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Biegler MT, Fedrigo O, Collier P, Mountcastle J, Haase B, Tilgner HU, Jarvis ED. Induction of an immortalized songbird cell line allows for gene characterization and knockout by CRISPR-Cas9. Sci Rep 2022; 12:4369. [PMID: 35288582 PMCID: PMC8921232 DOI: 10.1038/s41598-022-07434-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2021] [Accepted: 02/14/2022] [Indexed: 12/20/2022] Open
Abstract
The zebra finch is one of the most commonly studied songbirds in biology, particularly in genomics, neuroscience and vocal communication. However, this species lacks a robust cell line for molecular biology research and reagent optimization. We generated a cell line, designated CFS414, from zebra finch embryonic fibroblasts using the SV40 large and small T antigens. This cell line demonstrates an improvement over previous songbird cell lines through continuous and density-independent growth, allowing for indefinite culture and monoclonal line derivation. Cytogenetic, genomic, and transcriptomic profiling established the provenance of this cell line and identified the expression of genes relevant to ongoing songbird research. Using this cell line, we disrupted endogenous gene sequences using S.aureus Cas9 and confirmed a stress-dependent localization response of a song system specialized gene, SAP30L. The utility of CFS414 cells enhances the comprehensive molecular potential of the zebra finch and validates cell immortalization strategies in a songbird species.
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Affiliation(s)
- Matthew T Biegler
- Laboratory of Neurogenetics of Language, The Rockefeller University, 1230 York Avenue, New York, NY, 10065, USA.
- Howard Hughes Medical Institute, Chevy Chase, MD, USA.
| | - Olivier Fedrigo
- Vertebrate Genome Laboratory, The Rockefeller University, New York, NY, 10065, USA
| | - Paul Collier
- Center for Neurogenetics, Graduate School of Medical Sciences, Weil Cornell Medical Center, New York, NY, 10065, USA
| | | | - Bettina Haase
- Vertebrate Genome Laboratory, The Rockefeller University, New York, NY, 10065, USA
| | - Hagen U Tilgner
- Center for Neurogenetics, Graduate School of Medical Sciences, Weil Cornell Medical Center, New York, NY, 10065, USA
| | - Erich D Jarvis
- Laboratory of Neurogenetics of Language, The Rockefeller University, 1230 York Avenue, New York, NY, 10065, USA.
- Howard Hughes Medical Institute, Chevy Chase, MD, USA.
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Diddens J, Coussement L, Frankl-Vilches C, Majumdar G, Steyaert S, Ter Haar SM, Galle J, De Meester E, De Keulenaer S, Van Criekinge W, Cornil CA, Balthazart J, Van Der Linden A, De Meyer T, Vanden Berghe W. DNA Methylation Regulates Transcription Factor-Specific Neurodevelopmental but Not Sexually Dimorphic Gene Expression Dynamics in Zebra Finch Telencephalon. Front Cell Dev Biol 2021; 9:583555. [PMID: 33816458 PMCID: PMC8017237 DOI: 10.3389/fcell.2021.583555] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Accepted: 02/17/2021] [Indexed: 12/13/2022] Open
Abstract
Song learning in zebra finches (Taeniopygia guttata) is a prototypical example of a complex learned behavior, yet knowledge of the underlying molecular processes is limited. Therefore, we characterized transcriptomic (RNA-sequencing) and epigenomic (RRBS, reduced representation bisulfite sequencing; immunofluorescence) dynamics in matched zebra finch telencephalon samples of both sexes from 1 day post hatching (1 dph) to adulthood, spanning the critical period for song learning (20 and 65 dph). We identified extensive transcriptional neurodevelopmental changes during postnatal telencephalon development. DNA methylation was very low, yet increased over time, particularly in song control nuclei. Only a small fraction of the massive differential expression in the developing zebra finch telencephalon could be explained by differential CpG and CpH DNA methylation. However, a strong association between DNA methylation and age-dependent gene expression was found for various transcription factors (i.e., OTX2, AR, and FOS) involved in neurodevelopment. Incomplete dosage compensation, independent of DNA methylation, was found to be largely responsible for sexually dimorphic gene expression, with dosage compensation increasing throughout life. In conclusion, our results indicate that DNA methylation regulates neurodevelopmental gene expression dynamics through steering transcription factor activity, but does not explain sexually dimorphic gene expression patterns in zebra finch telencephalon.
