GEO DataSets

(Submitter supplied) To uncover exon junction complex (EJC) deposition sites on cellular mRNAs, RNA footprints of EJC immuo-purified from HEK293 cells were deep sequenced. The analysis of these data revealed that major “canonical” EJC occupancy site in vivo lies 24 nucleotides upstream of exon junctions (-24 position) and that the majority of exon junctions carry an EJC. Unexpectedly, we find that many sites further upstream of -24 position are also enriched in these EJC footprints. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing; Other

Platforms:

GPL9442 GPL11154 GPL13393

12 Samples

Download data: BED

(Submitter supplied) The exon junction complex (EJC) deposited upstream of mRNA exon junctions shapes structure, composition and fate of spliced mRNA ribonucleoprotein particles (mRNPs). To achieve this, the EJC core nucleates assembly of a dynamic shell of peripheral proteins that function in diverse post-transcriptional processes. In this study we show that EJC exists in two mutually exclusive compositions characterized by peripheral proteins RNPS1 and CASC3. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL16791

15 Samples

Download data: XLSX

(Submitter supplied) We demonstrates that pre-translational mammalian mRNPs fold as linear rod-like structures with no strong propensity for 5' and 3' end interaction.

Organism:

Homo sapiens

Type:

Other

Platform:

GPL18573

6 Samples

Download data: TXT

(Submitter supplied) Signaling pathways are controlled by a vast array of post-translational mechanisms. By contrast, little is known regarding the mechanisms that regulate the expression of their core components. We conducted an RNAi screen in Drosophila for factors modulating RAS/MAPK signaling and identified the Exon Junction Complex (EJC) as a novel key element of this pathway. The EJC binds the exon-exon junctions of mRNAs, and thus far, has been linked exclusively to post-splicing events. more...

Organism:

Drosophila melanogaster

Type:

Expression profiling by high throughput sequencing

Platform:

GPL10942

6 Samples

Download data: BAM, TXT, WIG

(Submitter supplied) Splicing of pre-mRNAs results in the deposition of the exon junction complex (EJC) upstream of exon-exon boundaries. The EJC plays crucial post-splicing roles in export, translation, localization and nonsense-mediated decay of mRNAs. It also aids faithful splicing of pre-mRNAs containing large introns, albeit via an unknown mechanism. Here, we show that the core EJC plus the accessory factors RnpS1 and Acinus aid in definition and efficient splicing of neighboring introns. more...

Organism:

Drosophila melanogaster

Type:

Expression profiling by high throughput sequencing

Platform:

GPL13304

9 Samples

Download data: BW, TXT

(Submitter supplied) We report that knockdown of EJC core proteins, eIF4A3, Y14, Magoh, causes a transcript-wide changes in alternative splicing, as well as some transcriptional changes. These changes are specific to EJC core proteins, and KD of UPF1 protein caused different sets of alterantive splicing changes. These changes are linked to the rate of transcription.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL11154

10 Samples

Download data: TSV

(Submitter supplied) The exon junction complex (EJC) is a central effector of mRNAs fate, linking nuclear processing to mRNA transport, translation and surveillance. Little is known about its transcriptome-wide targets. We used high-throughput sequencing after crosslinking and immunoprecipitation (HITS-CLIP) in human cells to identify the binding sites of the DEAD-box helicase eIF4AIII, an EJC core component. CLIP reads form peaks mainly located in spliced mRNAs. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing; Other

Platforms:

GPL10999 GPL11154

3 Samples

Download data: BEDGRAPH

(Submitter supplied) ChIP-seq Y14

Organism:

Drosophila melanogaster

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL14601

2 Samples

Download data: WIG

(Submitter supplied) Using the TSG101 pre-mRNA, we previously discovered cancer-specific re-splicing of mature mRNA that generates aberrant transcripts/proteins. The fact that mRNA is aberrantly re-spliced in various cancer cells implies there must be an important mechanism to prevent deleterious re-splicing on the spliced mRNA in normal cells. We thus postulated that the mRNA re-splicing is controlled by specific repressors and we searched for repressor candidates by siRNA-based screening for mRNA re-splicing activity. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL23159

