GEO DataSets

(Submitter supplied) Alternative cleavage and polyadenylation (APA) is a mechanism generating multiple mRNA isoforms with different 3'UTRs and/or coding sequences from a single gene. Here we used 3' Region Extraction And Deep Sequencing (3'READS) to systematically map cleavage and polyadenylation sites (PAS) in Drosophila and analyzsed APA in the RpII215 C4 mutant strain, which harbors a mutant RNA polymerase II (RNAPII) with a slower elongation rate. more...

Organism:

Drosophila melanogaster

Type:

Expression profiling by high throughput sequencing

Platform:

GPL17275

12 Samples

Download data: TXT

(Submitter supplied) Alternative cleavage and polyadenylation (APA) results in mRNA isoforms containing different 3’ untranslated regions (3’UTRs) and/or coding sequences. How core cleavage and polyadenylation (C/P) factors regulate APA is not well understood. Using siRNA knockdown coupled with deep sequencing, we found that several C/P factors can play significant roles in 3’UTR-APA. Whereas Pcf11 and Fip1 enhance usage of proximal poly(A) sites (pAs), CFI-25/68, PABPN1, and PABPC1 promote usage of distal pAs. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL13112 GPL17021 GPL9250

54 Samples

Download data: TXT

(Submitter supplied) Alternative cleavage and polyadenylation (APA) generates diverse mRNA isoforms. We developed 3' region extraction and deep sequencing (3'READS) to address mispriming issues that commonly plague poly(A) site (pA) identification, and we used the method to comprehensively map pAs in the mouse genome. Thorough annotation of gene 3' ends revealed over 5,000 previously overlooked pAs (~8% of total) flanked by A-rich sequences, underscoring the necessity of using an accurate tool for pA mapping. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL11002

4 Samples

Download data: BED

(Submitter supplied) Most mammalian genes display alternative cleavage and polyadenylation (APA). Previous studies have indicated preferential expression of APA isoforms with short 3’UTRs in testes. Here we show widespread shortening of 3’UTR by APA during the first wave of spermatogenesis in mouse, with 3’UTRs being the shortest in spermatids. Shortening of 3’UTR eliminates destabilizing elements, such as U-rich elements and transposable elements, which appear to be highly potent for transcript elimination during spermatogenesis. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing; Other

Platform:

GPL13112

6 Samples

Download data: TXT

(Submitter supplied) Using 3ʹ region extraction and deep sequencing coupled to ribonucleoprotein immunoprecipitation (3’READS+RIP), together with reanalyzing previous STAU1 binding and RNA structure data, we delineate STAU1 interactions transcriptome-wide, including binding differences between alternative polyadenylation (APA) isoforms. Consistent with previous reports, RNA structures are dominant features for STAU1 binding to CDSs and 3ʹUTRs. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing; Other

Platforms:

GPL18573 GPL11154

12 Samples

Download data: CSV

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

Organism:

Mus musculus

Type:

Other; Expression profiling by high throughput sequencing

Platforms:

GPL13112 GPL19057

46 Samples

Download data

(Submitter supplied) Alternative polyadenylation (APA) refers to the regulated selection of polyadenylation sites (PASs) in transcripts, which determines the length of their 3’ untranslated regions (3’UTRs). APA regulates stage- and tissue-specific gene expression by affecting the stability, subcellular localization and translation rate of transcripts. We have recently shown that SRSF3 and SRSF7, two closely related SR proteins, connect APA with mRNA export. more...

Organism:

Mus musculus

Type:

Other

Platform:

GPL13112

6 Samples

Download data: BED

(Submitter supplied) Alternative polyadenylation (APA) refers to the regulated selection of polyadenylation sites (PASs) in transcripts, which determines the length of their 3’ untranslated regions (3’UTRs). APA regulates stage- and tissue-specific gene expression by affecting the stability, subcellular localization and translation rate of transcripts. We have recently shown that SRSF3 and SRSF7, two closely related SR proteins, connect APA with mRNA export. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL19057

16 Samples

Download data: CSV

(Submitter supplied) Alternative polyadenylation (APA) refers to the regulated selection of polyadenylation sites (PASs) in transcripts, which determines the length of their 3’ untranslated regions (3’UTRs). APA regulates stage- and tissue-specific gene expression by affecting the stability, subcellular localization and translation rate of transcripts. We have recently shown that SRSF3 and SRSF7, two closely related SR proteins, connect APA with mRNA export. more...

Organism:

Mus musculus

Type:

Other

Platform:

GPL13112

24 Samples

Download data: BW

(Submitter supplied) Sequencing of the 3’ end of poly(A)+ RNA identifies cleavage and polyadenylation sites (pAs) and measures transcript expression. We previously developed a method, 3’ region extraction and deep sequencing (3’READS), to address mispriming issues that often plague 3’ end sequencing. Here we report a new version, named 3’READS+, which has vastly improved accuracy and sensitivity. Using a special locked nucleic acid oligo to capture poly(A)+ RNA and to remove bulk of the poly(A) tail, 3’READS+ generates RNA fragments with an optimal number of terminal As that balance data quality and detection of genuine pAs. more...

