Epigenetic dynamics shaping melanophore and iridophore cell fate in zebrafish

Genetic control over biogenic crystal morphogenesis in zebrafish

Organisms evolve mechanisms that regulate the properties of biogenic crystals to support a wide range of functions, from vision and camouflage to communication and thermal regulation. Yet, the mechanism underlying the formation of diverse intracellular crystals remains enigmatic. Here we unravel the biochemical control over crystal morphogenesis in zebrafish iridophores. We show that the chemical composition of the crystals determines their shape, particularly through the ratio between the nucleobases guanine and hypoxanthine. We reveal that these variations in composition are genetically controlled through tissue-specific expression of specialized paralogs, which exhibit remarkable substrate selectivity. This orchestrated combination grants the organism with the capacity to generate a broad spectrum of crystal morphologies. Overall, our findings suggest a mechanism for the morphological and functional diversity of biogenic crystals and may, thus, inspire the development of genetically designed biomaterials and medical therapeutics.

Keratinocytes drive the epithelial hyperplasia key to sea lice resistance in coho salmon

BACKGROUND

Salmonid species have followed markedly divergent evolutionary trajectories in their interactions with sea lice. While sea lice parasitism poses significant economic, environmental, and animal welfare challenges for Atlantic salmon (Salmo salar) aquaculture, coho salmon (Oncorhynchus kisutch) exhibit near-complete resistance to sea lice, achieved through a potent epithelial hyperplasia response leading to rapid louse detachment. The molecular mechanisms underlying these divergent responses to sea lice are unknown.

RESULTS

We characterized the cellular and molecular responses of Atlantic salmon and coho salmon to sea lice using single-nuclei RNA sequencing. Juvenile fish were exposed to copepodid sea lice (Lepeophtheirus salmonis), and lice-attached pelvic fin and skin samples were collected 12 h, 24 h, 36 h, 48 h, and 60 h after exposure, along with control samples. Comparative analysis of control and treatment samples revealed an immune and wound-healing response that was common to both species, but attenuated in Atlantic salmon, potentially reflecting greater sea louse immunomodulation. Our results revealed unique but complementary roles of three layers of keratinocytes in the epithelial hyperplasia response leading to rapid sea lice rejection in coho salmon. Our results suggest that basal keratinocytes direct the expansion and mobility of intermediate and, especially, superficial keratinocytes, which eventually encapsulate the parasite.

CONCLUSIONS

Our results highlight the key role of keratinocytes in coho salmon's sea lice resistance and the diverged biological response of the two salmonid host species when interacting with this parasite. This study has identified key pathways and candidate genes that could be manipulated using various biotechnological solutions to improve Atlantic salmon sea lice resistance.

The TET-Sall4-BMP regulatory axis controls craniofacial cartilage development

Craniofacial microsomia (CFM) is a congenital defect that usually results from aberrant development of embryonic pharyngeal arches. However, the molecular basis of CFM pathogenesis is largely unknown. Here, we employ the zebrafish model to investigate mechanisms of CFM pathogenesis. In early embryos, tet2 and tet3 are essential for pharyngeal cartilage development. Single-cell RNA sequencing reveals that loss of Tet2/3 impairs chondrocyte differentiation due to insufficient BMP signaling. Moreover, biochemical and genetic evidence reveals that the sequence-specific 5mC/5hmC-binding protein, Sall4, binds the promoter of bmp4 to activate bmp4 expression and control pharyngeal cartilage development. Mechanistically, Sall4 directs co-phase separation of Tet2/3 with Sall4 to form condensates that mediate 5mC oxidation on the bmp4 promoter, thereby promoting bmp4 expression and enabling sufficient BMP signaling. These findings suggest the TET-BMP-Sall4 regulatory axis is critical for pharyngeal cartilage development. Collectively, our study provides insights into understanding craniofacial development and CFM pathogenesis.

Divergent expression of aristaless1 and aristaless2 during embryonic appendage and pupal wing development in butterflies

BACKGROUND

Gene duplication events are critical for the evolution of new gene functions. Aristaless is a major regulator of distinct developmental processes. It is most known for its role during appendage development across animals. However, more recently other distinct biological functions have been described for this gene and its duplicates. Butterflies and moths have two copies of aristaless, aristaless1 (al1) and aristaless2 (al2), as a result of a gene duplication event. Previous work in Heliconius has shown that both copies appear to have novel functions related to wing color patterning. Here we expand our knowledge of the expression profiles associated with both ancestral and novel functions of Al1 across embryogenesis and wing pigmentation. Furthermore, we characterize Al2 expression, providing a comparative framework between gene copies within the same species, allowing us to understand the origin of new functions following gene duplication.

RESULTS

Our work shows that the expression of both Al1 and Al2 is associated with the ancestral function of sensory appendage (leg, mouth, spines, and eyes) development in embryos. Interestingly, Al1 exhibits higher expression earlier in embryogenesis while the highest levels of Al2 expression are shifted to later stages of embryonic development. Furthermore, Al1 localization appears extranuclear while Al2 co-localizes tightly with nuclei earlier, and then also expands outside the nucleus later in development. Cellular expression of Al1 and Al2 in pupal wings is broadly consistent with patterns observed during embryogenesis. We also describe, for the first time, how Al1 localization appears to correlate with zones of anterior/posterior elongation of the body during embryonic growth, showcasing a possible new function related to Aristaless' previously described role in appendage extension.

CONCLUSIONS

Overall, our data suggest that while both gene copies play a role in embryogenesis and wing pigmentation, the duplicates have diverged temporally and mechanistically across those functions. Our study helps clarify principles behind sub-functionalization and gene expression evolution associated with developmental functions following gene duplication events.

