Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Regulation of gene expression and RNA editing in Drosophila adapting to divergent microclimates

ABSTRACT: Regulation of gene expression and RNA editing in Drosophila adapting to divergent microclimates

PROVIDER: PRJNA408172 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR6055360_1.fastq.gz	Fastqsanger.gz
	SRR6055360_2.fastq.gz	Fastqsanger.gz
	SRR6055370_1.fastq.gz	Fastqsanger.gz
	SRR6055370_2.fastq.gz	Fastqsanger.gz
	SRR6055380_1.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 384

Similar Datasets

Measuring gene expression and RNA editing in Drosophila adapting to divergent microclimates

Project description:Measuring gene expression and RNA editing in Drosophila adapting to divergent microclimates

| PRJNA408160 | ENA

Measuring gene expression and RNA editing in Drosophila adapting to divergent microclimates

Project description:We performed RNA-seq to profile gene expression in the heads and whole bodies of 32 isofemale fly lines from two divergent microclimates at 'Evolution Canyon' in Israel (16 fly lines from each microclimate). We also measured RNA editing levels in the head tissue of these flies.

2017-09-20 | GSE104073 | GEO

Measuring RNA editing through mmPCR-seq in Drosophila adapting to divergent microclimates and raised at different temperatures

Project description:Measuring RNA editing through mmPCR-seq in Drosophila adapting to divergent microclimates and raised at different temperatures

| PRJNA408169 | ENA

Measuring RNA editing through mmPCR-seq in Drosophila adapting to divergent microclimates and raised at different temperatures

Project description:We applied microfluidic multiplex PCR and deep sequencing (mmPCR-seq) to quantify RNA editing levels at targeted sites in 32 isofemale lines from two divergent microclimates at 'Evolution Canyon' in Israel (16 fly lines from each microclimate). Editing levels were compared between different populations at 25˚C , and were also compared between 25˚C and 18˚C within populations.

2017-09-20 | GSE104084 | GEO

Regulation of gene expression and RNA editing in Drosophila adapting to divergent microclimates.

Project description:Determining the mechanisms by which a species adapts to its environment is a key endeavor in the study of evolution. In particular, relatively little is known about how transcriptional processes are fine-tuned to adjust to different environmental conditions. Here we study Drosophila melanogaster from 'Evolution Canyon' in Israel, which consists of two opposing slopes with divergent microclimates. We identify several hundred differentially expressed genes and dozens of differentially edited sites between flies from each slope, correlate these changes with genetic differences, and use CRISPR mutagenesis to validate that an intronic SNP in prominin regulates its editing levels. We also demonstrate that while temperature affects editing levels at more sites than genetic differences, genetically regulated sites tend to be less affected by temperature. This work shows the extent to which gene expression and RNA editing differ between flies from different microclimates, and provides insights into the regulation responsible for these differences.

| S-EPMC5691062 | biostudies-literature

Regulation of gene expression and RNA editing in Drosophila adapting to divergent microclimates

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

2017-09-20 | GSE104085 | GEO

Divergent evolutionary strategies for selective sex chromosome regulation in Drosophila

Project description:The dosage compensation complex (DCC) of Drosophila identifies its X chromosomal binding sites with exquisite selectivity. The principles that assure this vital targeting are known from the D. melanogaster model: DCC-intrinsic specificity of DNA binding, cooperativity with the CLAMP protein, and non-coding roX2 RNA transcribed from the X chromosome. We found that in D. virilis, a species separated from melanogaster by 40 million years of evolution, all principles are active, but contribute differently to X-specificity. In melanogaster, the DCC subunit MSL2 evolved intrinsic DNA-binding selectivity for rare PionX sites, which mark the X chromosome. In virilis, PionX sites are abundant and not X-enriched. Accordingly, MSL2 lacks specific recognition. Here, roX2 RNA plays a more instructive role, counteracting a non-productive interaction of CLAMP and modulating DCC binding selectivity. Remarkably, roX2 triggers a low-diffusion chromatin binding mode characteristic of DCC. Evidently, X-specific regulation is achieved by divergent evolution of similar components.

2021-06-23 | PXD023747 | Pride

Divergent transcription from lentiviral gene editing of cancer cells

Project description:We explored a gene editing approach to depleting ephrinB2 from colorectal cancer cells using an inducible lentiviral vector encoding a short hairpin (sh) RNA for ephrinB2 silencing via RNA interference. We discovered that lentiviral integration in the host DNA frequently drives divergent gene transcription generating antisense reads by forcing splicing and read-through into the host DNA resulting in expression of chimeric vector/host transcripts.

2022-05-25 | GSE186796 | GEO

Nascent-seq indicates widespread cotranscriptional RNA editing in Drosophila

Project description:The RNA editing enzyme ADAR chemically modifies adenosine (A) to inosine (I), which is interpreted by the ribosome as a guanosine. Here we assess cotranscriptional A-to-I editing in Drosophila, by isolating nascent RNA from adult fly heads and subjecting samples to high-throughput sequencing. There are a large number of edited sites within nascent exons. Nascent RNA from an ADAR null mutant strain was also sequenced, indicating that almost all A-to-I events require ADAR. Moreover, mRNA editing levels correlate with editing levels within the cognate nascent RNA sequence, indicating that the extent of editing is set cotranscriptionally. Surprisingly, the nascent data also identify an excess of intronic over exonic editing sites. These intronic sites occur preferentially within introns that are poorly spliced cotranscriptionally, suggesting a link between editing and splicing. We conclude that ADAR-mediated editing is more widespread than previously indicated and largely occurs cotranscriptionally. GSM914095: Fly genomic DNA sequencing. Sequenced on the Illumina GA II. GSM914102-GSM914113: Fly head nascent RNA profiles over 6 time points of a 12hr light:dark cycle in duplicate; sequenced on the Illumina GA II. GSM914114-GSM914119: Fly head nascent RNA profiles of yw, FM7, ADAR0 males in duplicate; sequenced on the HiSeq2000. GSM915213-GSM915214: Fly head mRNA profiles over 2 time points of a 12hr light:dark cycle; sequenced on the Illumina GA II. GSM915215-GSM915220: Fly head mRNA profiles over 6 time points of a 12hr light:dark cycle; paired-end sequenced on the Illumina GA II. GSM915221-GSM91526: Fly head mRNA profiles over 6 time points of a 12hr light:dark cycle; sequenced on the Illumina GA II.

2012-05-31 | E-GEOD-37232 | biostudies-arrayexpress

Divergent transcription from lentiviral gene editing of cancer cells

Project description:Divergent transcription from lentiviral gene editing of cancer cells

| PRJNA776033 | ENA