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TranscriptomicsThreonine-4 of the budding yeast RNAP II CTD couples transcription with Htz1-mediated chromatin remodeling
The C-terminal domain (CTD) of the largest subunit of RNA polymerase II (RNAP II) consists of repeated YSPTSPS heptapeptides and connects transcription with cotranscriptional events. Threonine-4 (Thr4) of the CTD repeats has been shown to function in histone mRNA 3'-end processing in chicken cells a...
ORGANISM(S): Saccharomyces cerevisiae 
2014-08-08 | E-GEOD-60181 | biostudies-arrayexpress
TranscriptomicsGlobal regulation of neuronal transcriptome by miR-9/tristetraprolin circuitry
Nervous system (NS) development relies on coherent up-regulation of extensive sets of genes in a precise spatiotemporal manner. How such transcriptome-wide effects are orchestrated at the molecular level remains an open question. Here we show that 3’-untranslated regions (3’UTRs) of multiple neurona...
ORGANISM(S): Mus musculus 
2015-04-01 | E-GEOD-61098 | 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
TranscriptomicsAnalysis of Caenorhabditis elegans intestinal gene expression and alternative polyadenylation using fluorescence-activated nuclei sorting (FANS) and 3' end deep sequencing (3'end-seq)
Caenorhabditis elegans is a major eukaryotic experimental system employed to unravel a broad range of cellular and biological processes. Despite the many advantages of C. elegans, biochemical approaches to study tissue-specific gene expression in postembryonic stages are challenging. Here we report ...
ORGANISM(S): Caenorhabditis elegans 
2011-12-01 | E-GEOD-32165 | biostudies-arrayexpress
TranscriptomicsTranscriptional activity regulates alternative cleavage and polyadenylation
Genes containing multiple polyadenylation (polyA) sites express mRNA isoforms with variable 3’ untranslated regions (3’UTRs). We found that short and long 3’UTR isoforms were relatively more abundant when genes were highly and lowly expressed, respectively, in human and mouse cells. Consistently, up...
ORGANISM(S): Mus musculus 
2011-08-15 | E-GEOD-26512 | biostudies-arrayexpress
TranscriptomicsRBBP6 isoforms regulate the human polyadenylation machinery and modulate expression of mRNAs with AU-rich 3' UTRs
Polyadenylation of mRNA precursors is mediated by a large multisubunit protein complex. Here we show that RBBP6 (retinoblastoma-binding protein 6), identified initially as an Rb- and p53-binding protein, is a component of this complex and functions in 3' processing in vitro and in vivo. RBBP6 associ...
ORGANISM(S): Homo sapiens 
2014-11-06 | E-GEOD-63036 | biostudies-arrayexpress
TranscriptomicsAnalysis of alternative cleavage and polyadenylation by 3' region extraction and deep sequencing
Alternative cleavage and polyadenylation (APA) generates diverse mRNA isoforms. We developed 3' region extraction and deep sequencing (3'READS) to address mispriming issues that commonly plague poly(A) site (pA) identification, and we used the method to comprehensively map pAs in the mouse genome. T...
ORGANISM(S): Mus musculus 
2012-12-17 | E-GEOD-42398 | biostudies-arrayexpress
TranscriptomicsAlternative cleavage and polyadenylation in spermatogenesis coordinates chromatin regulation and post-transcriptional control
Most mammalian genes display alternative cleavage and polyadenylation (APA). Previous studies have indicated preferential expression of APA isoforms with short 3’UTRs in testes. Here we show widespread shortening of 3’UTR by APA during the first wave of spermatogenesis in mouse, with 3’UTRs be...
ORGANISM(S): Mus musculus 
2016-01-11 | E-GEOD-73973 | biostudies-arrayexpress
TranscriptomicsA post-translational regulatory switch on UPF1 controls targeted mRNA degradation.
Nonsense-mediated mRNA decay (NMD) controls the quality of eukaryotic gene expression and also degrades physiologic mRNAs. How NMD targets are identified is incompletely understood. A central NMD factor is the ATP-dependent RNA helicase UPF1. Neither the distance in space between the termination cod...
ORGANISM(S): Homo sapiens 
2014-08-15 | E-GEOD-60045 | biostudies-arrayexpress
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