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Affiliation(s)
- Jolien Diddens
- Laboratory of Protein Chemistry, Proteomics and Epigenetic Signaling (PPES), Department of Biomedical Sciences, University of Antwerp, Antwerp, Belgium
| | - Louis Coussement
- Biobix: Laboratory of Bioinformatics and Computational Genomics, Department of Data Analysis and Mathematical Modeling, Ghent University, Ghent, Belgium
| | - Carolina Frankl-Vilches
- Department of Behavioral Neurobiology, Max Planck Institute for Ornithology, Seewiesen, Germany
| | - Gaurav Majumdar
- Bio-Imaging Lab, Department of Biomedical Sciences, University of Antwerp, Antwerp, Belgium
| | - Sandra Steyaert
- Biobix: Laboratory of Bioinformatics and Computational Genomics, Department of Data Analysis and Mathematical Modeling, Ghent University, Ghent, Belgium
| | - Sita M Ter Haar
- Laboratory of Behavioral Neuroendocrinology, GIGA Neuroscience, University of Liège, Liège, Belgium
| | - Jeroen Galle
- Biobix: Laboratory of Bioinformatics and Computational Genomics, Department of Data Analysis and Mathematical Modeling, Ghent University, Ghent, Belgium
| | - Ellen De Meester
- Laboratory of Pharmaceutical Biotechnology, Faculty of Pharmaceutical Sciences, Ghent University, Ghent, Belgium
| | - Sarah De Keulenaer
- Laboratory of Pharmaceutical Biotechnology, Faculty of Pharmaceutical Sciences, Ghent University, Ghent, Belgium
| | - Wim Van Criekinge
- Biobix: Laboratory of Bioinformatics and Computational Genomics, Department of Data Analysis and Mathematical Modeling, Ghent University, Ghent, Belgium
| | - Charlotte A Cornil
- Laboratory of Behavioral Neuroendocrinology, GIGA Neuroscience, University of Liège, Liège, Belgium
| | - Jacques Balthazart
- Laboratory of Behavioral Neuroendocrinology, GIGA Neuroscience, University of Liège, Liège, Belgium
| | - Annemie Van Der Linden
- Bio-Imaging Lab, Department of Biomedical Sciences, University of Antwerp, Antwerp, Belgium
| | - Tim De Meyer
- Biobix: Laboratory of Bioinformatics and Computational Genomics, Department of Data Analysis and Mathematical Modeling, Ghent University, Ghent, Belgium
| | - Wim Vanden Berghe
- Laboratory of Protein Chemistry, Proteomics and Epigenetic Signaling (PPES), Department of Biomedical Sciences, University of Antwerp, Antwerp, Belgium
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Bentz AB, Niederhuth CE, Carruth LL, Navara KJ. Prenatal testosterone triggers long-term behavioral changes in male zebra finches: unravelling the neurogenomic mechanisms. BMC Genomics 2021; 22:158. [PMID: 33676394 PMCID: PMC7937265 DOI: 10.1186/s12864-021-07466-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2020] [Accepted: 02/22/2021] [Indexed: 11/12/2022] Open
Abstract
BACKGROUND Maternal hormones, like testosterone, can strongly influence developing offspring, even generating long-term organizational effects on adult behavior; yet, the mechanisms facilitating these effects are still unclear. Here, we experimentally elevated prenatal testosterone in the eggs of zebra finches (Taeniopygia guttata) and measured male aggression in adulthood along with patterns of neural gene expression (RNA-seq) and DNA methylation (MethylC-Seq) in two socially relevant brain regions (hypothalamus and nucleus taenia of the amygdala). We used enrichment analyses and protein-protein interaction networks to find candidate processes and hub genes potentially affected by the treatment. We additionally identified differentially expressed genes that contained differentially methylated regions. RESULTS We found that males from testosterone-injected eggs displayed more aggressive behaviors compared to males from control eggs. Hundreds of genes were differentially expressed, particularly in the hypothalamus, including potential aggression-related hub genes (e.g., brain derived neurotrophic factor). There were also enriched processes with well-established links to aggressive phenotypes (e.g., somatostatin and glutamate signaling). Furthermore, several highly connected genes identified in protein-protein interaction networks also showed differential methylation, including adenylate cyclase 2 and proprotein convertase 2. CONCLUSIONS These results highlight genes and processes that may play an important role in mediating the effects of prenatal testosterone on long-term phenotypic outcomes, thereby providing insights into the molecular mechanisms that facilitate hormone-mediated maternal effects.
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Affiliation(s)
- Alexandra B Bentz
- Department of Biology, Indiana University, Bloomington, IN, 47405, USA.
- Center for the Integrative Study of Animal Behavior, Indiana University, Bloomington, IN, 47405, USA.
