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CSHLIn a role reversal, RNAs proofread themselves | News & Features

CSHLIn a role reversal, RNAs proofread themselves | News & Features

CSHLIn a role reversal, RNAs proofread themselves | News & Features.

Forget the Selfish Gene: Evolution of Life Is Driven by the Selfish Ribosome, Research Suggests

Since the discovery of how DNA encodes genetic information, most research on the evolution of life has focused on genes. According to the ‘selfish gene’ theory, cells and organisms exist … Jan. 7, 2015 

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Crystal structure of the RNA-guided immune surveillance Cascade complex in Escherichia coli.

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Crystal structure of the RNA-guided immune surveillance Cascade complex in Escherichia coli.

Nature. 2014 Nov 6;515(7525):147-50

Authors: Zhao H, Sheng G, Wang J, Wang M, Bunkoczi G, Gong W, Wei Z, Wang Y

Abstract
Clustered regularly interspaced short palindromic repeats (CRISPR) together with CRISPR-associated (Cas) proteins form the CRISPR/Cas system to defend against foreign nucleic acids of bacterial and archaeal origin. In the I-E subtype CRISPR/Cas system, eleven subunits from five Cas proteins (CasA1B2C6D1E1) assemble along a CRISPR RNA (crRNA) to form the Cascade complex. Here we report on the 3.05 Å crystal structure of the 405-kilodalton Escherichia coli Cascade complex that provides molecular details beyond those available from earlier lower-resolution cryo-electron microscopy structures. The bound 61-nucleotide crRNA spans the entire 11-protein subunit-containing complex, where it interacts with all six CasC subunits (named CasC1-6), with its 5′ and 3′ terminal repeats anchored by CasD and CasE, respectively. The crRNA spacer region is positioned along a continuous groove on the concave surface generated by the aligned CasC1-6 subunits. The five long β-hairpins that project from individual CasC2-6 subunits extend across the crRNA, with each β-hairpin inserting into the gap between the last stacked base and its adjacent splayed counterpart, and positioned within the groove of the preceding CasC subunit. Therefore, instead of continuously stacking, the crRNA spacer region is divided into five equal fragments, with each fragment containing five stacked bases flanked by one flipped-out base. Each of those crRNA spacer fragments interacts with CasC in a similar fashion. Furthermore, our structure explains why the seed sequence, with its outward-directed bases, has a critical role in target DNA recognition. In conclusion, our structure of the Cascade complex provides novel molecular details of protein-protein and protein-RNA alignments and interactions required for generation of a complex mediating RNA-guided immune surveillance.

PMID: 25118175 [PubMed – indexed for MEDLINE]

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tRFs and the Argonautes: gene silencing from antiquity – BioMed Central blog

tRFs and the Argonautes: gene silencing from antiquity – BioMed Central blog.

Viroids: Survivors from the RNA World?

Originally posted on MicrobiologyBytes:

Viroid A new review in Annual Review of Microbiology gives an excellent introduction to viroids.

Contents:

  • Introduction: Why The Need For An RNA World?
  • Viroids: Essential Features
  • Discovery of a Subviral World
  • Structure: Small Circular RNAs with Compact Folding
  • Replication: Rolling-Circle Mechanism Catalyzed by Enzymes and Ribozymes
  • Sequence Diversity
  • Viroid-Related Replicons
  • Viroid-Like Satellite RNAs
  • Retroviroid-Like Elements
  • Hepatitis δ virus
  • Why Are Viroids And Viroid-Related Replicons Regarded As Survivors Of The RNA World?
  • Early Speculations on the Origin of Viroids
  • Circular RNAs: Relics of Precellular Evolution?
  • Viroid-Related Replicons
  • Summary

Viroids: Survivors from the RNA World? (2014) Annual Review of Microbiology, 68(1): 395-414. doi: 10.1146/annurev-micro-091313-103416

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The functional role of long non-coding RNAs and epigenetics

Long non-coding RNAs (lncRNAs) are non-protein coding transcripts longer than 200 nucleotides. The post-transcriptional regulation is influenced by these lncRNAs by interfering with the microRNA pathways, involving in diverse cellular processes. The regulation of gene expression by lncRNAs at the epigenetic level, transcriptional and post-transcriptional level have been well known and widely studied. Recent recognition

The functional role of long non-coding RNAs and epigenetics is a post from: lncRNA Blog

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RCas9: A Programmable RNA Editing Tool

newscenter.lbl.gov
– lcyarris
A powerful scientific tool for editing the DNA instructions in a genome can now also be applied to RNA, the molecule that translates DNA’s genetic instructions into the production of proteins. A team of researchers with Berkeley Lab and the University of California (UC) Berkeley has demonstrated a means by which the CRISPR/Cas9 protein complex can be programmed to recognize and cleave RNA at sequence-specific target sites. This finding has the potential to transform the study of RNA function by…  show all text
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@NIGMS on Twitter
@NIGMS: Boost for Synthetic #Biology: Powerful #DNA editing tool can now be programmed to edit RNA. bit.ly/cas9r http://ift.tt/1tnrJ9j
@SeqComplete on Twitter
@SeqComplete: mt #igem #synbio RCas9: A Programmable RNA Editing Tool http://ift.tt/1vInd7S, see more http://ift.tt/1s6DmVA
@anamika13 on Twitter
@anamika13: A powerful scientific tool for editing the DNA instructions in a genome can be applied to RNA: http://ift.tt/1vInd7S http://ift.tt/1vD8083
@idtdna on Twitter
@idtdna: Boost for Synthetic #Biology: Powerful #DNA editing tool can now be programmed to edit RNA. bit.ly/cas9r http://ift.tt/1tnrJ9j
@GeneRef on Twitter
@GeneRef: RCas9: A programmable RNA editing tool ow.ly/2OAc4k
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Prediction of uridine modifications in tRNA sequences

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Rfam 12.0 is out | Xfam Blog

We are pleased to announce the release of Rfam 12.0!
This release contains some major changes when compared with previous releases of Rfam, so please take a minute to read our release notes. Rfam 12.0 is the first version of Rfam which is based on Infernal 1.1, and as such contains many significant changes. In particular, the curator-defined thresholds have all been manually altered to ensure compatability with Infernal 1.1. This means that many families have seen significant increases or decre…  show all text
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@emblebi on Twitter
@emblebi: Some huge changes in @Xfam_EBI‘s new Rfam release: no BLAST, no full alns, no genomes, motifs, … Congrats folks! http://ift.tt/1rbv7by
@ppgardne on Twitter
@ppgardne: Some huge changes in @Xfam_EBI‘s new Rfam release: no BLAST, no full alns, no genomes, motifs, … Congrats folks! http://ift.tt/1rbv7by
@ppgardne on Twitter
@ppgardne: Rfam 12 released today. No more BLAST filters – Infernal’s now fast enough for complete database searches for RNAs.
http://ift.tt/1rbv7by
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Origin of Life | The Advanced Apes | PBS Digital Studios

Origin of Life | The Advanced Apes | PBS Digital Studios.

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