Associate Professor Ozren Bogdanovic
Adjunct Associate Professor

Associate Professor Ozren Bogdanovic

2012 – PhD (Molecular Biology) Radboud University Nijmegen - the Netherlands
2004 – BSc / MSc (Molecular Biology) University of Zagreb - Croatia

Science
School of Biotech & Biomolecular Science

Ozren Bogdanovic is a Lab Head at the  Garvan Institute of Medical Research.  Ozren obtained his PhD from Radboud University (Nijmegen, the Netherlands), where he worked on DNA methylation and methyl CpG-binding proteins during early embryogenesis in the lab of Gert Jan Veenstra. Ozren then moved to the Andalusian Centre for Developmental Biology (CABD, Seville - Spain) to work with Jose Luis Gomez-Skarmeta and Juan Ramon Martinez-Morales on various aspects of embryonic gene regulation. There he led a number of developmental genetics projects and participated in the adaptation of next-generation sequencing technologies to vertebrate embryonic material. In 2013 Ozren started his postdoctoral studies at the University of Western Australia in the laboratory of Ryan Lister where he conducted research in the field of developmental and evolutionary epigenomics. His work at UWA includes the discovery of a highly conserved epigenome remodeling event associated with vertebrate body plan formation. Ozren joined the Garvan Institute of Medical Research as a Lab Head in February 2017. At the Garvan Ozren is applying integrative approaches to study the contribution of the epigenome to vertebrate embryogenesis and cancer formation.

