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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
TranscriptomicsMIWI and piRNA-mediated cleavage of messenger RNAs in mouse testes
The piRNA machinery is known for its role in mediating epigenetic silencing of transposons. Recent studies suggest that this function also involves piRNA-guided cleavage of transposon-derived transcripts. As many piRNAs also appear to have the capacity to target diverse mRNAs, this raises the intrig...
ORGANISM(S): Mus musculus 
2015-04-09 | E-GEOD-67683 | biostudies-arrayexpress
TranscriptomicsThe DSIF subunits Spt4 and Spt5 have several unexpected, distinct roles in regulating immunoglobulin class switch recombination
Class-switch recombination (CSR), induced by activation-induced cytidine deaminase, can be divided into two phases: DNA cleavage of the switch (S) regions, and the joining of the cleaved ends of the different S regions. Here, we show that the DSIF complex (Spt4 and Spt5), a transcription elongation ...
ORGANISM(S): Mus musculus 
2013-10-22 | E-GEOD-33206 | biostudies-arrayexpress
TranscriptomicsRNA Polymerase II CoTC Terminator Elements in the Human Genome (CstF-64 CLIP-seq from the nucleoplasm)
CLIP-seq experiment using immunoprecipitation with CstF-64 antibody from the nucleoplasmic fraction, was employed to specifically target pre-mRNAs that are released from the DNA template before cleavage at the poly(A) site. This lead to the identification of genes that utilize the co-transcriptional...
ORGANISM(S): Homo sapiens 
2013-02-14 | E-MTAB-1375 | biostudies-arrayexpress
ProteomicsFunctional surface expression of immunoglobulin cleavage systems in a candidate Mycoplasma vaccine chassis
The Mycoplasma Immunoglobulin Binding/Protease (MIB-MIP) system is a candidate virulence factor present in multiple pathogenic species of the Mollicutes, including the fast-growing species Mycoplasma feriruminatoris. The MIB-MIP system cleaves the heavy chain of host immunoglobulins, hence affecting...
ORGANISM(S): Mycoplasma feriruminatoris 
2024-06-28 | PXD053286 | Pride
Genome transplantation Immunoglobulin cleavage Mesomycoplasma hyorhinis Oric-plasmids Mycoplasma feriruminatoris 
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
UnknownRelaxed cleavage specificity of an immunoglobulin A1 protease from Neisseria meningitidis.
Not available
S-EPMC1932897 | biostudies-literature
TranscriptomicsPachytene piRNAs target endogenous mRNAs for silencing during meiosis
During embryonic germ cell development in mice, transposon-enriched, piwi-interacting RNAs (piRNAs) guide MILI and MIWI2 to direct silencing of potentially active mobile element families. In contrast, we know much less about the function of the highly abundant and extremely diverse class of piRNAs, ...
ORGANISM(S): Mus musculus 
2015-05-22 | E-GEOD-64138 | 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
UnknownU1A inhibits cleavage at the immunoglobulin M heavy-chain secretory poly(A) site by binding between the two downstream GU-rich regions.
Not available
S-EPMC434241 | biostudies-literature
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