Project description:We have developed an imaging-free framework to localize nucleic acids within a tissue by combining a compressed sensing tissue-sampling strategy based on multi-angle-sectioning and an associated image reconstruction algorithm. Initially, the tissue is cut into consecutive thin slices. Subsequently these are further sliced along an orthogonal plane at predefined orientations resulting in tissue strips that are subject to RNA sequencing. We implemented this framework to transform a single-cell RNA sequencing protocol into an imaging-free spatial transcriptomics technique. The method was validated by profiling the transcriptome of the Murine brain, and used to spatially profile the brain transcriptome of the Australian Central bearded dragon, Pogona vitticeps.
Project description:Hibernation is a physiological state employed by many animals that are exposed to limited food and adverse winter conditions. Controlling tissue-specific and organism wide changes in metabolism and cellular function requires precise regulation of gene expression, including by microRNAs (miRNAs). Here we profile miRNA expression in the central bearded dragon (Pogona vitticeps) using small RNA sequencing of brain, heart, and skeletal muscle from individuals in late hibernation and four days post-arousal. A total of 1295 miRNAs were identified in the central bearded dragon genome; 664 of which were novel to central bearded dragon. We identified differentially expressed miRNAs (DEmiRs) in all tissues and correlated mRNA expression with known and predicted target mRNAs. Functional analysis of DEmiR targets revealed an enrichment of differentially expressed mRNA targets involved in metabolic processes. However, we failed to reveal biologically relevant tissue-specific processes subjected to miRNA-mediated regulation in heart and skeletal muscle. In brain, neuroprotective pathways were identified as potential targets regulated by miRNAs. Our data suggests that miRNAs are necessary for modulating the shift in cellular metabolism during hibernation and regulating neuroprotection in the brain. This study is the first of its kind in a hibernating reptile and provides key insight into this ephemeral phenotype.