- Poultry Science Department, University of Georgia, Athens, GA, 30602, USA.
| | - Chad E Niederhuth
- Department of Plant Biology, Michigan State University, East Lansing, MI, 48823, USA
| | - Laura L Carruth
- Neuroscience Institute, Georgia State University, Atlanta, GA, 30303, USA
| | - Kristen J Navara
- Poultry Science Department, University of Georgia, Athens, GA, 30602, USA
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Effects of 5-Aza on p-Y1472 NR2B related to learning and memory in the mouse hippocampus. Biomed Pharmacother 2018; 109:701-707. [PMID: 30551522 DOI: 10.1016/j.biopha.2018.10.090] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2018] [Revised: 10/15/2018] [Accepted: 10/15/2018] [Indexed: 12/23/2022] Open
Abstract
BACKGROUND We have previously reported that 5-Aza-2-deoxycytidine (5-Aza-cdR) can repress protein serine/threonine phosphatase-1γ (PP1γ) expression and activity in the mouse hippocampus and affect the behaviour of mice in a water maze. It is well known that the phosphorylation of N-methyl-d-aspartate receptor 2B subunit (NR2B) plays a role in behaviour. In this study, we examined whether 5-Aza-cdR affects NR2B phosphorylation at tyrosine 1472 (p-Y1472 NR2B) and whether it affected the responses of the mice in a passive avoidance test. METHODS 5-Aza-cdR (10 μM) was administered to mice via intracerebroventricular injection (i.c.v). The learning and memory behaviour of the mice were evaluated by measuring their response in a step-down type passive avoidance test 24 h after the injection. The mRNA level of NR2B was measured by real-time PCR. NR2B and p-Y1472 NR2B protein expression in the mouse hippocampus was detected by western blot and immunofluorescence. CDK5 activity was detected by the ADP-Glo™ + CDK5/p35 Kinase Enzyme System. To further clarify whether the 5-Aza-cdR effects on behaviour were dependent on cellular proliferation or not, the effect of 5-Aza-cdR on the expression level of NR2B, the phosphorylation level of p-Y1472 NR2B, cell viability and the cell cycle were analysed using the immortalized mouse hippocampal neuronal cells neural cell line HT22 treated with 10 μM 5-Aza-cdR compared with an untreated control group. RESULTS After injection with 5-Aza-cdR, the behaviour of the mice in the step-down test was improved, while their phosphorylation level of p-Y1472 NR2B was increased and their CDK5 activity was decreased in the hippocampus. In vitro experiments showed 10 μM 5-Aza-cdR increased the p-Y1472 NR2B phosphorylation level with inhibition of cell viability and cell cycle arrest. CONCLUSIONS Our results suggested that the effect of 5-Aza-cdR on behaviour may be related to the increase in phosphorylation of p-Y1472 NR2B in the hippocampus.
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Guerrero-Bosagna C, Morisson M, Liaubet L, Rodenburg TB, de Haas EN, Košťál Ľ, Pitel F. Transgenerational epigenetic inheritance in birds. ENVIRONMENTAL EPIGENETICS 2018; 4:dvy008. [PMID: 29732172 PMCID: PMC5920295 DOI: 10.1093/eep/dvy008] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/08/2018] [Revised: 03/02/2018] [Accepted: 03/12/2018] [Indexed: 05/04/2023]
Abstract
While it has been shown that epigenetics accounts for a portion of the variability of complex traits linked to interactions with the environment, the real contribution of epigenetics to phenotypic variation remains to be assessed. In recent years, a growing number of studies have revealed that epigenetic modifications can be transmitted across generations in several animal species. Numerous studies have demonstrated inter- or multi-generational effects of changing environment in birds, but very few studies have been published showing epigenetic transgenerational inheritance in these species. In this review, we mention work conducted in parent-to-offspring transmission analyses in bird species, with a focus on the impact of early stressors on behaviour. We then present recent advances in transgenerational epigenetics in birds, which involve germline linked non-Mendelian inheritance, underline the advantages and drawbacks of working on birds in this field and comment on future directions of transgenerational studies in bird species.
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Affiliation(s)
- Carlos Guerrero-Bosagna
- Avian Behavioural Genomics and Physiology Group, IFM Biology, Linköping University, Linköping 58 183, Sweden
| | - Mireille Morisson
- GenPhySE, Université de Toulouse, INRA, ENVT, F-31326 Castanet-Tolosan, France
| | - Laurence Liaubet
- GenPhySE, Université de Toulouse, INRA, ENVT, F-31326 Castanet-Tolosan, France
| | - T Bas Rodenburg
- Behavioural Ecology Group, Wageningen University, 6700 AH Wageningen, The Netherlands
| | - Elske N de Haas
- Behavioural Ecology Group, Wageningen University, 6700 AH Wageningen, The Netherlands
| | - Ľubor Košťál
- Centre of Biosciences, Slovak Academy of Sciences, 840 05 Bratislava, Slovakia
| | - Frédérique Pitel
- GenPhySE, Université de Toulouse, INRA, ENVT, F-31326 Castanet-Tolosan, France
- Correspondence address. GenPhySE, INRA, 31326 Castanet-Tolosan, France. Tel:+33 561 28 54 35. E-mail:
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