RNomics

Home » Posts tagged 'Saved for Later'

Tag Archives: Saved for Later

Crystallization and preliminary X-ray diffraction analysis of the CRISPR-Cas RNA-silencing Cmr complex.

Crystallization and preliminary X-ray diffraction analysis of the CRISPR-Cas RNA-silencing Cmr complex.

Acta Crystallogr F Struct Biol Commun. 2015 Jun 1;71(Pt 6):735-740

Authors: Osawa T, Inanaga H, Numata T

Abstract
Clustered regularly interspaced short palindromic repeat (CRISPR)-derived RNA (crRNA) and CRISPR-associated (Cas) proteins constitute a prokaryotic adaptive immune system (CRISPR-Cas system) that targets and degrades invading genetic elements. The type III-B CRISPR-Cas Cmr complex, composed of the six Cas proteins (Cmr1-Cmr6) and a crRNA, captures and cleaves RNA complementary to the crRNA guide sequence. Here, a Cmr1-deficient functional Cmr (CmrΔ1) complex composed of Pyrococcus furiosus Cmr2-Cmr3, Archaeoglobus fulgidus Cmr4-Cmr5-Cmr6 and the 39-mer P. furiosus 7.01-crRNA was prepared. The CmrΔ1 complex was cocrystallized with single-stranded DNA (ssDNA) complementary to the crRNA guide by the vapour-diffusion method. The crystals diffracted to 2.1 Å resolution using synchrotron radiation at the Photon Factory. The crystals belonged to the triclinic space group P1, with unit-cell parameters a = 75.5, b = 76.2, c = 139.2 Å, α = 90.3, β = 104.8, γ = 118.6°. The asymmetric unit of the crystals is expected to contain one CmrΔ1-ssDNA complex, with a Matthews coefficient of 2.03 Å(3) Da(-1) and a solvent content of 39.5%.

PMID: 26057804 [PubMed – as supplied by publisher]

from pubmed: ArchaeaWeb http://ift.tt/1B85GO5
via IFTTT

Small RNAs, 5′ UTR elements and RNA-binding proteins in intracellular bacteria: impact on metabolism and virulence.

Small RNAs, 5′ UTR elements and RNA-binding proteins in intracellular bacteria: impact on metabolism and virulence.

FEMS Microbiol Rev. 2015 May;39(3):331-349

Authors: Oliva G, Sahr T, Buchrieser C

Abstract
Sequencing-based studies have illuminated increased transcriptional complexity within the genome structure of bacteria and have resulted in the identification of many small regulatory RNAs (sRNA) and a large amount of antisense transcription. It remains an open question whether these sRNAs all indeed play regulatory roles, but their identification led to an exponential increase in studies searching for their function. This allowed to show that sRNAs may modulate virulence gene expression, cellular differentiation, metabolic functions, adaptation to environmental conditions and pathogenesis. In this review we will provide mechanistic insights into how sRNAs bind mRNAs and/or proteins. Furthermore, the important roles of the RNA chaperone Hfq, the CsrA system and the CRISPR RNA will be discussed. We will then focus on sRNAs and 5(‘) untranslated region (UTR) elements of intracellular bacteria like Chlamydia, Listeria, Legionella, or Salmonella, and place emphasis on those that are expressed during replication in host cells and are implicated in virulence and metabolism. In addition, sRNAs that regulate motility, iron homeostasis, and differentiation or stress responses will be highlighted. Taken together sRNAs constitute key elements in many major regulatory networks governing the intracellular life and virulence of pathogenic bacteria.

PMID: 26009640 [PubMed – as supplied by publisher]

from pubmed: hfqrnabinding http://ift.tt/1BoL2nJ
via IFTTT

SNORD76, a box C/D snoRNA, acts as a tumor suppressor in glioblastoma.

SNORD76, a box C/D snoRNA, acts as a tumor suppressor in glioblastoma.

