Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

A comprehensive map of alternative polyadenylation in African American and European American lung cancer patients

ABSTRACT: We report the application of a novel method and analysis pipeline that sequences 3’end -enriched RNA to comprehensively map the APA landscape in lung cancer. The goals of this study are to identify the functional role of APA in determining transcriptomic heterogeneity in lung cancer and population differences in APA.

ORGANISM(S): Homo sapiens

PROVIDER: GSE174330 | GEO | 2021/05/13

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

A comprehensive map of alternative polyadenylation in African American and European American lung cancer patients.

Project description:Deciphering the post-transcriptional mechanisms (PTM) regulating gene expression is critical to understand the dynamics underlying transcriptomic regulation in cancer. Alternative polyadenylation (APA)-regulation of mRNA 3'UTR length by alternating poly(A) site usage-is a key PTM mechanism whose comprehensive analysis in cancer remains an important open challenge. Here we use a method and analysis pipeline that sequences 3'end-enriched RNA directly to overcome the saturation limitation of traditional 5'-3' based sequencing. We comprehensively map the APA landscape in lung cancer in a cohort of 98 tumor/non-involved tissues derived from European American and African American patients. We identify a global shortening of 3'UTR transcripts in lung cancer, with notable functional implications on the expression of both coding and noncoding genes. We find that APA of non-coding RNA transcripts (long non-coding RNAs and microRNAs) is a recurrent event in lung cancer and discover that the selection of alternative polyA sites is a form of non-coding RNA expression control. Our results indicate that mRNA transcripts from EAs are two times more likely than AAs to undergo APA in lung cancer. Taken together, our findings comprehensively map and identify the important functional role of alternative polyadenylation in determining transcriptomic heterogeneity in lung cancer.

| S-EPMC8460807 | biostudies-literature

A comprehensive map of alternative polyadenylation in African American and European American lung cancer patients

Project description:A comprehensive map of alternative polyadenylation in African American and European American lung cancer patients

| PRJNA729468 | ENA

CFIm25 links alternative polyadenylation to glioblastoma tumour suppression

Project description:Purpose: To identify all of the APA targets of CFIm25 on a global scale and develop an algorithm that can idenitify APA events from standard RNA-seq data Methods: RNA from HeLa cells treated with control siRNA and CFIm25 siRNA were subject to RNA-Seq. Using a custom-designed algorithm to mine RNA-seq data for novel APA events regulated by CFIm25. Results: We identified over 1,400 genes with shortened 3’UTRs after CFIm25 knockdown. Importantly, we show that as a consequence of APA, many of these mRNAs have greatly enhanced protein expression due to the loss of destabilizing features within the 3’UTR. Conclusions: Our study underscored the critical function of the CFIm complex members in governing APA and establish a previously unknown link between APA and metabolic pathways important for tumor progression. Hela cell line mRNA profiles of control treated and CFIm25 Knockdown were generated by RNA-Seq using Illumina GAIIx.

2014-05-15 | E-GEOD-42420 | biostudies-arrayexpress

The transcriptome-wide alternative polyadenylation alteration in herbal formula YYJD-induced activity in A549 lung adenocarcinoma cells

Project description:The Herbal Formula YYJD inhibit migration and invasion of lung adenocarcinoma cells, we aims to profile a comprehensive alternative polyadenylation (APA) dynamic pattern of Lung Adenocarcinoma Cells under YYJD treatment unsing 3T-seq method.

2019-10-31 | E-MTAB-8151 | biostudies-arrayexpress

Cleavage Factor 25 Deregulation Contributes to Pulmonary Fibrosis through Alternative Polyadenylation

Project description:The purpose of this experiment is to identify the APA targets of CFIm25 in human lung fibroblasts. Following the knockdown of CFIm25 in normal human lung fibroblasts, we identified 808 genes with shortened 3’UTRs, including those involved in the transforming growth factor-beta signaling pathway, the Wnt signaling pathway, and cancer pathways.

