In vivo analysis of Caenorhabditis elegans noncoding RNA promoter motifs Aug 5, 2008
Upstream motifs 2 and 3 do not drive GFP expression, and termination at consecutive T runs suggests transcription by RNA polymerase III. The UM2 sequence resembles the tRNA promoter, and is actually embedded within its own short-lived, primary transcript. This is a structure which is also found at a few plant and yeast loci, and may indicate an evolutionarily very old dicistronic transcription pattern in which a tRNA serves as a promoter for an adjacent snoRNA.. (BioMed Central)
'Dragon' protein may hold key to bird flu cure Jul 17, 2008
In H5N1, the most important of these proteins is thought to be RNA polymerase, which contains the instructions that allows the virus to copy itself along with all of its genetic material. Researchers focussed on H5N1's RNA polymerase protein, which contains three subunits: PA, PB1 and PB2. (Sify.com, India)
Specific genetic markers for detecting subtypes of dengue virus serotype-2 in isolates from the states of Oaxaca and Veracruz, Mexico. Jul 15, 2008
Partial nucleotide sequences of the genes encoding C- prM (14 sequences), the NS3 helicase domain (7 sequences), the NS5 S-adenosyl methionine transferase domain (7 sequences) and the RNA-dependent RNA polymerase (RdRp) domain (18 sequences) were obtained. Phylogenetic analysis showed that DENV-2 isolates belonged to the Asian/American genotype. (BioMed Central)
RNA Emerges From DNA's Shadow Jul 14, 2008
Quite simply, this speeds up the transcription process of reading the gene because the enzyme concerned, RNA Polymerase, can just keep on encircling the loop. As Proudfoot explained, this is relevant for quality control as well. (Science Daily)
Genome communication Jun 27, 2008
The gene mediator of paramutation1 (mop1), an RNA dependent RNA polymerase is absolutely required for paramutation silencing at the b1 locus as well as for several other maize genes. In Arabidopsis, this RNA polymerase is associated with the production of small, interfering RNAs (siRNA) that function in gene silencing in other contexts. (EurekAlert!)
New Role For Factor Critical To Transcription Identified Jun 24, 2008
ScienceDaily (June 24, 2008) The Stowers Institute s Shilatifard Lab has identified a new role for the elongation factor ELL in gene transcription by RNA polymerase II (Pol II) the enzyme that synthesizes messenger RNA to carry genetic information from DNA to the protein-synthesizing machinery of the cell ... 18, 2005) The transcriptional activator, HIV-1 Tat, not only acts by promoting RNA polymerase processivity, but it is able to promote transcription complex assembly in the absence of... (Science Daily)
How Cell's Master Transcribing Machine Achieves Near Perfection Jun 7, 2008
Now, researchers have discovered new details of how the cell's major transcriptional machinery, RNA polymerase II (Pol II), functions with such exquisite precision ... Instead, the enzyme RNA polymerase II and ... 3, 2007) Scientists reveal a surprising new role for tDNAs and RNA polymerase III-associated proteins in sister chromatid cohesion. (Science Daily)
'PLoS ONE' STUDY: A Low Dose of Dietary Resveratrol Partially Mimics Caloric Restriction and Retards Aging Parameters in Mice Jun 4, 2008
Only four GO terms were impacted by both CR and resveratrol across all tissues (), and these were chromatin assembly or disassembly (GO:0006333), regulation of transcription from RNA Polymerase II promoter (GO:0006357), transcription from RNA polymerse II promoter (GO:0006366), and ubiquitin cycle (GO:0006512). Analysis of individual genes within these classes suggests that both CR and resveratrol have a major impact on expression of genes that play important roles in chromatin remodeling that... (USA Today -- Tech)
An Ancient Protein Balances Gene Activity And Silences Foreign DNA In Bacteria May 20, 2008
RNA polymerase moves along the DNA molecule, copying its sequence of letters into ribonucleic acid. A protein called Rho binds to the newly-synthesized RNA and blocks the polymerase, preventing it from expressing toxic genes. (Science Daily)
Key Roadblock To Gene Expression Identified: Implications For AIDS May 10, 2008
They also showed that RNA polymerase--the enzyme that reads genes as the first step in making proteins--is stopped at the first nucleosome, where it remains idle until it is directed to continue moving forward. "This discovery is important because nucleosomes are barriers to transcription and we now are seeing the impact of nucleosome organization on RNA polymerase," said lead investigator B. Franklin Pugh, professor and Willaman Chair in Molecular Biology at Penn State University ... In yeast,... (Science Daily)
Cold Spring Harbor Protocols features classic approaches for analyzing chromosomes May 2, 2008
Spread polytene chromosomes of salivary glands from a Drosophila larva were triple-stained with fluorescently tagged antibodies to Heat Shock Transcription Factor (red), RNA Polymerase II (green), and P-TEFb kinase (blue). COLD SPRING HARBOR, N.Y. (Thursday, May 1, 2008) Recent discoveries have led to a revolution in the field of epigenetics, the study of gene regulation through the modulation of chromatin. (EurekAlert!)
