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Epigenetic alterations are cell type-specific and require methods like single cell sequencing and cell type sorting by flow cytometry. These methods often rely on the availability of fresh tissue, yet postmortem frozen tissue is typically the only material available from non-experimental subjects, including humans and other nonhuman primates (NHP). Many insights can be gained from analysis of these precious samples. To this end, we developed a protocol for isolating intact nuclei from small starting amounts of postmortem frozen chimpanzee ( ) cerebral cortex tissue. Isolated nuclei can be input directly into single cell epigenomics protocols like ATAC-seq or can be immunostained for enrichment of neuronal nuclei via fluorescent-activated nuclei sorting (FANS) followed by bulk epigenetic methods like methylome sequencing. We adapted and optimized this protocol based on existing human brain tissue protocols. Our protocol specifically addresses challenges presented by postmortem frozen NHP brain tissue, including high levels of myelin debris and reduced RNA integrity. We include key steps and troubleshooting guidance to improve nuclei quality and sorting outcomes, and we also discuss limitations and considerations for researchers interested in using these methods.

The X‐chromosomal MECP2/Mecp2 gene encodes methyl‐CpG‐binding protein 2, a transcriptional activator and repressor regulating many other genes. We discovered in male FVB/N mice that mild (~50%) transgenic overexpression of Mecp2 enhances aggression. Surprisingly, when the same transgene was expressed in C57BL/6N mice, transgenics showed reduced aggression and social interaction. This suggests that Mecp2 modulates aggressive social behavior. To test this hypothesis in humans, we performed a phenotype‐based genetic association study (PGAS) in >1000 schizophrenic individuals. We found MECP2 SNPs rs2239464 (G/A) and rs2734647 (C/T; 3′UTR) associated with aggression, with the G and C carriers, respectively, being more aggressive. This finding was replicated in an independent schizophrenia cohort. Allele‐specific MECP2 mRNA expression differs in peripheral blood mononuclear cells by ~50% (rs2734647: C > T). Notably, the brain‐expressed, species‐conserved miR‐511 binds to MECP2 3′UTR only in T carriers, thereby suppressing gene expression. To conclude, subtle MECP2/Mecp2 expression alterations impact aggression. While the mouse data provides evidence of an interaction between genetic background and mild Mecp2 over expression, the human data convey means by which genetic variation affects MECP2 expression and behavior. Synopsis The transcriptional regulator MECP2 is known to affect neurodevelopment. This study associates aggressive social behavior with MECP2 genotype and expression changes in both male schizophrenic patients and mouse models of different genetic background. Mild (50%) overexpression of Mecp2 in mice influences male social aggression. The genetic background (FVB/N versus C57Bl/6N) modulates this overexpression‐associated phenotype. Normal genetic variation of MECP2 (single nucleotide polymorphisms) co‐determines the level of aggression in two independent cohorts of schizophrenic men. miR‐511 downregulates MECP2 expression in T but not C carriers of SNP rs2734647, suggesting miR‐511 targeted therapies in MECP2 gene duplication syndrome. Graphical Abstract The transcriptional regulator MECP2 is known to affect neurodevelopment. This study associates aggressive social behavior with MECP2 genotype and expression changes in both male schizophrenic patients and mouse models of different genetic background.

The X‐chromosomal MECP2/Mecp2 gene encodes methyl‐CpG‐binding protein 2, a transcriptional activator and repressor regulating many other genes. We discovered in male FVB/N mice that mild (~50%) transgenic overexpression of Mecp2 enhances aggression. Surprisingly, when the same transgene was expressed in C57BL/6N mice, transgenics showed reduced aggression and social interaction. This suggests that Mecp2 modulates aggressive social behavior. To test this hypothesis in humans, we performed a phenotype‐based genetic association study (PGAS) in >1000 schizophrenic individuals. We found MECP2 SNPs rs2239464 (G/A) and rs2734647 (C/T; 3′UTR) associated with aggression, with the G and C carriers, respectively, being more aggressive. This finding was replicated in an independent schizophrenia cohort. Allele‐specific MECP2 mRNA expression differs in peripheral blood mononuclear cells by ~50% (rs2734647: C > T). Notably, the brain‐expressed, species‐conserved miR‐511 binds to MECP2 3′UTR only in T carriers, thereby suppressing gene expression. To conclude, subtle MECP2/Mecp2 expression alterations impact aggression. While the mouse data provides evidence of an interaction between genetic background and mild Mecp2 over expression, the human data convey means by which genetic variation affects MECP2 expression and behavior. image The transcriptional regulator MECP 2 is known to affect neurodevelopment. This study associates aggressive social behavior with MECP 2 genotype and expression changes in both male schizophrenic patients and mouse models of different genetic background. Mild (50%) overexpression of Mecp2 in mice influences male social aggression. The genetic background ( FVB /N versus C57Bl/6N) modulates this overexpression‐associated phenotype. Normal genetic variation of MECP 2 (single nucleotide polymorphisms) co‐determines the level of aggression in two independent cohorts of schizophrenic men. miR‐511 downregulates MECP 2 expression in T but not C carriers of SNP rs2734647, suggesting miR‐511 targeted therapies in MECP 2 gene duplication syndrome.

