Project description:Input control for ChIP-seq on transgenic flies expressing sna-eGFP fusion proteins. For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf
Project description:ChIP-seq on transgenic flies expressing sna-eGFP fusion proteins. The IP was performed using an anti-GFP antibody. For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf
Project description:This study aimed to identify RNAs bound to the C. elegans SNA-2, SNA-3, SUT-1 and SNR-2 proteins involved in spliced leader 1 trans-splicing through use of RNA immunoprecipitation sequencing (RIP-Seq). Four IP sample replicates and four control sample replicates were sequenced for each protein.
Project description:Radial glial cells (RGCs) are the most abundant macroglia in the teleost brain and have established roles in neurogenesis and neurosteroidogenesis; however, their transcriptome remains unstudied, limiting functional understanding of this crucial cell type. Using cultured goldfish RGCs, RNA sequencing and de novo transcriptome assembly were performed, generating the first reference transcriptome for fish RGCs with 17,620 unique genes identified. These data revealed that RGCs express a diverse repertoire of receptors and signaling molecules, suggesting that RGCs may respond to and synthesize an array of hormones, peptides, cytokines, and growth factors. Expanding on recent neuroanatomical data and possible direct neuronal regulation of RGC physiology, differential gene expression analysis identified transcriptional networks that are responsive to the conserved secretogranin II-derived neuropeptide secretoneurin A (SNa). Pathway analysis indicated that cellular processes related to the central nervous system (e.g., neurogenesis, synaptic plasticity, glial cell development) and immune functions (e.g., immune system activation, leukocyte function, macrophage response) were preferentially modulated by SNa. These data reveal an array of new functions that are proposed to be critical to neuronal-glial interactions through the mediator SNa.
Project description:Spliced leader trans-splicing is an essential RNA processing step that is required for the formation of mRNA in many eukaryotes, including C. elegans. However, the role of factors involved in this reaction is not well known. Here we further characterise the function of SNA-2, SNA-3, SUT-1 and SNR-2 involved in spliced leader 1 trans-splicing through identification of interacting proteins by immunoprecipitation followed by LC-MS/MS and label-free quantification.
Project description:Spliced leader trans-splicing is an essential RNA processing step that is required for the formation of mRNA in many eukaryotes, including C. elegans. However, the factors involved in this reaction are not well known. Here we perform a molecular analysis of key components in this reaction by immunoprecipitation of GFP-tagged SNA-1 and SNA-3 proteins from C. elegans embryonic extracts treated with/without RNAseA/T1 followed by the identification of associated proteins using LC-MS/MS and label-free quantification. As control, embryonic extract from wild type N2 animals were also subjected to the same treatment. Note file names (e.g. PE906_SNA1_RNase_IP_anti-GFP_beads) indicate the name of the C. elegans line (PE906_), the name of the protein tagged with GFP (SNA1) and whether samples were treated with RNases A and T1 (RNase), and for raw files whether immunoprecipitation was done with anti-GFP nanobody coupled agarose beads (IP_anti_GFP_beads), or control agarose beads (IP_control_beads), respectively. Note that SNA-3 protein is only identified by its Uniprot identifier Q9GYR5.
Project description:This study aimed to identify RNAs bound to the C. elegans SL1 snRNP SNA-1 protein through use of RNA immunoprecipitation sequencing. Three IP sample replicates and three control sample replicates were sequenced.
Project description:Abasic (AP) sites are one of the most common forms of DNA damage which can lead to polymerase stalling, strand breaks and mutations. We developed snA-seq, a mapping method that reveals the location of abasic sites at base-resolution. Using synthetic DNA, we show that high selectivity for AP DNA is achieved. We use this method to explore the distribution of thymine modifications in the Leishmania major genome, by converting these into abasic sites using a glycosylase enzyme. We also apply snAP-seq to the human genome to study the distribution of endogenous AP sites, in both APE1 knockdown and control cells.
Project description:Adaptation of liver to the postprandial state requires coordinate regulation of protein synthesis and folding aligned with changes in lipid metabolism. Here we demonstrate that sensory food perception is sufficient to elicit early activation of hepatic mTOR-signaling, Xbp1-splicing, increased expression of ER-stress genes and phosphatidylcholine synthesis, which translate into a rapid morphological ER-remodeling. These responses overlap with those activated during refeeding, where they are maintained and constantly increase upon nutrient supply. Sensory food perception activates POMC-neurons in the hypothalamus, optogenetic activation of POMC-neurons activates hepatic mTOR-signaling and Xbp1-splicing and lack of MC4R-expression attenuates these responses to sensory food perception. Chemogenetic POMC-neuron activation promotes sympathetic nerve activity (SNA) subserving the liver, and norepinephrine evokes the same responses in hepatocytes in vitro and liver in vivo as observed upon sensory food perception. Collectively, our experiments unravel that sensory food perception coordinatly primes postprandrial liver ER adaption through a melanocortin-SNA-mTOR-Xbp1s-axis