Abstract:The strategic importance of the genome sequence of the gray, short-tailed opossum, Monodelphis domestica, accrues from both the unique phylogenetic position of metatherian (marsupial) mammals and the fundamental biologic characteristics of metatherians that distinguish them from other mammalian species. Metatherian and eutherian (placental) mammals are more closely related to one another than to other vertebrate groups, and owing to this close relationship they share fundamentally similar genetic structures an… Show more
“…This creates "conflict" between paternal and maternal genomes for genes that influence resource allocation and is generally couched in terms of fetal growth regulation, and/or in neurologic development that can enhance or inhibit postnatal growth rates through variation in feeding competence [75,77-79]. The Conflict Model is pleasingly consistent with the known roles of several imprinted genes in fetal growth and postnatal nutritionally related behaviors, but for most imprinted genes agreement with the Conflict Model has been assumed rather than demonstrated [12]. …”
BackgroundImprinted genes have been extensively documented in eutherian mammals and found to exhibit significant interspecific variation in the suites of genes that are imprinted and in their regulation between tissues and developmental stages. Much less is known about imprinted loci in metatherian (marsupial) mammals, wherein studies have been limited to a small number of genes previously known to be imprinted in eutherians. We describe the first ab initio search for imprinted marsupial genes, in fibroblasts from the opossum, Monodelphis domestica, based on a genome-wide ChIP-seq strategy to identify promoters that are simultaneously marked by mutually exclusive, transcriptionally opposing histone modifications.ResultsWe identified a novel imprinted gene (Meis1) and two additional monoallelically expressed genes, one of which (Cstb) showed allele-specific, but non-imprinted expression. Imprinted vs. allele-specific expression could not be resolved for the third monoallelically expressed gene (Rpl17). Transcriptionally opposing histone modifications H3K4me3, H3K9Ac, and H3K9me3 were found at the promoters of all three genes, but differential DNA methylation was not detected at CpG islands at any of these promoters.ConclusionsIn generating the first genome-wide histone modification profiles for a marsupial, we identified the first gene that is imprinted in a marsupial but not in eutherian mammals. This outcome demonstrates the practicality of an ab initio discovery strategy and implicates histone modification, but not differential DNA methylation, as a conserved mechanism for marking imprinted genes in all therian mammals. Our findings suggest that marsupials use multiple epigenetic mechanisms for imprinting and support the concept that lineage-specific selective forces can produce sets of imprinted genes that differ between metatherian and eutherian lines.
“…This creates "conflict" between paternal and maternal genomes for genes that influence resource allocation and is generally couched in terms of fetal growth regulation, and/or in neurologic development that can enhance or inhibit postnatal growth rates through variation in feeding competence [75,77-79]. The Conflict Model is pleasingly consistent with the known roles of several imprinted genes in fetal growth and postnatal nutritionally related behaviors, but for most imprinted genes agreement with the Conflict Model has been assumed rather than demonstrated [12]. …”
BackgroundImprinted genes have been extensively documented in eutherian mammals and found to exhibit significant interspecific variation in the suites of genes that are imprinted and in their regulation between tissues and developmental stages. Much less is known about imprinted loci in metatherian (marsupial) mammals, wherein studies have been limited to a small number of genes previously known to be imprinted in eutherians. We describe the first ab initio search for imprinted marsupial genes, in fibroblasts from the opossum, Monodelphis domestica, based on a genome-wide ChIP-seq strategy to identify promoters that are simultaneously marked by mutually exclusive, transcriptionally opposing histone modifications.ResultsWe identified a novel imprinted gene (Meis1) and two additional monoallelically expressed genes, one of which (Cstb) showed allele-specific, but non-imprinted expression. Imprinted vs. allele-specific expression could not be resolved for the third monoallelically expressed gene (Rpl17). Transcriptionally opposing histone modifications H3K4me3, H3K9Ac, and H3K9me3 were found at the promoters of all three genes, but differential DNA methylation was not detected at CpG islands at any of these promoters.ConclusionsIn generating the first genome-wide histone modification profiles for a marsupial, we identified the first gene that is imprinted in a marsupial but not in eutherian mammals. This outcome demonstrates the practicality of an ab initio discovery strategy and implicates histone modification, but not differential DNA methylation, as a conserved mechanism for marking imprinted genes in all therian mammals. Our findings suggest that marsupials use multiple epigenetic mechanisms for imprinting and support the concept that lineage-specific selective forces can produce sets of imprinted genes that differ between metatherian and eutherian lines.
