Project description:Various species of teleost fish, amphibians, and neonatal mammals can regenerate their hearts following injury. Certain processes, including extracellular matrix remodelling, a switch from oxidative to glycolytic metabolism and sarcomere disorganization are believed to be critical to heart regeneration. However, whether all regenerating species follow the same pathway to regeneration is not known. Here, we use mass-spectrometry based proteomics to characterize the cellular processes that occur in the heart of a reptile, the leopard gecko (Eublepharis macularius) following injury. The hearts were damaged using a cryoprobe and wound sites were sampled at 3-, 14-, 30- and 100-days post injury (dpi). The proteomes of these were compared to those from sham operated geckos. Overall, 1116 proteins were identified in the wound sites and 579 were differentially expressed across at least two time points. This includes an increase in agrin at 14-dpi, a protein thought to be required for cardiomyocyte proliferation and heart regeneration. Interaction network analysis indicates that there is enrichment of Gene Ontology (GO) terms related to transcription and translation by 14-dpi, but a concurrent decrease in GO terms related to oxidative and glycolytic metabolism, and sarcomere organization. Importantly, GO terms related to the structure and function of mitochondria as well as sarcomere organization were enriched at 100-dpi compared to 3-dpi, and 14-dpi. There were no GO terms identified as differing between sham and 100 dpi hearts, suggesting full regeneration. This work indicates that the gecko heart can regenerate and that this involves reorganization of cellular pathways associated with mitosis, energy production and contractile function.
Project description:In this study, a population of knockout cells was generated using the GeCKO v2 sgRNA library. The population of knockout cells was treated with the PARP inhibitor olaparib for 14 days. Over this time, knockout cells that were sensitive to olaparib treatment would die and a population of knockout cells that was resistant to olaparib treatment remained. Cells from olaparib and DMSO conditions and the sgRNA cassette in the knockout cells was amplified and sequenced to identify synthetic lethal or suppressor interactions with olaparib treatment.
Project description:The current understanding of regulatory sequences in the vertebrate genome is still incomplete. By introducing an adapter switching strategy, we developed an ultra-throughput ultra-sensitivity single-nucleus ATAC-seq (UUATAC-seq) protocol that enables construction of high-quality chromatin accessibility landscape from one species in a one-day experiment. By using UUATAC-seq, we mapped open chromatin regions for five representative vertebrate species at the landscape scale.
