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2. Evolution of coding and non-coding genes in HOX clusters of a marsupial

Author

Yu Hongshi, Lindsay James, Feng Zhi-Ping, Frankenberg Stephen, Hu Yanqiu, Carone Dawn, Shaw Geoff, Pask Andrew J, O’Neill Rachel, Papenfuss Anthony T, and Renfree Marilyn B

Subjects
Marsupial, HOX cluster, MicroRNAs, Long non-coding RNAs, Biotechnology, TP248.13-248.65, Genetics, QH426-470
Abstract

Abstract Background The HOX gene clusters are thought to be highly conserved amongst mammals and other vertebrates, but the long non-coding RNAs have only been studied in detail in human and mouse. The sequencing of the kangaroo genome provides an opportunity to use comparative analyses to compare the HOX clusters of a mammal with a distinct body plan to those of other mammals. Results Here we report a comparative analysis of HOX gene clusters between an Australian marsupial of the kangaroo family and the eutherians. There was a strikingly high level of conservation of HOX gene sequence and structure and non-protein coding genes including the microRNAs miR-196a, miR-196b, miR-10a and miR-10b and the long non-coding RNAs HOTAIR, HOTAIRM1 and HOXA11AS that play critical roles in regulating gene expression and controlling development. By microRNA deep sequencing and comparative genomic analyses, two conserved microRNAs (miR-10a and miR-10b) were identified and one new candidate microRNA with typical hairpin precursor structure that is expressed in both fibroblasts and testes was found. The prediction of microRNA target analysis showed that several known microRNA targets, such as miR-10, miR-414 and miR-464, were found in the tammar HOX clusters. In addition, several novel and putative miRNAs were identified that originated from elsewhere in the tammar genome and that target the tammar HOXB and HOXD clusters. Conclusions This study confirms that the emergence of known long non-coding RNAs in the HOX clusters clearly predate the marsupial-eutherian divergence 160 Ma ago. It also identified a new potentially functional microRNA as well as conserved miRNAs. These non-coding RNAs may participate in the regulation of HOX genes to influence the body plan of this marsupial.

Published
2012
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3. Evolution of vertebrate interferon inducible transmembrane proteins

Author

Hickford Danielle, Frankenberg Stephen, Shaw Geoff, and Renfree Marilyn B

Subjects
Marsupial, Tammar wallaby, Opossum, Gene cluster, Biotechnology, TP248.13-248.65, Genetics, QH426-470
Abstract

Abstract Background Interferon inducible transmembrane proteins (IFITMs) have diverse roles, including the control of cell proliferation, promotion of homotypic cell adhesion, protection against viral infection, promotion of bone matrix maturation and mineralisation, and mediating germ cell development. Most IFITMs have been well characterised in human and mouse but little published data exists for other animals. This study characterised IFITMs in two distantly related marsupial species, the Australian tammar wallaby and the South American grey short-tailed opossum, and analysed the phylogeny of the IFITM family in vertebrates. Results Five IFITM paralogues were identified in both the tammar and opossum. As in eutherians, most marsupial IFITM genes exist within a cluster, contain two exons and encode proteins with two transmembrane domains. Only two IFITM genes, IFITM5 and IFITM10, have orthologues in both marsupials and eutherians. IFITM5 arose in bony fish and IFITM10 in tetrapods. The bone-specific expression of IFITM5 appears to be restricted to therian mammals, suggesting that its specialised role in bone production is a recent adaptation specific to mammals. IFITM10 is the most highly conserved IFITM, sharing at least 85% amino acid identity between birds, reptiles and mammals and suggesting an important role for this presently uncharacterised protein. Conclusions Like eutherians, marsupials also have multiple IFITM genes that exist in a gene cluster. The differing expression patterns for many of the paralogues, together with poor sequence conservation between species, suggests that IFITM genes have acquired many different roles during vertebrate evolution.

Published
2012
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4. A novel MSMB-related microprotein in the postovulatory egg coats of marsupials

Author

Frankenberg Stephen, Fenelon Jane, Dopheide Bonnie, Shaw Geoff, and Renfree Marilyn B

Subjects
Evolution, QH359-425
Abstract

Abstract Background Early marsupial conceptuses differ markedly from those of eutherian mammals, especially during cleavage and early blastocyst stages of development. Additionally, in marsupials the zona pellucida is surrounded by two acellular layers, the mucoid coat and shell, which are formed from secretions from the reproductive tract. Results We report the identification of a novel postovulatory coat component in marsupials, which we call uterinesecreted microprotein (USM). USM belongs to a family of disulfide-rich microproteins of unconfirmed function that is found throughout deuterostomes and in some protostomes, and includes β-microseminoprotein (MSMB) and prostate-associated microseminoprotein (MSMP). We describe the evolution of this family in detail, including USM-related sequences in other vertebrates. The orthologue of USM in the tammar wallaby, USM1, is expressed by the endometrium with a dynamic temporal profile, possibly under the control of progesterone. Conclusions USM appears to have evolved in a mammalian ancestor specifically as a component of the postovulatory coats. By analogy with the known properties of MSMB, it may have roles in regulating sperm motility/survival or in the immune system. However, its C-terminal domain is greatly truncated compared with MSMB, suggesting a divergent function.

