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Series GSE149204 Query DataSets for GSE149204
Status Public on Aug 26, 2022
Title Alternative cleavage and polyadenylation generates downstream uncapped RNA isoforms with translation potential
Organism Homo sapiens
Experiment type Expression profiling by high throughput sequencing
Other
Summary Here, we uncovered the expression of thousands of previously unnoticed 5’-Uncapped and Polyadenylated Transcripts (5’UPTs). We show that 5’UPTs appear downstream of APA points that occur within the coding and intronic regions of their host genes. Furthermore, 5’UPTs are marked with N6-methyladenosine (m6A) at their 5’ termini, and this modification is linked to their expression. We also demonstrate that 5’UPTs are strongly enriched in polysomal RNA fractions, suggesting protein production capacity. In addition, we examined the expression of 5’UPTs in the biological context of T cell activation, known to induce APA usage. In line with a causal link between APA and 5’UPTs, T cell activation induced 5’UPTs expression and their incorporation into heavy polysomal fractions. Our findings indicate that APA does not only generates shorter upstream mRNA isoforms, but is also responsible for the generation of downstream uncapped and polyadenylated transcripts that possess potential translational capacity.
 
Overall design Examination of mRNA levels and cleavage across CDS within transcripts in U2OS, 293, HeLa cells and mouse T-cells (2/3 replicates each).
 
Contributor(s) Malka Y, Alkan F, Ju S, Körner P, Pataskar A, Shulman E, Loayza-Puch F, Champagne J, Wenzel C, Faller W, Elkon R, Lee C, Agami R
Citation(s) 36270248
Submission date Apr 23, 2020
Last update date Oct 24, 2022
Contact name Pierre-Rene Körner
Organization name Netherlands Cancer Institute (NKI)
Department Oncogenomics
Street address Plesmanlaan 121
City Amsterdam
ZIP/Postal code 1066CX
Country Netherlands
 
Platforms (2)
GPL16791 Illumina HiSeq 2500 (Homo sapiens)
GPL24106 MinION (Homo sapiens)
Samples (70)
GSM4492160 Polysomal_RNA_sequencing_Control_1.fastq.gz
GSM4492162 Polysomal_RNA_sequencing_Control_2.fastq.gz
GSM4492164 RNA_sequencing_Control_for TEX_XRN1_1.fastq.gz
Relations
BioProject PRJNA627652
SRA SRP258098

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE149204_3prime_htseq_readcounts.txt.gz 342.8 Kb (ftp)(http) TXT
GSE149204_3prime_sequencing_readcounts.txt.gz 263.9 Kb (ftp)(http) TXT
GSE149204_5prime_htseq_readcounts.txt.gz 285.5 Kb (ftp)(http) TXT
GSE149204_5prime_sequencing_readcounts.txt.gz 285.6 Kb (ftp)(http) TXT
GSE149204_Nanopore_Readcounts.txt.gz 263.0 Kb (ftp)(http) TXT
GSE149204_Nanopore_sequencing_readcounts.txt.gz 263.0 Kb (ftp)(http) TXT
GSE149204_Polysome_htseq_readcounts.txt.gz 501.7 Kb (ftp)(http) TXT
GSE149204_Polysome_sequencing_readcounts.txt.gz 267.2 Kb (ftp)(http) TXT
GSE149204_RAW.tar 18.1 Gb (http)(custom) TAR (of BW, PSL)
GSE149204_Ribosome_htseq_readcounts.txt.gz 286.6 Kb (ftp)(http) TXT
GSE149204_Ribosome_sequencing_readcounts.txt.gz 251.1 Kb (ftp)(http) TXT
GSE149204_Total_RNAs_Readcounts.txt.gz 2.1 Mb (ftp)(http) TXT
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Raw data are available in SRA
Processed data are available on Series record
Processed data provided as supplementary file

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