6 Samples

Download data: CEL, TXT

(Submitter supplied) RNA sequencing of E10.5 neocortices from control, Magoh, Rbm8a, and Eif4a3 haploinsufficient embryos (generated with Emx1-Cre)

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL13112

20 Samples

Download data: XLSX

(Submitter supplied) Biogenesis of eukaryotic messenger ribonucleoprotein complexes (mRNPs) involves the synthesis, splicing, and 3’-processing of pre-mRNA, and the assembly of mature mRNPs for nuclear export. We mapped 23 mRNP biogenesis factors onto the newly synthesized yeast transcriptome, providing ~10^5-10^6 high-confidence RNA interaction sites per factor.

Organism:

Saccharomyces cerevisiae

Type:

Other

Platforms:

GPL18085 GPL13272

23 Samples

Download data: TXT

(Submitter supplied) Exon junction complexes (EJCs) are deposited to mRNAs during splicing and displaced from mRNAs by ribosomes in the pioneer round of translation. The understanding of EJC-bound mRNA degradation before steady-state translation has been limited to nonsense-mediated mRNA decay (NMD) due to a lack of suitable methodologies. Here, we show that RNA degradome data of Arabidopsis, rice, worm and human cells all exhibit a predominant accumulation of 5′ monophosphate (5′P) ends in the canonical EJC region. more...

Organism:

Arabidopsis thaliana

Type:

Other

Platform:

GPL17639

14 Samples

Download data: TXT

(Submitter supplied) N6–methyladenosine (m6A) is the most abundant mRNA modification and plays crucial roles in diverse physiological processes. Utilizing a Massively Parallel Assay for m6A (MPm6A), we discover that m6A specificity is globally regulated by “suppressors” that prevent m6A deposition in unmethylated transcriptome regions. We identify Exon Junction Complexes (EJCs) as m6A suppressors that protect exon junction-proximal RNA within coding sequences from methylation and regulate mRNA stability through m6A suppression. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing; Other

Platforms:

GPL20301 GPL24676 GPL18573

166 Samples

Download data: BED, BEDGRAPH, TXT

(Submitter supplied) The exon junction complex (EJC) is a highly conserved ribonucleoprotein complex which binds RNAs during splicing and remains associated with them following export to the cytoplasm. While the role of this complex in mRNA localization, translation and degradation has been well characterized, its mechanism of action in splicing a subset of Drosophila and human transcripts remains to be elucidated. Here, we describe a novel function for the EJC and its splicing subunit RnpS1 in preventing transposon accumulation in both Drosophila germline and surrounding somatic follicle cells. more...

Organism:

Drosophila melanogaster

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL9061

6 Samples

Download data: CSV, TXT

(Submitter supplied) The exon junction complex (EJC) is a highly conserved ribonucleoprotein complex which binds RNAs at a late stage of the splicing reaction and remains associated following export to the cytoplasm. This complex is involved in several cellular post-transcriptional processes including mRNA localization, translation and degradation. The EJC plays an additional role in the splicing of a subset of genes in Drosophila and in human cells but the underlying mechanism remains to be elucidated. more...

Organism:

Drosophila melanogaster

Type:

Expression profiling by high throughput sequencing

Platform:

GPL13304

8 Samples

Download data: TXT

(Submitter supplied) This study was designed to identify changes in gene expression resulting from depletion of Mago nashi (Mago), a core subunit of the exon junction complex. Drosophila S2R+ cells were treated with double-stranded RNA targeting either LacZ or Mago for 6 days. Poly(A)+ RNA was purified from each sample and sequenced using 54 bp reads on an Illumina Genome Analyzer II. Fold changes in expression were calculated for each gene as the ratio of the reads per kilobase per million reads (RPKM) for Mago relative to LacZ. more...

Organism:

Drosophila melanogaster

Type:

Expression profiling by high throughput sequencing

Platform:

GPL9061

2 Samples

Download data: TXT