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GenomicsGenome-wide distribution of RNA-DNA hybrids identifies RNase H targets in tRNA genes, retrotransposons and mitochondria
During transcription the nascent RNA can invade the DNA template, forming extended RNA-DNA duplexes (R-loops). Here we employ ChIP-seq in strains expressing or lacking RNase H to map targets of RNase H activity throughout budding yeast genome. In wild-type strains, R-loops were readily detected over...
ORGANISM(S): Saccharomyces cerevisiae 
2014-11-03 | E-GEOD-53420 | biostudies-arrayexpress
ProteomicsProteomic profiling of RNase III-dependent asRNA regulation in E. coli
In an effort to determine if the RNase III-dependent asRNA regulation had an effect on protein production in E. coli we conducted two TMT 6-plex experiments comparing cultures of wildtype E. coli, rnc-14, rnc-38, hfq in the stationary and exponential phase.
ORGANISM(S): Escherichia coli 
2020-06-18 | PXD011180 | Pride
E. coli Antisense rnas Rnase iii 
TranscriptomicsTranscriptome Wide Annotation of Eukaryotic RNase III Reactivity and Degradation Signals
Here we present complete genomic and biochemical annotations of the signals required for RNA degradation by the dsRNA specific ribonuclease III (Rnt1p) and examine its impact on transcriptome stability. Rnt1p cleavage signals are randomly distributed in the yeast genome and encompass wide variety of...
ORGANISM(S): Saccharomyces cerevisiae 
2015-02-16 | E-GEOD-57390 | biostudies-arrayexpress
TranscriptomicsTranscriptome Wide Annotation of Eukaryotic RNase III Reactivity and Degradation Signals
Here we present complete genomic and biochemical annotations of the signals required for RNA degradation by the dsRNA specific ribonuclease III (Rnt1p) and examine its impact on transcriptome stability. Rnt1p cleavage signals are randomly distributed in the yeast genome and encompass wide variety of...
ORGANISM(S): Saccharomyces cerevisiae 
2015-02-16 | E-GEOD-57448 | biostudies-arrayexpress
TranscriptomicsTranscriptome wide annotation of eukaryotic RNase III reactivity and degradation signals
Here we present complete genomic and biochemical annotations of the signals required for RNA degradation by the dsRNA specific ribonuclease III (Rnt1p) and examine its impact on transcriptome expression. Rnt1p cleavage signals are randomly distributed in the yeast genome and encompass wide variety o...
ORGANISM(S): Saccharomyces cerevisiae 
2015-02-16 | E-GEOD-57447 | biostudies-arrayexpress
GenomicsBacterial RNase III cleaves long dsRNA at preferred sites
Bacterial RNase III cleaves long dsRNA at preferred sites
PRJNA491502 | ENA
TranscriptomicsIn vivo cleavage rules and target repertoire of RNase III in Escherichia coli
In this study we generated 5'P libraries in wt and RNAse III mutant strains, grown to exponential and stationary phases. Libraries that retain short RNA fragments were also generated in both growth phases. After sequencing by Illumina NextSeq 500 system, reads were mapped to E. coli genome NC_00091...
ORGANISM(S): Escherichia coli str. K-12 substr. MG1655 
2018-09-30 | E-MTAB-6704 | biostudies-arrayexpress
GenomicsIdentification of RNase III cleavage sites in Escherichia coli
Identification of RNase III cleavage sites in Escherichia coli
PRJEB26394 | ENA
TranscriptomicsGene expression profiling of constitutively competent comR and proQ mutants and RNase R (rnr) mutant of L. pneumophila
Bacterial competence is a genetically programmed process that is triggered as a response to environmental stimuli. DNA uptake from the extracellular milieu by competence requires the expression of a complex machinery composed of a competence pseudopilus and a DNA translocase. In L. pneumophila, it ...
ORGANISM(S): Legionella pneumophila 
2010-05-20 | E-GEOD-12796 | biostudies-arrayexpress
TranscriptomicsTranscriptome Wide Annotation of Eukaryotic RNase III Reactivity and Degradation Signals
This SuperSeries is composed of the SubSeries listed below. Refer to individual Series
ORGANISM(S): Saccharomyces cerevisiae 
2015-02-16 | E-GEOD-57450 | biostudies-arrayexpress
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