The Kdm/Kmt gene families in the self-fertilizing mangrove rivulus fish, Kryptolebias marmoratus, suggest involvement of histone methylation machinery in development and reproduction

Fellous, Alexandre; Earley, Ryan L.; Silvestre, Frédéric

doi:10.1016/j.gene.2018.11.046

Cited by 25 publications

(20 citation statements)

References 67 publications

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“…The PR domain could interact with some essential proteins, such as histone methyltransferase [26,27]. There have been reports showing that PRDM6, as a methyltransferase, was considered to be involved in the histone methylation mechanism in development and reproduction [28,29]. Histone methylation could regulate organic growth and development by epigenetic modification [30,31].…”

Section: Discussionmentioning

confidence: 99%

Screening of Deletion Variants within the Goat PRDM6 Gene and Its Effects on Growth Traits

Wang

Guo

et al. 2020

Animals

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Simple Summary: Genome-wide association studies found that the PR/SET Domain 6 (PRDM6) gene mutation was associated with bone development, bone density, and body mass index. This study found a 12 bp deletion variation within the PRDM6 gene in Shaanbei white cashmere goats in a large sample size (n = 1044). This variation polymorphism was associated with multiple goat growth traits in the yearling period, including heart girth (p = 0.027), cannon circumference (p = 0.008), chest depth (p = 2.10 × 10 −5 ), chest width (p = 0.004), body height (p = 0.032), body length (p = 0.044), and hip-width (p = 0.014). The effects of the 12 bp variation were found to make no difference on adult goat growth traits. Taken together, these results demonstrate that the 12 bp deletion variant plays an important role in the early growth and development of goats and could be considered as a useful and effective molecular marker for goat breeding selection in the growth stage.Abstract: By genome-wide association studies, the PRDM6 gene has been shown to affect multiple, apparently unrelated inherited traits, including bone density and body mass index. Therefore, it is considered a potentially pleiotropic gene. In this study, we identified a 12 bp deletion variant (NC_030814.1:rs651603667, g: 79985625-79985636delTTGACTGATCCA) within the PRDM6 gene in a large sample (SBWC goats; n = 1044). All goat samples were collected in Shaanxi province in July 2018. The frequency of the wt allele was higher than the frequency of the del allele, and this mutation polymorphism confirmed to be consistent with the Hardy-Weinberg equilibrium (p > 0.05). Further results showed that in a group of goats in the yearling period (18 months old, n = 567), this deletion variant of the PRDM6 gene was associated with heart girth (p = 0.027), cannon circumference (p = 0.008), chest depth (p = 2.10 × 10 −5 ), chest width (p = 0.004), body height (p = 0.032), body length (p = 0.044) and hip-width (p = 0.014). For adult SBWC goats (36 months old, n = 477), the effects of the 12 bp variation on growth-related traits were found to make no difference. These findings show that the 12 bp deletion within the goat PRDM6 gene plays an important role in the early growth and development of goats. Using the 12 bp mutation, breeders can quickly and effectively select excellent individual goats at an early stage.

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Section: Discussionmentioning

confidence: 99%

Screening of Deletion Variants within the Goat PRDM6 Gene and Its Effects on Growth Traits

Wang

Guo

et al. 2020

Animals

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“…Interestingly, PRMT8, which is duplicated in stickleback, plays a critical role during zebrafish embryonic and neural development (Wang and Li, 2012), and is the only enzyme with tissue-restricted expression. Whereas they are less known outside of other non-model species (Best et al, 2018), the KMTs seem to be conserved in stickleback, as well as in mangrove rivulus (Fellous et al, 2019b), insects (Jiang et al, 2017), and humans (Petrossian and Clarke, 2011), although species-specific loss/duplication events have occurred.…”

Section: Histone Methylationmentioning

confidence: 94%

“…The number of KDMs in stickleback differs slightly from other fish species (Qian et al, 2015;Fellous et al, 2019b). However, despite being well documented in taxa ranging from fruit flies to mammals and crucial in development and adaptation of a number of organisms, as well as being temperature sensitive (Takeuchi et al, 1999;Sasai et al, 2007;Fellous et al, 2014Fellous et al, , 2015Zhang et al, 2019), these fundamental proteins remain understudied in fishes, with the exception of zebrafish (Stewart et al, 2009;Akerberg et al, 2017).…”

Section: Histone Methylationmentioning

confidence: 99%

Genome Survey of Chromatin-Modifying Enzymes in Threespine Stickleback: A Crucial Epigenetic Toolkit for Adaptation?

Fellous

Shama

2019

Front. Mar. Sci.

