Genome-wide histone state profiling of fibroblasts from the opossum, Monodelphis domestica, identifies the first marsupial-specific imprinted gene

Douglas, Kory C.; Wang, Xiaozhu; Jasti, Madhuri; Wolff, Abigail; VandeBerg, John L.; Clark, Andrew G.; Samollow, Paul B.

doi:10.1186/1471-2164-15-89

Cited by 9 publications

(8 citation statements)

References 88 publications

(79 reference statements)

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“…Much as RNA-Seq has become the workhorse technique in transcriptomic studies, chromatin immunoprecipitation sequencing (ChIP-Seq) has been widely used for CRE discovery and characterization (Douglas et al, 2014;Johnson et al, 2007;Roy et al, 2010;Visel et al, 2009). This technique works by cross-linking proteins bound to DNA, fragmenting the genome, and immunoprecipitating proteins of interest using a specific antibody.…”

Section: Identifying Cresmentioning

confidence: 99%

The GRN concept as a guide for evolutionary developmental biology

Feigin

Moreno

et al. 2022

J Exp Zool Pt B

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Organismal phenotypes result largely from inherited developmental programs, usually executed during embryonic and juvenile life stages. These programs are not blank slates onto which natural selection can draw arbitrary forms. Rather, the mechanisms of development play an integral role in shaping phenotypic diversity and help determine the evolutionary trajectories of species. Modern evolutionary biology must, therefore, account for these mechanisms in both theory and in practice. The gene regulatory network (GRN) concept represents a potent tool for achieving this goal whose utility has grown in tandem with advances in “omic” technologies and experimental techniques. However, while the GRN concept is widely utilized, it is often less clear what practical implications it has for conducting research in evolutionary developmental biology. In this Perspective, we attempt to provide clarity by discussing how experiments and projects can be designed in light of the GRN concept. We first map familiar biological notions onto the more abstract components of GRN models. We then review how diverse functional genomic approaches can be directed toward the goal of constructing such models and discuss current methods for functionally testing evolutionary hypotheses that arise from them. Finally, we show how the major steps of GRN model construction and experimental validation suggest generalizable workflows that can serve as a scaffold for project design. Taken together, the practical implications that we draw from the GRN concept provide a set of guideposts for studies aiming at unraveling the molecular basis of phenotypic diversity.

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Section: Identifying Cresmentioning

confidence: 99%

The GRN concept as a guide for evolutionary developmental biology

Feigin

Moreno

et al. 2022

J Exp Zool Pt B

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“…Marsupials are characterised by specific epigenetic imprinting on X chromosomes in females which preferentially silences paternally-derived X chromosomes [103,104]. However, to date, apart from selected imprinted genes [105], there is no evidence of widespread and parental origin based epigenetic profiling in marsupials beyond the X chromosome.…”

Section: Parental Control Of Telomere Lengthmentioning

confidence: 99%

Untitled

2016

AIMS Genetics

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There has been increasing interest in the use of telomeres as biomarkers of stress, cellular ageing and life-histories. However, the telomere landscape is a diverse feature, with noticeable differences between species, a fact which is highlighted by the unusual telomeres of various vertebrate organisms. We broadly review differences in telomere dynamics among vertebrates, and emphasize the need to understand more about telomere processes and trends across species. As part of these species differences, we review unusual telomeres in vertebrates. This includes mega-telomeres, which are present across a diverse set of organisms, but also focusing on the unusual telomeres traits of marsupials and monotremes, which have seen little to no prior discussion, yet uniquely stand out from other unusual telomere features discovered thus far. Due to the presence of at least two unique telomere features in the marsupial family Dasyuridae, as well as to the presence of physiological strategies semelparity and torpor, which have implications for telomere life-histories in these species, we suggest that this family has a very large potential to uncover novel information on telomere evolution and dynamics.

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“…However, of these, only 9 genes have been con rmed to be imprinted in marsupials (Ager et al, 2007;Das et al, 2012;Ishihara et al, 2022;Killian et al, 2000;O'Neill et al, 2000;Smits et al, 2008;Suzuki et al, 2007Suzuki et al, , 2005. In addition, there are ve marsupial-speci c imprinted genes (Douglas et al, 2014;Grant et al, 2012;Mahadevaiah et al, 2020;Stringer et al, 2012;Suzuki et al, 2018). These common imprinted genes could provide insights into the evolutionary conserved and/or lineage speci c imprinting mechanisms between marsupials and eutherians.…”

Section: Introductionmentioning

confidence: 99%

Marsupials have monoallelic MEST expression with a conserved antisense lncRNA but MEST is not imprinted

Ishihara,

Suzuki,

Newman

et al. 2023

Heredity

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The imprinted isoform of the Mestgene in mice is involved in key mammalian traits such as placental and fetal growth, maternal care and mammary gland maturation. MEST has a distinct promoter differentially methylated region (DMR) in eutherian mammals but in marsupials, while MEST was thought to be imprinted, it had no DMR. In this study, we examined similarities and differences in the MEST gene locus across mammals using a marsupial, the tammar wallaby, a monotreme, the platypus, and a eutherian, the mouse, to investigate how MEST imprinting evolved in mammals. By con rming the presence of the short isoform in all mammalian groups (which is imprinted in eutherians), this study suggests that an alternative promoter for the short isoform has evolved at the MESTgene locus in the common ancestor of mammals. In the tammar, the short isoform of MEST shared the putative promoter CpG island with an antisense lncRNA previously identi ed in humans and an isoform of a neighbouring gene CEP41. The antisense lncRNA was expressed in tammar sperm, as seen in humans. This suggested that the conserved lncRNA might play an important part in the establishment of MEST imprinting in therian mammals, but it was not imprinted in the tammar. In contrast to previous studies, this study showed that MEST is non-imprinted and mono-allelically expressed in marsupials. This suggests that selection of MEST imprinting in eutherians must have occurred after the marsupial-eutherian split with the acquisition of a key epigenetic imprinting control region, the DMR.

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Genome-wide histone state profiling of fibroblasts from the opossum, Monodelphis domestica, identifies the first marsupial-specific imprinted gene

Cited by 9 publications

References 88 publications

The GRN concept as a guide for evolutionary developmental biology

The GRN concept as a guide for evolutionary developmental biology

Untitled

Marsupials have monoallelic MEST expression with a conserved antisense lncRNA but MEST is not imprinted

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