Non-coding RNAs and RNA modifiers in cancer progression and cancer cells resistance to therapies
Three-dimensional super-resolution microscopy of the inactive X chromosome territory reveals a collapse of its active nuclear compartment harboring distinct Xist RNA foci
A Xist RNA decorated Barr body is the structural hallmark of the compacted inactive X territory in female mammals. Using super-resolution three-dimensional structured illumination microscopy (3D-SIM) and quant...Epigenetics & Chromatin 2014 7:8The Related Article to this article has been published in Nature Protocols 2017 12:BFnprot2017020Differential expression of histone H3 genes and selective association of the variant H3.7 with a specific sequence class in Stylonychia macronuclear development
Regulation of chromatin structure involves deposition of selective histone variants into nucleosome arrays. Numerous histone H3 variants become differentially expressed by individual nanochromosomes in the cou...Epigenetics & Chromatin 2014 7:4Limited evidence for evolutionarily conserved targeting of long non-coding RNAs by microRNAs
Long non-coding RNAs (lncRNAs) are emerging as important regulators of cell physiology, but it is yet unknown to what extent lncRNAs have evolved to be targeted by microRNAs. Comparative genomics has previousl...Silence 2013 4:4XIST-induced silencing of flanking genes is achieved by additive action of repeat a monomers in human somatic cells
The establishment of facultative heterochromatin by X-chromosome inactivation requires the long non-coding RNA XIST/Xist. However, the molecular mechanism by which the RNA achieves chromosome-wide gene silenci...Epigenetics & Chromatin 2013 6:23Analysis of hairpin RNA transgene-induced gene silencing in Fusarium oxysporum
Hairpin RNA (hpRNA) transgenes can be effective at inducing RNA silencing and have been exploited as a powerful tool for gene function analysis in many organisms. However, in fungi, expression of hairpin RNA t...Silence 2013 4:3UpSETing chromatin during non-coding RNA production
The packaging of eukaryotic DNA into nucleosomal arrays permits cells to tightly regulate and fine-tune gene expression. The ordered disassembly and reassembly of these nucleosomes allows RNA polymerase II (RN...Epigenetics & Chromatin 2013 6:16cWords - systematic microRNA regulatory motif discovery from mRNA expression data
Post-transcriptional regulation of gene expression by small RNAs and RNA binding proteins is of fundamental importance in development of complex organisms, and dysregulation of regulatory RNAs can influence on...Silence 2013 4:2Generation of a luciferase-based reporter for CHH and CG DNA methylation inArabidopsis thaliana
DNA methylation ensures genome integrity and regulates gene expression indiverse eukaryotes. In Arabidopsis, methylation occurs in threesequence contexts: CG, CHG and CHH. The initial establishment of DNAmethylat...Silence 2013 4:1Strand-specific libraries for high throughput RNA sequencing (RNA-Seq) prepared without poly(A) selection
High throughput DNA sequencing technology has enabled quantification of all the RNAs in a cell or tissue, a method widely known as RNA sequencing (RNA-Seq). However, non-coding RNAs such as rRNA are highly abu...Silence 2012 3:9Mediator regulates non-coding RNA transcription at fission yeast centromeres
In fission yeast, centromeric heterochromatin is necessary for the fidelity of chromosome segregation. Propagation of heterochromatin in dividing cells requires RNA interference (RNAi) and transcription of cen...Epigenetics & Chromatin 2012 5:19MicroRNAs from the same precursor have different targeting properties
The processing of a microRNA results in an intermediate duplex of two potential mature products that derive from the two arms (5′ and 3′) of the precursor hairpin. It is often suggested that one of the sequenc...Silence 2012 3:8Development of a luciferase-based reporter of transcriptional gene silencing that enables bidirectional mutant screening in Arabidopsis thaliana
Cytosine methylation is an important chromatin modification that maintains genome integrity and regulates gene expression through transcriptional gene silencing. Major players in de novo methylation guided by siR...Silence 2012 3:6Application of RNA silencing to plant disease resistance
To reduce the losses caused by plant pathogens, plant biologists have adopted numerous methods to engineer resistant plants. Among them, RNA silencing-based resistance has been a powerful tool that has been us...Silence 2012 3:5Reducing ligation bias of small RNAs in libraries for next generation sequencing
The use of nucleic acid-modifying enzymes has driven the rapid advancement in molecular biology. Understanding their function is important for modifying or improving their activity. However, functional analysi...Silence 2012 3:4Target gene expression levels and competition between transfected and endogenous microRNAs are strong confounding factors in microRNA high-throughput experiments
MicroRNA (miRNA) target genes tend to have relatively long and conserved 3' untranslated regions (UTRs), but to what degree these characteristics contribute to miRNA targeting is poorly understood. Different h...Silence 2012 3:3Noncoding RNA localisation mechanisms in chromatin regulation