Algorithm Finds The Network -- For Genes Or The Internet Mar 20, 2008
"We've identified the substructures of three different RNA polymerase complexes from noisy data, for instance, which are crucial for gene transcription." ... Using machine learning techniques, Zhang and his collaborators showed that almost all intergenic microRNA genes in four model species, human, mouse, rice and mustard plant (Arabidopsis), are transcribed by RNA polymerase II, which transcribes protein-coding genes. (Science Daily)
Scientists see Norwalk virus' Achilles heel Mar 19, 2008
The Norwalk virus uses the enzyme, RNA polymerase, to make new strands of RNA using an existing RNA strand as a template. The copying, which occurs within an area of the enzyme called an active site, can be blockedor inhibited--with a drug molecule shaped to fit the site, like a key in a key hole. (EurekAlert!)
First Direct Observation Of 3-D Molecule Folding In Real Time Feb 22, 2008
To make RNA, a protein called RNA polymerase moves along the length of a strand of DNA. It reads a pattern in the building blocks of DNA, nucleic acids whose names are abbreviated A, C, G and T, and it makes RNA with a complementary pattern. This long strand of RNA is then the recipe for a specific protein. (Science Daily)
Solubility enhancement of aggregation-prone heterologous proteins by fusion expression using stress-responsive Escherichia coli protein, RpoS Feb 19, 2008
We analyzed the Escherichia coli proteome response to the exogenous stress of guanidine hydrochloride using 2-dimensional gel electrophoresis and found that RpoS (RNA polymerase sigma factor) was significantly stress responsive. While under the stress condition the total number of soluble proteins decreased by about 7 %, but a 6-fold increase in the level of RpoS was observed, indicating that RpoS is a stress-induced protein. (BioMed Central)
Location Matters, Even For Genes Feb 16, 2008
Instead, the enzyme RNA polymerase II and. (Mar. (Science Daily)
'Molecular Glue' Cohesin Acts As Regulator Of Gene Expression Feb 14, 2008
3, 2007) Scientists reveal a surprising new role for tDNAs and RNA polymerase III-associated proteins in sister chromatid cohesion. Sister chromatid cohesion (the binding together of the two identical copies. (Science Daily)
All and only CpG containing sequences are enriched in promoters abundantly bound by RNA polymerase II in multiple tissues Feb 6, 2008
The promoters of housekeeping genes are well-bound by RNA polymerase II (RNAP) in different tissues. Although the promoters of these genes are known to contain CpG islands, the specific DNA sequences that are associated with high RNAP binding to housekeeping promoters has not been described. (BioMed Central)
New Light Shed On The Mechanics Of Gene Transcription Jan 10, 2008
Instead, the enzyme RNA polymerase II (Pol II) and other key molecules can assemble at the site of an activated gene, regardless of the gene's position. See also. (Science Daily)
Evolution With A Restricted Number Of Genes Dec 19, 2007
18, 2007) The development of higher forms of life would appear to have been influenced by RNA polymerase II. This enzyme transcribes the information coded by genes from DNA into messenger-RNA (mRNA), which in turn is the basis for the production of proteins. RNA polymerase II is highly conserved through evolution, with many of its structural characteristics being conserved between bacteria and humans ... Dirk Eick at the Institute of Clinical Molecular Biology and Tumor Genetics, GSF National... (Science Daily)
