Project description:The brushtail possum, Trichosurus vulpecula, is threatened in parts of its native range in Australia, but has also become a devastating mammalian pest following introduction into New Zealand from the mid 1800s. We have completed the first chromosome-level assembly of the possum genome and, using nuclear and mitochondrial analyses, traced southern New Zealand possums to distinct Tasmanian and mainland Australian subspecies, which have subsequently hybridised. This admixture is reflected in high levels of genetic diversity within New Zealand populations despite a founding bottleneck. Functional genomics revealed unique adaptations to altricial birth and extending weaning, including novel chemo-sensory genes, and at least four genes with imprinted, parent-specific expression not yet detected in other species (MLH1, EPM2AIP1, UBP1 and GPX7). We found that reprogramming of possum germline imprints and the wider epigenome was similar to eutherian mammals, except onset occurs after birth. Together, our data and analysis is useful for genetic-based control and conservation of possums, and contributes to understanding of the evolution of novel mammalian epigenetic traits such as germline methylation erasure and genomic imprinting.
Project description:The brushtail possum, Trichosurus vulpecula, is threatened in parts of its native range in Australia, but has also become a devastating mammalian pest following introduction into New Zealand from the mid 1800s. We have completed the first chromosome-level assembly of the possum genome and, using nuclear and mitochondrial analyses, traced southern New Zealand possums to distinct Tasmanian and mainland Australian subspecies, which have subsequently hybridised. This admixture is reflected in high levels of genetic diversity within New Zealand populations despite a founding bottleneck. Functional genomics revealed unique adaptations to altricial birth and extending weaning, including novel chemo-sensory genes, and at least four genes with imprinted, parent-specific expression not yet detected in other species (MLH1, EPM2AIP1, UBP1 and GPX7). We found that reprogramming of possum germline imprints and the wider epigenome was similar to eutherian mammals, except onset occurs after birth. Together, our data and analysis is useful for genetic-based control and conservation of possums, and contributes to understanding of the evolution of novel mammalian epigenetic traits such as germline methylation erasure and genomic imprinting.
Project description:We compared the binding patterns in embryonic stem cells of KAP1 and KRAB Zinc Finger (KZNF) proteins as well as H3K4me3 DNA under several conditions. Native human stem cells. Mouse stem cells containing a transchromosomic copy of human chromosome 11, with and without the introduction of plasmids containing KRAB Zinc Finger sequences. We show that certain KZNFs are responsible for the repression of certain retrotransposons in embryonic stem cells, preventing their spread across the genome. ChIP-seq of HESCs and mouse TC11 ESCs with ZNF91 plasmids and with empty vector plasmids. ChIP of KAP1, ZNF486, H3K4me3. At least 2 replicates of each condition.
Project description:ChIP-seq experiments using low numbers of input cells, scaled down to the point where data quality is unnacceptably compromised, reveals limits of the technique. Two-part ChIPseq study using native chromatin (non-crosslinked) generated with MNase from human CD4+ cells. Part 1: Previously published protocol (Barski et al, 2007, Cell 129:823, hereafter called "Benchmark") used with 2x10e7 cells / ChIP with H3K4me3 antibody, compared to modified method ("new") with decreasing input cell numbers spanning 1000-fold range from 2x10e7 cells / IP to 2x10e4 cells/ IP. Part 2: reproducibility of new method studied using triplicate samples at lowest two cell numbers tested: 1x10e5 and 2x10e4 / ChIP, using H3K4me3 and H3K27me3 antisera.