An important challenge in biology has been to understand how cell-type-specific expression programs are orchestrated through regulated access to chromatin. Knowledge of the interaction between noncoding RNAs (...Silence 2012 3:2Inhibition of microRNA function by antimiR oligonucleotides
MicroRNAs (miRNAs) have emerged as important post-transcriptional regulators of gene expression in many developmental and cellular processes. Moreover, there is now ample evidence that perturbations in the lev...Silence 2012 3:1Enhancer-driven chromatin interactions during development promote escape from silencing by a long non-coding RNA
Gene regulation in eukaryotes is a complex process entailing the establishment of transcriptionally silent chromatin domains interspersed with regions of active transcription. Imprinted domains consist of clus...Epigenetics & Chromatin 2011 4:21The dose can make the poison: lessons learned from adverse in vivotoxicities caused by RNAi overexpression
For the past five years, evidence has accumulated that vector-mediated robust RNA interference (RNAi) expression can trigger severe side effects in small and large animals, from cytotoxicity and accelerated tu...Silence 2011 2:8Helicobacter pylori interferes with an embryonic stem cell micro RNA cluster to block cell cycle progression
MicroRNAs, post-transcriptional regulators of eukaryotic gene expression, are implicated in host defense against pathogens. Viruses and bacteria have evolved strategies that suppress microRNA functions, result...Silence 2011 2:7Pluripotency factor binding and Tsix expression act synergistically to repress Xist in undifferentiated embryonic stem cells
Expression of Xist, the master regulator of X chromosome inactivation, is extinguished in pluripotent cells, a process that has been linked to programmed X chromosome reactivation. The key pluripotency transcript...Epigenetics & Chromatin 2011 4:17Noncoding RNAs and cancer
The study of miRNAs and other noncoding RNAs has revolutionised our understanding of gene expression regulation during cancer development and progression, creating one of the fastest-growing research fields in...Silence 2011 2:6Posttranslational modification of Argonautes and their role in small RNA-mediated gene regulation
Shortly after their discovery, repertoires of miRNA were identified, together with proteins involved in their biogenesis and action. It is now obvious that miRNA-mediated gene regulation itself is regulated at...Silence 2011 2:5A 5′-uridine amplifies miRNA/miRNA* asymmetry in Drosophilaby promoting RNA-induced silencing complex formation
MicroRNA (miRNA) are diverse in sequence and have a single known sequence bias: they tend to start with uridine (U).Silence 2011 2:4Off-target effects dominate a large-scale RNAi screen for modulators of the TGF-β pathway and reveal microRNA regulation of TGFBR2
RNA interference (RNAi) screens have been used to identify novel components of signal-transduction pathways in a variety of organisms. We performed a small interfering (si)RNA screen for novel members of the t...Silence 2011 2:3Experimental design, preprocessing, normalization and differential expression analysis of small RNA sequencing experiments
Prior to the advent of new, deep sequencing methods, small RNA (sRNA) discovery was dependent on Sanger sequencing, which was time-consuming and limited knowledge to only the most abundant sRNA. The innovation...Silence 2011 2:2Effect of small interfering RNA 3'-end overhangs on chemosensitivity to thymidylate synthase inhibitors
Small interfering RNAs (siRNAs) are double-stranded RNAs that effectively inhibit expression of its complimentary target mRNA. Standard siRNAs contain two nucleotide overhangs on their 3' end. While these over...Silence 2011 2:1MicroR159 regulation of most conserved targets in Arabidopsis has negligible phenotypic effects
A current challenge of microRNA (miRNA) research is the identification of biologically relevant miRNA:target gene relationships. In plants, high miRNA:target gene complementarity has enabled accurate target pr...Silence 2010 1:18A structural-based statistical approach suggests a cooperative activity of PUM1 and miR-410 in human 3'-untranslated regions
Micro (mi)RNAs comprise a large family of small non-coding RNAs that are thought to regulate a large fraction of protein-coding genes. Generally, miRNAs downregulate messenger (m)RNA expression by binding to t...Silence 2010 1:17In vivo quantification of formulated and chemically modified small interfering RNA by heating-in-Triton quantitative reverse transcription polymerase chain reaction (HIT qRT-PCR)
While increasing numbers of small interfering RNA (siRNA) therapeutics enter into clinical trials, the quantification of siRNA from clinical samples for pharmacokinetic studies remains a challenge. This challe...Silence 2010 1:16An endogenous F-box protein regulates ARGONAUTE1 in Arabidopsis thaliana
ARGONAUTE1 (AGO1) mediates microRNA- and small interfering RNA-directed posttranscriptional gene silencing in Arabidopsis thaliana. Mutant alleles of SQUINT (SQN) slightly reduce AGO1 activity and have weak effec...Silence 2010 1:15A status report on RNAi therapeutics
Fire and Mello initiated the current explosion of interest in RNA interference (RNAi) biology with their seminal work in Caenorhabditis elegans. These observations were closely followed by the demonstration of RN...Silence 2010 1:14RNA silencing in plants: Flash report!
