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RNA, Untranslated (9):
Recent article
RNA, Untranslated
Journal of Neurochemistry (119)5 2011
Abstract
We have used neuroblastoma cells expressing NDM29 at its basal level (Mock cells) or at 5.4-fold higher levels (S1 cells) to investigate whether a functional differentiation correlates with morphological and biochemical development induced by NDM29 expression. First, analyzing the expression of spec...
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PMID: 21933186
PDF is available here.
PDF is available here.
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Abstract
We generated parthenogenetic human induced pluripotent stem cells (iPSCs) with a homozygote diploid karyotype. Global gene expression and DNA methylation analyses of the parthenogenetic cells enabled the identification of the entire repertoire of paternally expressed genes. We thus demonstrated that...
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PMID: 21572443
PDF is available here.
PDF is available here.
Abstract
We describe the ways in which pseudogenes exert their effect on coding genes and explore the role of pseudogenes in the increasingly complex web of noncoding RNA that contributes to normal cellular regulation....
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PMID: 21398401
PDF is available here.
PDF is available here.
Abstract
Our results support the model that the QS sRNAs bind to the 5' untranslated region of multiple mRNAs and alter the fate of one in a positive manner and several others in a negative manner. This mechanism ensures the proper timing of the QS response, which includes the expression of traits critical f...
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PMID: 21031313
PDF is available here.
PDF is available here.
Abstract
Our understanding of siRNA and miRNA-based regulation has direct implications for fundamental biology as well as disease aetiology and treatment as it is discussed in this review on 'new techniques in molecular biology'.
2011 S. Karger AG, Basel....
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PMID: 21252559
PDF is available here.
PDF is available here.
Abstract
We hypothesize that genes in different orientations will have differing degrees of coupled expression and, in turn, different noise levels. Divergently organized gene pairs, in particular those with bidirectional promoters, have close promoters, maximizing the likelihood that expression of one gene...
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PMID: 21402863
PDF is available here.
PDF is available here.
Abstract
We aimed to identify novel sRNAs and sORFs in Shigella, the principal etiologic agents of bacillary dysentery.
We identified 64 sRNAs in Shigella, which were experimentally validated in other bacteria based on sequence conservation. We employed computer-based and tiling array-based m...
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PMID: 21483688
PDF is available here.
PDF is available here.
Abstract
RNA-based pathways that regulate protein expression are much more widespread than previously thought. Regulatory RNAs, including 5' and 3' untranslated regions next to the coding sequence, cis-acting antisense RNAs and trans-acting small non-coding RNAs, are effective regulatory mole...
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PMID: 21079634
PDF is available here.
PDF is available here.
Abstract
We have shown that key factors supporting pluripotency-Nanog, Oct4 and Sox2-bind within Xist intron 1 in undifferentiated embryonic stem cells (ESC) to repress Xist transcription. However, the relationship between transcription factors of the pluripotency network and Tsix regulation has remained unc...
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PMID: 21085182
PDF is available here.
PDF is available here.
Abstract
We identify Xic-encoded Jpx as an Xist activator. Jpx is developmentally regulated and accumulates during XCI. Deleting Jpx blocks XCI and is female lethal. Posttranscriptional Jpx knockdown recapitulates the knockout, and supplying Jpx in trans rescues lethality. Thus, Jpx is trans-acting and funct...
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PMID: 21029862
PDF is available here.
PDF is available here.
Abstract
Epigenetic signals are responsible for the establishment, maintenance, and reversal of metastable transcriptional states that are fundamental for the cell's ability to "remember" past events, such as changes in the external environment or developmental cues. Complex epigenetic states are orchestrate...
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PMID: 21030644
PDF is available here.
PDF is available here.
Pediatric Research (68)5 2010
Abstract
We tested 18 single nucleotide polymorphisms (SNPs) in the IGF2, H19, and IGF2R genes for associations with birth weight variation in 342 mother-newborn pairs (birth weight 2.1-4.7 kg at term) and 527 parent-newborn trios (birth weight 2.1-5.1 kg) across three localities. SNPs in the IGF2R (rs819175...
