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TranscriptomicsExtensive alternative polyadenylation during zebrafish development
The post-transcriptional fate of messenger RNAs (mRNAs) is largely dictated by their 3' untranslated regions (3'UTRs), which are defined by cleavage and polyadenylation (CPA) of pre-mRNAs. We used poly(A)-position profiling by sequencing (3P-Seq) to map poly(A) sites at eight developmental stages an...
ORGANISM(S): Danio rerio 
2012-06-17 | E-GEOD-37453 | biostudies-arrayexpress
TranscriptomicsProgressive lengthening of 3' untranslated regions of mRNAs by alternative polyadenylation during mouse embryonic development
The 3' untranslated regions (3' UTRs) of mRNAs contain cis-acting elements for posttranscriptional regulation of gene expression. Here, we report that mouse genes tend to express mRNAs with longer 3' UTRs as embryonic development progresses. This global regulation is controlled by alternative polyad...
ORGANISM(S): Mus musculus 
2010-08-31 | E-GEOD-23871 | biostudies-arrayexpress
TranscriptomicsPaf1C plays novel subunit-specific roles in alternative cleavage and polyadenylation
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 bo...
ORGANISM(S): Mus musculus 
2016-01-15 | E-GEOD-72574 | biostudies-arrayexpress
TranscriptomicsThe genetics and regulatory logic of alternative polyadenylation in human lymphoblastoid cells
We set out to investigate genomic mechanisms by which alternative polyadenylation impacts gene expression and its variation across genetically distinct human individuals. We used 3’-end RNA-seq to maximize genome coverage and precision of transcript end positions, and to measure quantitative express...
ORGANISM(S): Homo sapiens 
2012-08-27 | E-GEOD-33154 | biostudies-arrayexpress
TranscriptomicsGenome-wide gene expression analysis in Thoc5- and CFIm68-depleted HeLa cells
We found that CFIm68, a mRNA cleavage and polyadenylation factor implicated for alternative polyadenylation site choice, was co-purified with Thoc5, a component of human THO/TREX. Microarray analysis using human HeLa cells reveals knockdown of Thoc5 affects the expression of a subset of non-heat sho...
ORGANISM(S): Homo sapiens 
2013-05-21 | E-GEOD-42327 | biostudies-arrayexpress
TranscriptomicsCoupling between alternative polyadenylation and alternative splicing is limited to terminal introns
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 alternat...
ORGANISM(S): Homo sapiens 
2016-03-14 | E-GEOD-79157 | biostudies-arrayexpress
TranscriptomicsCFIm25 links alternative polyadenylation to glioblastoma tumour suppression
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-s...
ORGANISM(S): Homo sapiens 
2014-05-15 | E-GEOD-42420 | biostudies-arrayexpress
GenomicsMouse alternative polyadenylation
Divergence of alternative polyadenylation in mouse
PRJEB15336 | ENA
TranscriptomicsCPEB inducible knock-down in a H.D. Myz cell line
Messenger RNA stability, localization, and translation are largely determined by sequences in their 3M-bM-^@M-2 untranslated regions (3M-bM-^@M-^YUTRs), which recruit regulatory proteins and RNAs. More than half of the mammalian genes generate multiple mRNA isoforms differing in their 3M-bM-^@M-2UTR...
ORGANISM(S): Homo sapiens 
2013-02-25 | E-GEOD-32440 | biostudies-arrayexpress
TranscriptomicsAlternative Isoform Regulation in Human Tissue Transcriptomes
Through alternative processing of pre-mRNAs, individual mammalian genes often produce multiple mRNA and protein isoforms that may have related, distinct or even opposing functions. Here we report an in-depth analysis of 15 diverse human tissue and cell line transcriptomes based on deep sequencing of...
ORGANISM(S): Homo sapiens 
2008-09-30 | E-GEOD-12946 | biostudies-arrayexpress
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