Published
2011
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5. Comparative analysis of the ATRX promoter and 5' regulatory region reveals conserved regulatory elements which are linked to roles in neurodevelopment, alpha-globin regulation and testicular function

Author

Argentaro Anthony, Frankenberg Stephen, Tang Paisu, Graves Jennifer M, and Familari Mary

Subjects
Medicine, Biology (General), QH301-705.5, Science (General), Q1-390
Abstract

Abstract Background ATRX is a tightly-regulated multifunctional protein with crucial roles in mammalian development. Mutations in the ATRX gene cause ATR-X syndrome, an X-linked recessive developmental disorder resulting in severe mental retardation and mild alpha-thalassemia with facial, skeletal and genital abnormalities. Although ubiquitously expressed the clinical features of the syndrome indicate that ATRX is not likely to be a global regulator of gene expression but involved in regulating specific target genes. The regulation of ATRX expression is not well understood and this is reflected by the current lack of identified upstream regulators. The availability of genomic data from a range of species and the very highly conserved 5' regulatory regions of the ATRX gene has allowed us to investigate putative transcription factor binding sites (TFBSs) in evolutionarily conserved regions of the mammalian ATRX promoter. Results We identified 12 highly conserved TFBSs of key gene regulators involved in biologically relevant processes such as neural and testis development and alpha-globin regulation. Conclusions Our results reveal potentially important regulatory elements in the ATRX gene which may lead to the identification of upstream regulators of ATRX and aid in the understanding of the molecular mechanisms that underlie ATR-X syndrome.

Published
2011
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6. Genome of the endangered eastern quoll (Dasyurus viverrinus) reveals signatures of historical decline and pelage color evolution

Author

Hartley, Gabrielle A., primary, Frankenberg, Stephen R., additional, Robinson, Natasha M., additional, MacDonald, Anna J., additional, Hamede, Rodrigo K., additional, Burridge, Christopher P., additional, Jones, Menna E., additional, Faulkner, Tim, additional, Shute, Hayley, additional, Rose, Karrie, additional, Brewster, Rob, additional, O’Neill, Rachel J., additional, Renfree, Marilyn B., additional, Pask, Andrew J., additional, and Feigin, Charles Y., additional

Published
2024
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7. Embryology of the fat‐tailed dunnart (Sminthopsis crassicaudata): A marsupial model for comparative mammalian developmental and evolutionary biology

Author

Newton, Axel H., primary, Hutchison, Jennifer C., additional, Farley, Ella R., additional, Scicluna, Emily L., additional, Youngson, Neil A., additional, Liu, Jun, additional, Menzies, Brandon R., additional, Hildebrandt, Thomas B., additional, Lawrence, Ben M., additional, Sutherland, Angus H. W., additional, Potter, David L., additional, Tarulli, Gerard A., additional, Selwood, Lynne, additional, Frankenberg, Stephen, additional, Ord, Sara, additional, and Pask, Andrew J., additional

Published
2024
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14. Population genomics of a predatory mammal reveals patterns of decline and impacts of exposure to toxic toads

Author

von Takach, Brenton, primary, Ranjard, Louis, additional, Burridge, Christopher P., additional, Cameron, Skye F., additional, Cremona, Teigan, additional, Eldridge, Mark D. B., additional, Fisher, Diana O., additional, Frankenberg, Stephen, additional, Hill, Brydie M., additional, Hohnen, Rosemary, additional, Jolly, Chris J., additional, Kelly, Ella, additional, MacDonald, Anna J., additional, Moussalli, Adnan, additional, Ottewell, Kym, additional, Phillips, Ben L., additional, Radford, Ian J., additional, Spencer, Peter B. S., additional, Trewella, Gavin J., additional, Umbrello, Linette S., additional, and Banks, Sam C., additional

Published
2022
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15. Evolutionary Origin of Vertebrate OCT4/POU5 Functions in Supporting Pluripotency