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PMID: 20639793
PDF is available here.
PDF is available here.
Abstract
We show, by targeting a conditional knockout of Rnf12 to oocytes where RLIM accumulates to high levels, that the maternal transmission of the mutant X chromosome (Δm) leads to lethality in female embryos as a result of defective imprinted XCI. We provide evidence that in Δm female embryos the in...
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PMID: 20962847
PDF is available here.
PDF is available here.
Genetika (Moskva) (46)10 2010
Abstract
The Tsix regulatory region was examined in vole Microtus rossiaemeridionalis. The minimal promoter region, three potential enhancer regulatory elements and one transcription suppressor element were identified. The enhancer regions contained potential binding sites of transcription activators, while...
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PMID: 21254563
PDF is available here.
PDF is available here.
Genetika (Moskva) (46)10 2010
Abstract
Interaction of transcription factor CTCF with the minimal promoter of Xist gene was investigated in intraspecific hybrids ofcommon voles. CTCF was shown to bind with the minimal promoter region in vivo. However, the experiments of the delay in gel resulted in the absence of interaction between the C...
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PMID: 21254564
PDF is available here.
PDF is available here.
Genetika (Moskva) (46)10 2010
Abstract
The Xist gene belongs to the class of long noncoding regulatory RNA genes which play a key role in the process of inactivation of one of the X chromosomes in females of placental mammals. Based on interspecific comparative sequence analysis performed using a set ofbioinformatic programs and approach...
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PMID: 21254561
PDF is available here.
PDF is available here.
Genetika (Moskva) (46)10 2010
Abstract
Mouse X chromosome inactivation center contains the DXPas34 minisatellite locus which plays an important role in expression regulation of the Tsix and Xist genes, involved into female dosage compensation. Comparative analysis of the DXPas34 locus from mouse, rat, and four common vole species reveale...
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PMID: 21254565
PDF is available here.
PDF is available here.
Biochimica et Biophysica Acta (1799)9 2010
Abstract
We turn our attention to the larger, in number and size, long non-coding RNAs (lncRNAs), and review their evolutionary complexity and the growing evidence for their diverse mechanisms of action and functional roles in basic molecular and cellular biology and in human disease. In contrast to the focu...
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PMID: 20951849
PDF is available here.
PDF is available here.
Abstract
Oncology Reports (24)3 2010
Abstract
We identified a new splice variant of ANRIL and introduced it into HeLa cells to uncover functional aspects of ANRIL towards cellular function. For this purpose, we monitored global mRNA expressional changes and conducted gene ontology enrichment. The majority of mRNAs was down-regulated by ANRIL ov...
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PMID: 20664976
PDF is available here.
PDF is available here.
Journal of Virology (84)16 2010
Abstract
We have employed a genomewide tiling array to examine the lytic transcriptome of the Kaposi's sarcoma-associated herpesvirus, KSHV. Our results reveal that during lytic growth (but not during latency), there is extensive transcription from noncoding regions, including both intergenic regions and, es...
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PMID: 20534856
PDF is available here.
PDF is available here.
Developmental Biology (344)1 2010
Abstract
We posit that more than a dozen additional miRNAs are excellent candidates for influencing the generation of iPS cells as well as for providing new insights into the process of reprogramming.
Copyright (c) 2010 Elsevier Inc. All rights reserved....
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PMID: 20478297
PDF is available here.
PDF is available here.
Abstract
MicroRNAs (miRNAs) are an abundant class of small non-coding RNAs that collectively regulate the expression of a large number of mRNAs by either promoting destabilization or repressing translation, or both. Therefore, they play a major role in shaping the transcriptomes and proteomes...
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PMID: 20596726
PDF is available here.
PDF is available here.
