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Aggressive behavior is an evolutionary conserved phenomenon and wide-spread among animal kingdom. Using aggression, animals of many species establish dominance hierarchy to regulate social interactions. Previous studies on dominance using fish mainly centered on the differences in brain gene expression between dominants and subordinates after their fighting interactions have ended. Thus, information on how brain gene expression changes according to each stage of aggression generation across different stages of fighting remains to be understood. This study aims to fill the gap by evaluating brain gene expression changes across different fighting stages in males of the fish Betta splendens using RNA-seq approach. I discover that brain gene expression between two opponents within a fighting pair changed in a synchrony fashion during fighting, reflecting mutual assessment between them at molecular level. The genes mediated this process are associated with ion transport, signal transduction, and long-term memory. Additionally, the transcriptomic synchronization pattern during fighting was gradually lost after fighting, and brain gene activity reduced to minimum leading to the emergence of a unique neurogenomic state, which is considered to be an energy-saving strategy to adapt to energy depletion among all individuals after fighting. Furthermore, a higher impact of losing in comparison with winning in the nerogenomic state of the individuals was found as indicated by a greater number of long-term memory and autism-risk genes in loser relative to winner. Interestingly, alternative splicing was found to play key roles in response to oxygen stress across the fighting stages among all individuals. Altogether, the findings from this thesis sufficiently elucidate the genes and molecular events underlying aggression generation across different stages of fighting in B. splendens, and provide comprehensive information for future research on aggression in vertebrates at molecular levels.

Intron retention (IR) is an important regulatory mechanism that affects gene expression and protein functions. Using klotho mice as a model, we proposed that retained introns are an excellent marker for the pre-disease state. Surprisingly, among widespread retained introns that accumulated during aging in the liver, a subset was recovered to the normal state by a Japanese traditional herbal medicine. IR-recovered genes fell into two categories: (1) those involved in the spliceosome and (2) those involved in liver-specific metabolism. By integrating data for splicing patterns, transcriptomes, and metabolomes, we hypothesize that this medicine-related IR recovery under the pre-disease state reflects the actual recovery of liver-specific function to the healthy state. Accordingly, the study provides proof-of-concept evidence related to the ancient Chinese statement proposing the medicine’s usefulness for treating the pre-disease state. This approach lays out a method for elucidating unknown molecular mechanisms of an herbal medicine with multiple ingredients.

Conspecific male animals fight for resources such as food and mating opportunities but typically stop fighting after assessing their relative fighting abilities to avoid serious injuries. Physiologically, how the fighting behavior is controlled remains unknown. Using the fighting fish Betta splendens, we studied behavioral and neurotranscriptomic changes during the fight between the two opponents. At the behavioral level, surface-breathing and biting/striking occurred only during intervals between mouth-lockings. Eventually, the behaviors of the two opponents became synchronized, with each pair showing a unique behavioral pattern. At the physiological level, we examined the expression patterns of 23,306 brain transcripts using RNA-sequencing data from brains of fighting pairs after a 20-min (D20) and a 60-min (D60) fight. The two opponents in each D60 fighting pairs showed a strong gene expression correlation, whereas those D20 fighting pair showed a weak correlation. Moreover, each fighting pair in the D60 group showed pair-specific gene expression patterns in the grade of membership analysis (GoM) and were grouped as a pair in the heatmap clustering. The observed pair-specific individualization in neurotranscriptomic synchronization (PINS) suggested that this synchronization provides physiological bases for the behavioral synchronization. An analysis using the synchronized genes in fighting pairs of the D60 found genes enriched for ion transport, synaptic function, and learning and memory. PINS could be a general phenomenon and may provide a new cornerstone to investigate coordinating and sustaining social interactions between two interacting partners of higher animals.

Generation of neurons through direct reprogramming has emerged as a promising therapeutic approach for neurodegenerative diseases. Despite successful applications in vitro , in vivo implementation has been hampered by low efficiency. In this study, we present a highly efficient strategy for reprogramming retinal glial cells into neurons by simultaneously inhibiting key negative regulators. By suppressing Notch signaling through the removal of its central mediator Rbpj, we induced mature Müller glial cells to reprogram into bipolar and amacrine neurons in uninjured adult mouse retinas, and observed that this effect was further enhanced by retinal injury. We found that specific loss of function of Notch1 and Notch2 receptors in Müller glia mimicked the effect of Rbpj deletion on Müller glia-derived neurogenesis. Integrated analysis of multiome (scRNA- and scATAC-seq) and CUT&Tag data revealed that Rbpj directly activates Notch effector genes and genes specific to mature Müller glia while also indirectly represses the expression of neurogenic bHLH factors. Furthermore, we found that combined loss of function of Rbpj and Nfia/b/x resulted in a robust conversion of nearly all Müller glia to neurons. Finally, we demonstrated that inducing Müller glial proliferation by AAV (adeno-associated virus)-mediated overexpression of dominant- active Yap supports efficient levels of Müller glia-derived neurogenesis in both Rbpj - and Nfia/b/x/Rbpj - deficient Müller glia. These findings demonstrate that, much like in zebrafish, Notch signaling actively represses neurogenic competence in mammalian Müller glia, and suggest that inhibition of Notch signaling and Nfia/b/x in combination with overexpression of activated Yap could serve as an effective component of regenerative therapies for degenerative retinal diseases.

The transition from natal downs for heat conservation to juvenile feathers for simple flight is a remarkable environmental adaptation process in avian evolution. However, the underlying epigenetic mechanism for this primary feather transition is mostly unknown. Here we conducted time-ordered gene co-expression network construction, epigenetic analysis, and functional perturbations in developing feather follicles to elucidate four downy-juvenile feather transition events. We discovered that LEF1 works as a key hub of Wnt signaling to build rachis and converts radial downy to bilateral symmetry. Extracellular matrix reorganization leads to peripheral pulp formation, which mediates epithelial -mesenchymal interactions for branching morphogenesis. ACTA2 compartments dermal papilla stem cells for feather cycling. Novel usage of scale keratins strengthens feather sheath with SOX14 as the epigenetic regulator. We found this primary feather transition largely conserved in chicken (precocious) and zebra finch (altricial) and discussed the possibility that this evolutionary adaptation process started in feathered dinosaurs., Competing Interests: Competing interests The authors declare no competing or financial interests.