Phone
+61 (02) 9295 8340
Location
Garvan Institute of Medical Research 384 Victoria Street Darlinghurst, NSW, 2010
  • Book Chapters | 2021
    2021, 'Erratum: Correction to: TET Proteins and DNA Demethylation (Methods in molecular biology (Clifton, N.J.) (2021) 2272 (29-44))', in , pp. C1, http://dx.doi.org/10.1007/978-1-0716-1294-1_18
    Book Chapters | 2021
    2021, 'Generation and Molecular Characterization of Transient TET1/2/3 Zebrafish Knockouts', in TET Proteins and DNA Demethylation: Methods and Protocols, pp. 281 - 317, http://dx.doi.org/10.1007/978-1-0716-1294-1_17
    Book Chapters | 2021
    2021, 'TAB-seq and ACE-seq Data Processing for Genome-Wide DNA hydroxymethylation Profiling', in TET Proteins and DNA Demethylation: Methods and Protocols, pp. 163 - 178, http://dx.doi.org/10.1007/978-1-0716-1294-1_9
  • Journal articles | 2023
    2023, 'Memory of stochastic single-cell apoptotic signaling promotes chemoresistance in neuroblastoma', Science Advances, 9, pp. eabp8314, http://dx.doi.org/10.1126/sciadv.abp8314
    Journal articles | 2023
    2023, 'The Australasian dingo archetype: de novo chromosome-length genome assembly, DNA methylome, and cranial morphology', GigaScience, 12, http://dx.doi.org/10.1093/gigascience/giad018
    Journal articles | 2023
    2023, 'The little skate genome and the evolutionary emergence of wing-like fins', Nature, 616, pp. 495 - 503, http://dx.doi.org/10.1038/s41586-023-05868-1
    Journal articles | 2022
    2022, 'A developmentally programmed splicing failure contributes to DNA damage response attenuation during mammalian zygotic genome activation', Science Advances, 8, pp. eabn4935, http://dx.doi.org/10.1126/sciadv.abn4935
    Journal articles | 2022
    2022, 'Active DNA demethylation of developmental cis-regulatory regions predates vertebrate origins', Science Advances, 8, pp. eabn2258, http://dx.doi.org/10.1126/sciadv.abn2258
    Journal articles | 2022
    2022, 'Large-scale manipulation of promoter DNA methylation reveals context-specific transcriptional responses and stability', Genome Biology, 23, http://dx.doi.org/10.1186/s13059-022-02728-5
    Journal articles | 2022
    2022, 'Multiomic atlas with functional stratification and developmental dynamics of zebrafish cis-regulatory elements', Nature Genetics, 54, pp. 1037 - 1050, http://dx.doi.org/10.1038/s41588-022-01089-w
    Journal articles | 2022
    2022, 'Nanopore Sequencing and Data Analysis for Base-Resolution Genome-Wide 5-Methylcytosine Profiling', Methods in molecular biology (Clifton, N.J.), 2458, pp. 75 - 94, http://dx.doi.org/10.1007/978-1-0716-2140-0_5
    Journal articles | 2022
    2022, 'The Australian dingo is an early offshoot of modern breed dogs', Science Advances, 8, http://dx.doi.org/10.1126/sciadv.abm5944
    Journal articles | 2021
    2021, 'Analysis of gene network bifurcation during optic cup morphogenesis in zebrafish', Nature Communications, 12, pp. 3866, http://dx.doi.org/10.1038/s41467-021-24169-7
    Journal articles | 2021
    2021, 'Author Correction: Analysis of gene network bifurcation during optic cup morphogenesis in zebrafish (Nature Communications, (2021), 12, 1, (3866), 10.1038/s41467-021-24169-7)', Nature Communications, 12, http://dx.doi.org/10.1038/s41467-021-24834-x
    Journal articles | 2021
    2021, 'Chromosome-length genome assembly and structural variations of the primal Basenji dog (Canis lupus familiaris) genome', BMC Genomics, 22, http://dx.doi.org/10.1186/s12864-021-07493-6
    Journal articles | 2021
    2021, 'Developmental Accumulation of Gene Body and Transposon Non-CpG Methylation in the Zebrafish Brain', Frontiers in Cell and Developmental Biology, 9, http://dx.doi.org/10.3389/fcell.2021.643603
    Journal articles | 2021
    2021, 'Krüppel-like factor 1 is a core cardiomyogenic trigger in zebrafish', Science, 372, pp. 201 - 205, http://dx.doi.org/10.1126/science.abe2762
    Journal articles | 2021
    2021, 'Sequence determinants, function, and evolution of CpG islands', Biochemical Society Transactions, 49, pp. 1109 - 1119, http://dx.doi.org/10.1042/BST20200695
    Journal articles | 2021