Enzyme Mutation Disrupts Organ Growth Nov 29, 2007
A key player in the process--called transcription--is the enzyme RNA polymerase III. A new study reports that a mutation of this enzyme prevents cell division, but surprisingly, only affects the development of specific organs ... A team of researchers led by Dr. Michael Pack, at the University of Pennsylvania, investigated the mutation in RNA polymerase III of the zebrafish, an animal model system that is increasingly being used to study human development and disease ... Seventeen different... (Science Daily)
Comparison of chicken 7SK and U6 RNA polymerase III promoters for short hairpin RNA expression Nov 20, 2007
RNA polymerase III (pol III) type 3 promoters such as U6 or 7SK are commonly used to express short-hairpin RNA (shRNA) effectors for RNA interference (RNAi). To extend the use of RNAi for studies of development using the chicken as a model system, we have developed a system for expressing shRNAs using the chicken 7SK (ch7SK) promoter. (BioMed Central)
Localization of TFIIB binding regions using serial analysis of chromatin occupancy Nov 13, 2007
RNA Polymerase II (RNAP II) is recruited to core promoters by the pre-initiation complex (PIC) of general transcription factors. Within the PIC, transcription factor for RNA polymerase IIB (TFIIB) determines the start site of transcription. (BioMed Central)
Regulation of TATA-less promoters Nov 2, 2007
"This study surprised us on 2 levels; one was the preponderance of TRF2 dependent promoters; the other was the differential usage of TRF2 versus TBP within a gene cluster generally thought to be coordinately regulated. Just goes to show that dogma shifts constantly in this field of transcriptional control, explains Dr. Tjian. In eukaryotic cells, gene transcription is initiated when the RNA polymerase II machinery recognizes and binds to specific core promoter sequences in the gene. While some... (EurekAlert!)
Systematic identification of non-coding RNA 2,2,7-trimethylguanosine cap structures in Caenorhabditis elegans Sep 30, 2007
Our results showed that most ncRNAs predicted to be transcribed by RNA polymerase II had a TMG cap, while those predicted to be transcribed by RNA plymerase III or located in introns did not have a TMG cap structure. Compared to ncRNAs without a TMG cap, TMG-capped ncRNAs tended to have higher expression levels. (BioMed Central)
New Mechanism In Development Of Severe Inherited Disease Discovered Sep 6, 2007
Only if the genes are accessible can the enzyme RNA polymerase go about its work and synthesize new RNA molecules according to the DNA code ... Xuejun Yuan, Weiijun Feng, Axel Imhof, Ingrid Grummt and Yonggang Zhou: Activation of RNA polymerase I transcription by Cockayne Syndrome group B (CSB) protein and histone methyltransferase G9a. (Science Daily)
Enzyme alerts cell's powerful army to repair DNA damage Sep 6, 2007
Scientists know that inside each cell, a little engine called RNA polymerase II does one essential job: It copies instructions from genes in the nucleus that get carried to production units in the rest of the cell to support our daily needs. Now researchers at the University of Michigan Medical School have shown that RNA polymerase II also constantly scans the cells DNA for damage ... When certain types of damage in DNA halt the action of RNA polymerase II, a stress signal is generated that... (EurekAlert!)