2018-05-01 | GSE108352 | GEO

Arginine methylation regulates widespread alternative polyadenylation

Project description:Alternative polyadenylation (APA) has recently been recognized as a universal mechanism for gene regulation, but it remains unclear how APA is controlled. Here we report that the Arabidopsis thaliana Protein Arginine Methyltransferase 10 (AtPRMT10) regulates global APA with its protein partner HLP1, a conserved hnRNP A/B protein. HLP1 binds preferentially to A-rich and U-rich cis-elements around polyadenylation sites, thereby linking AtPRMT10 to the control of APA through protein-protein interactions. AtPRMT10 mutations cause significant proximal-to-distal poly(A) site shifts largely overlapping with those in hlp1-1 mutants. Proximal polyadenylation is maintained by AtPRMT10-directed methylation and is mediated in part by methylation of HLP1 at specific arginine residues. Our findings demonstrate that arginine methylation of an RNA-binding protein adds a novel layer of regulation to widespread alternative polyadenylation.

2019-01-01 | GSE69904 | GEO

CFIm25 links alternative polyadenylation to glioblastoma tumour suppression

2014-05-15 | GSE42420 | GEO

Saccharomyces Cerevisiae Modulates Cell Growth via Alternative Polyadenylation

Project description:Dynamic 3' UTRs variation mediated by APA is one of the major determinants of post-transcriptional regulation. Though some progress has been made in understanding its function in mammalian cells, the role of APA in the model organism S. cerevisiae, which lack of miRNAs, is a matter of debate. Unlike mammalian cells, most of S. cerevisiae genes tend to express mRNAs with longer 3′ UTRs in proliferating cells. Further analysis demonstrated that 3' UTRs length and mRNA expression were negatively correlated in different growth conditions. By combining APA sequencing and polysome profiling, we observed that mRNA isoforms with shorter 3' UTRs with a higher translational efficiency in proliferating cells but not quiescent. Further analysis demonstrated that different function genes translational efficiency control by APA are differential modulated and closely related with growth conditions. Furthermore, we observed the correlation between asRNAs and translational efficiency of different length 3′ UTR transcripts, suggests asRNAs may involve in the regulation of translational efficiency mediated by APA. Thus, this study indicates conservation of molecular function of APA in different Eukaryotes, highlighting the importance of APA in regulating gene function.

2024-09-15 | GSE242763 | GEO

Cancer-specific alternative polyadenylation shapes tumor phenotypes in vivo

Project description:Alternative polyadenylation (APA) is strikingly dysregulated in many cancers. Although APA dysregulation is frequently associated with poor prognosis, the biological importance of most APA events remains unclear simply because few have been functionally studied. Here, we performed a CRISPR/Cas9-based screen to assess individual APA events’ contributions to tumor growth in vivo. Forcing use of specific polyadenylation sites altered mRNA and protein levels to modify mouse melanoma growth in an immunocompetent host. Our screen highlighted APA events of potential clinical relevance. For example, forced Atg7 3′ UTR lengthening in mouse melanoma reduced ATG7 protein levels and tumor immune infiltration; similarly, in human melanoma, a long ATG7 3′ UTR and low mRNA levels were significantly associated with reduced anti-tumor T cell activity and failure of immune checkpoint blockade. Our data demonstrate that cancer-associated APA plays a causative role in tumorigenesis and motivate future studies of the therapeutic potential of modulating APA.

2023-06-01 | GSE212278 | GEO

Dynamic Landscape of Alternative Polyadenylation during Retinal Development

Project description: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. Here we conducted global analysis of APA during mouse retinal development, and identified stage-specific polyadenylation (pA) sites that are enriched for genes critical for retinal development and visual perception. Moreover, we demonstrated 3’UTR lengthening and increased usage of intronic pA sites over development that would result in gaining many different RBP (RNA binding protein) and miRNA target sites. Furthermore, we showed that a considerable number of polyadenylated lncRNAs are co-expressed with protein-coding genes involved in retinal development and functions. Together, our data indicate that APA is highly and dynamically regulated during retinal development and maturation, suggesting that APA may serve as a crucial mechanism of gene regulation underlying the delicate process of CNS development.

2017-04-09 | GSE80206 | GEO

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data