Project description:Comparison of whole genome exome array CGH to a commercial SNP array for detection of de novo and homozygous copy number variants in 99 autism simplex trios. Will update once manuscript is prepared.
Project description:Deep whole genome sequencing of Drosophila melanogaster inbred lines: DGRP-28, DGRP-307, DGRP-399, DGRP-57, DGRP-639, DGRP-712, DGRP-714, DGRP-852 and Virginizer (VGN). The lines were sequenced deeply giving between 54M and 92M reads to achieve a whole genome coverage that ranged between 74X and 125X. The sequencing was used for de novo genotyping.
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.
2021-06-29 | PXD025736 | Pride
Project description:Vitis berlandieri de novo whole genome sequencing