A flexible group decision-making method for green supplier selection integrating MABAC and CRITIC method under the linguistic Z-numbers environment

This paper intends to treat the green supplier selection (GSS) problem as a multi-attribute group decision making (MAGDM) problem, adopt the linguistic Z-number that can more flexibly and accurately express the evaluation information, and expand the traditional multi-attribute boundary approximate area comparison (MABAC) method, combine the CRITIC method of standard importance and consider the risk vector to finally determine the optimal solution. More specifically, the linguistic Z-number is used to describe the fuzzy evaluation information of experts on alternatives under attributes, then the expanded CRITIC method is used to obtain the weight of each given attribute, and finally the MABAC method with added risk vector and expanded is used to obtain the ranking of alternatives and obtain the best solution. Finally, taking green supplier selection as an example, and comparing with other methods, the reliability and effectiveness of the constructed method are verified. The results show that this method can express the evaluation information of experts flexibly and completely, and obtain the ranking results of given schemes through fewer steps, which is reliable and effective.

Genome-wide chromatin accessibility analysis unveils open chromatin convergent evolution during polyploidization in cotton

Allopolyploidization, resulting in divergent genomes in the same cell, is believed to trigger a “genome shock”, leading to broad genetic and epigenetic changes. However, little is understood about chromatin and gene-expression dynamics as underlying driving forces during allopolyploidization. Here, we examined the genome-wide DNase I-hypersensitive site (DHS) and its variations in domesticated allotetraploid cotton ( Gossypium hirsutum and Gossypium barbadense , AADD) and its extant AA ( Gossypium arboreum ) and DD ( Gossypium raimondii ) progenitors. We observed distinct DHS distributions between G. arboreum and G. raimondii . In contrast, the DHSs of the two subgenomes of G. hirsutum and G. barbadense showed a convergent distribution. This convergent distribution of DHS was also present in the wild allotetraploids Gossypium darwinii and G. hirsutum var. yucatanense , but absent from a resynthesized hybrid of G. arboreum and G. raimondii , suggesting that it may be a common feature in polyploids, and not a consequence of domestication after polyploidization. We revealed that putative cis -regulatory elements (CREs) derived from polyploidization-related DHSs were dominated by several families, including Dof, ERF48, and BPC1. Strikingly, 56.6% of polyploidization-related DHSs were derived from transposable elements (TEs). Moreover, we observed positive correlations between DHS accessibility and the histone marks H3K4me3, H3K27me3, H3K36me3, H3K27ac, and H3K9ac, indicating that coordinated interplay among histone modifications, TEs, and CREs drives the DHS landscape dynamics under polyploidization. Collectively, these findings advance our understanding of the regulatory architecture in plants and underscore the complexity of regulome evolution during polyploidization.

Epigenetic effect of putrescine supplementation during in vitro maturation of oocytes on offspring in mice

PURPOSE

To investigate the epigenetic safety of putrescine supplementation during in vitro maturation (IVM) to offspring.

METHODS

Germinal vesicle oocytes retrieved from 12-week-old mice were randomly divided into two groups and cultured in IVM medium with or without 1 mmol/L putrescine for 16 h. Then, in vitro fertilization and embryo transplantation were conducted to produce the F1 offspring. The F1 mated with ordinary mice and bred the F2 offspring. The DNA methylation patterns in the brain and heart of F1 were investigated by reduced representation bisulfite sequencing. Imprinted gene expression levels of F1 oocytes were tested. The global methylation of F2 was examined by dot blot.

RESULTS

The weight, organ coefficient, and histology were normal in the F1 and F2 offspring from the putrescine-treated oocytes. An overall methylation level of 31.23 to 32.53% was observed for all CpG sites in the brain and heart of the two groups. The DNA methylation patterns of the brain and heart in F1 were not altered in general, with subtle differences. The expression levels of imprinted genes including H19, Snrpn, Peg3, Igf2, and Igf2r did not statistically change. The global 5mC level of F2 was consistent with the control group.

CONCLUSION

Putrescine supplementation during IVM did not directly affect the development, health, and reproduction, and did not affect the genome and global epigenetics of mouse offspring derived from those oocytes. The transient putrescine treatment for improving oocyte maturation shows its long-term safety of genome and epigenetics in the offspring of mice.

Epigenetic dynamics shaping melanophore and iridophore cell fate in zebrafish

BACKGROUND

Zebrafish pigment cell differentiation provides an attractive model for studying cell fate progression as a neural crest progenitor engenders diverse cell types, including two morphologically distinct pigment cells: black melanophores and reflective iridophores. Nontrivial classical genetic and transcriptomic approaches have revealed essential molecular mechanisms and gene regulatory circuits that drive neural crest-derived cell fate decisions. However, how the epigenetic landscape contributes to pigment cell differentiation, especially in the context of iridophore cell fate, is poorly understood.

RESULTS

We chart the global changes in the epigenetic landscape, including DNA methylation and chromatin accessibility, during neural crest differentiation into melanophores and iridophores to identify epigenetic determinants shaping cell type-specific gene expression. Motif enrichment in the epigenetically dynamic regions reveals putative transcription factors that might be responsible for driving pigment cell identity. Through this effort, in the relatively uncharacterized iridophores, we validate alx4a as a necessary and sufficient transcription factor for iridophore differentiation and present evidence on alx4a's potential regulatory role in guanine synthesis pathway.

CONCLUSIONS

Pigment cell fate is marked by substantial DNA demethylation events coupled with dynamic chromatin accessibility to potentiate gene regulation through cis-regulatory control. Here, we provide a multi-omic resource for neural crest differentiation into melanophores and iridophores. This work led to the discovery and validation of iridophore-specific alx4a transcription factor.