Abstract
We systematically screened 71 fully sequenced archaeal genomes, and identified some proteins containing homologous regions to the functional domains of eukaryotic RNA silencing pathway key proteins. The phylogenetic relationships of these proteins were analyzed. The conserved functional amino acids...
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PMID: 20816382
PDF is available here.
PDF is available here.
Abstract
We have also introduced Penelope into Drosophila melanogaster, which are otherwise naive to the element. We have taken advantage of these natural and experimentally induced colonization processes to probe the evolution of small RNA pathways in response to transposon challenge. In both species, Penel...
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PMID: 20581131
PDF is available here.
PDF is available here.
Abstract
We defined complementary DNAs (cDNAs) lacking any positive-strand open reading frames (ORFs) longer than 30 amino acids, as well as cDNAs lacking any evidence of interspecies conservation of their longer-than-30-amino acid ORFs, as noncoding. We have identified 5446 lncRNA genes in the human genome...
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PMID: 20587619
PDF is available here.
PDF is available here.
Nature Reviews: Genetics (11)8 2010
Abstract
We discuss the implications of phenotypic transcription factor retention on mitotic chromosomes in biological control and disease....
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PMID: 20628351
PDF is available here.
PDF is available here.
Small RNA profiling reveals antisense transcription throughout the KSHV genome and novel small RNAs.
Abstract
We developed a method to profile small RNAs ( approximately 18-75 nt) from populations of cells undergoing predominantly lytic infection. Using two different next-generation sequencing platforms, we cloned and sequenced both pre-miRNAs and derivative miRNAs. Our analysis shows that the vast majority...
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PMID: 20566670
PDF is available here.
PDF is available here.
Abstract
Abstract
We show that peptides of 11 to 32 amino acids encoded by the polished rice (pri) sORF gene control epidermal differentiation in Drosophila by modifying the transcription factor Shavenbaby (Svb). Pri peptides trigger the amino-terminal truncation of the Svb protein, which converts Svb from a represso...
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PMID: 20647469
PDF is available here.
PDF is available here.
Abstract
Molecular Pharmacology (78)1 2010
Abstract
We report a previously unsuspected role for the nonprotein-coding RNA GAS5 in the inhibition of T-cell proliferation produced by mTOR antagonists such as rapamycin. GAS5 transcripts are up-regulated during growth arrest and after rapamycin treatment, and GAS5 has recently been shown to be necessary...
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PMID: 20421347
PDF is available here.
PDF is available here.
Nucleic Acids Research (38)12 2010
Abstract
We report the discovery of 34 novel small RNAs (sRNAs) in the TB-complex M. bovis BCG, using a combination of experimental and computational approaches. Putative homologues of many of these sRNAs were also identified in M. tuberculosis and/or M. smegmatis. Those sRNAs that are also expressed in the...
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PMID: 20181675
PDF is available here.
PDF is available here.
Abstract
We summarise recent advances in our knowledge of the regulation of Xist and Tsix in embryonic stem (ES) and differentiating ES cells....
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PMID: 20544740
PDF is available here.
PDF is available here.
Molecular Plant (3)4 2010
Abstract
We discuss the interactions between RBPs and npcRNAs in the context of nuclear-related processes and their implication in plant development and stress responses. We propose that these interactions may add a regulatory layer that modulates the interactions between the nuclear genome and the environme...
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PMID: 20603381
PDF is available here.
PDF is available here.
Molecular Plant (3)4 2010
Abstract
We discuss the interactions between RBPs and npcRNAs in the context of nuclear-related processes and their implication in plant development and stress responses. We propose that these interactions may add a regulatory layer that modulates the interactions between the nuclear genome and the environme...
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PMID: 20603381
PDF is available here.
PDF is available here.
PLoS Genetics (6)7 2010
Abstract
We examined intra- and inter-individual variation in DNA methylation at the differentially methylated regions (DMRs) of the IGF2/H19 and IGF2R loci in a population of children conceived in vitro or in vivo. We found substantial variation in allele-specific methylation at both loci in both groups. Ab...
