Small RNA expression in swi6 mutants or dcr1 delta fission yeast Schizosaccharomyces pombe
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ABSTRACT:
ORGANISM(S): Schizosaccharomyces pombe
SUBMITTER: Tim Roloff
PROVIDER: E-GEOD-42849 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
Similar Datasets
Project description:Small RNA expression in swi6 mutants, dcr1 delta, and wild type fission yeast Schizosaccharomcyces pombe
2013-07-20 | GSE42849 | GEO
Project description:Small RNA produced by Dicer (Dcr1) are used to map dsRNA in wild-type strain and a xrn1-delta mutant of S. cerevisiae, inactivated for the cytoplasmic 5'-3' RNA decay pathway. Small RNA sequencing in wild-type and xrn1-delta strains of S. cerevisiae, with or without reconstituted RNAi pathway.
2015-08-11 | E-GEOD-64090 | biostudies-arrayexpress
Project description:The Dicer ribonuclease III (RNase III) enzymes process long double-stranded RNA (dsRNA) into the small interfering RNAs (siRNAs) that direct RNA interference. Here, we describe the structure and activity of a catalytically active fragment of Kluyveromyces polysporus Dcr1, which represents the noncanonical Dicers found in budding yeast. The crystal structure reveals a homodimer that resembles bacterial RNase III but includes a novel N-terminal domain and newly identified catalytic residues conserved throughout eukaryotic RNase III enzymes. Biochemical analyses show that Dcr1 dimers bind cooperatively along the dsRNA substrate and cleave at precise intervals based on the distance between consecutive active sites. Thus, unlike canonical Dicers, which successively remove siRNA duplexes from the dsRNA termini, Dcr1 initiates processing in the interior and works outward. The distinct mechanism of budding-yeast Dicers establishes a novel paradigm for natural protein-based molecular rulers and imparts substrate preferences with ramifications for biological function. High-throughput sequencing of small RNAs generated by in vitro processing of long dsRNA using Kluyveromyces polysporus Dicer
2011-05-11 | E-GEOD-29168 | biostudies-arrayexpress
Project description:Small RNA expression in swi6 mutants or dcr1 delta fission yeast Schizosaccharomyces pombe
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Project description:The mRNA profiles of [delta]rgsA, [delta]nopA, [delta]rgdA ([delta]swi4), [delta]mbpA ([delta]swi6) mutants and wild-type (AF293) of A. fumigatus.
2019-12-17 | GSE123744 | GEO
Project description:We have established a novel sequencing approach to characterise usage of replicative DNA polymerases in S. pombe. This approach allows us to determine the roles of DNA polymerase delta and epsilon in lagging strand and leading strand DNA synthesis, respectively in genome-wide scale. Utilising the dataset of usage of these polymerases, we also successfully identified DNA replication initiation sites at high resolution. Furthermore, our informatics analysis establishes genome-wide datasets of fork direction rates, replication timing and the probability of replication termination. We mapped ribonucleotide-incorporation by the mutated DNA polymerase delta and epsilon at single-nucleotide resolution and subsequent informatics analysis was performed to generate datasets listed here.
2015-02-03 | E-GEOD-62108 | biostudies-arrayexpress
Project description:Dicer proteins function in RNA interference (RNAi) pathways by generating small RNAs (sRNAs). Here we report the solution structure of the C-terminal domain of Schizosaccharomyces pombe Dicer (Dcr1). The structure reveals an unusual double-stranded RNA binding domain (dsRBD) fold embedding a novel zinc-binding motif that is conserved among dicers in yeast. Although the C-terminal domain of Dcr1 still binds nucleic acids, this property is dispensable for proper functioning of Dcr1. In contrast, disruption of zinc coordination renders Dcr1 mainly cytoplasmic and leads to remarkable changes in gene expression and loss of heterochromatin assembly. In summary, our results reveal novel insights into the mechanism of nuclear retention of Dcr1 and raise the possibility that this new class of dsRBDs might generally function in nucleo-cytoplasmic trafficking and not substrate binding. The C-terminal domain of Dcr1 constitutes a novel regulatory module that might represent a potential target for therapeutic intervention with fungal diseases. Small RNA libraries from total RNA isolations of wild-type, dcr1Delta, dcr1SHSS, and dcr1Deltaloop2 cells and subjected to high-throughput sequencing.
2011-09-22 | E-GEOD-30549 | biostudies-arrayexpress
Project description:small RNA profiles of 6 human tonsillar B cell populatios (naive B cells, pre-germinal center B cells, centrocytes, centroblasts, memory B cells, and plasma cells) were determined by deep sequencing. These samples were compared to mouse developing lymphocytes, various hematopoietic cell lineages, and tissues. small RNA expression profiles of 6 well defined B cell populations isolated from human tonsils.
2010-07-23 | E-GEOD-23090 | biostudies-arrayexpress
Project description:Canonical microRNAs (miRNAs) require two processing steps: the first by the Microprocessor, a complex of DGCR8 and Drosha, and the second by Dicer. dgcr8delta/delta mouse embryonic stem cells (mESCs) have less severe phenotypes than dicer1delta/delta mESCs, suggesting a physiological role for Microprocessor-independent, Dicer-dependent small RNAs. To identify these small RNAs with unusual biogenesis, we performed high-throughput sequencing from wild type, dgcr8delta/delta, and dicer1delta/delta mESCs. Several of the DGCR8-independent, Dicer-dependent RNAs were non-canonical miRNAs. These derived from mirtrons and a newly identified subclass of miRNA precursors, which appears to be the endogenous counterpart of short hairpin RNAs (shRNAs). Our analyses also revealed endogenous siRNAs resulting from Dicer cleavage of long hairpins, the vast majority of which originated from one genomic locus with tandem, inverted short interspersed nuclear elements (SINEs). Our results extend the known diversity of mammalian small-RNA generating pathways and show that mammalian siRNAs exist in tissues outside of oocytes. Small RNAs were sequenced from wt, dgcr8(-), and dicer(-) mouse ES cells and the frequencies of small RNA types compared between the three. This record includes Illumina-platform-generated datasets from all three samples and 454-platform-generated datasets from wt and dgcr8(-) samples. [raw data files are unavailable]
2008-09-09 | E-GEOD-12521 | biostudies-arrayexpress
Project description:Small RNA diversity and function has been widely characterized in various tissues of the sporophytic generation of the angiosperm model Arabidopsis thaliana. In contrast, there is limited knowledge about small RNA diversity and their roles in developing male gametophytes. We thus carried out small RNA sequencing on RNA isolated from four stages of developing Arabidopsis thaliana pollen. Spores from 4 stages of pollen development (UNM: Uninucleate microspore M-bM-^@M-^S BCP: Bicellular pollen M-bM-^@M-^S TCP: Tricellular pollen M-bM-^@M-^S MP: Mature pollen) were isolated using a percoll gradient-based method (Honys and Twell, 2004) and the small RNA fraction for each sample was isolated and sequenced by Illumina technology. Reference: Honys, D. and Twell, D. (2004) Transcriptome analysis of haploid male gametophyte development in Arabidopsis. Genome Biol. 5/11/R85.
2014-07-01 | E-GEOD-34190 | biostudies-arrayexpress