Real-Time Dynamics of RNA Polymerase II Clustering in Live Human Cells. Transcription is reported to be spatially compartmentalized in nuclear transcription factories with clusters of RNA polymerase II (Pol II). However, little is known about when these foci assemble or their relative stability. We developed a quantitative single-cell approach to characterize protein spatiotemporal organization, with single-molecule sensitivity in live eukaryotic cells. We observed that Pol II clusters form transiently, with an average lifetime of 5.1 (± 0.4) seconds, which refutes the notion that they are statically assembled substructures. Stimuli affecting transcription yielded orders-of-magnitude changes in the dynamics of Pol II clusters, which implies that clustering is regulated and plays a role in the cell’s ability to effect rapid response to external signals.
In higher eukaryotes, messenger RNA (mRNA) synthesis is thought to involve foci of clustered RNA polymerase II (Pol II) called transcription factories. Science Magazine: Sign In. Science Magazine: Sign In. Transcription is reported to be spatially compartmentalized in nuclear transcription factories with clusters of RNA polymerase II (Pol II). However, little is known about when these foci assemble or their relative stability. We developed a quantitative single-cell approach to characterize protein spatiotemporal organization, with single-molecule sensitivity in live eukaryotic cells.
More Transcription is reported to be spatially compartmentalized in nuclear transcription factories with clusters of RNA polymerase II (Pol II). However, little is known about when these foci assemble or their relative stability. Science Magazine: Sign In. Science Magazine: Sign In. Science Magazine: Sign In. Broad-scale genome tinkering with help of an RNA guide. Duke researchers have devised a way to quickly and easily target and tinker with any gene in the human genome. The new tool, which builds on an RNA-guided enzyme they borrowed from bacteria, is being made freely available to researchers who may now apply it to the next round of genome discovery.
The new method also has obvious utility for gene therapy and for efforts to reprogram stem or adult cells into other cell types -- for example, to make new neurons from skin cells. "We have the genome sequence and we know what all the parts are, but we are still in need of methods to manipulate it easily and precisely," says assistant professor Charles Gersbach, of Duke's Pratt School of Engineering and the Duke Institute for Genome Sciences & Policy.
"That's where this engineering tool comes in. " Gersbach's team had already been in the business of tinkering with the genome using specially engineered proteins, but the process was difficult and slow. Source: Duke University. Sanford-Burnham researchers develop novel nanoparticle to deliver powerful RNA interference drugs. Silencing genes that have malfunctioned is an important approach for treating diseases such as cancer and heart disease. One effective approach is to deliver drugs made from small molecules of ribonucleic acid, or RNA, which are used to inhibit gene expression. The drugs, in essence, mimic a natural process called RNA interference. In a new paper appearing today online in the journal, ACS Medicinal Chemistry Letters, researchers at Sanford-Burnham Medical Research Institute have developed nanoparticles that appear to solve a big challenge in delivering the RNA molecules, called small interfering RNA, or siRNA, to the cells where they are needed.
By synthesizing a nanoparticle that releases its siRNA cargo only after it enters targeted cells, Dr. Tariq M. "Our study describes a strategy to reduce toxic effects of nanoparticles, and deliver a cargo to its target," said Dr. Dr. The next step, Dr. Source: Sanford-Burnham Medical Research Institute. Science Magazine: Sign In. Science Magazine: Sign In. Science Magazine: Sign In. Science Magazine: Sign In. Science Magazine: Sign In. Science Magazine: Sign In. Science Magazine: Sign In. Science Magazine: Sign In. Science Magazine: Sign In. Science Magazine: Sign In. Science Magazine: Sign In. Science Magazine: Sign In. Science Magazine: Sign In. Science Magazine: Sign In. Science Magazine: Sign In. RNA chaperones are ubiquitous, heterogeneous proteins essential for RNA structural biogenesis and function. We investigated the mechanism of chaperone-mediated RNA folding by following the time-resolved dimerization of the packaging domain of a retroviral RNA at nucleotide resolution.
In the absence of the nucleocapsid (NC) chaperone, dimerization proceeded through multiple, slow-folding More RNA chaperones are ubiquitous, heterogeneous proteins essential for RNA structural biogenesis and function. We investigated the mechanism of chaperone-mediated RNA folding by following the time-resolved dimerization of the packaging domain of a retroviral RNA at nucleotide resolution.
In the absence of the nucleocapsid (NC) chaperone, dimerization proceeded through multiple, slow-folding intermediates. In the presence of NC, dimerization occurred rapidly through a single structural intermediate. Science Magazine: Sign In. Science Magazine: Sign In. Science Magazine: Sign In. Science Magazine: Sign In. Science Magazine: Sign In. MicroRNAs (miRNAs) control gene expression through both translational repression and degradation of target messenger RNAs (mRNAs).