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PMID: 20661447
PDF is available here.
PDF is available here.
Abstract
We show that shRNAs, which target the vector genomic RNA, strongly reduced lentiviral vector titers but inhibition of the RNAi pathway via saturation could rescue vector production. The presence of miRNAs in the vector RNA genome (sense orientation) results in a minor titer reduction due to Drosha p...
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PMID: 20498457
PDF is available here.
PDF is available here.
Abstract
We currently define as epigenetics evolved over time as our knowledge on DNA methylation and chromatin modifications and their effects on gene expression increased. The current explosion of research on epigenetics and the increasing documentation of the effects of various environmental factors on DN...
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PMID: 20381512
PDF is available here.
PDF is available here.
Biophysics (39)1 2010
Abstract
Large noncoding RNAs fold into their biologically functional structures via compact yet disordered intermediates, which couple the stable secondary structure of the RNA with the emerging tertiary fold. The specificity of the collapse transition, which coincides with the assembly of helical domains,...
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PMID: 20192764
PDF is available here.
PDF is available here.
Abstract
We constructed and analyzed a size-fractionated cDNA library (20-35 nt) from epimastigotes forms of T. cruzi. Our results showed the production of an abundant class of tRNA-derived small RNAs preferentially restricted to specific isoacceptors and whose production was more accentuated under nutrition...
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PMID: 20156490
PDF is available here.
PDF is available here.
Nucleic Acids Research (38)11 2010
Abstract
We used exhaustive PSI-BLAST and TBLASTN searches across 774 bacterial genomes to identify homologs of known type I toxins. These searches substantially expanded the collection of predicted type I toxins, revealed homology of the Ldr and Fst toxins, and suggested that type I toxin-antitoxin loci are...
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PMID: 20156992
PDF is available here.
PDF is available here.
Abstract
RNA interference (RNAi), an evolutionarily conserved sequence-specific post-transcriptional gene silencing mechanism, is triggered by double-stranded RNA (dsRNA) that results in the degradation of homologous mRNA or in the inhibition of mRNA translation. The naturally occurring trigg...
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PMID: 20455856
PDF is available here.
PDF is available here.
Abstract
We propose a new non-coding RNA named B2 discovered by differential display. B2 is a nuclear RNA which is 51,011 bp long with no significant open reading frame. This RNA has a continuous homology with the genomic DNA of the HEF1/ NEDD9/Cas-L gene located on 6p24-p25. This homology has enabled us to...
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PMID: 20428794
PDF is available here.
PDF is available here.
Abstract
We report a next-generation sequencing technique designed to facilitate the inference of function of uncharacterized transcript forms by improving their coverage in sequencing libraries, in parallel with the detection of canonical mRNAs. We piloted this protocol, which is based on the capture of 3'...
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PMID: 20421314
PDF is available here.
PDF is available here.
Abstract
We show that Bunyamwera virus (BUNV), the prototype of the Bunyaviridae family of segmented negative-sense RNA viruses, also can repair its genomic termini. When an intact nontranslated region (NTR) was added to the anti-genomic 3' end, it was precisely removed, to restore both length and RNA synthe...
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PMID: 20430858
PDF is available here.
PDF is available here.
Abstract
We show that both Hfq and this Hfq binding site are required for RprA or ArcZ to act in vivo and to form a stable complex with rpoS mRNA in vitro; both were partially dispensable for DsrA at 37 degrees C. ArcZ sRNA is processed from 121 nt to a stable 56 nt species that contains the pairing region;...
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PMID: 20457943
PDF is available here.
PDF is available here.
Epigenetics (5)4 2010
Abstract
We explored the epigenetic modulation of IGF2/H19 during human development in 60 normal and 66 idiopathic IUGR (Intrauterine Growth Restriction) pregnancies, studying embryonic (cord blood) and extraembryonic (placenta and umbilical cord) tissues. We found ICR1 normal methylation levels ( approximat...
