repeats.\u00a0Nucleic Acids Res<\/a>. 2020 Dec 16;48(22):12675-12688.<\/p>\n

6. de Mendoza A, Lister R,\u00a0Bogdanovic O<\/strong>. Evolution of DNA Methylome Diversity in Eukaryotes.\u00a0J Mol Biol<\/a>. 2019 Nov 11:S0022-2836(19)30659-X.<\/p>\n

7. Skvortsova K, Tarbashevich K, Stehling M, Lister R, Irimia M, Raz E,\u00a0Bogdanovic O<\/strong>. Retention of paternal DNA methylome in the developing zebrafish germline.\u00a0Nat Commun<\/a>. 2019 Jul 11;10(1):3054.<\/p>\n

8. Marl\u00e9taz F*, Firbas PN*, Maeso I*, Tena JJ*,\u00a0Bogdanovic O<\/strong>*, Perry M*, Wyatt CDR, de la Calle-Mustienes E, Bertrand S, Burguera D, Acemel RD, van Heeringen SJ, Naranjo S, Herrera-Ubeda C, Skvortsova K, Jimenez-Gancedo S, Aldea D, Marquez Y, Buono L, Kozmikova I, Permanyer J, Louis A, Albuixech-Crespo B, Le Petillon Y, Leon A, Subirana L, Balwierz PJ, Duckett PE, Farahani E, Aury JM, Mangenot S, Wincker P, Albalat R, Benito-Guti\u00e9rrez \u00c8, Ca\u00f1estro C, Castro F, D’Aniello S, Ferrier DEK, Huang S, Laudet V, Marais GAB, Pontarotti P, Schubert M, Seitz H, Somorjai I, Takahashi T, Mirabeau O, Xu A, Yu JK, Carninci P, Martinez-Morales JR, Crollius HR, Kozmik Z, Weirauch MT, Garcia-Fern\u00e0ndez J, Lister R, Lenhard B, Holland PWH, Escriva H, G\u00f3mez-Skarmeta JL, Irimia M. Amphioxus functional genomics and the origins of vertebrate gene regulation.\u00a0Nature<\/a>. 2018 Dec;564(7734):64-70.<\/p>\n

9. Skvortsova K, Iovino N,\u00a0Bogdanovic O<\/strong>. Functions and mechanisms of epigenetic inheritance in animals.\u00a0Nat Rev Mol Cell Biol<\/a>. 2018 Dec;19(12):774-790.<\/p>\n

10.\u00a0Bogdanovic O<\/strong>, Smits AH, de la Calle Mustienes E, Tena JJ, Ford E, Williams R, Senanayake U, Schultz MD, Hontelez S, van Kruijsbergen I, Rayon T, Gnerlich F, Carell T, Veenstra GJ, Manzanares M, Sauka-Spengler T, Ecker JR, Vermeulen M, G\u00f3mez-Skarmeta JL, Lister R. Active DNA demethylation at enhancers during the vertebrate phylotypic period.\u00a0Nat Genet<\/a>. 2016 Apr;48(4):417-26.<\/p>\n<\/div>\n

For more detailed information about our work please check out the\u00a0lab website<\/a>.<\/p>\n<\/div>\n<\/div>\n<\/div>\n<\/div>\n<\/div>\n<\/div>\n<\/div>\n<\/div>\n<\/div>\n<\/div>\n<\/div>\n<\/div>\n

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Lab members & collaborators<\/h2>\n
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Lab members<\/h3>\n

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Principal Investigator:<\/h4>\n

Dr Ozren Bogdanovic, CSIC Tel: 954 34 86 87<\/p>\n

Associate Professor (adjunct) \u2013 UNSW (Sydney, Australia) Tel: 954 34 86 87<\/p>\n

Collaborators<\/h3>\n

Dr Alex de Mendoza (QMUL, UK)
Dr Manuel Irimia (CRG, ES)
Prof Susan Clark (Garvan Institute, AU)
Dr Daniel Hesselson (University of Sydney, AU)
Prof Greg Neely (University of Sydney, AU)
Dr Maria Ina Arnone (Stazione Zoologica Anton Dohrn, IT)
Dr Hector Escriva (CNRS, FR)
Prof Vanessa Hayes (University of Sydney, AU)
Prof Scott Cummins (University of Sunshine Coast, AU)
Dr Andrea Pauli (IMP, AT)
Prof Michiel Vermeulen (Radboud University, NL)<\/p>\n

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Genome Dynamics Developmental Epigenomics Dr Ozren Bogdanovic Principal Investigator Summary   How a complex, multicellular organism develops from a single fertilised egg is one of the most intriguing concepts in […]<\/p>\n","protected":false},"author":3052,"featured_media":0,"parent":21588,"menu_order":0,"comment_status":"closed","ping_status":"closed","template":"","meta":{"_et_pb_use_builder":"on","_et_pb_old_content":"","_et_gb_content_width":"","footnotes":""},"class_list":["post-20349","page","type-page","status-publish","hentry"],"_links":{"self":[{"href":"https:\/\/cabd.es\/en\/wp-json\/wp\/v2\/pages\/20349","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/cabd.es\/en\/wp-json\/wp\/v2\/pages"}],"about":[{"href":"https:\/\/cabd.es\/en\/wp-json\/wp\/v2\/types\/page"}],"author":[{"embeddable":true,"href":"https:\/\/cabd.es\/en\/wp-json\/wp\/v2\/users\/3052"}],"replies":[{"embeddable":true,"href":"https:\/\/cabd.es\/en\/wp-json\/wp\/v2\/comments?post=20349"}],"version-history":[{"count":12,"href":"https:\/\/cabd.es\/en\/wp-json\/wp\/v2\/pages\/20349\/revisions"}],"predecessor-version":[{"id":24237,"href":"https:\/\/cabd.es\/en\/wp-json\/wp\/v2\/pages\/20349\/revisions\/24237"}],"up":[{"embeddable":true,"href":"https:\/\/cabd.es\/en\/wp-json\/wp\/v2\/pages\/21588"}],"wp:attachment":[{"href":"https:\/\/cabd.es\/en\/wp-json\/wp\/v2\/media?parent=20349"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}