Sci Rep. 2015;5:8588

Authors: Chen L, Han L, Wei J, Zhang K, Shi Z, Duan R, Li S, Zhou X, Pu P, Zhang J, Kang C

Abstract
Glioblastoma (GBM) is associated with disproportionately high morbidity and mortality, reflecting the need to develop new diagnostic and therapeutic targets for this disease. Recently, accumulating evidence has suggested that small nucleolar RNAs (snoRNAs) are gaining prominence and are more actively involved in tumorigenesis than previously thought. However, no report concerning the implication of snoRNAs in glioma has been published to date. In our study, SNORD76 was first found to be inversely associated with Hox Transcript Antisense Intergenic RNA (HOTAIR) knockdown, and surprisingly, forcibly expressed SNORD76 inhibited proliferation and growth of glioma cells. Moreover, downregulation of SNORD76 led to a more malignant phenotype. The pleiotropy of SNORD76 overexpression could be achieved at least partially through inducing cell cycle arrest at S phase by affecting the Rb-associated cell cycle regulation. Enforced SNORD76 expression in orthotopic tumors resulted in decreased tumor growth and the reduction of tumor volume. Additionally, in surgically resected glioma tissues, SNORD76, not its host gene, was associated with the WHO classification and was selectively downregulated in GBM (WHO grade IV). Collectively, our study adds to a growing body of evidence for the participation of snoRNAs in gliomagenesis and is the first to implicate a snoRNA in glioblastoma.

PMID: 25715874 [PubMed – in process]

from pubmed: rna c/d box http://ift.tt/1Bho8BU
via IFTTT

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

Related Articles

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]

from pubmed: rna binding protein … http://ift.tt/1m0Wm1G
via IFTTT

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

from lncRNA Blog http://ift.tt/1pLta0a
via IFTTT

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
posted by friends:
(6)
@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
posted by followers of the list:
(0)

from All News on ‘The Twitter Times: rnomics/bioscience’ http://ift.tt/1tnrL16
via IFTTT

Prediction of uridine modifications in tRNA sequences

from BMC Bioinformatics – Latest Articles http://ift.tt/1xEwjXw
via IFTTT

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
posted by friends:
(2)
@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
posted by followers of the list:
(0)

from Top News on ‘The Twitter Times: rnomics/bioinfo’ http://ift.tt/1viCHPU
via IFTTT

XXI International Round Table on Nucleosides, Nucleotides and Nucleic Acids

from Isis Pharmaceuticals Calendar Events http://www.is3na.org/
via IFTTT

EMD-2660 — Cryo-EM structure of the Plasmodium falciparum 80S ribosome bound to the anti-protozoan drug emetine — Wong W, Bai XC, Brown A, Fernandez IS, Hanssen E, Condron M, Tan YH, Baum J, Schere…

EMD-2660 — Cryo-EM structure of the Plasmodium falciparum 80S ribosome bound to the anti-protozoan drug emetine — Wong W, Bai XC, Brown A, Fernandez IS, Hanssen E, Condron M, Tan YH, Baum J, Scheres SHW — The Electron Microscopy Data Bank (EMDB) is a public repository for electron microscopy density maps of macromolecular complexes and subcellular structures. It covers a variety of techniques, including single-particle analysis, electron tomography, and electron (2D) crystallography. …
posted by friends:
(1)
@PDBeurope on Twitter
@PDBeurope: News from @elife on cryo-em for anti-malarials. #EMDB entry pdbe.org/emd-2660 et al. http://ift.tt/1pDUXAj http://ift.tt/1rrA12y
@PDBeurope on Twitter
@PDBeurope: .@elife Here’s the cryoEM map archived in #EMDB. pdbe.org/EMD-2660 http://ift.tt/1rrA9Py
posted by followers of the list:
(0)

from All News on ‘The Twitter Times: rnomics/structbio’ http://ift.tt/1pDV9PP
via IFTTT

%d bloggers like this: