Deciphering the regulatory principles of metazoan development. This proposal aims to elucidate how regulatory elements in the genome, known as enhancers, determine the identity and function of animal tissues. Currently, it is believed that enhancers cannot be traced across evolutionarily distant animals. The project uses novel concepts, computational and molecular approaches to identify deeply conserved enhancers. It further dissects the mechanism of function by proteomics and high-throughput ge ....Deciphering the regulatory principles of metazoan development. This proposal aims to elucidate how regulatory elements in the genome, known as enhancers, determine the identity and function of animal tissues. Currently, it is believed that enhancers cannot be traced across evolutionarily distant animals. The project uses novel concepts, computational and molecular approaches to identify deeply conserved enhancers. It further dissects the mechanism of function by proteomics and high-throughput genomics. The expected outcomes will overturn our current view on enhancer evolution and reposition our understanding of how enhancers are functionally encoded in the genome. The work is an important contribution to understanding cellular complexity and species evolution with wide-ranging impact in genetics.Read moreRead less
Discovery Early Career Researcher Award - Grant ID: DE160100755
Funder
Australian Research Council
Funding Amount
$371,000.00
Summary
Evolution of genome architecture. The project aims to understand how changes to genome architecture over evolutionary time are linked to the diversity of animal morphology. Our genome sequence is arranged into higher order structures that enable coordinated gene expression. The appropriate expression of genes in time and space is necessary to produce the multitude of cell types that make up a multicellular organism. Yet, to date, genome topology is poorly explored, especially between species. Th ....Evolution of genome architecture. The project aims to understand how changes to genome architecture over evolutionary time are linked to the diversity of animal morphology. Our genome sequence is arranged into higher order structures that enable coordinated gene expression. The appropriate expression of genes in time and space is necessary to produce the multitude of cell types that make up a multicellular organism. Yet, to date, genome topology is poorly explored, especially between species. The project involves comparisons of the 3D structure of genomes in divergent species. These findings are expected to inform the underlying principles of gene regulation in animals and species evolution.Read moreRead less
Old genes learning new tricks: characterising regulatory changes driving increased heart complexity during vertebrate evolution. The heart has dramatically increased in morphological complexity during vertebrate evolution but the molecular basis driving these major changes remains unknown. Using comparative genomics approaches, this project will explore changes in the regulation of genes involved in heart formation that lead to changes in cardiac structure. It will elucidate for the first time t ....Old genes learning new tricks: characterising regulatory changes driving increased heart complexity during vertebrate evolution. The heart has dramatically increased in morphological complexity during vertebrate evolution but the molecular basis driving these major changes remains unknown. Using comparative genomics approaches, this project will explore changes in the regulation of genes involved in heart formation that lead to changes in cardiac structure. It will elucidate for the first time the cardiac regulatory repertoire in zebrafish and will compare it with that of fly and mouse using cutting-edge bioinformatics pipelines. This work will unravel cardiac-specific regulatory modifications that give rise to evolutionary changes. On a broader scale, it will shed new light on the role of regulatory innovations over gene innovations in the emergence of new traits.Read moreRead less
Developing the Dunnart as a Model Species for Marsupial Research. The project aims to develop a marsupial model capable of genome manipulations to take our understanding of marsupial biology to the next level. In doing so, the project would produce the first comprehensive transcriptome data defining early cell lineage specification in a marsupial. Combined with similar data from mouse and human, it would enable us to examine diversity in early mammals. In addition, it would identify cohorts of g ....Developing the Dunnart as a Model Species for Marsupial Research. The project aims to develop a marsupial model capable of genome manipulations to take our understanding of marsupial biology to the next level. In doing so, the project would produce the first comprehensive transcriptome data defining early cell lineage specification in a marsupial. Combined with similar data from mouse and human, it would enable us to examine diversity in early mammals. In addition, it would identify cohorts of genes with fundamental roles in differentiation of the earliest cell lineages: trophoblast, pluriblast and hypoblast. The project may identify maternally localised transcripts with a marsupial-specific role in trophoblast–pluriblast specification, giving new insights into the fundamental pathways maintaining pluripotency in mammals and the evolution of the mammalian genome.Read moreRead less
Heads or tails - which did echinoderms lose in the evolution of radial symmetry? Echinoderms, despite their unusual radial body plan, are closely related to chordates, but it is not known how this plan evolved. This project uses gene expression studies with uniquely suited Australian species to identify genes involved in radial body plan development and generate insights into origins of chordates and the vertebrate central nervous system (CNS).
Ancestral, conserved and novel mechanisms in marsupial genomic imprinting. Genomic imprinting is the differential expression pattern of some genes depending on whether the gene copy came from the mother or the father. This differential expression is essential for embryonic development and errors lead to disease. To date, most of our knowledge of the control of genomic imprinting comes from the mouse, but much less is known about this process in marsupials. Our comparative approach, using marsupi ....Ancestral, conserved and novel mechanisms in marsupial genomic imprinting. Genomic imprinting is the differential expression pattern of some genes depending on whether the gene copy came from the mother or the father. This differential expression is essential for embryonic development and errors lead to disease. To date, most of our knowledge of the control of genomic imprinting comes from the mouse, but much less is known about this process in marsupials. Our comparative approach, using marsupial mammals that are distantly related to mice and humans, aims to clarify how genomic imprinting mechanisms have evolved, which patterns are conserved across mammals, and which vary. Our proposed research aims to provide new approaches and understanding of this fundamental process essential for the continuation of life.
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Reprogramming maternal and paternal genomes during development: new perspectives from marsupials. This project will use marsupials to examine programming of the germ cell lineage (cells that become eggs and sperm) and the evolution of these mechanisms that control their development. Using the unique features of our Australian native animals, this research will contribute to the understanding of the transmission of life.
Discovery Early Career Researcher Award - Grant ID: DE150101150
Funder
Australian Research Council
Funding Amount
$362,000.00
Summary
Using sponge transcriptomes to understand ancestral animal development. The invention of a basic developmental program was likely a key step in the transition to multicellularity in animals, one of the major transitions in the tree of life. By combining next-generation sequencing of a representative panel of sponges and functional studies on an oviparous sponge, this project aims to identify gene interactions and networks that built the first animal embryos over 680 million years ago. Furthermor ....Using sponge transcriptomes to understand ancestral animal development. The invention of a basic developmental program was likely a key step in the transition to multicellularity in animals, one of the major transitions in the tree of life. By combining next-generation sequencing of a representative panel of sponges and functional studies on an oviparous sponge, this project aims to identify gene interactions and networks that built the first animal embryos over 680 million years ago. Furthermore, the role of Wingless (Wnt) signalling in patterning these ancestral embryos along a primordial anterior-posterior axis will be investigated. Piecing together the fundamental molecular machinery shared by all animal embryos will shed light on the molecular basis for the complex development of most animals on Earth.Read moreRead less
Origin of genomically-encoded communication in animals: deciphering the role of peptide signalling in the sea sponge Amphimedon queenslandica. The purpose of this research is to understand the evolutionary origin and essential roles of peptide communication in humans and other animals. Knowledge gleaned from this study will shed light on how peptide signalling influences animal life at its most fundamental level, including potentially how abnormal cell communication causes disease.
Evolutionary origin of stem cells and the emergence of animal complexity. The project aims to decipher the fundamental mechanisms governing stem cell specification and formation. All animals rely on stem cells to replenish, repair and regenerate tissues. Stem cells are also often a conduit to malignant tumours. This project seeks to uncover the rules governing stem cell formation through the study of a simple and ancient animal – the marine sponge Amphimedon queenslandica. The project plans to c ....Evolutionary origin of stem cells and the emergence of animal complexity. The project aims to decipher the fundamental mechanisms governing stem cell specification and formation. All animals rely on stem cells to replenish, repair and regenerate tissues. Stem cells are also often a conduit to malignant tumours. This project seeks to uncover the rules governing stem cell formation through the study of a simple and ancient animal – the marine sponge Amphimedon queenslandica. The project plans to combine insights from the simple, experimentally-tractable sponge stem cell system with existing knowledge of stem cell specification in humans and other animals, to reveal the essential features of stem cell formation. These insights may inform future pursuits to generate, control and use stem cells in cancer and regenerative medicines.Read moreRead less