Tag Archives: Nature
Scientists home in on a short list of interesting RNA ‘machines.’
by Elizabeth Dougherty, MIT News correspondent
DNA stores the information of life, proteins provide the action, and in between sits elusive RNA, which serves both as a database of information and as a molecular machine. RNA is more flexible than DNA, and its three-dimensional structures are more complex than proteins. When studied in the laboratory, RNA bends into so many convolutions that it is nearly impossible to tease out which folds are worthy of scientific inquiry and which can safely be ignored.
New collaborative work from computational biologists at MIT and experimental biologists at the University of California at San Francisco (UCSF), however, is easing that distinction by combining computational and experimental approaches to identifying biologically meaningful RNA folds. The work, published this week in Nature, could open the door to a better understanding of RNA machinery — which ranges from the ribosome, a molecular factory that manufactures proteins, to microRNAs and riboswitches, tiny devices that regulate gene expression, to long noncoding RNAs whose diverse functions are only beginning to be understood.
Origins of Genomic ‘Dark Matter’ Discovered
from Science Daily
A duo of scientists at Penn State University has achieved a major milestone in understanding how genomic “dark matter” originates. This “dark matter” — called non-coding RNA — does not contain the blueprint for making proteins and yet it comprises more than 95 percent of the human genome. The researchers have discovered that essentially all coding and non-coding RNA originates at the same types of locations along the human genome. The team’s findings eventually may help to pinpoint exactly where complex-disease traits reside, since the genetic origins of many diseases reside outside of the coding region of the genome.
The research, which will be published as an Advance Online Publication in the journal Nature on 18 September 2013, was performed by B. Franklin Pugh, holder of the Willaman chair in Molecular Biology at Penn State, and postdoctoral scholar Bryan Venters, who now holds a faculty position at Vanderbilt University.
RNA: The genome’s rising stars
from Nature by Amy Maxmen
When Saba Valadkhan lingered in the hallways at conferences, absorbed in discussions about the strands of ‘junk’ DNA that litter the human genome, she was not looking for work. She was consumed with curiosity about the possibility that long RNA sequences that do not encode proteins nevertheless have a function — enhancing or suppressing gene expression. Valadkhan’s enthusiasm about the budding field of long non-coding RNA (lncRNA) did not go unnoticed: senior investigators were on the hunt for young researchers willing to pursue the topic. “Before I was even looking for job opportunities, I was told about people who were hiring,” says Valadkhan. Soon after receiving her PhD for studies on small nuclear RNA — a type of non-coding RNA — at Columbia University in New York in 2003, she took a position as an assistant professor at Case Western Reserve University in Cleveland, Ohio.
John Rinn, now a molecular biologist at Harvard University and the Broad Institute of MIT and Harvard in Cambridge, Massachusetts, also had a rapid career launch; as a postdoc at Stanford University in California, he was noticed at meetings where he spoke about his research on how lncRNA silences genes involved in embryonic development. Rinn was offered several faculty positions, but was sold on the Cambridge post when Stuart Schreiber, a chemical biologist and a founding member of the Broad Institute, told him: “Every day I come to work dreaming of how I will bend the genome to my will.” Rinn wanted to bend the genome with lncRNA to learn how to prevent and cure diseases.
Incoming search terms:
- How much of the human genome encodes protein
Long non-coding RNAs act like enhancers of gene regulation
from The Max Planck Institute for Molecular Medicine
LncRNA, the Place to Be
from GenomeWeb
The field of long non-coding RNAs is moving from the fringe into mainstream research, bringing a number of young researchers with it, writes Amy Maxmen at Nature. While there is enthusiasm for the field, she adds, lncRNA studies can still be difficult to tackle. “There are no optimized experimental protocols and few clues to the habits of individual lncRNAs, so experiments often fail,” she says. “And when they do work, investigators need to go the extra mile to convince reviewers that their results are real.”
“I have had so many conversations where people think I’m just full of crap,” Kevin Morris, from the Scripps Research Institute tells Nature. “You need a thick skin to be in this field. You need to do it because you love it.”
And researchers who are taking on the problem are in demand, Maxmen says. Case Western Reserve University’s Saba Valadkhan “was consumed with curiosity about the possibility that long RNA sequences that do not encode proteins nevertheless have a function — enhancing or suppressing gene expression,” and more senior researchers noticed. Valadkhan says that before she even began to look for a job, she was hearing about job openings.
Further, there are funding opportunities for lncRNA studies. Maxmen notes that 28 grant applications for lncRNA studies were approved in 2012, and that more a announcements are specifically targeted at lncRNA studies.
(read more…)