Surprising New Role For Proteins In Sister Chromatid Cohesion Sep 4, 2007
Rudra Dubey and Marc Gartenberg (UMDNJ) reveal a surprising new role for tDNAs and RNA polymerase III-associated proteins in sister chromatid cohesion. Sister chromatid cohesion (the binding together of the two identical copies of each chromosome that are formed during replication) helps to ensure that chromosomes are accurately segregated during the anaphase of the cell cycle. (Science Daily)
Scientists Discover The Dynamics Of Transcription In Living Mammalian Cells Aug 8, 2007
The study focused on RNA polymerase II--the enzyme responsible for transcription. During transcription, growing numbers of RNA polymerase II molecules assemble on DNA and then synthesize RNA by sequentially recruiting complementary RNA nucleotides ... Then, by attaching fluorescent tags to RNA polymerase II, they were able to closely monitor all three phases of the transcription process: binding of the enzyme molecules to DNA, initiation (when the enzyme links the first few RNA nucleotides... (Science Daily)
Researchers Watch Antibiotics, Bacteria Meet At Atomic Level Jul 31, 2007
The green "noodles" represent RNA polymerase ... In the first study, the team found that they could create a detailed image of the elongation complex, a structure formed by RNA polymerase ... RNA polymerase is the enzyme responsible for setting gene expression in motion, a process called transcription. (Science Daily)
Gene-transcription machinery seen poised for action, held in check until needed Jul 26, 2007
Once that molecule is removed, the machinery with a molecule known as RNA polymerase II at its core is released and transcription is set into motion. The research was done in yeast, an often-used model organism for genetic studies. (EurekAlert!)
Biochemical characterization of a recombinant Japanese encephalitis virus RNA-dependent RNA polymerase Jul 11, 2007
Japanese encephalitis virus (JEV) NS5 is a viral nonstructural protein that carries both methyltransferase and RNA-dependent RNA polymerase (RdRp) domains. It is a key component of the viral RNA replicase complex that presumably includes other viral nonstructural and cellular proteins. (BioMed Central)
New Pathway Found To Thwart Antibiotic Resistance Jun 25, 2007
In findings published today online in two complementary papers in Nature, the research team describe the differences in an enzyme called RNA polymerase in bacterial cells as opposed to human cells ... RNA polymerase is the key enzyme regulating the transfer of genetic information from DNA to RNA, said Dmitry Vassylyev, Ph ... Specifically, Vassylyev s team traced the similarities and differences between human RNA polymerase and bacteria RNA polymerase, painting a more complete picture of the... (Science Daily)
The promoter and transcribed regions of the Leishmania tarentolae spliced leader RNA gene array are devoid of nucleosomes May 22, 2007
This small nuclear RNA is transcribed by RNA polymerase II from individual promoters. In Leishmania tarentolae the SL RNA genes reside in two multi-copy tandem arrays designated MINA and MINB. The transcript accumulation from the SL promoter on the drug-selected, episomal SL RNA gene cassette pX-tSL is ~10% that of the genomic array in uncloned L. tarentolae transfectants. (BioMed Central)
Researchers Identify Process That Enables Access To Genes May 19, 2007
Tanny used a chromosome immunoprecipitation assay to determine where RNA polymerase the large protein machine that copies DNA into RNA is located in these genes. He found that RNA polymerase had no problem getting to the gene promoter the first step in transcription but there were problems downstream, at the body of the gene ... The real effect of the ubiquitylation mutation on transcription is on the ability of RNA polymerase to get through the gene, rather than the ability of RNA polymerase to... (Science Daily)
Genelabs Technologies Announces Presentation of Data on Non-Nucleoside HCV Polymerase Inhibitor at 20th International Conference on Antiviral Research Meeting May 3, 2007
D., Director of Medicinal Chemistry at Genelabs, entitled "GL59728: A Potent Allosteric Inhibitor of the HCV NS5b RNA Dependent RNA Polymerase with Excellent Pharmacokinetic Properties." GL59728 is one of a number of non-nucleoside HCV polymerase inhibitors discovered by Genelabs. In the presentation, Dr. Roberts outlined the lead optimization of certain non-nucleoside HCV polymerase inhibitors through an iterative process involving testing for potency in directly inhibiting HCV NS5b polymerase,... (PR Newswire)
