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A-to-I RNA editing signatures of neuronal populations within the Drosophila brain

ABSTRACT: A-to-I RNA editing signatures of neuronal populations within the Drosophila brain

PROVIDER: PRJNA453549 | ENA |

REPOSITORIES: ENA

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Measuring A-to-I RNA editing signatures of neuronal populations within the Drosophila brain

Project description:We used an improved INTACT (Isolation of Nuclei Tagged in A specific Cell Type) technique to isolate RNA from purified nuclei from different neuronal populations of the Drosophila brain. Using microfluidic multiplex PCR and sequencing (mmPCR-seq), we determined gene expression and A-to-I RNA editing levels at editing sites across nine distinct neuronal sub-populations and a pan-neuronal control.

2019-01-18 | GSE113662 | GEO

Measuring A-to-I RNA editing signatures of neuronal populations within the Drosophila brain

Project description:Measuring A-to-I RNA editing signatures of neuronal populations within the Drosophila brain

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Measuring A-to-I RNA editing and gene expression signatures of neuronal populations within the Drosophila brain

Project description:We used an improved INTACT (Isolation of Nuclei Tagged in A specific Cell Type) technique to isolate RNA from purified nuclei from different neuronal populations of the Drosophila brain. Using RNA-seq, we determined gene expression and A-to-I RNA editing levels at editing sites across nine distinct neuronal sub-populations and a pan-neuronal control.

2019-01-18 | GSE113661 | GEO

Measuring A-to-I RNA editing and gene expression signatures of neuronal populations within the Drosophila brain

Project description:Measuring A-to-I RNA editing and gene expression signatures of neuronal populations within the Drosophila brain

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A-to-I RNA editing signatures of neuronal populations within the Drosophila brain

Project description:This SuperSeries is composed of the SubSeries listed below.

2019-01-18 | GSE113663 | GEO

Genetic Diversity Through RNA Editing: Apobec1-mediated RNA editing in bulk and single cell macrophages and dendritic cells

Project description:RNA editing is a mutational mechanism that specifically alters the nucleotide content in sets of transcripts while leaving their cognate genomic blueprint intact. Editing has been detected from bulk RNA-seq data in thousands of distinct transcripts, but apparent editing rates can vary widely (from under 1% to almost 100%). These observed editing rates could result from approximately equal rates of editing within each individual cell in the bulk sample, or alternatively, editing estimates from a population of cells could reflect an average of distinct, biologically significant editing signatures that vary substantially between individual cells in the population. To distinguish between these two possibilities we have constructed a hierarchical Bayesian model which quantifies the variance of editing rates at specific sites using RNA-seq data from both single cells and a cognate bulk sample consisting of ∼ 106 cells. The model was applied to data from murine bone-marrow derived macrophages and dendritic cells, and predicted high variance for specific edited sites in both cell types tested. We then 1 validated these predictions using targeted amplification of specific editable transcripts from individual macrophages. Our data demonstrate substantial variance in editing signatures between single cells, supporting the notion that RNA editing generates diversity within cellular populations. Such editing-mediated RNA-level sequence diversity could contribute to the functional heterogeneity apparent in cells of the innate immune system.

2016-07-11 | GSE74720 | GEO

Single Cell Methylome Signatures Reveal Distinct Neuronal Populations and Regulatory Elements in the Mammalian Cortex

Project description:Single Cell Methylome Signatures Reveal Distinct Neuronal Populations and Regulatory Elements in the Mammalian Cortex

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Exon-activated functional rescue secures neuronal transcript signatures

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Alu sequences in undifferentiated human embryonic stem cells display high levels of A-to-I RNA editing

Project description:Adenosine to Inosine (A-to-I) RNA editing is a site-specific modification of RNA transcripts, catalyzed by members of the ADAR (Adenosine Deaminase Acting on RNA) protein family. RNA editing occurs in human RNA in thousands of different sites. Some of the sites are located in protein-coding regions but the majority is found in non-coding regions, such as 3âUTRs, 5âUTRs and introns - mainly in Alu elements. While editing is found in all tissues, the highest levels of editing are found in the brain. It was shown that editing levels within protein-coding regions are increased during embryogenesis and after birth and that RNA editing is crucial for organism viability as well as for normal development. In this study we characterized the A-to-I RNA editing phenomenon during neuronal and spontaneous differentiation of human embryonic stem cells (hESCs). We identified high editing levels of Alu repetitive elements in hESCs and demonstrated a global decrease in editing levels of non-coding Alu sites when hESCs are differentiating, particularly into the neural lineage. Using RNA interference, we showed that the elevated editing levels of Alu elements in undifferentiated hESCs are highly dependent on ADAR1. DNA microarray analysis showed that ADAR1 knockdown has a global effect on gene expression in hESCs and leads to a significant increase in RNA expression levels of genes involved in differentiation and development processes, including neurogenesis. Taken together, our data suggest that A-to-I editing of Alu sequences plays a role in the regulation of hESC early differentiation decisions. Two samples, One control and the second treated

2010-07-29 | E-GEOD-19719 | biostudies-arrayexpress

Identification of the hypothalamic neuronal populations that derive from Pomc-expressing precursors

Project description:Hypothalamic neuronal populations are central regulators of energy homeostasis and reproductive function. However, the ontogeny of these critical hypothalamic neuronal populations is largely unknown. Here, we reveal novel cellular fates of the hypothalamic Pomc-expressing precursors by combining mouse genetics with a conditional viral ribosome-tagging approach to phenotype neurons. Our results show that the Pomc-expressing precursors differentiate into discrete neuronal subpopulations that mediate not only energy balance (POMC and AgRP) but also reproductive physiology (Kisspeptin).

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