Structure of yeast Argonaute with guide RNA
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA162877 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR493531.fastq.gz | Fastqsanger.gz | |||
| SRR493532.fastq.gz | Fastqsanger.gz | |||
| SRR493535.fastq.gz | Fastqsanger.gz | |||
| SRR493536.fastq.gz | Fastqsanger.gz |
Items per page: 5 1 - 4 of 4 |
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Project description:The RNA-induced silencing complex, comprising Argonaute and guide RNA, mediates RNA interference. Here we report the 3.2 Å crystal structure of Kluyveromyces polysporus Argonaute (KpAGO) fortuitously complexed with guide RNA originating from small-RNA duplexes autonomously loaded by recombinant KpAGO. Despite their diverse sequences, guide-RNA nucleotides 1-8 are positioned similarly, with sequence-independent contacts to bases, phosphates and 2'-hydroxyl groups pre-organizing the backbone of nucleotides 2-8 in a near-A-form conformation. Compared with prokaryotic Argonautes, KpAGO has numerous surface-exposed insertion segments, with a cluster of conserved insertions repositioning the N domain to enable full propagation of guide-target pairing. Compared with Argonautes in inactive conformations, KpAGO has a hydrogen-bond network that stabilizes an expanded and repositioned loop, which inserts an invariant glutamate into the catalytic pocket. Mutation analyses and analogies to ribonuclease H indicate that insertion of this glutamate finger completes a universally conserved catalytic tetrad, thereby activating Argonaute for RNA cleavage.
| S-EPMC3853139 | biostudies-literature
Project description:This SuperSeries is composed of the following subset Series: GSE37723: Degradome sequencing from S. castellii GSE37724: Bacteria-derived small RNAs that co-purify with KpAGO Refer to individual Series
2012-05-13 | E-GEOD-37725 | biostudies-arrayexpress
Project description:This SuperSeries is composed of the SubSeries listed below.
2012-05-14 | GSE37725 | GEO
Project description:Argonaute proteins lie at the heart of the RNA-Induced Silencing Complex (RISC), wherein they use small RNA guides to recognize targets. Some Argonaute proteins can directly cleave their targets, whereas others recruit co-factors to repress independently of “slicing.” Prior studies established the architecture of Argonaute proteins; however, we have not yet had a detailed picture of an Argonaute whose biochemical and biological functions were well established. Here we describe the crystal structure of human Argonaute-2 bound to miR-20a at 2.2 Å resolution. Overall architecture and domain organization is shared with its prokaryotic counterparts, though Ago2 is somewhat more open, with its PAZ domain further removed from the other domains. The miRNA is anchored at both ends by the Mid and PAZ domains but makes several kinks and turns along the binding groove. The RNA confers remarkable stability on the Argonaute protein, locking this otherwise flexible enzyme into a stable conformation. total small RNAs (19-29nt) and small RNAs associated with purified hArgonaute2 purified from SF9 cells. These were processed and sequenced on Illumina GA-II platform.
2012-05-12 | E-GEOD-37931 | biostudies-arrayexpress
Project description:Argonaute proteins lie at the heart of the RNA-Induced Silencing Complex (RISC), wherein they use small RNA guides to recognize targets. Some Argonaute proteins can directly cleave their targets, whereas others recruit co-factors to repress independently of “slicing.” Prior studies established the architecture of Argonaute proteins; however, we have not yet had a detailed picture of an Argonaute whose biochemical and biological functions were well established. Here we describe the crystal structure of human Argonaute-2 bound to miR-20a at 2.2 Å resolution. Overall architecture and domain organization is shared with its prokaryotic counterparts, though Ago2 is somewhat more open, with its PAZ domain further removed from the other domains. The miRNA is anchored at both ends by the Mid and PAZ domains but makes several kinks and turns along the binding groove. The RNA confers remarkable stability on the Argonaute protein, locking this otherwise flexible enzyme into a stable conformation.
