ResearchBlogs : Patterns of RNA methylatio... Patterns of RNA methylation 2. In a recent post I discussed the extent of adenosine methylation in RNAs. Meyer et al. found that m6A was found in many mRNAs and showed a bias in its distribution towards the end of coding sequence, stop codons, and the proximal section of 3’UTRs. The main chemically modified base of DNA is 5-methylcytosine. Squires et al. have surveyed the presence of m5C in human RNAs, and find that this modification is also common in tRNAs, rRNAs, mRNAs and ncRNAs. The principal method for detecting methylated cytosines in nucleic acids is bisulphite sequencing. Bisulphite converts cytosine residues to uracil, but modified cytosines are left unchanged. Surveying RNAs from HeLa cells, Squires et al discovered 255 modified Cs in tRNAs. Most interestingly, the researchers discovered 10, 275 m5C candidate sites in mRNAs and ncRNAs.
Two different methyltransferases are known to catalyse the m5C modification in eukaryotic RNAs, NSUN2 and TRDMT1. Like this: Like Loading... Esciencenews : UMass Medical School resea... Physorg_com : Researchers discover a new... Researchers discover a new role for RNAi. Organisms employ a fascinating array of strategies to identify and restrain invasive pieces of foreign DNA, such as those introduced by viruses. For example, many viruses produce double-stranded (ds)RNA during their life cycle and the RNA interference (RNAi) mechanism is thought to recognize this structural feature to initiate a silencing response. Now, UMass Medical School researchers have identified a mechanism related to RNAi that scans for intruders not by recognizing dsRNA or some other aberrant feature of the foreign sequence, but rather by comparing the foreign sequences to a memory of previously expressed native RNA. Once identified, an "epigenetic memory" of the foreign DNA fragments is created and can be passed on from one generation to the next, permanently silencing the gene.
A remarkable feature of this RNAi-related phenomenon (referred to as RNA-induced epigenetic silencing, or RNAe), is that the animal carries a memory of previous gene expression. Dr. ScienceIndex_ : RNA I... ScienceIndex_ : MetaM... ScienceIndex_ : RNAi-... ScienceIndex_ : A Mov... SciReports : Involvement of RDR6 in sho... Toni10juan : RT @Alexis_Verger: Want to... Sciencedaily : Structure of RNAi complex... Esciencenews : Structure of RNAi complex... Structure of RNAi complex now crystal clear. Researchers at Whitehead Institute and Memorial Sloan-Kettering Cancer Center have defined and analyzed the crystal structure of a yeast Argonaute protein bound to RNA. This complex plays a key role in the RNA interference (RNAi) pathway that silences gene expression. Describing the molecular structure of a eukaryotic Argonaute protein has been a goal of the RNAi field for close to a decade. "You can learn a lot from biochemical experiments, but to more fully understand a protein like Argonaute, it's useful to know where all of the atoms are and which amino acids are playing important roles," says Whitehead Institute Member David Bartel, who is also an MIT professor of biology and a Howard Hughes Medical Institute (HHMI) investigator.
"Learning the Argonaute crystal structure is an important step in understanding the RNAi biochemical pathway and will be the basis for many future experiments. " The yeast Argonaute structure is described in the June 21st print issue of Nature. Physorg_com : Structure of RNAi complex... Structure of RNAi complex now crystal clear. Researchers at the Whitehead Institute and Memorial Sloan-Kettering Cancer Center have defined and analyzed the crystal structure of a yeast Argonaute protein bound to RNA. This complex plays a key role in the RNA interference (RNAi) pathway that silences gene expression. Describing the molecular structure of a eukaryotic Argonaute protein has been a goal of the RNAi field for close to a decade.