Author

Sukparangsi, Woranop, primary, Morganti, Elena, additional, Lowndes, Molly, additional, Mayeur, Hélène, additional, Weisser, Melanie, additional, Hammachi, Fella, additional, Peradziryi, Hanna, additional, Roske, Fabian, additional, Hölzenspies, Jurriaan, additional, Livigni, Alessandra, additional, Godard, Benoit Gilbert, additional, Sugahara, Fumiaki, additional, Kuratani, Shigeru, additional, Montoya, Guillermo, additional, Frankenberg, Stephen R., additional, Mazan, Sylvie, additional, and Brickman, Joshua M, additional

Published
2022
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19. The evolution of class V POU domain transcription factors in vertebrates and their characterisation in a marsupial

Author

Frankenberg, Stephen, Pask, Andrew, and Renfree, Marilyn B.

Subjects
Stem cells, Platypus, DNA binding proteins, Biological sciences
Abstract

To link to full-text access for this article, visit this link: http://dx.doi.org/10.1016/j.ydbio.2009.10.017 Byline: Stephen Frankenberg, Andrew Pask, Marilyn B. Renfree Keywords: POU5F1; POU2; Pluripotency; Tammar wallaby; Platypus; Germ cells Abstract: POU5F1 (OCT4) encodes a master regulator of pluripotency that is present in all mammals. A paralogue, POU2, is also present in the genomes of marsupials and monotremes and is an orthologue of zebrafish pou2 and chicken POUV. We explored the evolution of class V POU domain transcription factors and show that POU5F1 arose by gene duplication of pou2 early in the evolution of tetrapods and is not mammal-specific, as previously thought. Instead, either POU5F1 or POU2/POUV has become extinct independently in various lineages, although all gnathostomes appear to possess at least one or the other. In the tammar wallaby, POU5F1 expression is limited to pluripotent cell types (embryonic tissues and germ cells). POU2 is similarly expressed in pluripotent tissues but is also expressed in a broad range of adult tissues. Thus, unlike POU5F1, the role of POU2 may not be restricted to pluripotent cell types but could have a related function such as maintaining multipotency in adult stem cells. Author Affiliation: Department of Zoology, University of Melbourne, 3010, Victoria, Australia Article History: Received 31 May 2009; Revised 7 October 2009; Accepted 8 October 2009

Published
2010

20. Chromosome-Scale Hybrid Genome Assembly of the Extinct Tasmanian Tiger (Thylacinus cynocephalus).

Author

Feigin, Charles, Frankenberg, Stephen, and Pask, Andrew

Subjects
*GENOMES, *SKULL morphology, *CONVERGENT evolution, *BIOLOGICAL extinction, *MARSUPIALS, *TWENTIETH century, *HETEROZYGOSITY
Abstract

The extinct Tasmanian tiger or thylacine (Thylacinus cynocephalus) was a large marsupial carnivore native to Australia. Once ranging across parts of the mainland, the species remained only on the island of Tasmania by the time of European colonization. It was driven to extinction in the early 20th century and is an emblem of native species loss in Australia. The thylacine was a striking example of convergent evolution with placental canids, with which it shared a similar skull morphology. Consequently, it has been the subject of extensive study. While the original thylacine assemblies published in 2018 enabled the first exploration of the species' genome biology, further progress is hindered by the lack of high-quality genomic resources. Here, we present a new chromosome-scale hybrid genome assembly for the thylacine, which compares favorably with many recent de novo marsupial genomes. In addition, we provide homology-based gene annotations, characterize the repeat content of the thylacine genome, and show that consistent with demographic decline, the species possessed a low rate of heterozygosity even compared to extant, threatened marsupials. [ABSTRACT FROM AUTHOR]

Published
2022
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26. The mammalian blastocyst

Author

Frankenberg, Stephen R., primary, de Barros, Flavia R.O., additional, Rossant, Janet, additional, and Renfree, Marilyn B., additional

Published
2016
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29. Anatomy of a blastocyst: cell behaviors driving cell fate choice and morphogenesis in the early mouse embryo

Author

Schrode, Nadine, Xenopoulos, Panagiotis, Piliszek, Anna, Frankenberg, Stephen, Plusa, Berenika, and Hadjantonakis, Anna-Katerina

Subjects
Mice, Blastocyst, embryonic structures, Morphogenesis, Animals, Cell Differentiation, Cell Lineage, Article, Embryonic Stem Cells
Abstract

The preimplantation period of mouse early embryonic development is devoted to the specification of two extra-embryonic tissues and their spatial segregation from the pluripotent epiblast. During this period two cell fate decisions are made while cells gradually lose their totipotency. The first fate decision involves the segregation of the extra-embryonic trophectoderm (TE) lineage from the inner cell mass (ICM); the second occurs within the ICM and involves the segregation of the extra-embryonic primitive endoderm (PrE) lineage from the pluripotent epiblast (EPI) lineage, which eventually gives rise to the embryo proper. Multiple determinants, such as differential cellular properties, signaling cues and the activity of transcriptional regulators, influence lineage choice in the early embryo. Here, we provide an overview of our current understanding of the mechanisms governing these cell fate decisions ensuring proper lineage allocation and segregation, while at the same time providing the embryo with an inherent flexibility to adjust when perturbed.