However, the interplay between these processes and the precise molecular mechanisms involved remain unclear. Here, we show that translational inhibition is the primary event required for mRNA degradation. Translational inhibition depends on miRNAs impairing More MicroRNAs (miRNAs) control gene expression through both translational repression and degradation of target messenger RNAs (mRNAs).
However, the interplay between these processes and the precise molecular mechanisms involved remain unclear. Here, we show that translational inhibition is the primary event required for mRNA degradation. Translational inhibition depends on miRNAs impairing the function of the eIF4F initiation complex. Science Magazine: Sign In. Science Magazine: Sign In. Science Magazine: Sign In.
Science Magazine: Sign In. Science Magazine: Sign In. 'Activating' RNA takes DNA on a loop through time and space. Long segments of RNA -- encoded in our DNA but not translated into protein -- are key to physically manipulating DNA in order to activate certain genes. These non-coding RNA-activators (ncRNA-a) have a crucial role in turning genes on and off during early embryonic development, researchers say, and have also been connected with diseases, including some cancers, in adults.
In an online article of the journal Nature, a team of scientists led by Wistar's Ramin Shiekhattar, Ph.D., detail the mechanism by which long non-coding RNA-activators promote gene expression. They show how these RNA molecules help proteins in the cell to create a loop of DNA in order to open up genes for transcription. Their experiments have also described how particular ncRNA-a molecules are related to FG syndrome, a genetic disease linked to severe neurological and physical deficits.
Source: The Wistar Institute. Science Magazine: Sign In. Science Magazine: Sign In. The presence of DNA in the cytoplasm of mammalian cells is a danger signal that triggers host immune responses such as the production of type I interferons. Cytosolic DNA induces interferons through the production of cyclic guanosine monophosphate–adenosine monophosphate (cyclic GMP-AMP, or cGAMP), which binds to and activates the adaptor More The presence of DNA in the cytoplasm of mammalian cells is a danger signal that triggers host immune responses such as the production of type I interferons.
Cytosolic DNA induces interferons through the production of cyclic guanosine monophosphate–adenosine monophosphate (cyclic GMP-AMP, or cGAMP), which binds to and activates the adaptor protein STING. Through biochemical fractionation and quantitative mass spectrometry, we identified a cGAMP synthase (cGAS), which belongs to the nucleotidyltransferase family.
Overexpression of cGAS activated the transcription factor IRF3 and induced interferon-β in a STING-dependent manner. Science Magazine: Sign In. Bacteria and archaea have evolved adaptive immune defenses, termed clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated (Cas) systems, that use short RNA to direct degradation of foreign nucleic acids. Here, we engineer the type II bacterial CRISPR system to function with custom guide RNA (gRNA) in human cells. For the More Bacteria and archaea have evolved adaptive immune defenses, termed clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated (Cas) systems, that use short RNA to direct degradation of foreign nucleic acids. Here, we engineer the type II bacterial CRISPR system to function with custom guide RNA (gRNA) in human cells.
Science Magazine: Sign In. Science Magazine: Sign In. The retinoic acid–inducible gene I (RIG-I)–like receptor (RLR) melanoma differentiation–associated protein 5 (MDA5) senses cytoplasmic viral RNA and activates antiviral innate immunity. To reveal how paramyxoviruses counteract this response, we determined the crystal structure of the MDA5 adenosine 5′-triphosphate (ATP)–hydrolysis domain in complex with the viral inhibitor V protein. The More The retinoic acid–inducible gene I (RIG-I)–like receptor (RLR) melanoma differentiation–associated protein 5 (MDA5) senses cytoplasmic viral RNA and activates antiviral innate immunity.
To reveal how paramyxoviruses counteract this response, we determined the crystal structure of the MDA5 adenosine 5′-triphosphate (ATP)–hydrolysis domain in complex with the viral inhibitor V protein. The V protein unfolded the ATP-hydrolysis domain of MDA5 via a β-hairpin motif and recognized a structural motif of MDA5 that is normally buried in the conserved helicase fold. Science Magazine: Sign In. Science Magazine: Sign In. Science Magazine: Sign In. Metazoan replication-dependent histone messenger RNAs (mRNAs) have a conserved stem-loop (SL) at their 3′-end. The stem-loop binding protein (SLBP) specifically recognizes the SL to regulate histone mRNA metabolism, and the 3′-5′ exonuclease 3′hExo trims its 3′-end after processing. We report the crystal structure of a ternary complex of human SLBP More Metazoan replication-dependent histone messenger RNAs (mRNAs) have a conserved stem-loop (SL) at their 3′-end.
