RNA‐seq of the aging brain in the short‐lived fish N. furzeri – conserved pathways and novel genes associated with neurogenesis

Abstract

The brains of teleost fish show extensive adult neurogenesis and neuronal regeneration. The patterns of gene regulation during fish brain aging are unknown. The short-lived teleost fish Nothobranchius furzeri shows markers of brain aging including reduced learning performances, gliosis, and reduced adult neurogenesis. We used RNA-seq to quantify genome-wide transcript regulation and sampled five different time points to characterize whole-genome transcript regulation during brain aging of N. furzeri. Comparison with human datasets revealed conserved up-regulation of ribosome, lysosome, and complement activation and conserved down-regulation of synapse, mitochondrion, proteasome, and spliceosome. Down-regulated genes differ in their temporal profiles: neurogenesis and extracellular matrix genes showed rapid decay, synaptic and axonal genes a progressive decay. A substantial proportion of differentially expressed genes (∼40%) showed inversion of their temporal profiles in the last time point: spliceosome and proteasome showed initial down-regulation and stress-response genes initial up-regulation. Extensive regulation was detected for chromatin remodelers of the DNMT and CBX families as well as members of the polycomb complex and was mirrored by an up-regulation of the H3K27me3 epigenetic mark. Network analysis showed extensive coregulation of cell cycle/DNA synthesis genes with the uncharacterized zinc-finger protein ZNF367 as central hub. In situ hybridization showed that ZNF367 is expressed in neuronal stem cell niches of both embryonic zebrafish and adult N. furzeri. Other genes down-regulated with age, not previously associated with adult neurogenesis and with similar patterns of expression are AGR2, DNMT3A, KRCP, MEX3A, SCML4, and CBX1. CBX7, on the other hand, was up-regulated with age.

The African turquoise killifish: A research organism to study vertebrate aging and diapause

“…In 2015, two independent groups de novo assembled and annotated the turquoise killifish genome: Anne Brunet's laboratory at Stanford University (African Turquoise Killifish Genome Browser: http://africanturquoisekillifishbrowser.org/; Valenzano et al., 2015) and Matthias Platzer's laboratory in Jena, Germany ( Nothobranchius furzeri Genome Browser: http://nfingb.leibniz-fli.de/; Reichwald et al., 2015). Additionally, other genomic resources have also been established through the years, including genetic linkage maps, quantitative trait loci, over 150 microsatellite markers (Blazek et al., 2017; Kirschner et al., 2012; Valenzano et al., 2009), and numerous transcriptomic and epigenomic datasets of different tissues at different ages using various strains (Baumgart et al., 2012, 2014, 2016, 2017; D'Angelo et al., 2014; Ng'oma, Groth, Ripa, Platzer & Cellerino, 2014; Petzold et al., 2013). A reference genome from the NCBI pipeline was made available online in 2016 (NCBI Genome ID: 2642, URL: https://www.ncbi.nlm.nih.gov/genome/2642).…”

“…Aging in the turquoise killifish has been extensively characterized at both the phenotypical and molecular level in both the GRZ strain and other strains such as MZM0403 and 0410 (Baumgart et al., 2012, 2014; Di Cicco, Tozzini, Rossi & Cellerino, 2011; Hartmann et al., 2009, 2011; Priami et al., 2015; Terzibasi Tozzini et al., 2014; Terzibasi et al., 2008; Tozzini, Baumgart, Battistoni & Cellerino, 2012). Indeed, despite their short lifespan compared to other vertebrates, various strains of the turquoise killifish recapitulate numerous stereotypical aging traits that have been reported in other vertebrates (Figure 5), including decline in reproduction, fertility, cognition, mobility, regeneration, and tissue homeostasis, along with increased incidence of senescence, neural and muscular degeneration, and cancerous lesions (Di Cicco et al., 2011; Terzibasi, Valenzano & Cellerino, 2007; Terzibasi et al., 2008; Valenzano, Terzibasi, Cattaneo, Domenici & Cellerino, 2006; Wendler, Hartmann, Hoppe & Englert, 2015).…”

“…However, in canonical vertebrate research organisms such as mice and zebrafish, it is more difficult to reconstruct the aging process from a few points, because the age points are often too far apart. The turquoise killifish provides a great opportunity to fill this gap, as its compressed lifespan requires fewer data points to capture the kinetics of the aging process (Baumgart et al., 2014). In addition, the turquoise killifish exhibits various complex behaviors such as learning that could be monitored and measured (Valenzano, Terzibasi, Vattaneo et al., 2006a, 2006b).…”

Developmentally arrested Austrofundulus limnaeus embryos have changes in post-translational modifications of histone H3

“…Histone H3 post-translational modifications are extensively studied because of their impact on chromatin structure and function and their central role in epigenetic mechanisms. However, our understanding of chromatin modification in developing vertebrate embryos is limited and has only been examined in a few species including mice (Dahl et al, 2010;VerMilyea et al, 2009), zebrafish (Havis et al, 2006;Lindeman et al, 2010;Wardle et al, 2006), N. furzeri (Baumgart et al, 2014) and Xenopus tropicalis embryos (van Heeringen et al, 2014). The chromatin state in an arrested vertebrate embryo has not been fully examined.…”

“…We investigated the changes in chromatin of preDII, arrested DII and postDII embryos. We elected to analyze the post-translational modifications of histone H3 because there are commercially available antibodies that recognize specific histone H3 modifications, and have been used in many systems including yeast, humans, mice and fish (Baumgart et al, 2014;Wu et al, 2011). Furthermore, the predicted histone H3 protein in A. limnaeus shows 100% protein identity to the histone H3 protein in zebrafish and another annual killifish (Nothobranchius furzeri) and the fish protein has only two amino acid differences when compared with human histone H3 (Fig.…”