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Alternative intronic polyadenylation influences cancer metastasis and response to therapy [3'-seq]

ABSTRACT: We explored the impact of alternative polyadenylation regulation during tumor cell spreading.

ORGANISM(S): Mus musculus

PROVIDER: GSE94373 | GEO | 2018/01/01

SECONDARY ACCESSION(S): PRJNA369527

REPOSITORIES: GEO

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Alternative intronic polyadenylation influences cancer metastasis and response to therapy

Project description:Alternative intronic polyadenylation influences cancer metastasis and response to therapy

| PRJNA369518 | ENA

Alternative intronic polyadenylation influences cancer metastasis and response to therapy

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

2018-01-01 | GSE94375 | GEO

Alternative intronic polyadenylation influences cancer metastasis and response to therapy [CLIP-seq]

Project description:CLIP-seq analysis of TIA1 protein in 4T1 invasive mammary tumor cells

2018-01-01 | GSE94369 | GEO

Mouse alternative polyadenylation

Project description:Divergence of alternative polyadenylation in mouse

| PRJEB15336 | ENA

Genome-wide profiling of Alternative polyadenylation sites in mouse female germline stem cells

Project description:Alternative polyadenylation (APA) is an important post-transcriptional modification implicated in development. Female germline stem cell (FGSC) is unipotent and capable of giving rise to oocyte. However, whether alternative polyadenylation plays a role in self-renew and cell fate determination of FGSCs remain elusive. Here, we used 3T-Seq developed in our lab to profile genome-wide 3a termini of transcripts and delineate APA sites in mouse FGSCs and explored the biological significance of APA modulation in FGSC identity.

2015-11-20 | E-MTAB-4038 | biostudies-arrayexpress

Coupling between alternative polyadenylation and alternative splicing is limited to terminal introns

Project description:Alternative polyadenylation has been implicated as an important regulator of gene expression. In some cases, alternative polyadenylation is known to couple with alternative splicing to influence last intron removal. However, it is unknown whether alternative polyadenylation events influence alternative splicing decisions at upstream exons. Knockdown of the polyadenylation factors CFIm25 or CstF64 was used as an approach in identifying alternative polyadenylation and alternative splicing events on a genome-wide scale. Although hundreds of alternative splicing events were found to be differentially spliced in the knockdown of CstF64, genes associated with alternative polyadenylation did not exhibit an increased incidence of alternative splicing. These results demonstrate that the coupling between alternative polyadenylation and alternative splicing is usually limited to defining the last exon. The striking influence of CstF64 knockdown on alternative splicing can be explained through its effects on UTR selection of known splicing regulators such as hnRNP A2/B1, thereby indirectly influencing splice site selection. We conclude that changes in the expression of the polyadenylation factor CstF64 influences alternative splicing through indirect effects. HeLa cell line was stably transfected with shRNA plasmids targeting CstF64. Total RNA was isolated from CstF64 KD cells and wild-type control cells using Trizol according to manufacturerâs protocols. Samples were deep sequenced in duplicate using the Illumina GAIIx system.

2016-03-14 | E-GEOD-79157 | biostudies-arrayexpress

Coupling between alternative polyadenylation and alternative splicing is limited to terminal introns

2016-03-14 | GSE79157 | GEO

Alternative polyadenylation is a minor feature of primary human muscle differentiation

Project description:Alternative polyadenylation has been explored in multiple native and disease transitions. The prevailing hypothesis being that differentiated cells use longer 3’UTRs with more scope for regulation, whereas undifferentiated cells use shorter, less regulated 3’UTRs. Here we describe gene-expression and alternative polyadenylation of human primary myocytes over a time course differentiation. Contrary to expectation, only minor changes to 3’-end choice were detected. To reconcile this finding with published differentiation data in the immortalized C2C12 myocyte cell line, a systematic comparison was undertaken. Less than half the genes differentially expressed in the immortalized model were recapitulated in primary cells, and of these, important metabolic states were either absent, underrepresented or regulated in the opposite direction. A new bioinformatic approach, developed to quantitate the degree of alternative polyadenylation between unrelated experiments demonstrated that alternative polyadenylation was reduced by ~50% with less than 1/10 of the genes that underwent alternative polyadenylation in C2C12 differentiation showing alternative processing in primary muscle differentiation. A possible explanation for this difference was a less pronounced down regulation of the cleavage and polyadenylation factors in the differentiation primary cell. In sum, the data promote the use of primary human myocytes to model muscle biogenesis over immortalized models that may not fully recapitulate human muscle development.

2024-03-12 | GSE168897 | GEO

Genome-wide profiling reveals cancer-related genes have switched alternative polyadenylation sites in colorectal cancer

Project description:Alternative polyadenylation (APA) is a kind of important post-transcriptional modification in eukaryotic cells. It plays considerable roles in many biological processes and diseases, such as cell differentiation, proliferation and cancer. Here, we used a high-throughput sequencing-based method 3T-seq to investigate the APA pattern in three colorectal cancer patients and explored the biological significance of APA modulation in all the three patients.

2018-02-02 | E-MTAB-6403 | biostudies-arrayexpress

Comprehensive profiling of rhizome-associated alternative splicing and alternative polyadenylation reveals in moso bamboo (Phyllostachys edulis)

Project description:Moso bamboo (Phyllostachys edulis) represents one of the fastest-spreading plants in the world, due in part to their well-developed rhizomes system. However, the post-transcriptional regulation mechanism has not been comprehensively studied for the development of rhizome system in bamboo. We therefore used single-molecule long-read sequencing technology to re-annotate the bamboo genome, and genome-wide identify alternative splicing (AS) and alternative polyadenylation (APA) in the rhizomes system. In total, 145,522 mapped full-length non-chimeric (FLNC) reads were analyzed, resulting in the correction of 2,241 mis-annotated genes and identification of 8,091 previously unannotated loci. Markedly, more than 42,280 contiguous exon connectivity were derived from full-length splicing isoforms, including a large number of AS events that associated with rhizome systems. In addition, we characterized 25,069 polyadenylation sites from 11,450 genes, 6,311 of which have APA sites. Further analysis of intronic polyadenylation revealed that LTR/Gypsy and LTR/Copia were two major transposable elements (TEs) within the intronic polyadenylation region. Furthermore, this study provided a quantitative altas of poly(A) usage and identified several hundreds of differential poly(A) sites in rhizome-root system using a combination of polyadenylation site sequencing (PAS-seq) and PacBio reads. Taken together, these results suggest that posttranscriptional regulation may potentially play vital role in the underground rhizome-root system.

2017-05-10 | GSE90517 | GEO

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