ABSTRACT: Whole genome sequencing and de novo assembly of the collared flycatcher. Population resequencing of additional 9 collared flycatchers and 10 pied flycatchers
Project description:Whole genome sequencing and de novo assembly of the collared flycatcher. Population resequencing of additional 9 collared flycatchers and 10 pied flycatchers. Transcriptome sequencing of male/female samples, 9 tissues and embryos of collared and pied flycatchers.
Project description:DNA methylation plays a critical role in development, particularly in repressing retrotransposons. The mammalian methylation landscape is dependent on the combined activities of the canonical maintenance enzyme Dnmt1 and the de novo Dnmts, 3a and 3b. Here we demonstrate that Dnmt1 displays de novo methylation activity in vitro and in vivo with specific retrotransposon targeting. We used whole-genome bisulfite and long-read Nanopore sequencing in genetically engineered methylation depleted embryonic stem cells to provide an in-depth assessment and quantification of this activity. Utilizing additional knockout lines and molecular characterization, we show that Dnmt1's de novo methylation activity depends on Uhrf1 and its genomic recruitment overlaps with targets that enrich for Trim28 and H3K9 trimethylation. Our data demonstrate that Dnmt1 can de novo add and maintain DNA methylation, especially at retrotransposons and that this mechanism may provide additional stability for long-term repression and epigenetic propagation throughout development.
Project description:Whole genome resequencing of extreme phenotypes in collared flycatchers highlights the difficulty of detecting quantitative trait loci in natural populations
Project description:Shot-gun whole cell lysate proteomics data from pure and enriched microbes were de-novo sequenced using PEAKS de Novo. The obtained peptide sequence lists serves as a test data for the peptide-centric taxonomy database Unipept.