"You can learn a lot from biochemical experiments, but to more fully understand a protein like Argonaute, it's useful to know where all of the atoms are and which amino acids are playing important roles," says Whitehead Institute Member David Bartel, who is also an MIT professor of biology and a Howard Hughes Medical Institute (HHMI) investigator. "Learning the Argonaute crystal structure is an important step in understanding the RNAi biochemical pathway and will be the basis for many future experiments.
" The yeast Argonaute structure is described in the June 21st print issue of Nature. ScienceIndex_ : Lack... ScienceIndex_ : Genom... Physorg_com : Lariats: How RNA splicing... Lariats: How RNA splicing decisions are made. Lariats are discarded byproducts of RNA splicing, the process by which genetic instructions for making proteins are assembled. A new study has found hundreds more lariats than ever before, yielding new information about how splicing occurs and how it can lead to disease. Tiny, transient loops of genetic material, detected and studied by the hundreds for the first time at Brown University, are providing new insights into how the body transcribes DNA and splices (or missplices) those transcripts into the instructions needed for making proteins.
The lasso-shaped genetic snippets — they are called lariats — that the Brown team reports studying in the June 17 edition of Nature Structural & Molecular Biology are byproducts of gene transcription. "We used modern genomic methods, deep sequencers, to detect these rare intermediates of splicing," said William Fairbrother, associate professor of biology and senior author of the study. That specific step is known as RNA splicing. Modeling splicing. ScienceIndex_ : RNAiA... ScienceIndex_ : Evalu... ScienceIndex_ : Evolu...
Sciencedaily: Living microprocessor tune... ScienceIndex_ : Oxida... ScienceIndex_ : Isola... ScienceIndex_ : An En... ScienceIndex_ : Prima... ScienceIndex_ : Relat... ScienceIndex_ : The m... Esciencenews : Researchers achieve RNA in... Researchers achieve RNA interference, in a lighter package. Using a technique known as "nucleic acid origami," chemical engineers have built tiny particles made out of DNA and RNA that can deliver snippets of RNA directly to tumors, turning off genes expressed in cancer cells. To achieve this type of gene shutdown, known as RNA interference, many researchers have tried -- with some success -- to deliver RNA with particles made from polymers or lipids. However, those materials can pose safety risks and are difficult to target, says Daniel Anderson, an associate professor of health sciences and technology and chemical engineering, and a member of the David H. Koch Institute for Integrative Cancer Research at MIT.
The new particles, developed by researchers at MIT, Alnylam Pharmaceuticals and Harvard Medical School, appear to overcome those challenges, Anderson says. Because the particles are made of DNA and RNA, they are biodegradable and pose no threat to the body. Genetic disruption Circulate and accumulate. NatureBlogs : RT @m_m_campbell: Ironing... Physorg_com : Researchers achieve RNA in... Researchers achieve RNA interference, in a lighter package. Using a technique known as “nucleic acid origami,” chemical engineers have built tiny particles made out of DNA and RNA that can deliver snippets of RNA directly to tumors, turning off genes expressed in cancer cells. To achieve this type of gene shutdown, known as RNA interference, many researchers have tried — with some success — to deliver RNA with particles made from polymers or lipids.
However, those materials can pose safety risks and are difficult to target, says Daniel Anderson, an associate professor of health sciences and technology and chemical engineering, and a member of the David H. Koch Institute for Integrative Cancer Research at MIT. The new particles, developed by researchers at MIT, Alnylam Pharmaceuticals and Harvard Medical School, appear to overcome those challenges, Anderson says. Anderson is senior author of a paper on the particles appearing in the June 3 issue of Nature Nanotechnology.
Genetic disruption Circulate and accumulate. ScienceIndex_ : IL-6... NatureBlogs : Dissolved iron may have be... Dissolved iron may have been key to RNA-based life. Iron now locked in ancient rock formations may have once enabled an 'RNA world'. More than three billion years ago, in the primordial soup that was the cradle of life on Earth, RNA took on many of the roles that its sister molecule DNA fills today — or so some scientists have speculated. A paper published 31 May in PLoS ONE posits one way that such an ‘RNA world’ could have worked: by making use of iron, a common element in the watery environs of ancient Earth. In an RNA-dominated world, “RNA would have been the genetic material, and would have been the primary enzyme in metabolism,” says Loren Dean Williams, a chemist at the Georgia Institute of Technology in Atlanta and a co-author on the paper.