2012-05-12 | GSE37931 | GEO
Project description:The structures of RNA molecules are often important for their function and regulation, yet there are no experimental techniques for genome-scale measurement of RNA structure. Here, we describe a novel strategy termed Parallel Analysis of RNA Structure (PARS), which is based on deep sequencing fragments of RNAs that were treated with structure-specific enzymes, thus providing simultaneous in-vitro profiling of the secondary structure of thousands of RNA species at single nucleotide resolution. We apply PARS to profile the secondary structure of the mRNAs of the budding yeast S. cerevisiae and obtain structural profiles for over 3000 distinct transcripts. Analysis of these profiles reveals several RNA structural properties of yeast transcripts, including the existence of more secondary structure over coding regions compared to untranslated regions, a three-nucleotide periodicity of secondary structure across coding regions, and a relationship between the efficiency with which an mRNA is translated and the lack of structure over its translation start site. PARS is readily applicable to other organisms and to profiling RNA structure in diverse conditions, thus enabling studies of the dynamics of secondary structure at a genomic scale. RNA sample was treated with one of two structure-specific enzymes (RNase V1 or RNase S1). Four independent V1 experiments and three independent S1 experiments were carried out. Processed data file linked below. Data processing involves merging (or rather log-ratio-ing) the 7 lanes of SOLiD sequencing data against each other. Also linked below are the genome and transcriptome FASTA files used for mapping, and the annotation file having the format: gene_ID, chromosome, start, end, feature. Start and end are 1-based; feature is "Transcript" for the entire transcript (including introns), "Intron", "Exon", "5UTR" or "3UTR". Genome-wide measurement of RNA secondary structure in yeast, Kertesz et al., Nature Volume:467, Pages:103-107, Date published:(02 September 2010) http://www.nature.com/nature/journal/v467/n7311/abs/nature09322.html
2010-08-24 | E-GEOD-22393 | biostudies-arrayexpress
Project description:The structures of RNA molecules are often important for their function and regulation, yet there are no experimental techniques for genome-scale measurement of RNA structure. Here, we describe a novel strategy termed Parallel Analysis of RNA Structure (PARS), which is based on deep sequencing fragments of RNAs that were treated with structure-specific enzymes, thus providing simultaneous in-vitro profiling of the secondary structure of thousands of RNA species at single nucleotide resolution. We apply PARS to profile the secondary structure of the mRNAs of the budding yeast S. cerevisiae and obtain structural profiles for over 3000 distinct transcripts. Analysis of these profiles reveals several RNA structural properties of yeast transcripts, including the existence of more secondary structure over coding regions compared to untranslated regions, a three-nucleotide periodicity of secondary structure across coding regions, and a relationship between the efficiency with which an mRNA is translated and the lack of structure over its translation start site. PARS is readily applicable to other organisms and to profiling RNA structure in diverse conditions, thus enabling studies of the dynamics of secondary structure at a genomic scale.
2010-08-24 | GSE22393 | GEO
Project description:Box C/D snoRNAs snR4 and snR45, whose role was unknown, guide 18S rRNA acetylations by Kre33 in yeast. UV-crosslinking (CRAC) was used to determine binding sites of Kre33 on RNA.
2017-07-25 | GSE87480 | GEO
Project description:MicroRNAs are regulators of gene expression whose functions are critical for normal development and physiology. We have previously characterized mutations in a Caenorhabditis elegans microRNA-specific Argonaute ALG-1 (Argonaute-like gene) that are antimorphic [alg-1(anti)]. alg-1(anti) mutants have dramatically stronger microRNA-related phenotypes than animals with a complete loss of ALG-1. ALG-1(anti) miRISC (microRNA induced silencing complex) fails to undergo a functional transition from microRNA processing to target repression. To better understand this transition, we characterized the small RNA population associated with ALG-1(anti) complexes in vivo. alg-1(anti) mutants dramatically overaccumulated microRNA* (passenger) strands, and immunoprecipitated ALG-1(anti) complexes contained nonstoichiometric yields of mature microRNA and microRNA* strands, with some microRNA* strands present in the ALG-1(anti) Argonaute far in excess of the corresponding mature microRNAs. We show complex and microRNA-specific defects in microRNA strand selection and microRNA* strand disposal. For certain microRNAs (for example mir-58), microRNA guide strand selection by ALG-1(anti) appeared normal, but microRNA* strand release was inefficient. For other microRNAs (such as mir-2), both the microRNA and microRNA* strands were selected as guide by ALG-1(anti), indicating a defect in normal specificity of the strand choice. Our results suggest that wild-type ALG-1 complexes recognize structural features of particular microRNAs in the context of conducting the strand selection and microRNA* ejection steps of miRISC maturation. Deep-sequencing was performed on cDNA libraries made from total RNA and RNA immunoprecipitated with ALG-1 from mixed-staged populations of three strains: three biological replicates from wild-type animals and two biological replicates each from alg-1(ma192) and alg-1(ma202) mutant animals. In addition, deep-sequencing was performed on cDNA libraries made from L2-staged total RNA in two biological replicates from wildtype and alg-1(ma202) animals and one biological replicate of alg-1(ma192).
2015-09-07 | E-GEOD-72659 | biostudies-arrayexpress
Project description:MicroRNAs are regulators of gene expression whose functions are critical for normal development and physiology. We have previously characterized mutations in a Caenorhabditis elegans microRNA-specific Argonaute ALG-1 (Argonaute-like gene) that are antimorphic [alg-1(anti)]. alg-1(anti) mutants have dramatically stronger microRNA-related phenotypes than animals with a complete loss of ALG-1. ALG-1(anti) miRISC (microRNA induced silencing complex) fails to undergo a functional transition from microRNA processing to target repression. To better understand this transition, we characterized the small RNA population associated with ALG-1(anti) complexes in vivo. alg-1(anti) mutants dramatically overaccumulated microRNA* (passenger) strands, and immunoprecipitated ALG-1(anti) complexes contained nonstoichiometric yields of mature microRNA and microRNA* strands, with some microRNA* strands present in the ALG-1(anti) Argonaute far in excess of the corresponding mature microRNAs. We show complex and microRNA-specific defects in microRNA strand selection and microRNA* strand disposal. For certain microRNAs (for example mir-58), microRNA guide strand selection by ALG-1(anti) appeared normal, but microRNA* strand release was inefficient. For other microRNAs (such as mir-2), both the microRNA and microRNA* strands were selected as guide by ALG-1(anti), indicating a defect in normal specificity of the strand choice. Our results suggest that wild-type ALG-1 complexes recognize structural features of particular microRNAs in the context of conducting the strand selection and microRNA* ejection steps of miRISC maturation.
2015-09-07 | GSE72659 | GEO