Marsupial genetics and genomics

Marsupial genomics and genetics provide invaluable data for comparative analysis because these mammals are distantly related cousins of humans and other eutherian mammals (∼148 million years), but they are more closely related to eutherians compared to monotremes (∼166 million years) and birds (∼310 million years). This divergence time places them uniquely on the phylogenetic tree whereby comparative gene mapping and genome sequences of marsupials enable us to trace the evolution of the therian X chromosome. It is shown by comparative gene mapping that the marsupial X chromosome is homologous to the long arm and pericentric region of the short arm of the human X chromosome (X conserved region). However, it is homologous to autosomes in the platypus and the chicken, suggesting that a novel XY system evolved in therian mammals after they diverged from monotremes 166 million years ago but before marsupials diverged from eutherians 148 million years ago. Apart from the X conserved region, eutherian mammals have an autosomal addition on the X chromosome (X added region) since their divergence from marsupials. Although the marsupial X chromosome is similar in composition to that of the eutherian X chromosome, it has accumulated numerous rearrangements, has become GC rich and has acquired a higher synonymous substitution rate since divergence of marsupial and eutherian mammals. Similarly, the marsupial X chromosome undergoes X inactivation like eutherian mammals, but the mechanisms, which regulates X inactivation, is very different from that observed in eutherian mammal, and may be the ancestral state. The XIST gene responsible for X inactivation in eutherian mammals is absent from the marsupial lineage suggesting that the evolution of XIST in early eutherians set up selection for accumulation of LINE sequences that aided the spread of X inactivation. Unlike the LINE accumulation on the eutherian X chromosome, the marsupial X has accumulated and expanded a microRNA family that could be involved in the marsupial X inactivation. This chapter provides a comprehensive review of the organization and evolution of the marsupial X chromosome and the implications this may have for X inactivation.

Organization and Evolution of the Marsupial X Chromosome

Understanding the evolution and regulation of nucleolar organizing regions (NORs) is important to elucidate genome structure and function. This is because ribosomal gene (rDNA) copy number and activity mediate protein biosynthesis, stress response, ageing, disease, dosage compensation and genome stability. Here, we found contrasting dosage compensation of sex‐linked NORs in turtles with male and female heterogamety. Most taxa examined exhibit homomorphic rRNA gene clusters in a single autosome pair (determined by 28S rDNA fluorescence in situ hybridization), whereas NORs are sex‐linked in Apalone spinifera, Pelodiscus sinensis and Staurotypus triporcatus. Full‐dosage compensation upregulates the male X‐NOR (determined via silver staining—AgNOR) in Staurotypus (who lacks Y‐NOR) compared with female X‐AgNORs. In softshell Apalone and Pelodiscus, who share homologous ZZ/ZW micro‐chromosomes, their enlarged W‐NOR is partially active (due to 28S rDNA invasion by R2 retroelements), whereas their smaller Z‐NOR is silent in females but active in both male‐Zs (presumably because the W‐NOR meets cellular demands and excessive NOR activity is costly). We hypothesize that R2 disruption favoured W enlargement to add intact 28S‐units, perhaps facilitated by reduced recombination during sex chromosome evolution. The molecular basis of the potentially adaptive female Z‐silencing is likely intricate and perhaps epigenetic, as non‐ribosomal Z genes are active in Apalone females. Yet, Emydura maquarii exhibit identical heteromorphism in their autosomal NOR (R2 invaded 28S‐units and the small‐autosome NOR is silent), suggesting that the softshell turtle pattern can evolve independent of sex chromosome evolution. Our study illuminates the complex sex chromosome evolution and dosage compensation of non‐model systems that challenges classic paradigms.

https://onlinelibrary.wiley.com/doi/pdfdirect/10.1111/jeb.14064

Evolution and dosage compensation of nucleolar organizing regions (NORs) mediated by mobile elements in turtles with female (ZZ/ZW) but not with male (XX/XY) heterogamety

Upstream Binding Factor, an Evolutionarily Conserved Protein that Organises Ribosomal Gene Chromatin

The class Mammalia is divided into three subclasses: (1) Prototheria including monotremes, (2) Metatheria including marsupials, and (3) Eutheria that include all other mammalian species. Eutherian mammals, which include humans, have chromosome numbers ranging from 2n = 6 (lowest) to 2n = 102 (highest). The karyotype which consists of the chromosome number and morphology is considered to be the characteristic of a given species. Some mammalian species have either only acrocentric chromosomes, as in the case of laboratory mouse, or only metacentric and/or submetacentric chromosomes, as in the case of most hamster species. Some species, on the other hand, have a combination of acrocentric, submetacentric, and metacentric chromosomes, as in the case of humans. In a few rare mammalian species, the X and the Y chromosomes may be fused to an autosome. With the discovery and application of various chromosome identification (banding) techniques, it became apparent that diverse groups of mammalian species share large chromosomal segments or even many intact chromosomes. Here, I have discussed in brief chromosomal characteristics of various mammalian species with special reference to the laboratory mouse, Mus musculus, and human, Homo sapiens sapiens and concluded that laboratory mouse may not be a suitable animal model representing all mammalian species including humans. In addition, the discussions presented here suggest that mouse is not the best or ideal laboratory animal model for cancer research and anticancer drug development. In the era of personalized medicine, the time has come to use human mini-organs (organoids) produced in culture vessels following the various somatic cell cloning techniques including the somatic cell nuclear transfer (SCNT), induced pluripotent stem (iPS) cells, and other small molecules induced newly discovered reprogramming methods. Such reprogrammed iPS or SCNT stem cells can be monitored in culture to produce patient-specific different human organoids and used instead of using mouse by the pharmaceutical companies and research institutes for testing drug toxicity and production of more effective new anticancer drugs.

Diversity of Chromosomal Characteristics Among Mammals: With Special Reference to Laboratory Mouse in Cancer Research

Silver staining of cells in metaphase and interphase nuclei of both sexes of the Bennett wallaby, Macropus rufogriseus, has shown that (1) the nucleolus organizer region (NOR) is located only on the X chromosome (single Ag-NOR); (2) both X chromosomes in the female cells stain with silver; (3) the amounts of silver staining of metaphase chromosomes and interphase nuclei of both sexes are very similar; (4) the single X chromosome is hyperactive in male cells to equalize the expression of rRNA genes in the female cells with two X chromosomes; and (5) the mechanism of dosage compensation for rRNA genes in this species is similar to that reported for Drosophila salivary gland cells.

Shirley Lr

Papers

Ag-NOR staining in the Bennett wallaby, Macropus rufogriseus: evidence for dosage compensation