Project description:Using ATAC-seq, we aimed to identify regions of open chromatin in the developing C. elegans nervous system. This dataset was used to determine regions of chromatin and compare it to ChIP-seq data of TFs of interest, to assist us in identifying ChIP-seq peaks which are solely expressed in neurons (vs. general, total worm binding). Specifically, since EGL-43 is expressed in many tissues, including both neuronal and the somatic gonad, ATAC-seq was particularly helpful in identifying neuronal-specific ChIP-seq peaks and NanoDam peaks of interest (GSE227552).
Project description:These three arrays are replicate extractions and hybridizations. Each array hybridizes C. elegans labeled RNA from NGM plate grown, mixed stage, animals (Channel 1) against labled RNA from liquid CeMM grown, mixed stage, animals (Channel 2).
Project description:We performed comprehensive DNA methylation analysis in neuronal and non-neuronal nuclei obtained from the human prefrontal cortex. This revealed that neuronal and non-neuronal nuclei manifest qualitatively and quantitatively distinctive DNA methylation patterns.
Project description:Neurons are categorised into many subclasses, and each subclass displays different morphology, expression patterns, connectivity and function. Changes in protein synthesis are critical for neuronal function. Therefore, analysing protein expression patterns in individual neuronal subclass will elucidate molecular mechanisms for memory and other functions. In this study, we used neuronal subclass-selective proteomic analysis with cell-selective Bio-Orthogonal Non-Canonical Amino acid Tagging (BONCAT). We selected Caenorhabditis elegans as a model organism because it shows diverse neuronal functions and simple neural circuitry. We performed proteomic analysis of all neurons or AFD subclass neurons that regulate thermotaxis in C. elegans. Mutant phenylalanyl tRNA synthetase (MuPheRS) was selectively expressed in all neurons or AFD subclass neurons, and azido-phenylalanine was incorporated into proteins in cells of interest. Azide-labelled proteins were enriched and proteomic analysis was performed. We identified 4412 and 1834 proteins from strains producing MuPheRS in all neurons and AFD subclass neuron, respectively. F23B2.10 (RING-type domain-containing protein) was identified only in neuronal cell-enriched proteomic analysis. We expressed GFP under the control of the 5' regulatory region of F23B2.10 and found GFP expression in neurons. We expect that more single-neuron specific proteomic data will clarify how protein composition and abundance affect characteristics of neuronal subclasses.
Project description:To discover new miRNA targets, we generated a C. elegans transgenic line expressing a functional N-terminally Tandem Affinity Purification (TAP) tagged ALG-1 protein We purified TAP::ALG-1 complexes from mixed-stage TAP::ALG-1 transgenic (WS4303) and wild-type (N2, serving as a mock control) animals and hybridized the associated mRNAs to two-color microarrays
Project description:We recently reported that a significant subpopulation of adult mouse brain cellular nuclei (NeuN-High) have highly decondensed chromatin characteristic of multipotent cells types (Yu et al., DNEU, 2015). Herein we show that NeuN-High nuclei also have significantly higher levels of 5´-hydroxymethylcytosine (5hmC), a rate limiting intermediate in the turnover of modified cytosine. TET-assisted bisulfite sequencing demonstrated that 5hmC levels in NeuN-High nuclei spiked rapidly from 20% to nearly 40% of CG dinucleotides at the start of gene regions for various classes of the most highly transcribed neuron-specific genes, but were variably distributed among different functional gene categories and in well-defined gene regions. NeuN-Low neuronal and non-nueronal neuronal nuclei had significantly lower levels of 5hmC for all classes of expressed genes. In summary, these data support the view that an elevated turnover rate for chromatin modifications may potentiate the cellular memory of the most active subclasses of neurons.
Project description:High-throughput sequencing of mixed-stage Caenorhabditis elegans small RNAs. total RNA, ~18-26nt RNAs isolated using PAGE, ligation to adapters requires 5' monophosphate and 3' OH Keywords: high-throughput 454 sequencing