    2021, 'The emergence of the brain non-CpG methylation system in vertebrates', Nature Ecology and Evolution, 5, pp. 369 - 378, http://dx.doi.org/10.1038/s41559-020-01371-2
    Journal articles | 2020
    2020, 'A developmentally programmed splicing failure attenuates the DNA damage response during mammalian zygotic genome activation', , http://dx.doi.org/10.1101/2020.11.25.397794
    Journal articles | 2020
    2020, 'A zebrafish functional genomics model to investigate the role of human A20 variants in vivo', Scientific Reports, 10, http://dx.doi.org/10.1038/s41598-020-75917-6
    Journal articles | 2020
    2020, 'A zebrafish functional genomics model to investigate the role of human A20 variantsin vivo', , http://dx.doi.org/10.1101/2020.02.23.961763
    Journal articles | 2020
    2020, 'Analysis of gene network bifurcation during optic cup morphogenesis in zebrafish', , http://dx.doi.org/10.1101/2020.05.28.121038
    Journal articles | 2020
    2020, 'Canfam-GSD: De novo chromosome-length genome assembly of the German Shepherd Dog (Canis lupus familiaris) using a combination of long reads, optical mapping, and Hi-C', GigaScience, 9, http://dx.doi.org/10.1093/gigascience/giaa027
    Journal articles | 2020
    2020, 'Chromosome-length genome assembly and structural variations of the primal Basenji dog (Canis lupus familiaris) genome', bioRxiv, http://dx.doi.org/10.1101/2020.11.11.379073
    Journal articles | 2020
    2020, 'Depletion of Foxk transcription factors causes genome-wide transcriptional misregulation and developmental arrest in zebrafish embryos.', MicroPubl Biol, 2020, http://dx.doi.org/10.17912/micropub.biology.000341
    Journal articles | 2020
    2020, 'Developmental accumulation of gene body and transposon non-CpG methylation in the zebrafish brain', , http://dx.doi.org/10.1101/2020.12.17.423365
    Journal articles | 2020
    2020, 'Developmental remodelling of non-CG methylation at satellite DNA repeats', Nucleic Acids Research, 48, pp. 12675 - 12688, http://dx.doi.org/10.1093/nar/gkaa1135
    Journal articles | 2020
    2020, 'Evolution of DNA Methylome Diversity in Eukaryotes', Journal of Molecular Biology, 432, pp. 1687 - 1705, http://dx.doi.org/10.1016/j.jmb.2019.11.003
    Journal articles | 2020
    2020, 'José Luis Gómez-Skarmeta (1966-2020)', Nature genetics, 52, pp. 1267 - 1268, http://dx.doi.org/10.1038/s41588-020-00743-5
    Journal articles | 2020
    2020, 'Pervasive non-CpG methylation at zebrafish mosaic satellite repeats', , http://dx.doi.org/10.1101/2020.05.13.093203
    Journal articles | 2019
    2019, 'Convergent evolution of a vertebrate-like methylome in a marine sponge', Nature Ecology and Evolution, 3, pp. 1464 - 1473, http://dx.doi.org/10.1038/s41559-019-0983-2
    Journal articles | 2019
    2019, 'DNA Hypermethylation Encroachment at CpG Island Borders in Cancer Is Predisposed by H3K4 Monomethylation Patterns', Cancer Cell, 35, pp. 297 - 314.e8, http://dx.doi.org/10.1016/j.ccell.2019.01.004
    Journal articles | 2019
    2019, 'Enhancer DNA methylation: implications for gene regulation.', Essays Biochem, pp. EBC20190030 - EBC20190030, http://dx.doi.org/10.1042/EBC20190030
    Journal articles | 2019
    2019, 'Retention of paternal DNA methylome in the developing zebrafish germline', Nature Communications, 10, http://dx.doi.org/10.1038/s41467-019-10895-6
    Journal articles | 2019
    2019, 'TET enzymes, DNA demethylation and pluripotency', Biochemical Society Transactions, 47, pp. 875 - 885, http://dx.doi.org/10.1042/BST20180606
    Journal articles | 2018
    2018, 'Amphioxus functional genomics and the origins of vertebrate gene regulation', Nature, 564, pp. 64 - 70, http://dx.doi.org/10.1038/s41586-018-0734-6
    Journal articles | 2018
    2018, 'Functions and mechanisms of epigenetic inheritance in animals', Nature Reviews Molecular Cell Biology, 19, pp. 774 - 790, http://dx.doi.org/10.1038/s41580-018-0074-2
    Journal articles | 2017
    Bogdanović O; Lister R, 2017, 'DNA methylation and the preservation of cell identity', Current Opinion in Genetics and Development, 46, pp. 9 - 14, http://dx.doi.org/10.1016/j.gde.2017.06.007
    Journal articles | 2017
    Crisp PA; Ganguly DR; Smith AB; Murray KD; Estavillo GM; Searle I; Ford E; Bogdanović O; Lister R; Borevitz JO; Eichten SR; Pogson BJ, 2017, 'Rapid recovery gene downregulation during excess-light stress and recovery in arabidopsis', Plant Cell, 29, pp. 1836 - 1863, http://dx.doi.org/10.1105/tpc.16.00828
    Journal articles | 2017
    Elurbe DM; Paranjpe SS; Georgiou G; van Kruijsbergen I; Bogdanovic O; Gibeaux R; Heald R; Lister R; Huynen MA; van Heeringen SJ; Veenstra GJ C, 2017, 'Regulatory remodeling in the allo-tetraploid frog Xenopus laevis', Genome biology, 18, pp. 198, http://dx.doi.org/10.1186/s13059-017-1335-7
    Journal articles | 2017
    Westhorpe F; Tiengwe C; Hunsberger H; Jain G; Wells M; Yu M; Bogdanovic O; Absalon S; Sen P; Madrigal P; Natarajan K, 2017, 'Postdocs, What Would You Tell Your Younger Self?', CELL, 168, pp. 745 - 748, http://dx.doi.org/10.1016/j.cell.2017.02.016
    Journal articles | 2017
    Zenk F; Loeser E; Schiavo R; Kilpert F; Bogdanovic O; Iovino N, 2017, 'Germ line–inherited H3K27me3 restricts enhancer function during maternal-to-zygotic transition', Science, 357, pp. 212 - 216, http://dx.doi.org/10.1126/science.aam5339
    Journal articles | 2017
    2017, 'Frequent lack of repressive capacity of promoter DNA methylation identified through genome-wide epigenomic manipulation', , http://dx.doi.org/10.1101/170506
    Journal articles | 2017
    2017, 'Regulatory remodeling in the allo-tetraploid frog Xenopus laevis', , http://dx.doi.org/10.1101/120212
    Journal articles | 2017
    2017, 'Tet proteins: Master regulators of vertebrate body plan formation?', Epigenomics, 9, pp. 93 - 96, http://dx.doi.org/10.2217/epi-2016-0164
    Journal articles | 2016
    Bogdanović O; 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 C; Manzanares M; Sauka-Spengler T; Ecker JR; Vermeulen M; Gómez-Skarmeta JL; Lister R, 2016, 'Active DNA demethylation at enhancers during the vertebrate phylotypic period', Nature Genetics, 48, pp. 417 - 426, http://dx.doi.org/10.1038/ng.3522
    Journal articles | 2016
    Bogdanović O; Van Heeringen SJ, 2016, 'ChiP-seq data processing for PcG proteins and associated Histone modifications', Methods in Molecular Biology, 1480, pp. 37 - 53, http://dx.doi.org/10.1007/978-1-4939-6380-5_4
    Journal articles | 2016
    Hontelez S; van Kruijsbergen I; Georgiou G; van Heeringen SJ; Bogdanovic O; Lister R; Veenstra GJ C, 2016, 'Embryonic transcription is controlled by maternally defined chromatin state (vol 6, 10148, 2015)', NATURE COMMUNICATIONS, 7, http://dx.doi.org/10.1038/ncomms12208
    Journal articles | 2016
    Session AM; Uno Y; Kwon T; Chapman JA; Toyoda A; Takahashi S; Fukui A; Hikosaka A; Suzuki A; Kondo M; Van Heeringen SJ; Quigley I; Heinz S; Ogino H; Ochi H; Hellsten U; Lyons JB; Simakov O; Putnam N; Stites J; Kuroki Y; Tanaka T; Michiue T; Watanabe M; Bogdanovic O; Lister R; Georgiou G; Paranjpe SS; Van Kruijsbergen I; Shu S; Carlson J; Kinoshita T; Ohta Y; Mawaribuchi S; Jenkins J; Grimwood J; Schmutz J; Mitros T; Mozaffari SV; Suzuki Y; Haramoto Y; Yamamoto TS; Takagi C; Heald R; Miller K; Haudenschild C; Kitzman J; Nakayama T; Izutsu Y; Robert J; Fortriede J; Burns K; Lotay V; Karimi K; Yasuoka Y; Dichmann DS; Flajnik MF; Houston DW; Shendure J; Dupasquier L; Vize PD; Zorn AM; Ito M; Marcotte EM; Wallingford JB; Ito Y; Asashima M; Ueno N; Matsuda Y; Veenstra GJ C; Fujiyama A; Harland RM; Taira M; Rokhsar DS, 2016, 'Genome evolution in the allotetraploid frog Xenopus laevis', Nature, 538, pp. 336 - 343, http://dx.doi.org/10.1038/nature19840
    Journal articles | 2015
    2015, 'Embryonic transcription is controlled by maternally defined chromatin state', Nature Communications, 6, http://dx.doi.org/10.1038/ncomms10148
    Journal articles | 2015
    2015, 'Genome-wide epigenetic cross-talk between DNA methylation and H3K27me3 in zebrafish embryos', Genomics Data, 6, pp. 7 - 9, http://dx.doi.org/10.1016/j.gdata.2015.07.020
    Journal articles | 2015
    2015, 'Meis1 coordinates a network of genes implicated in eye development and microphthalmia', Development (Cambridge), 142, pp. 3009 - 3020, http://dx.doi.org/10.1242/dev.122176