The stem-loop binding protein (SLBP) specifically recognizes the SL to regulate histone mRNA metabolism, and the 3′-5′ exonuclease 3′hExo trims its 3′-end after processing. We report the crystal structure of a ternary complex of human SLBP RNA binding domain, human 3′hExo, and a 26-nucleotide SL RNA. Only one base of the SL is recognized specifically by SLBP, and the two proteins primarily recognize the shape of the RNA.
Science Magazine: Sign In. The Structure of Native Influenza Virion Ribonucleoproteins. Developmental Progression to Infectivity in Trypanosoma brucei Triggered by an RNA-Binding Protein. Science Magazine: Sign In. Organization of the Influenza Virus Replication Machinery. Science Magazine: Sign In. Science Magazine: Sign In. Making a Flu Vaccine Without the Virus. A new vaccine strategy could make flu shots cheaper, safer, and easier to produce. Using synthetic messenger RNA (mRNA) instead of proteins purified from viruses, German scientists have shown they can protect mice, ferrets, and pigs against influenza.
"This is a very interesting new approach," says Hans-Dieter Klenk, a virologist at the University of Marburg in Germany who was not involved in the work. Now, most flu vaccines consist of hemagglutinin and neuraminidase, the two proteins covering the surface of the virus. To produce these molecules, the three predominant influenza strains are cultured in fertilized chicken eggs or, increasingly, in cell culture. Virus is then harvested and broken up so that the two proteins can be purified. How well a given strain grows in either eggs or cells is hard to predict, however, and producing enough virus for millions of vaccine doses takes many months every year. An mRNA vaccine could have other advantages. Science Magazine: Sign In. Multiplex Genome Engineering Using CRISPR/Cas Systems.
Science/AAAS | News - Up to the minute news and features from Science. Science Magazine: Sign In. RNA-Guided Human Genome Engineering via Cas9. Making a Flu Vaccine Without the Virus. Gene Loops Enhance Transcriptional Directionality. Science Magazine: Sign In. Influenza virus ribonucleoprotein complexes (RNPs) are central to the viral life cycle and in adaptation to new host species. RNPs are composed of the viral genome, viral polymerase, and many copies of the viral nucleoprotein. In vitro cell expression of all RNP protein components with four of the eight influenza More Influenza virus ribonucleoprotein complexes (RNPs) are central to the viral life cycle and in adaptation to new host species. RNPs are composed of the viral genome, viral polymerase, and many copies of the viral nucleoprotein.
Science Magazine: Sign In. The influenza viruses cause annual epidemics of respiratory disease and occasional pandemics, which constitute a major public-health issue. The segmented negative-stranded RNAs are associated with the polymerase complex and nucleoprotein (NP), forming ribonucleoproteins (RNPs), which are responsible for virus transcription and replication. We describe the structure of native RNPs derived More The influenza viruses cause annual epidemics of respiratory disease and occasional pandemics, which constitute a major public-health issue. The segmented negative-stranded RNAs are associated with the polymerase complex and nucleoprotein (NP), forming ribonucleoproteins (RNPs), which are responsible for virus transcription and replication.
We describe the structure of native RNPs derived from virions. They show a double-helical conformation in which two NP strands of opposite polarity are associated with each other along the helix. Science Magazine: Sign In. Science Magazine: Sign In. Widespread RNA and DNA Sequence Differences in the Human Transcriptome. Science Magazine: Sign In. Science Magazine: Sign In. Science Magazine: Sign In. Eukaryotic genomes are extensively transcribed, forming both messenger RNAs (mRNAs) and noncoding RNAs (ncRNAs). ncRNAs made by RNA polymerase II often initiate from bidirectional promoters (nucleosome-depleted chromatin) that synthesize mRNA and ncRNA in opposite directions.
We demonstrate that, by adopting a gene-loop conformation, actively transcribed mRNA encoding genes restrict divergent More Eukaryotic genomes are extensively transcribed, forming both messenger RNAs (mRNAs) and noncoding RNAs (ncRNAs). ncRNAs made by RNA polymerase II often initiate from bidirectional promoters (nucleosome-depleted chromatin) that synthesize mRNA and ncRNA in opposite directions.
We demonstrate that, by adopting a gene-loop conformation, actively transcribed mRNA encoding genes restrict divergent transcription of ncRNAs. Science Magazine: Sign In. Science Magazine: Sign In. The Crystal Structure of Human Argonaute2. Science Magazine: Sign In. RNA Plays Meiotic Matchmaker. Science Magazine: Sign In. Science Magazine: Sign In. Science Magazine: Sign In. Science Magazine: Sign In. Response to Comments on “Widespread RNA and DNA Sequence Differences in the Human Transcriptome”
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