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TranscriptomicsC. elegans piRNAs are processed from capped-small RNAs transcribed at promoters throughout the genome
Piwi-interacting (pi) RNAs are a class of germline-expressed small RNAs that have been linked to epigenetic programming in metazoa. C. elegans piRNAs known as 21U-RNAs are defined by more than 15,000 genome-encoded species. To explore the origin of 21U-RNAs we employed methods to enrich the 5' ends ...
ORGANISM(S): Mus musculus 
2012-12-22 | E-GEOD-40053 | biostudies-arrayexpress
TranscriptomicspiRNAs initiate an epigenetic memory of non-self RNA in the C. elegans germline.
Organisms exhibit a fascinating array of gene-silencing pathways, which have evolved in part, to confront invasive nucleic acids such as transposons and viruses. A key question raised by the existence of these pathways is how do they distinguish M-bM-^@M-^\selfM-bM-^@M-^] from M-bM-^@M-^\non-selfM-b...
ORGANISM(S): Caenorhabditis elegans 
2012-07-17 | E-GEOD-38724 | biostudies-arrayexpress
TranscriptomicsThe Translin-TRAX complex/C3PO is a ribonuclease in tRNA processing
The endogenous RNA substrates of Translin-TRAX complexes (also known as C3POs) and how they regulate diverse biological processes remain unknown. Here we show that Translin and TRAX do not play a significant role in RNAi in the filamentous fungus Neurospora crassa. Instead, the Neurospora C3PO compl...
ORGANISM(S): Neurospora crassa 
2012-07-30 | E-GEOD-38334 | biostudies-arrayexpress
TranscriptomicsHigh throughput sequencing of endogenous small RNAs from AGO pathway mutants
High-throughput pyrosequencing of endogenous small RNAs from >95% male enriched populations of alg-3(tm1155);alg-4(ok1041);fog-2(q71) and fog-2(q71) worms as well as purified spermatids from fem-3(q20) adult worms. Gametogenesis is thermosensitive in numerous metazoa ranging from worms to man. In C...
ORGANISM(S): Caenorhabditis elegans 
2010-02-24 | E-GEOD-18729 | biostudies-arrayexpress
TranscriptomicsHigh throughput sequencing of mutants in the WAGO pathway
Diverse naturally-occurring small RNA species interact with Argonaute proteins to mediate sequence-specific regulation in animals. In addition to micro-RNAs (miRNAs), which collectively regulate thousands of target mRNAs, other endogenous small RNA species include the Piwi-associated piRNAs that are...
ORGANISM(S): Caenorhabditis elegans 
2009-10-01 | E-GEOD-18215 | biostudies-arrayexpress
TranscriptomicsSequential rounds of RNA-dependent RNA transcription drive endogenous small-RNA biogenesis in ERGO-1/Argonaute pathway
Argonaute (AGO) proteins interact with distinct classes of small RNAs to direct multiple regulatory outcomes. In many organisms, including plants, fungi and nematodes, cellular RNAdependent RNA polymerases (RdRPs) utilize AGO targets as templates for amplification of silencing signals. Here, we show...
ORGANISM(S): Caenorhabditis elegans 
2010-02-25 | E-GEOD-18714 | biostudies-arrayexpress
TranscriptomicsDiverse pathways generate microRNA-like RNAs and Dicer-independent small interfering RNAs in fungi
A variety of small RNAs, including the Dicer-dependent miRNAs and the Dicer-independent Piwi-interacting RNAs, associate with Argonaute family proteins to regulate gene expression in diverse cellular processes. These two species of small RNA have not been found in fungi. Here, by analyzing small RN...
ORGANISM(S): Neurospora crassa 
2010-07-01 | E-GEOD-21175 | biostudies-arrayexpress
TranscriptomicsInfluenza A virus preferentially snatches non-coding RNA caps
Influenza A virus (IAV) lacks the enzyme for adding 5’ caps to its RNAs, and thus snatches the 5’ ends of host capped RNAs to prime transcription. Neither the preference of the host RNA sequences snatched, nor the effect of “cap-snatching” on host processes has been completely defined. Previ...
ORGANISM(S): Homo sapiens 
2015-11-23 | E-GEOD-67493 | biostudies-arrayexpress
TranscriptomicsSuppression of pervasive noncoding transcription in embryonic stem cells by esBAF
Approximately 75% of the human genome is transcribed, the majority of which does not encode protein. However, most noncoding RNA (ncRNA) is rapidly degraded after transcription, and relatively few have established functions, questioning the significance of this observation. Here we show that esBAF, ...
ORGANISM(S): Mus musculus 
2015-02-12 | E-GEOD-57170 | biostudies-arrayexpress
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