Organism:

Homo sapiens

Type:

Other; Expression profiling by high throughput sequencing

Platform:

GPL11154

9 Samples

Download data: CSV

(Submitter supplied) we generated developmental and tissue-specific 3'-seq libraries from D. yakuba and D. virilis to study the role of alternative polyadenylation across Drosophila species

Organism:

Drosophila virilis; Drosophila melanogaster; Drosophila yakuba

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL23800 GPL15334 GPL23801

44 Samples

Download data: BW, TAB

(Submitter supplied) APA mechanisms in S. pombe and S. cerevisiae are largely different, distinctly impacting gene expression, antisense transcripts and 3’UTR evolution, and core processing factors regulate APA in a PAS-dependent manner.

Organism:

Saccharomyces cerevisiae; Schizosaccharomyces pombe

Type:

Other

Platforms:

GPL17225 GPL17342

8 Samples

Download data: TXT

(Submitter supplied) Cleavage and polyadenylation is essential for 3’ end processing of almost all eukaryotic mRNAs. Recent studies have shown widespread alternative cleavage and polyadenylation (APA) events leading to mRNA isoforms with different 3’UTRs and/or coding sequences. Here we present a compendium of conserved cleavage and polyadenylation sites (PASs) in mammalian genes, based on ~1.2 billion 3’ end sequencing reads from over 360 human, mouse and rat samples. more...

Organism:

Rattus norvegicus; Homo sapiens; Mus musculus

Type:

Other

5 related Platforms

128 Samples

Download data: TXT

(Submitter supplied) Much of posttranscriptional mRNA regulation occurs through cis-acting sequences in mRNA 3´ untranslated regions (UTRs), which interact with specific proteins and ribonucleoprotein complexes that modulate translation, mRNA stability and subcellular localization. Studies in Caenorhabditis elegans have revealed indispensable roles for 3´UTR-mediated gene regulation, yet most C. elegans genes have lacked annotated 3´UTRs. more...

Organism:

Caenorhabditis elegans

Type:

Expression profiling by high throughput sequencing

Platform:

GPL9269

10 Samples

Download data: BED, TXT

(Submitter supplied) Alternative polyadenylation (APA) has been implicated in a variety of developmental and disease processes, such as stem cell differentiation and cancer. A particularly dramatic form of APA has been documented in the developing nervous system of flies and mammals, whereby a variety of neurogenic genes undergo coordinate extension of their 3’ UTRs. In Drosophila, the RNA-binding protein ELAV inhibits RNA processing at proximal polyadenylation (poly(A)) sites, thereby fostering the formation of 3’ extensions that can reach 12 kb in length. more...

Organism:

Drosophila melanogaster

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL13304

6 Samples

Download data: BEDGRAPH

(Submitter supplied) The 3' ends of most Drosophila melanogaster genes are poorly annotated or are determined by only a single EST or cDNA clone. To enhance the annotation of poly(A) site use in Drosophila, we performed deep sequencing on RNA isolated from 29 dissected tissues using an approach designed to enrich for poly(A) spanning reads. From these experiments, we identified 1.4 million poly(A) spanning reads leading to the identification of many new poly(A) sites and the identification of many tissue-specific poly(A) sites. more...

Organism:

Drosophila melanogaster

Type:

Other

Platforms:

GPL11203 GPL13304

58 Samples

Download data: GFF

(Submitter supplied) Background: Alternative polyadenylation (APA) is emerging as a widespread mechanism of gene regulation. The usage of APA sites allows a single gene to encode multiple mRNA transcripts with different 3'-untranslated region (3'UTR) lengths. Many disease processes reflect the importance of the regulation of APA site switching. The objective of this study was to explore the profiling of tandem APA sites in nasal polyps compared with nasal uncinate process mucosa. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL9115

4 Samples

Download data: TXT

(Submitter supplied) The PAF complex (Paf1C) has been shown to regulate chromatin modifications, gene transcription, and PolII elongation. Here, we provide the first genome-wide analysis of chromatin occupancy by the entire PAF complex in mammalian cells. We show that Paf1C is recruited not only to promoters and gene bodies, but also to regions downstream of cleavage/polyadenylation (pA) sites at 3’ ends, a profile that sharply contrasted with the yeast complex. more...

Organism:

Mus musculus

Type:

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

Platform:

GPL13112

66 Samples

Download data: BIGWIG, BW, TXT

(Submitter supplied) we observed distinct profiles of transcriptome-wide 3’UTR in the accurately dissected mitotic and meiotic cells of wildtype testes, also in the over-amplifying mitotic germ cells of mutant testes

Organism:

Drosophila melanogaster

Type:

Expression profiling by high throughput sequencing

Platform:

GPL17275

12 Samples

Download data: XLSX

(Submitter supplied) Analogous to alternative splicing, alternative polyadenylation (APA) has long been thought to result from competition between proximal and distal polyA sites. By Fractionation-seq, we unexpectedly identified several hundred APA genes where their distal polyA isoforms are retained in chromatin/nuclear matrix and proximal polyA isoforms released into the cytoplasm. Global metabolic PAS-seq and Nanopore long-read RNA-seq provided further evidence that the strong distal polyA sites are first processed and the resulting transcripts are anchored in chromatin/nuclear matrix for further processing at proximal polyA sites and removal of certain slowly spliced introns. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing; Other

Platforms:

GPL24106 GPL11154 GPL24676

18 Samples

Download data: BED, BEDGRAPH, BW