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PMID: 20418667
PDF is available here.
PDF is available here.
Lab Animal (39)5 2010
Abstract
PLoS Biology (8)5 2010
Abstract
We have characterized transcription sites located outside protein-coding genes in a highly regulated response, macrophage activation by endotoxin. Using chromatin signatures, we could unambiguously classify extragenic Pol_II binding sites as belonging to either canonical RNA genes or transcribed enh...
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PMID: 20485488
PDF is available here.
PDF is available here.
Biological Bulletin (218)2 2010
Abstract
We crossed two inbred lines to produce inbred and hybrid larvae, which grew at different rates under the same environmental conditions. Using high-throughput cloning and sequencing methods, we identified 1.1 million expressed sequence tags from the mitochondrial genome, 96.7% of which were perfect m...
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PMID: 20413789
PDF is available here.
PDF is available here.
Abstract
We developed a cell-based crosslinking approach to determine at high resolution and transcriptome-wide the binding sites of cellular RBPs and miRNPs. The crosslinked sites are revealed by thymidine to cytidine transitions in the cDNAs prepared from immunopurified RNPs of 4-thiouridine-treated cells....
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PMID: 20371350
PDF is available here.
PDF is available here.
Biomaterials (31)10 2010
Abstract
We utilized a simple in vitro epigenetic reprogramming approach to convert skin fibroblasts into multipotent cells. After transient reprogramming, stem cell markers, including Oct4 and Nanog, became activated in the treated cells. The reprogrammed cells were multipotent as demonstrated by their abil...
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PMID: 20044135
PDF is available here.
PDF is available here.
Cellular Reprogramming (12)2 2010
Abstract
We aimed to determine the expression levels and methylation patterns of imprinted genes in placentas of live cloned piglets and dead ones. Quantitative real-time reverse transcriptase-polymerase chain reaction (RT-PCR) analysis showed that the expression of all four imprinted genes (IGF2, H19, PEG3,...
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PMID: 20677935
PDF is available here.
PDF is available here.
Abstract
We first address the synthesis, mechanisms of action, and functions of siRNAs. Then, we focus on recent advances and technologies in miRNA and protein research of the human placenta. Next, we discuss the clinical applications of miRNA in lung cancer. We also touch on "long" noncoding RNAs from inter...
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PMID: 20453418
PDF is available here.
PDF is available here.
Abstract
Chromatin remodeling guided by non-coding RNA (ncRNA) contributes mechanistically to the establishment of chromatin structure and to the maintenance of epigenetic memory. Various ncRNAs have been identified as regulators of chromatin structure and gene expression. The widespread occurrence of antise...
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PMID: 20373265
PDF is available here.
PDF is available here.
Methods in Molecular Biology (609)609 2010
Abstract
We give a short overview of fundamental computational techniques to analyze ncRNAs that can help us better understand their function. Topics covered include prediction of secondary structure from the primary sequence, prediction of consensus structures for homologous sequences, search for homologous...
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PMID: 20221926
PDF is available here.
PDF is available here.
Abstract
EMBO Reports (11)3 2010
Abstract
The biannual Abcam meeting on Chromatin: Structure & Function held last November covered many aspects of chromatin regulation in health and disease. Important discussion points were the dynamic aspects of chromatin and the ever-increasing involvement of non-coding RNAs in chromatin and epigenetic me...
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PMID: 20154643
PDF is available here.
PDF is available here.
Abstract
This report summarizes the information presented at the 2009 Keystone Conference on MicroRNAs and Cancer, held in Keystone, Colorado, USA, June 10th to 15th 2009. Soon after microRNAs (miRNAs) emerged as an abundant new class of non-coding RNAs (ncRNAs), evidence started to mount supporting importan...
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PMID: 20168081
PDF is available here.
PDF is available here.