Published
2013

30. The POU-er of gene nomenclature

Author

Frankenberg, Stephen R., primary, Frank, Dale, additional, Harland, Richard, additional, Johnson, Andrew D., additional, Nichols, Jennifer, additional, Niwa, Hitoshi, additional, Schöler, Hans R., additional, Tanaka, Elly, additional, Wylie, Chris, additional, and Brickman, Joshua M., additional

Published
2014
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41. Genome sequence of an Australian kangaroo, Macropus eugenii, provides insight into the evolution of mammalian reproduction and development

Author

Renfree, Marilyn B, primary, Papenfuss, Anthony T, additional, Deakin, Janine E, additional, Lindsay, James, additional, Heider, Thomas, additional, Belov, Katherine, additional, Rens, Willem, additional, Waters, Paul D, additional, Pharo, Elizabeth A, additional, Shaw, Geoff, additional, Wong, Emily SW, additional, Lefèvre, Christophe M, additional, Nicholas, Kevin R, additional, Kuroki, Yoko, additional, Wakefield, Matthew J, additional, Zenger, Kyall R, additional, Wang, Chenwei, additional, Ferguson-Smith, Malcolm, additional, Nicholas, Frank W, additional, Hickford, Danielle, additional, Yu, Hongshi, additional, Short, Kirsty R, additional, Siddle, Hannah V, additional, Frankenberg, Stephen R, additional, Chew, Keng Y, additional, Menzies, Brandon R, additional, Stringer, Jessica M, additional, Suzuki, Shunsuke, additional, Hore, Timothy A, additional, Delbridge, Margaret L, additional, Patel, Hardip, additional, Mohammadi, Amir, additional, Schneider, Nanette Y, additional, Hu, Yanqiu, additional, O'Hara, William, additional, Al Nadaf, Shafagh, additional, Wu, Chen, additional, Feng, Zhi-Ping, additional, Cocks, Benjamin G, additional, Wang, Jianghui, additional, Flicek, Paul, additional, Searle, Stephen MJ, additional, Fairley, Susan, additional, Beal, Kathryn, additional, Herrero, Javier, additional, Carone, Dawn M, additional, Suzuki, Yutaka, additional, Sugano, Sumio, additional, Toyoda, Atsushi, additional, Sakaki, Yoshiyuki, additional, Kondo, Shinji, additional, Nishida, Yuichiro, additional, Tatsumoto, Shoji, additional, Mandiou, Ion, additional, Hsu, Arthur, additional, McColl, Kaighin A, additional, Lansdell, Benjamin, additional, Weinstock, George, additional, Kuczek, Elizabeth, additional, McGrath, Annette, additional, Wilson, Peter, additional, Men, Artem, additional, Hazar-Rethinam, Mehlika, additional, Hall, Allison, additional, Davis, John, additional, Wood, David, additional, Williams, Sarah, additional, Sundaravadanam, Yogi, additional, Muzny, Donna M, additional, Jhangiani, Shalini N, additional, Lewis, Lora R, additional, Morgan, Margaret B, additional, Okwuonu, Geoffrey O, additional, Ruiz, San J, additional, Santibanez, Jireh, additional, Nazareth, Lynne, additional, Cree, Andrew, additional, Fowler, Gerald, additional, Kovar, Christie L, additional, Dinh, Huyen H, additional, Joshi, Vandita, additional, Jing, Chyn, additional, Lara, Fremiet, additional, Thornton, Rebecca, additional, Chen, Lei, additional, Deng, Jixin, additional, Liu, Yue, additional, Shen, Joshua Y, additional, Song, Xing-Zhi, additional, Edson, Janette, additional, Troon, Carmen, additional, Thomas, Daniel, additional, Stephens, Amber, additional, Yapa, Lankesha, additional, Levchenko, Tanya, additional, Gibbs, Richard A, additional, Cooper, Desmond W, additional, Speed, Terence P, additional, Fujiyama, Asao, additional, M Graves, Jennifer A, additional, O'Neill, Rachel J, additional, Pask, Andrew J, additional, Forrest, Susan M, additional, and Worley, Kim C, additional

Published
2011
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