    Journal articles | 2015
    2015, 'Of mice and man: Differential DNMT dependence in mammalian ESCs', Cell Stem Cell, 16, pp. 459 - 460, http://dx.doi.org/10.1016/j.stem.2015.04.009
    Journal articles | 2014
    2014, 'Embryonic DNA methylation: Insights from the genomics era', Briefings in Functional Genomics, 13, pp. 121 - 130, http://dx.doi.org/10.1093/bfgp/elt039
    Journal articles | 2014
    2014, 'Invertebrate epigenomics: The brave new world of the spineless', Briefings in Functional Genomics, 13, pp. 189 - 190, http://dx.doi.org/10.1093/bfgp/elu008
    Journal articles | 2013
    2013, 'The developmental epigenomics toolbox: ChIP-seq and MethylCap-seq profiling of early zebrafish embryos', Methods, 62, pp. 207 - 215, http://dx.doi.org/10.1016/j.ymeth.2013.04.011
    Journal articles | 2012
    2012, 'Extensive conservation of ancient microsynteny across metazoans due to cis-regulatory constraints', Genome Research, 22, pp. 2356 - 2367, http://dx.doi.org/10.1101/gr.139725.112
    Journal articles | 2012
    2012, 'Numb/Numbl-Opo Antagonism Controls Retinal Epithelium Morphogenesis by Regulating Integrin Endocytosis', Developmental Cell, 23, pp. 782 - 795, http://dx.doi.org/10.1016/j.devcel.2012.09.004
    Journal articles | 2011
    Bogdanović O; Veenstra GJ C, 2011, 'Affinity-based enrichment strategies to assay methyl-CpG binding activity and DNA methylation in early Xenopus embryos.', BMC Res Notes, 4, pp. 300, http://dx.doi.org/10.1186/1756-0500-4-300
  • Working Papers | 2021
    2021, Chromosome-length genome assembly and structural variations of the primal Basenji dog (Canis lupus familiaris) genome, BioMed Central, http://dx.doi.org10.1186/s12864-021-07493-6
    Working Papers | 2020
    2020, Desert Dingo (Canis lupus dingo) genome provides insights into their role in the Australian ecosystem, Cold Spring Harbor, http://dx.doi.org10.1101/2020.11.15.384057, https://www.biorxiv.org/content/10.1101/2020.11.15.384057v1
  • Preprints | 2023
    2023, The Australasian dingo archetype: De novo chromosome-length genome assembly, DNA methylome, and cranial morphology., , http://dx.doi.org/10.1101/2023.01.26.525801
    Preprints | 2022
    2022, The little skate genome and the evolutionary emergence of wing-like fin appendages, , http://dx.doi.org/10.1101/2022.03.21.485123
    Preprints | 2021
    2021, Active DNA demethylation of developmental cis-regulatory regions predates vertebrate origins, , http://dx.doi.org/10.1101/2021.11.07.467601
    Preprints | 2021
    2021, Integrated annotation and analysis of genomic features reveal new types of functional elements and large-scale epigenetic phenomena in the developing zebrafish, , http://dx.doi.org/10.1101/2021.08.09.454869

2017 - Millennium Science Award
2017 - Raine Research Prize
2016 - UWA Early Career Researcher Vice Chancellor’s Award
2016 - UWA Research Collaboration Award
2015 - UWA Research Collaboration Award
2014 - ECR Award to attend the annual meeting of the Australian Academy of Sciences
2014 - Cell Symposia – Transcriptional Regulation in Development, Poster Presentation Award 
2013 - ARC Discovery Early Career Researcher Award (DECRA)
2013 - EMBO travel grant
2003 - IAESTE internship to work at Friedrich Miescher Institute (Basel, CH)

How a complex, multicellular organism develops from a single fertilized egg is among 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.

The research in the Bogdanović lab aims to understand the contributions of the epigenome to embryonic development, cell differentiation and disease. We are particularly interested in how DNA methylation patterns are established, maintained and altered during those processes. Our interest in DNA methylation stems from the fact that this epigenetic mark can be stably propagated through cell division and that the presence or absence of DNA methylation correlates well with the activity of regulatory regions. Finally, a vast wealth of studies has demonstrated strong links between DNA methylation and various disease phenotypes suggestive of its potential applicability as a biomarker.

My Research Supervision

PhD