GEO DataSets

(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) 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) 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) 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) 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) Alternative polyadenylation (APA) of mRNAs has emerged as an important mechanism for post-transcriptional gene regulation in higher eukaryotes. Although microarrays have recently been used to characterize APA globally, they have a number of serious limitations that prevents comprehensive and highly quantitative analysis. To better characterize APA and its regulation, we have developed a deep sequencing-based method called Poly(A) Site Sequencing (PAS-Seq) for quantitatively profiling RNA polyadenylation at the transcriptome level. more...

Organism:

Mus musculus; Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL9052 GPL9185

4 Samples

Download data: PDF, TXT

(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) To determine the extent of alternative 3' end cleavage during Drosophila spermatogenesis, we performed 3' end sequencing of Drosophila testes from flies at different time points post heat shock (pHS) that were mutant for bam and also had a heat shock inducible transgene expressing Bam. We then performed Polysome profiling of testes at 24, 48 and 72 hours PHS and created 3' end sequencing libraries from the free, 40S, 60s, 80S, 2-3 ribosomes, and 4+ ribosomes fractions for each dataset

Organism:

Drosophila melanogaster

Type:

Expression profiling by high throughput sequencing

Platform:

GPL19132

48 Samples

Download data: TXT

(Submitter supplied) The development of the central nervous system (CNS) is a complex process that must be exquisitely controlled at multiple levels to ensure the production of appropriate types and quantity of neurons. RNA alternative polyadenylation (APA) contributes to transcriptome diversity and gene regulation and has recently been shown to be widespread in the CNS. However, previous studies have been primarily focused on the tissue specificity of APA and developmental APA change of whole model organisms, a systematic survey of APA usage is lacking during CNS development. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL13112

6 Samples

Download data: TXT

(Submitter supplied) mRNA isoform abundance and stability in HEK293T cells were examined by 4sU labeling and fractionation

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL11154

5 Samples

Download data: TXT

(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

(Submitter supplied) This experimental series concerns the position bias and extent of 3'-end choice in MCF7 cells after knock-down of the CFII subunits PCF11 and CLP1 in MCF7. Loss of either subunit results in 3'-lengthening by APA. Importantly this lengthening is toward a more 'normal-like' distribution. MCF7 cells show a native 3'-end distribution favoring short internal adenylation sites compared to MDAMD231 cells. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18460

11 Samples

Download data: CSV

(Submitter supplied) Genes with different sizes have distinct expression patterns and functions. Here we show that the 3' end processing PCF11 modulates gene expression according to gene size. Gene density and polyA site strength, but not orientation between neighboring genes, impact short gene regulation by PCF11. In contrast, long gene modulation involves intronic polyadenylation (IPA), which is widespread in large introns. more...

Organism:

Mus musculus

Type:

Other; Expression profiling by high throughput sequencing

Platforms:

GPL19057 GPL13112

22 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) To inverstigate off-target effects of CRISPR-iPAS, we transfected HEK293TAPA reporter cells with dPguCas13b and gUSE (showed most effective APA-interference) or non-targeting gRNA (gNT) respectively. 3'end-seq and RNA-seq were performed to investigate if the global change on the endogenous PAS usage and gene expression caused by CRISPR-iPAS. Comparing with gNT, dPguCas13b with gUSE showed high specificity.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24676

8 Samples

Download data: TSV

(Submitter supplied) Polyadenylation of mRNA precursors is mediated by a large multisubunit protein complex. Here we show that RBBP6 (retinoblastoma-binding protein 6), identified initially as an Rb- and p53-binding protein, is a component of this complex and functions in 3' processing in vitro and in vivo. RBBP6 associates with other core factors, and this interaction is mediated by an unusual ubiquitin-like domain, DWNN (domain with no name), that is required for 3' processing activity. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL5188

4 Samples

Download data: CEL

(Submitter supplied) Here, using genome wide analysis, we demonstrate that canonical mRNA is processed post-transcriptionally through an alternative cleavage and polyadenylation mechanism. As a result of this process, the downstream cleavage fragment of the 3′UTR remains uncapped and stable This finding indicates that different parts of gene mRNA are separate and independent, by re-annotating the human transcriptome using this model, we provide a new overview of the function and impact of microRNA (miRNA) Our results shed new light on the mammalian transcriptome and show that what were considered as 3′UTRs are in fact autonomous RNA fragments.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing; Other

Platform:

GPL18573

36 Samples

Download data: BIGWIG, TSV

(Submitter supplied) Poly(A)-ClickSeq is a new methodology for the sequencing of the 3'UTR/poly(A) tail junction of RNA. We analysed both wild-type and CF25Im knock-down HeLa cells in culture using Poly(A)-ClickSeq to find the distribution of poly(A) sites in these samples and determine the role of CF25Im in poly(A) site selection (alternative poly-adenylation, APA).

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL18460 GPL15520

11 Samples

Download data: BEDGRAPH

(Submitter supplied) We assayed the expression of millions of alternative polyadenylation reporters constructed from randomized sequences

Organism:

Homo sapiens

Type:

Other

Platforms:

GPL15520 GPL21697

14 Samples

Download data: CSV, MAT, TXT