A genome-wide search for epigenetically regulated genes in zebra finch using MethylCap-seq and RNA-seq

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

The genome of blue-capped cordon-bleu uncovers hidden diversity of ltr retrotransposons in zebra finch

Avian genomes have perplexed researchers by being conservative in both size and rearrangements, while simultaneously holding the blueprints for a massive species radiation during the last 65 million years (My). Transposable elements (TEs) in bird genomes are relatively scarce but have been implicated as important hotspots for chromosomal inversions. In zebra finch (Taeniopygia guttata), long terminal repeat (LTR) retrotransposons have proliferated and are positively associated with chromosomal breakpoint regions. Here, we present the genome, karyotype and transposons of blue-capped cordon-bleu (Uraeginthus cyanocephalus), an African songbird that diverged from zebra finch at the root of estrildid finches 10 million years ago (Mya). This constitutes the third linked-read sequenced genome assembly and fourth in-depth curated TE library of any bird. Exploration of TE diversity on this brief evolutionary timescale constitutes a considerable increase in resolution for avian TE biology and allowed us to uncover 4.5 Mb more LTR retrotransposons in the zebra finch genome. In blue-capped cordon-bleu, we likewise observed a recent LTR accumulation indicating that this is a shared feature of Estrildidae. Curiously, we discovered 25 new endogenous retrovirus-like LTR retrotransposon families of which at least 21 are present in zebra finch but were previously undiscovered. This highlights the importance of studying close relatives of model organisms

Data from: The genome of blue-capped cordon-bleu uncovers hidden diversity of LTR retrotransposons in zebra finch

Avian genomes have perplexed researchers by being conservative in both size and rearrangements, while simultaneously holding the blueprints for a massive species radiation during the last 65 My. Transposable elements (TEs) in bird genomes are relatively scarce but have been implicated as important hotspots for chromosomal inversions. In zebra finch (Taeniopygia guttata), long terminal repeat (LTR) retrotransposons have proliferated and are positively associated with chromosomal breakpoint regions. Here, we present the genome, karyotype and transposons of blue-capped cordon-bleu (Uraeginthus cyanocephalus), an African songbird that diverged from zebra finch at the root of estrildid finches 10 Mya. This constitutes the third linked-read sequenced genome assembly and fourth in-depth curated TE library of any bird. Exploration of TE diversity on this brief evolutionary timescale constitutes a considerable increase in resolution for avian TE biology and allowed us to uncover 4.5 Mb more LTR retrotransposons in the zebra finch genome. In blue-capped cordon-bleu, we likewise observed a recent LTR accumulation indicating that this is a shared feature of Estrildidae. Curiously, we discovered 25 new endogenous retrovirus-like LTR retrotransposon families of which at least 21 are present in zebra finch but were previously undiscovered. This highlights the importance of studying close relatives of model organisms

uraCya_heart_0.8

Genome assembly of an adult male blue-capped cordon-bleu (Uraeginthus cyanocephalus). NCBI BioProject (PRJNA531762) and NCBI BioSample (SAMN11381998). Note that this a "pseudohaploid" assembly created with Supernova 2.0 assembly software

The impact response of environmental-friendly sandwich structures

The low-velocity impact response of sandwich structures based on fully-recyclable skin and core materials has been investigated. Particular attention has been focused on structures based on self-reinforced polypropylene skins combined with a polypropylene honeycomb core. Two types of skin designs were considered, the first being based on a single 'as-supplied' monolithic self-reinforced polypropylene laminate and the second being manufactured from thin self-reinforced polypropylene sheets bonded together using a hot-melt polypropylene film. For comparative purposes, a limited number of tests have also been carried out on a more conventional GFRP/aluminium honeycomb sandwich structure. Drop-weight impact test have shown that all-polypropylene honeycomb sandwich structures absorb significant energy through plastic deformation in the composite skins as well as plastic buckling in the honeycomb core. It has also been shown that the design of the self-reinforced polypropylene skin has a significant effect on the energy-absorbing characteristics of the sandwich structure, with the performance of systems based on multiple layer skins greatly exceeding that observed following tests on a monolithic design. Tests on plain laminates also yielded similar conclusions, with multilayer systems offering much higher perforation resistances than their plain counterparts. Finally, it has been demonstrated that when the impact data are normalised by their respective areal densities, the all-polypropylene composites significantly out-perform GFRP/aluminium honeycomb sandwich structures

Schematic representation of the inversion found in TGU1 (GGA2).

<p>Schematic representation of the inversion found in TGU1 (GGA2).</p

DNA Methylation Regulates Transcription Factor-Specific Neurodevelopmental but Not Sexually Dimorphic Gene Expression Dynamics in Zebra Finch Telencephalon

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

Comparative Cytogenetics between Two Important Songbird, Models: The Zebra Finch and the Canary - Fig 2

<p>C-band patternsof zebra finch (A) and canary (B). Sex chromosomes are indicated.</p