RNA Enzyme Structure Offers A Glimpse Into The Origins Of Life Mar 17, 2007
Scott and postdoctoral researcher Michael Robertson determined the structure of a ribozyme that joins two RNA subunits together in the same reaction that is carried out in biological systems by the protein known as RNA polymerase ... "An RNA-dependent RNA polymerase ribozyme is the foundation of the entire RNA World hypothesis," Robertson said. (Science Daily)
Hairpins For Switches: Artificial RNA Ligands Differentiate Between On And Off States Of Riboswitches Dec 14, 2006
(June 19, 2006) -- Of the thousands of proteins produced in our cells, few are as important as the enzyme RNA polymerase (RNAP), which has the unique ability to faithfully copy genetic information from DNA. Now a team. . (Science Daily)
Detailed 3-D Image Catches A Key Regulator Of Neural Stem Cell Differentiation In Action Dec 11, 2006
When active, Scp1 prevents the enzyme RNA polymerase II from reading and switching on neuronal genes in tissues where they shouldn't be expressed, such as skin, muscle and liver. In the nervous system Scp1 is switched off, enabling RNA polymerase II to efficiently transcribe information encoded by neuronal genes and driving the maturation of neural stem cells into specialized neurons ... Scp1 is not the only protein that directly influences the activity of RNA polymerase II. A constantly... (Science Daily)
From A Lowly Yeast, Researchers Divine A Clue To Human Disease Dec 8, 2006
Normally, Sen1 acts like a molecular stop sign, telling another protein called RNA polymerase II when to stop transcribing genetic information from DNA into related threads of RNA. The polymerase reads along DNA strands, building RNA as it goes ... Without a properly functional Sen1, RNA polymerase II "reads through" the end of the gene and builds longer and longer RNA messages ... In other cases, Sen1 stop signs near the beginning of some genes normally prevent RNA polymerase II from making RNA... (Science Daily)
Nobel Laureate Finds 'Elegant' Explanation For DNA Transcribing Enzyme's High Fidelity Dec 3, 2006
The fundamental mechanism of transcription is conserved among cellular RNA polymerases, the researchers explained ... "The basis for the extraordinary specificity with which RNA polymerases transcribe DNA lies in a structural element termed the trigger loop, which makes both direct and indirect contact with all features of the nucleotide in the polymerase active center," the researchers concluded ... (June 19, 2006) -- Of the thousands of proteins produced in our cells, few are as important as... (Science Daily)
Scientists Explore Function Of 'Junk DNA' Nov 22, 2006
Expression of the microRNAs required an enzyme called RNA Polymerase III (Pol III) rather than the RNA Polymerase II (Pol II), which mediates expression of RNA that encode proteins. The study is published in Nature Structural and Molecular Biology Advance Online Publication (AOP) on Nov. 12. (Science Daily)
Researchers Unravel A Mystery About DNA Nov 20, 2006
Initial transcription by RNA polymerase proceeds through a "DNA scrunching" mechanism, in which the enzyme remains stationary on promoter DNA and pulls into itself downstream DNA. (Credit: Image provided by Achillefs Kapanidis, Shimon Weiss, and Richard H. Ebright) ... (November 23, 2005) -- By shooting lasers at an RNA polymerase (RNAP) and a strand of DNA, scientists have learned a critical component of how a complex protein ... (June 19, 2006) -- Of the thousands of proteins produced in our... (Science Daily)
Novel experiment documents evolution of genome in near-real time Nov 6, 2006
Mutations also appeared in a second, unrelated gene for an enzyme called RNA polymerase. "That was a surprise to almost everybody because RNA polymerase is involved in one of the core processes of any cell," said Palsson ... "You wouldn't expect that gene to change because a wide variety of cellular process would be affected; it's like replacing the wiring system in a building when a light bulb burns out. But we repeated the experiment more than 50 times and mutations in the RNA polymerase gene... (EurekAlert!)