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Ocean environments are changing rapidly and marine organisms need to cope with these changes in order to survive, develop, and reproduce. To do so, organisms can either migrate, adapt in situ or acclimate via phenotypic plasticity. In this context, the emerging field of environmental epigenetics investigates the contribution of genetic and epigenetic information to adaptive potential of wild populations. Epigenetic modifications are based on the highly dynamic combination of DNA methylation, histone modifications, and non-coding RNAs, which may facilitate phenotypic plasticity through genotype-epigenotype-environment interactions, and can drive rapid evolution in wild populations. However, while knowledge of epigenetic contributions to phenotypes across different developmental and generational timescales is increasing for medical research model species, the mechanistic and synergistic action of these modifications remain comparatively understudied in ecological models such as teleost fishes. Here, we characterized the evolution of the gene toolkit involved in key molecular epigenetic pathways including DNA methylation, histone modifications, macroH2A histone, and miRNA biogenesis/turnover in threespine stickleback, a model species in evolution and ecology. We then investigated these genes within a phylogenetic context by comparing them in stickleback to human, mouse, chicken, tropical clawed frog, zebrafish, medaka, green spotted puffer, channel catfish, and mangrove rivulus. We found that, in general, conserved domains, in conjunction with their phylogenetic positions, suggest evolutionary conservation of putative enzyme activity in stickleback. However, molecular epigenetic pathways also revealed that teleost gene evolution is diversified and complex. Specifically, the number of genes, gene loss/duplication events, identified conserved domains, and putative protein lengths vary greatly from one species to another, particularly within fishes, which exhibit a potentially new class of histone deacetylases. This suggests different biological functions specific to fish species, and that the action of genes regulating epigenetic modifications in model species are not necessarily applicable to other related species. We integrate our results into recent advances concerning epigenetic mechanisms in teleosts, and conclude by discussing the necessity to delve deeper into the fundamental mechanics of epigenetic modifications in a wide array of taxa, particularly those relevant for assisted evolution, conservation, aquaculture, fisheries, and climate change-adaptation studies.

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“…This protein, FSTL1, was only detected as light labelled in the CCM from one of the conceptuses in our study. The gene coding for SET domain containing 9 (SETD9), heavy labelled in four CCM and present in media from seven conceptuses, belongs to a greater family, Kmt methyltransferases, that has been found to peak in expression during gastrula stage with a later reduction during embryogenesis in mangrove rivulus fish [55]. Another of the heavy labelled proteins, DExH-box helicase 34 (DHX34), is involved in the complex comprising UPF1 and SMG1, two proteins that are present in the CCM from all the conceptuses as light labelled and that are involved in nonsense-mediated decay [56] and could therefore be important during development although it was only detected in three CCM as heavy labelled.…”

Section: De Novo Synthesised Proteins In Conceptus-conditioned Mediamentioning

confidence: 99%

Protein Synthesis by Day 16 Bovine Conceptuses during the Time of Maternal Recognition of Pregnancy

Estepa

Tinning

Vasconcelos

et al. 2020

IJMS

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Interferon Tau (IFNT), the conceptus-derived pregnancy recognition signal in cattle, significantly modifies the transcriptome of the endometrium. However, the endometrium also responds to IFNT-independent conceptus-derived products. The aim of this study was to determine what proteins are produced by the bovine conceptus that may facilitate the pregnancy recognition process in cattle. We analysed by mass spectrometry the proteins present in conceptus-conditioned media (CCM) after 6 h culture of Day 16 bovine conceptuses (n = 8) in SILAC media (arginine- and lysine-depleted media supplemented with heavy isotopes) and the protein content of extracellular vesicles (EVs) isolated from uterine luminal fluid (ULF) of Day 16 pregnant (n = 7) and cyclic (n = 6) cross-bred heifers on day 16. In total, 11,122 proteins were identified in the CCM. Of these, 5.95% (662) had peptides with heavy labelled amino acids, i.e., de novo synthesised by the conceptuses. None of these proteins were detected in the EVs isolated from ULF. Pregnancy-associated glycoprotein 11, Trophoblast Kunitz domain protein 1 and DExD-Box Helicase 39A were de novo produced and present in the CCM from all conceptuses and in previously published CCM data following 6 and 24 h. A total of 463 proteins were present in the CCM from all the conceptuses in the present study, and after 6 and 24 h culture in a previous study, while expression of their transcripts was not detected in endometrium indicating that they are likely conceptus-derived. Of the proteins present in the EVs, 67 were uniquely identified in ULF from pregnant heifers; 35 of these had been previously reported in CCM from Day 16 conceptuses. This study has narrowed a set of conceptus-derived proteins that may be involved in EV-mediated IFNT-independent embryo–maternal communication during pregnancy recognition in cattle.

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The Kdm/Kmt gene families in the self-fertilizing mangrove rivulus fish, Kryptolebias marmoratus, suggest involvement of histone methylation machinery in development and reproduction

Cited by 25 publications

References 67 publications

Screening of Deletion Variants within the Goat PRDM6 Gene and Its Effects on Growth Traits

Screening of Deletion Variants within the Goat PRDM6 Gene and Its Effects on Growth Traits

Genome Survey of Chromatin-Modifying Enzymes in Threespine Stickleback: A Crucial Epigenetic Toolkit for Adaptation?

Protein Synthesis by Day 16 Bovine Conceptuses during the Time of Maternal Recognition of Pregnancy

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