thisischristina : 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.
Expression of small nucleolar RNAs in leukemic cells submitted by toareno 1 year and 3 months ago How is competition to be understood as a time-bound activity? While the comparison of task completion success is a central feature of competition, time is routinely used as a principle through which contests are organized, either as a direct measure of success or as a constraining resource that i... submitted by gom 1 year and 1 month ago buildmodels : 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.
JChrisPires : RT @rnomics: Top #tweeted story... 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.
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.
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.
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.
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."
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."
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.
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.