GEO DataSets

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:

Human adenovirus 2

Type:

Other

Platform:

GPL30034

59 Samples

Download data

(Submitter supplied) The specific recognition of splice signals at or near the exon-intron junctions is not explained by their weak conservation across the mammalian transcriptome and postulated to require a multitude of features embedded in the pre-mRNA strand. We explored the possibility of three-dimensional structural scaffold of a pre-mRNA guiding early spliceosomal components to the splice signal sequences. We find that mutation in non-cognate splice signal sequences of a model pre-mRNA substrate could impede recruitment of early spliceosomal components due to disruption of global structure of the pre-mRNA. more...

Organism:

Human adenovirus 2

Type:

Other

Platform:

GPL30034

9 Samples

Download data: SHAPE

(Submitter supplied) The specific recognition of splice signals at or near exon-intron junctions is not explained by their weak conservation and instead is postulated to require a multitude of features embedded in the pre-mRNA strand. We explored the possibility of three-dimensional structural scaffold of AdML – a model pre-mRNA substrate – guiding early spliceosomal components to the splice signal sequences. We find that mutations in the non-cognate splice signal sequences impede recruitment of early spliceosomal components due to disruption of the global structure of the pre-mRNA. more...

Organism:

Human adenovirus 2

Type:

Other

Platform:

GPL30034

50 Samples

Download data: SHAPE

(Submitter supplied) Please refer to the summary of the Superseries.

Organism:

Human adenovirus 2

Type:

Expression profiling by high throughput sequencing

Platform:

GPL30034

5 Samples

Download data: SHAPE

(Submitter supplied) We recently reported that serine-arginine-rich (SR) protein-mediated pre-mRNA structural remodeling generates a pre-mRNA 3D structural scaffold that is stably recognized by the early spliceosomal components. However, the intermediate steps between the free pre-mRNA and the assembled early spliceosome are not yet characterized. By probing the early spliceosomal complexes in vitro and RNA-protein interactions in vivo, we show that the SR proteins bind the pre-mRNAs cooperatively generating a substrate that recruits U1 snRNP and U2AF65 in a splice signal-independent manner. more...

Organism:

Human adenovirus 2

Type:

Other

Platform:

GPL30034

22 Samples

Download data: SHAPE, TXT

(Submitter supplied) Please refer to the summary of the Superseries.

Organism:

Human adenovirus 2

Type:

Other

Platform:

GPL30034

6 Samples

Download data: TXT

(Submitter supplied) Please refer to the summary of the Superseries.

Organism:

Human adenovirus 2

Type:

Other

Platform:

GPL30034

11 Samples

Download data: SHAPE

(Submitter supplied) Individual-nucleotide resolution UV-crosslinking and immunoprecipitation (iCLIP) combined with high-throughput sequencing was performed to generate genome-wide binding maps of two U1-snRNP proteins: U1C and U1-70K in Trypanosoma brucei.

Organism:

Trypanosoma brucei

Type:

Other

Platforms:

GPL16561 GPL16563 GPL16562

5 Samples

Download data: TXT

(Submitter supplied) OThe N6-methyladenosine (m6A) RNA modification is widely used to alter the fate of mRNAs. Here we demonstrate that the C. elegans writer METT-10 (orthologue of mouse METTL16) deposits an m6A mark on the 3′ splice site (AG) of the SAM synthetase pre-mRNA which inhibits its proper splicing and protein production. The mechanism is triggered by a rich diet, and acts as an m6A-mediated switch to stop SAM production and regulate its homeostasis. more...

Organism:

Bombyx mori; Mus musculus; Caenorhabditis elegans

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL22765 GPL28266 GPL19757

42 Samples

Download data: BW, CSV, XLSX

(Submitter supplied) Internal modification of RNAs with N6-methyladenosine (m6A) is a highly conserved and widely used means of gene expression control. METTL16 is an m6A writer but how it recognizes its RNA targets and its physiological roles remain unknown. Here we describe the crystal structure of human METTL16 to reveal a classical methyltransferase domain but with an extra N-terminal module that is essential for catalysis. more...

Organism:

Mus musculus; synthetic RNA

Type:

Expression profiling by high throughput sequencing; Other

Platforms:

GPL19057 GPL24911

74 Samples

Download data: CSV

(Submitter supplied) Alternative splicing diversifies mRNA transcripts in human cells. While the spliceosome pairs exons with a high degree of accuracy, the rates of rare aberrant and non-canonical pre-mRNA splicing have not been evaluated at the nucleotide level to determine the quantity and identity of these events across splice junctions. Using ultra-deep sequencing the frequency of aberrant and non-canonical splicing events for three splice junctions flanking exon 7 of SMN1 were determined at single nucleotide resolution. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL11154

1 Sample

Download data: TXT

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL11154

18 Samples

Download data: BEDGRAPH, BW, TXT

(Submitter supplied) In the earliest step of spliceosome assembly, the two splice sites flanking an intron are brought into proximity by U1 snRNP and U2AF. The mechanism that facilitates this intron looping is poorly understood. Using a CRISPR interference-based approach to halt RNA polymerase II transcription in the middle of introns, we discovered that the 5 splice site base pairs with a U1 snRNA that is tethered to RNA polymerase II during intron synthesis. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL11154

1 Sample

Download data: TXT

(Submitter supplied) In the earliest step of spliceosome assembly, the two splice sites flanking an intron are brought into proximity by U1 snRNP and U2AF. The mechanism that facilitates this intron looping is poorly understood. Using a CRISPR interference-based approach to halt RNA polymerase II transcription in the middle of introns, we discovered that the 5 splice site base pairs with a U1 snRNA that is tethered to RNA polymerase II during intron synthesis. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL11154

10 Samples

Download data: BEDGRAPH, BW

(Submitter supplied) In the earliest step of spliceosome assembly, the two splice sites flanking an intron are brought into proximity by U1 snRNP and U2AF. The mechanism that facilitates this intron looping is poorly understood. Using a CRISPR interference-based approach to halt RNA polymerase II transcription in the middle of introns, we discovered that the 5 splice site base pairs with a U1 snRNA that is tethered to RNA polymerase II during intron synthesis. more...

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL11154

7 Samples

Download data: BW

(Submitter supplied) Removal of introns during pre-mRNA splicing, which is central to gene expression, initiates by base pairing of U1 snRNA with a 5' splice site (5'SS). In mammals, many introns contain weak 5'SSs that are not efficiently recognized by the canonical U1 snRNP, suggesting alternative mechanisms exist. Here, we develop a cross-linking immunoprecipitation coupled to a high-throughput sequencing method, BCLIP-seq, to identify NRDE2 (Nuclear RNAi defective-2) and CCDC174 (Coiled-Coil Domain-Containing 174) as novel RNA-binding proteins in mouse ES cells that associate with U1 snRNA and unspliced 5'SSs. more...

Organism:

Mus musculus

Type:

Other

Platform:

GPL17021

48 Samples

Download data: BIGWIG, BW, TXT

(Submitter supplied) Examination of transcriptome of SPF45 knockdown cells by Ribosomal RNA depleted RNA-Seq

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL16791

6 Samples

Download data: BW