A genome-wide search for epigenetically regulated genes in zebra finch using MethylCap-seq and RNA-seq
| Autor: | Sandra Steyaert, Anne-Marie Van Der Linden, Wim Vanden Berghe, Sarah De Keulenaer, Carolina Frankl-Vilches, Tim De Meyer, Antje Bakker, Ellen De Meester, Wim Van Criekinge, Jeroen Galle, Jolien Diddens, Nina Sohnius-Wilhelmi |
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| Jazyk: | angličtina |
| Rok vydání: | 2016 |
| Předmět: |
0301 basic medicine
animal structures SEQUENCING DATA CELL-LINES Biology 03 medical and health sciences Epigenetics of physical exercise SYNAPTIC PLASTICITY Epigenetics BRAIN EPIGENETIC REGULATION Gene RNA-Directed DNA Methylation Zebra finch DNA METHYLATION Epigenomics Genetics Multidisciplinary MEMORY Biology and Life Sciences Methylation ALZHEIMERS-DISEASE 030104 developmental biology nervous system DIFFERENTIAL EXPRESSION ANALYSIS DNA methylation behavior and behavior mechanisms BDNF GENE Human medicine Engineering sciences. Technology |
| Zdroj: | SCIENTIFIC REPORTS Scientific reports |
| ISSN: | 2045-2322 |
| Popis: | Learning and memory formation are known to require dynamic CpG (de)methylation and gene expression changes. Here, we aimed at establishing a genome-wide DNA methylation map of the zebra finch genome, a model organism in neuroscience, as well as identifying putatively epigenetically regulated genes. RNA- and MethylCap-seq experiments were performed on two zebra finch cell lines in presence or absence of 5-aza-2′-deoxycytidine induced demethylation. First, the MethylCap-seq methodology was validated in zebra finch by comparison with RRBS-generated data. To assess the influence of (variable) methylation on gene expression, RNA-seq experiments were performed as well. Comparison of RNA-seq and MethylCap-seq results showed that at least 357 of the 3,457 AZA-upregulated genes are putatively regulated by methylation in the promoter region, for which a pathway analysis showed remarkable enrichment for neurological networks. A subset of genes was validated using Exon Arrays, quantitative RT-PCR and CpG pyrosequencing on bisulfite-treated samples. To our knowledge, this study provides the first genome-wide DNA methylation map of the zebra finch genome as well as a comprehensive set of genes of which transcription is under putative methylation control. |
| Databáze: | OpenAIRE |
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