Aside from many genetic and environmental influences on the brain, aging itself is a significant risk factor for accelerated cognitive decline, making aging research crucial due to the increasing population age in our era. We aimed to discover gene expression differences in the aging zebrafish brain using three age groups in the first aim. We identified gjc2 (CX47) and alcamb (ALCAM) cell adhesion genes showing consistent downregulation with age across all experiments. ALCAM is also known to be associated with neuroinflammation, which has been implicated to be lowered using anti-aging, non-genetic nutrient interventions. In the second aim, we applied 12 weeks of two opposing nutrient interventions, caloric restriction (CR) and overfeeding (OF) in aging zebrafish, in order to be able to propose a reliable therapeutic approach for reversing age-related neurobiological changes. We measured protein and expression level differences of selected genes related to proliferation to inflammation with these diets. The results showed that sox2 gene expression was significantly upregulated following OF treatment than CR diet, and myca and tp53 mRNA levels were significantly downregulated with advanced age. Alcamb and tfdp1 expression levels were also marginally significantly lowered with CR compared to other groups. Meanwhile, we also conducted another transcriptomic approach using microarray to assess gene expression differences with CR compared to Ad-libitum (AL) feeding. Thus, lastly, in the third part, we found that CR causes changes in cell cycle regulation among several other functional regulatory pathways in zebrafish brains. We identified the tfdp1 gene, which showed downregulation with CR, as a possible CR regulator. Then, to create a CR mimic, we performed morpholino oligo (MO) injections to zebrafish embryos and adult brains to knock down tfdp1 gene expression levels. The injections were not successful in altering Tfdp1 protein levels in neither embryos and adults. However, 8ng tfdp1-MO injections in embryos significantly increased myca and tp53 expression levels, which are among the downstream targets of tfdp1. Our examinations shed light on healthy brain aging and possibly propose new drug targets.

Currently we know from rodent and fish studies that adult neuron generation is reduced but still continues in old animals with a dynamic change throughout aging. This process occurs mainly in hippocampal region, which is thought to be analogous to a region in telencephalon of the zebrafish brain. Changes in this neuron turnover are thought to be one contributing factor to cognitive change occuring with advanced age. Since we know that external factors can affect the process of neurogenesis, and as previous studies showed, dietary restriction (DR) extends life span; here, we hypothesized that DR should also alleviate several age associated alterations. In order to test this, we applied a 10-week feeding regimen to young (8-9 months) and old (26-32.5 months) male and female fish. We had two dietary regimen groups, one fed Ad libitum and one fed with a DR that was a pattern of every-other-day feeding, which is a widely accepted method of DR. A total of 124 animals were used in this study. As a result, a significant loss of body weight in both young and old DR groups was observed without an effect on body lengths. To be able to label actively dividing cells we used Bromodeoxyuridine (BrdU), which is a thymidine analog. It is injected into the fish intraperitoneally prior to euthanasia. Four hours later the brains were dissected and fixed for sectioning. We obtained cross-sectional slices of 50 m thickness with a vibratome, performed immunostaining with antibodies against BrdU, NeuN (neuronal marker), HuC (neuronal marker); and visualized the brain sections with confocal microscopy forming 3D reconstructed pictures. We counted the BrdU positive cells in all brain slices, forming a regional map of the telencephalic region of zebrafish brain, in which we documented the specific regions where the adult neurogenesis dominates the most and least. Our results confirmed that there are more BrdU positive cells in young animals than olds, and that age is correlated with an increased senescence associated fi-galactosidase (SA-fi-gal) activity, along with shortened telomere lengths. The 10-week diet was not found to be creating a significant change in cell proliferation rates, cellular senescence, or the differentiation pattern of glial cells. However, it was demonstrated to have a shortening effect on telomere lengths. Our data suggest that the potential effects of DR could be related to telomere regulation. Therefore, in order to detect differentially expressed genes that could be related to this mechanism between the groups, we performed microarray analysis with differing DR regimens. Initial data indicated no significant effects of a 4-week diet on gene expression differences among aged fish. Further analysis of the different periods of DR will be performed. Taken together, the effects of age are more robust than a short-term DR.