Today, RNA is best known as the messenger of genetic information, but large RNA molecules can fold into more complex structures, called ribozymes, with the ability to cut or glue other RNAs together. “We’re used to our world of oxygen, and oxygen and iron is just a terrible combination. ScienceIndex_ : Intra... Esciencenews : On early Earth, iron may h... Sciencedaily : Chemical substitution: On... Physorg_com : On early Earth, iron may h... Sciencescape : RT @Jen_Angela: Reducing s... ResearchBlogs : A dual purpose RNA and Hox... A dual purpose RNA and Hox regulation. A new paper in Plos Genetics shows that a long non-coding RNA regulates the expression of a Hox gene in Drosophila in cis. This finding suggests an explanation for the co-linearity displayed by Hox genes between genomic arrangement and expression pattern.
The Ultrabithorax mutant. Hox genes are master-regulators of positional identity along the anterior-posterior axis throughout bilaterian animals. Hox genes are found in genomic clusters in which their 3′-5′ organisation mirrors their expression pattern along the A-P axis. This correspondence between body axis and genomic organisation is termed co-linearity.
The Hox gene cluster is actually divided into two partial clusters in Drosophila; the Antennapedia complex (ANT-C) and the Bithorax complex (BX-C). Figure showing the expression of ABD-A (red), and ABD-B (green) in the embryonic CNS. Abd-A is expressed in the embryonic epidermis and CNS in parasegments (PS) 7-12 but is excluded from PS13. Like this: Like Loading... ScienceIndex_ : From... ScienceIndex_ : Drawb... ScienceIndex_ : Label... ScienceIndex_ : Phylo... ScienceIndex_ : The E... ScienceIndex_: Down-... ScienceIndex_ : Inhib... Sciencedaily : RNA: From messenger to gua... ResearchBlogging.org: Patterns of RNA methylatio... Patterns of RNA methylation. A new paper in Cell provides a transcriptome-wide survey of the methylation of adenosine residues in RNAs. Meyer et al find that this epitranscriptomic post-transcriptional modification is widespread and dynamically regulated, and likely to play important roles in cellular regulation.
Methylation of the N6 position of adenosine residues (m6A) has been known to be a post-transcriptional modification of RNAs for many years. Research in the 1960’s and 70’s demonstrated that m6A is present in tRNAs, rRNAs and viral RNAs, and made up between 0.1% and 0.4% or total adenosines in cellular RNA. However as m6A was not easily detectable by commonly available methods, research on this modified base foundered. A recent spur to experimentation on m6A has come from the analysis of a gene linked to obesity. As m6A is not detectable by sequencing or hybridisation based techniques, nor susceptible to chemical modification, Meyer et al. based their experiments on the use of an anti-m6A antibody (ά-m6A).
Science Index: RNA i... Science Index: Devel... E! Science News: CSHL study uncovers a new... PhysOrg Science News: Research uncovers new exce... E! Science News: Researchers reveal an RNA... Jenie J: Researchers have identifie... PhysOrg Science News: Researchers reveal an RNA... Science Index: RNA S... Science Index: MRNA... Science Index: The R... Science Index: A nov... Science Index: BC1-F... Science Index: Base... Science Index: Revea... Science Index: Meios... Science Index: RNA d... Science Index: The R... Science Index: Chara... Science Index: Compa... Science Index: Malac... ResearchBlogging.org: Fixing mitochindrial mutat... Science Index: RNA-b... RNA-based vaccines. Science Index: The T... View All.
Tom Reinard: Strange cousins: Molecular...