Earlier this year plant scientists met in Santa Fe, New Mexico at the Keystone Symposium "RNA Silencing Mechanisms in Plants". Sessions included small RNA biogenesis and signalling, development and stress resp...Silence 2010 1:13Naturally occurring variations in sequence length creates microRNA isoforms that differ in argonaute effector complex specificity
Micro(mi)RNAs are short RNA sequences, ranging from 16 to 35 nucleotides (miRBase; http://www.mirbase.org). The majority of the identified sequences ar...Silence 2010 1:12How do miRNAs mediate translational repression?
Micro(mi)RNAs regulate gene expression by what are believed to be related but separate mechanistic processes. The relative contribution that each process plays, their mechanistic overlap, and the degree by whi...Silence 2010 1:11Efficiency of Xist-mediated silencing on autosomes is linked to chromosomal domain organisation
X chromosome inactivation, the mechanism used by mammals to equalise dosage of X-linked genes in XX females relative to XY males, is triggered by chromosome-wide localisation of a cis-acting non-coding RNA, Xist....Epigenetics & Chromatin 2010 3:10Specificity and functionality of microRNA inhibitors
Micro(mi)RNAs regulate gene expression through translational attenuation and messenger (m)RNA degradation, and are associated with differentiation, homeostasis and disease. Natural miRNA target recognition is ...Silence 2010 1:10Inhibiting miRNA in Caenorhabditis elegans using a potent and selective antisense reagent
Antisense reagents can serve as efficient and versatile tools for studying gene function by inhibiting nucleic acids in vivo. Antisense reagents have particular utility for the experimental manipulation of the ac...Silence 2010 1:9Riding in silence: a little snowboarding, a lot of small RNAs
The recent symposium, RNA silencing: Mechanism, Biology and Applications, organized by Phillip D. Zamore (University of Massachusetts Medical School) and Beverly Davidson (University of Iowa), and held in Keyston...Silence 2010 1:8microRNA as a new immune-regulatory agent in breast milk
Breast milk is a complex liquid that provides nutrition to the infant and facilitates the maturation of the infant's immune system. Recent studies indicated that microRNA (miRNA) exists in human body fluid. Be...Silence 2010 1:7Development of the human cancer microRNA network
MicroRNAs are a class of small noncoding RNAs that are abnormally expressed in different cancer cells. Molecular signature of miRNAs in different malignancies suggests that these are not only actively involved...Silence 2010 1:6Expression patterns of intronic microRNAs in Caenorhabditis elegans
MicroRNAs (miRNA) are an abundant and ubiquitous class of small RNAs that play prominent roles in gene regulation. A significant fraction of miRNA genes reside in the introns of the host genes in the same orie...Silence 2010 1:5Aptamer-targeted cell-specific RNA interference
This potent ability of small interfering (si)RNAs to inhibit the expression of complementary RNA transcripts is being exploited as a new class of therapeutics for a variety of diseases. However, the efficient ...Silence 2010 1:4How to slice: snapshots of Argonaute in action
Argonaute is the principal protein component of the mechanisms of RNA silencing, providing anchor sites for the small guide RNA strand and the 'slicer' activity for cleavage of target mRNAs or short passenger ...Silence 2010 1:3Solution structure of the Drosha double-stranded RNA-binding domain
Drosha is a nuclear RNase III enzyme that initiates processing of regulatory microRNA. Together with partner protein DiGeorge syndrome critical region 8 (DGCR8), it forms the Microprocessor complex, which clea...Silence 2010 1:2Interaction of RNA polymerase II and the small RNA machinery affects heterochromatic silencing in Drosophila
Heterochromatin is the tightly packaged dynamic region of the eukaryotic chromosome that plays a vital role in cellular processes such as mitosis and meiotic recombination. Recent experiments in Schizosaccharomyc...Epigenetics & Chromatin 2009 2:15A role for non-coding Tsix transcription in partitioning chromatin domains within the mouse X-inactivation centre
Delimiting distinct chromatin domains is essential for temporal and spatial regulation of gene expression. Within the X-inactivation centre region (Xic), the Xist locus, which triggers X-inactivation, is juxtapos...Epigenetics & Chromatin 2009 2:8Dicer regulates Xist promoter methylation in ES cells indirectly through transcriptional control of Dnmt3a
X chromosome inactivation is the mechanism used in mammals to achieve dosage compensation of X-linked genes in XX females relative to XY males. Chromosome silencing is triggered in cis by expression of the non-co...Epigenetics & Chromatin 2008 1:2
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