Self-splicing proteins in eukaryotes Oct 29, 2006
Multiple, non-allelic, intein-coding sequences in eukaryotic RNA polymerase genes ... We identified seven intein coding sequences within nuclear genes coding for the second largest subunits of RNA polymerase ... These sequences were found in diverse eukaryotes: one is in the second largest subunit of RNA polymerase I (RPA2) from the ascomycete fungus Phaeosphaeria nodorum, one is in the RNA polymerase III (RPC2) of the slime mould Dictyostelium discoideum and four intein coding sequences are in... (BioMed Central)
DNA work earns chemistry Nobel Oct 5, 2006
In 2001, he published the first molecular snapshot of an enzyme called RNA polymerase II. Its job is to get the synthesis of proteins underway by copying their genes into RNAs. Medical importance. (BBC News -- Science)
Crystallography grabs chemistry Nobel Oct 5, 2006
Structural determination of RNA polymerase unlocked secrets of cells ... Kornberg, a professor of structural biology at Stanford University, California (where his father is an active emeritus professor), had his major breakthrough in 2001, when he solved the structure of RNA polymerase II an enzyme that helps messenger RNA take information from DNA. By exposing crystals of the polymerase, extracted from yeast, to a brilliant beam of X-rays, he was able to painstakingly determine their structure... (Nature News Service)
With Record Resolution And Sensitivity, Tool Images How Life Organizes In A Cell Membrane Oct 3, 2006
(November 23, 2005) -- By shooting lasers at an RNA polymerase (RNAP) and a strand of DNA, scientists have learned a critical component of how a complex protein. . (Science Daily)
Loss of the flagellum happened only once in the fungal lineage: phylogenetic structure of kingdom Fungi inferred from RNA polymerase II subunit genes Sep 30, 2006
BMC Evolutionary Biology 2006, 6:74 doi:10. Abstract (provisional). (BioMed Central)
Scientists Discuss New Frontiers In Single-molecule Research Sep 21, 2006
But Greenleaf and Block showed that DNA sequencing also can be done by measuring how long a single enzyme, called RNA polymerase, pauses at each base's location. "This process is unique because it uses the motion of RNA polymerase, not chemistry, to sequence DNA," Block said ... (November 23, 2005) -- By shooting lasers at an RNA polymerase (RNAP) and a strand of DNA, scientists have learned a critical component of how a complex protein. (Science Daily)
Molecular signatures (unique proteins and conserved Indels) that are specific for the epsilon proteobacteria (Campylobacterales) Jul 4, 2006
B subunit of exinuclease ABC, phenylalanyl-tRNA synthetase, RNA polymerase b-subunit and FtsH protein) that are specific for either all epsilon proteobacteria or different subgroups. In addition, a rare genetic event that caused fusion of the genes for the largest subunits of RNA polymerase (rpoB and rpoC) in Wolinella and Helicobacter is also described. (BioMed Central)
Basic work on E. coli identifies two new keys to regulation of bacterial gene expression Jun 17, 2006
MADISON - The cellular process of transcription, in which the enzyme RNA polymerase constructs chains of RNA from information contained in DNA, depends upon previously underappreciated sections of both the DNA promoter region and RNA polymerase, according to work done with the bacterium E. coli and published today (June 16) in the journal Cell by a team of bacteriologists from the University of Wisconsin-Madison ... In his most recent study, Gourse investigated the interaction between RNA... (EurekAlert!)
Towards a unified model of transcription termination Apr 7, 2006
The allosteric, or antiterminator, model proposes that transcription of the poly(A) site triggers conformational changes that destabilize the elongating RNA polymerase, resulting in termination. The torpedo model proposes that an exonuclease degrades the nascent RNA, and eventually catches up to the elongation complex, causing its termination. (EurekAlert!)
Idenix Announces Licensing of Valopicitabine (NM283) by Novartis Mar 29, 2006
Valopicitabine blocks hepatitis C virus (HCV) replication by specifically inhibiting the HCV RNA polymerase. In initial clinical trials, valopicitabine, administered orally once a day, was shown to reduce HCV viremia in patients infected with the genotype 1 strain of HCV. The ongoing phase IIb clinical trials are evaluating the combination of valopicitabine and pegylated interferon in hepatitis C patients who previously failed to respond to antiviral treatment, as well as in patients who have... (PR Newswire)
ANA Patterns Mar 14, 2006
A nucleolar pattern is caused by the following antibodies/antigens: RNA polymerase I, which is highly prevalent in scleroderma; fibrillarin and also DNA topoisomerase I (Scl-70), which are both seen in scleroderma; and PM-scL, which is seen in polymyositis. An MSA pattern is caused by antibodies to mitotic spindle apparatus and NuMa; these antibodies can be seen in carpal tunnel syndrome, SLE, and Sjogrens syndrome; the cytoplasmic nucleolus pattern is seen in polymyositis. (Suite101.com)