“…The gray short-tailed opossum (Monodelphis domestica) is arguably one of the better-developed model marsupial species and has been useful for comparative immunology and biomedical research (Samollow 2008). M. domestica is currently used as a model for melanoma, developmental biology, spinal cord injury, and genetics of cholesterol regulation (Samollow 2008). Significantly, it is one of the few non-eutherian mammals for which a well-annotated whole genome sequence is available (Mikkelsen et al 2007).…”
mentioning
confidence: 98%
“…Marsupials represent a lineage of mammals that diverged from the eutherians (placental mammals) over 150 million years ago and have provided insights into the evolution of mammalian MHC (Baker et al 2009;Belov et al 2006;Gouin et al 2006). The gray short-tailed opossum (Monodelphis domestica) is arguably one of the better-developed model marsupial species and has been useful for comparative immunology and biomedical research (Samollow 2008). M. domestica is currently used as a model for melanoma, developmental biology, spinal cord injury, and genetics of cholesterol regulation (Samollow 2008).…”
The gray short-tailed opossum Monodelphis domestica is one of the few marsupial species for which a high quality whole genome sequence is available and the major histocompatibility complex (MHC) region has been annotated. Previous analyses revealed only a single locus within the opossum MHC region, designated Modo-UA1, with the features expected for encoding a functionally classical class I α-chain. Nine other class I genes found within the MHC are highly divergent and have features usually associated with non-classical roles. The original annotation, however, was based on an early version of the opossum genome assembly. More recent analyses of allelic variation in individual opossums revealed too many Modo-UA1 sequences per individual to be accounted for by a single MHC class I locus found in the genome assembly. A reanalysis of a later generation assembly, MonDom5, revealed the presence of two additional loci, now designated Modo-UA3 and UA4, in a region that was expanded and more complete than in the earlier assembly. Modo-UA1, UA3, and UA4 are all transcribed, although Modo-UA4 transcripts are rarer. Modo-UA4 is also relatively non-polymorphic. Evidence presented support the accuracy of the later assembly and the existence of three related class I genes in the opossum, making opossums more typical of mammals and most tetrapods by having multiple apparent classical MHC class I loci.
“…It appears quite clear that TEs constitute from at least 30% to more than half of the sequences of mammalian genomes [Lander et al, 2001;Han et al, 2007;Mikkelsen et al, 2007;Pontius et al, 2007]. Recently published genomes of 3 early diverged mammals, the platypus (Ornithorhynchus anatinus) [O'Brien, 2008;Warren et al ., 2008], the short-tailed opossum (Monodelphis domestica) [Mikkelsen et al, 2007;Samollow, 2008], and the tammar wallaby (Macropus eugenii) [Renfree et al, 2011] allow us to get a scent of the mode/tempo of the TE relationship in a well time-frameworked specific example of the evolution process. The platypus genome is composed of a large proportion ( ϳ 50%) of interspersed repeats [O'Brien, 2008;Warren et al, 2008] mostly represented by the still active LINE-2 and its non-autonomous companion, the mammalian-wide interspersed repeat (MIR).…”
Section: Short and Long Interspersed Elementsmentioning
The study of genome size (GS) and its variation is so fascinating to the scientific community because it constitutes the link between the present-day analytical and molecular studies of the genome and the old trunk of the holistic and synthetic view of the genome. The GS of several taxa vary over a broad range and do not correlate with the complexity of the organisms (the C-value paradox). However, the biology of transposable elements has let us reach a satisfactory view of the molecular mechanisms that give rise to GS variation and novelties, providing a less perplexing view of the significance of the GS (C-enigma). The knowledge of the composition and structure of a genome is a pre-requisite for trying to understand the evolution of the main genome signature: its size. The radiation of mammals provides an approximately 180-million-year test case for theories of how GS evolves. It has been found from data-mining GS databases that GS is a useful cyto-taxonomical instrument at the level of orders/superorders, providing genomic signatures characterizing Monotremata, Marsupialia, Afrotheria, Xenarthra, Laurasiatheria, and Euarchontoglires. A hypothetical ancestral mammalian-like GS of 2.9–3.7 pg has been suggested. This value appears compatible with the average values calculated for the high systematic levels of the extant Monotremata (∼2.97 pg) and Marsupialia (∼4.07 pg), suggesting invasion of mobile DNA elements concurrently with the separation of the older clades of Afrotheria (∼5.5 pg) and Xenarthra (∼4.5 pg) with larger GS, leaving the Euarchontoglires (∼3.4 pg) and Laurasiatheria (∼2.8 pg) genomes with fewer transposable elements. However, the paucity of GS data (546 mammalian species sized from 5,488 living species) for species, genera, and families calls for caution. Considering that mammalian species may be vanished even before they are known, GS data are sorely needed to phenotype the effects brought about by their variation and to validate any hypotheses on GS evolution in mammals.
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