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TranscriptomicsGenome?wide analysis of pre?mRNA 3' end processing reveals a decisive role of human cleavage factor I in the regulation of 3' UTR length: A-seq
Through alternative polyadenylation, human mRNAs acquire longer or shorter 3' untranslated regions, the latter typically associated with higher transcript stability and increased protein production. To understand the dynamics of polyadenylation site usage, we mapped transcriptome?wide both binding s...
ORGANISM(S): Homo sapiens 
2012-05-15 | E-GEOD-37037 | biostudies-arrayexpress
TranscriptomicsGenome-wide analysis of pre-mRNA 3' end processing reveals a decisive role of human cleavage factor I in the regulation of 3' UTR length: CLIP
Through alternative polyadenylation, human mRNAs acquire longer or shorter 3' untranslated regions, the latter typically associated with higher transcript stability and increased protein production. To understand the dynamics of polyadenylation site usage, we mapped transcriptome‐wide both binding s...
ORGANISM(S): Homo sapiens 
2012-05-15 | E-GEOD-37398 | biostudies-arrayexpress
TranscriptomicssiRNA profiling of HeLa cells reveals strand-specific 5-O-methylation of siRNA duplexes controls guide strand selection and targeting specificity.
Small interfering RNAs (siRNAs) and microRNAs (miRNAs) guide catalytic sequence-specific cleavage of fully or nearly fully complementary target mRNAs or control translation and/or stability of many mRNAs that share 6-8 nucleotides (nt) of complementarity to the siRNA and miRNA 5' end. siRNA- and miR...
ORGANISM(S): Homo sapiens 
2008-06-11 | E-GEOD-10960 | biostudies-arrayexpress
TranscriptomicsThe systematic shortening of 3’ UTRs has limited influence on the relative change in protein abundance in proliferating cells
Alternative polyadenylation is an important cellular mechanism that enables generation of mRNA isoforms that differ in their 3' untranslated regions (3' UTRs) and consequently in their susceptibility to miRNA and RNA binding protein mediated regulation. A dramatic change in polyadenylation site usa...
ORGANISM(S): Homo sapiens 
2014-09-25 | E-GEOD-54950 | biostudies-arrayexpress
TranscriptomicsConserved generation of short products at piRNA loci
We analyzed small RNAs from three mammalian species, and found that in all these species piRNA-directed targeting is accompanied by the generation of short sequences that have a very precisely defined length and a specific spatial relationship with the guide piRNAs. small RNA-seq of testes lysate (b...
ORGANISM(S): Mus musculus 
2011-03-07 | E-GEOD-26160 | biostudies-arrayexpress
UnknownSplice variation in mouse full-length cDNAs identified by mapping to the mouse genome.
Not available
S-EPMC186662 | biostudies-literature
GenomicsPAPD5, a noncanonical poly(A) polymerase with an unusual RNA-binding motif [PAR-CLIP]
PAPD5 is one of the seven members of non-canonical poly(A) polymerases in human cells. There are previous reports about polyadenylation dependent degradation of pre-ribosomal RNAs and uridylation dependent degradation of histone mRNAs in vivo. In this study, we observed polyadenylation but not polyu...
ORGANISM(S): Homo sapiens 
2012-04-02 | E-GEOD-36987 | biostudies-arrayexpress
TranscriptomicsTranslation-dependent displacement of UPF1 from coding sequences causes its enrichment in 3M-bM-^@M-^Y UTRs
The RNA helicase UPF1 is best known for its key function in mRNA nonsense-mediated mRNA decay (NMD), but has also been implicated in additional mRNA turnover mechanisms, telomere homeostasis, and DNA replication. In NMD, UPF1 recruitment to target mRNAs is thought to occur through interaction with r...
ORGANISM(S): Homo sapiens 
2013-06-20 | E-GEOD-47976 | biostudies-arrayexpress
TranscriptomicsCleavage Factor Im as a key regulator of 3’ UTR length
In eukaryotes, the 3' ends of RNA polymerase II-generated transcripts are made in the majority of cases by site-specific endonucleolytic cleavage, followed by the addition of a poly(A) tail. By alternative polyadenylation, a gene can give rise to multiple mRNA isoforms that differ in the length of t...
ORGANISM(S): Homo sapiens 
2012-10-30 | E-GEOD-40137 | biostudies-arrayexpress
TranscriptomicsA quantitative analysis of CLIP methods for identifying binding sites of RNA-binding proteins (CLIP)
Crosslinking and immunoprecipitation (CLIP) is increasingly used to map transcriptome-wide binding sites of RNA-binding proteins (RBPs). We developed a method for CLIP data analysis and applied it to compare 254 nm CLIP with PAR-CLIP, which involves crosslinking of photoreactive nucleotides with 365...
ORGANISM(S): Homo sapiens 
2011-05-15 | E-GEOD-28859 | biostudies-arrayexpress
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