‘Junk DNA’

The Y chromosome has been notoriously difficult to sequence due to repetitive elements. Junk, right? Now, researchers from the University of Rochester have found a way to sequence a large portion of the Y chromosome in the fruit fly Drosophila melanogaster—the most that the Y chromosome has been assembled in fruit flies. The research, published in the journal GENETICS, provides new insights into the processes that shape the Y chromosome, “and adds to the evidence that, far from a genetic wasteland, Y chromosomes are highly dynamic and have mechanisms to acquire and maintain genes,” says Amanda Larracuente, an assistant professor of biology at Rochester. Using sequence data generated by new technology that reads long strands of individual DNA molecules, Chang Read More ›

Some researchers wondered whether all that junk DNA supposedly left over from Darwinian evolution actually did something after all so they tested the idea: Patches of seemingly meaningless DNA dotted throughout the genome might actually have a function: helping cells to survive starvation. Two studies published in Nature on 16 January suggest that these stretches of non-coding DNA called introns help to control the rate at which cells grow, conserving energy when food becomes scarce. Michael Marshall, “Cryptic DNA sequences may help cells survive starvation” at Nature Not just “junk DNA” any moreat The Scientist either, it would seem: Two studies contest the idea that the noncoding sequences are just “junk DNA,” demonstrating that they play important roles in the regulation of Read More ›

Researchers Nigel Goldenfeld and Thomas Kuhlman noticed that “half of the human genome is made up of retrotransposons [jumping genes, “junk DNA”], but bacteria hardly have them at all” and wondered what would happen if they just inserted some: “We thought a really simple thing to try was to just take one (retrotransposon) out of my genome and put it into the bacteria just to see what would happen,” Kuhlman said. “And it turned out to be really quite interesting.” Their results, published in the Proceedings of the National Academy of Sciences, give more depth to the history of how advanced life may have emerged billions of years ago—and could also help determine the possibility and nature of life on Read More ›

And we are not sure which ones they are. From ScienceDaily: Research Centre (CNIO) reveals that up to 20% of genes classified as coding (those that produce the proteins that are the building blocks of all living things) may not be coding after all because they have characteristics that are typical of non-coding or pseudogenes (obsolete coding genes). They don’t mean “junk DNA,” do they? Not this again. The work once again highlights doubts about the number of real genes present in human cells 15 years after the sequencing the human genome. Although the most recent data indicates that the number of genes encoding human proteins could exceed 20,000, Federico Abascal, of the Wellcome Trust Sanger Institute in the United Read More ›

From ScienceDaily: Scientists at the MDI Biological Laboratory and the University of Maine have discovered that genetic material in the cell that was previously thought to be “junk” because of its apparent lack of function likely plays a part in regulating genetic circuits responsible for regeneration in highly regenerative animals. … The discovery of these novel long noncoding RNAs and their role in regulating regeneration may lead to an answer to the paramount question that is being examined by scientists at the MDI Biological Laboratory: If highly regenerative animals such as zebrafish and salamanders can regenerate tissues and organs, why we can’t we? The answer could one day lead to the development of drugs to trigger humans’ dormant pathways for Read More ›

From ScienceDaily: Researchers have captured video showing how pieces of DNA once thought to be useless can act as on-off switches for genes. These pieces of DNA are part of over 90 percent of the genetic material that are not genes. Researchers now know that this “junk DNA” contains most of the information that can turn on or off genes. But how these segments of DNA, called enhancers, find and activate a target gene in the crowded environment of a cell’s nucleus is not well understood. Now a team led by researchers at Princeton University has captured how this happens in living cells. The video allows researchers to see the enhancers as they find and connect to a gene to Read More ›

Abstract: Seventeen years after the sequencing of the human genome, the human proteome is still under revision. One in eight of the 22 210 coding genes listed by the Ensembl/GENCODE, RefSeq and UniProtKB reference databases are annotated differently across the three sets. We have carried out an in-depth investigation on the 2764 genes classified as coding by one or more sets of manual curators and not coding by others. Data from large-scale genetic variation analyses suggests that most are not under protein-like purifying selection and so are unlikely to code for functional proteins. A further 1470 genes annotated as coding in all three reference sets have characteristics that are typical of non-coding genes or pseudogenes. These potential non-coding genes also Read More ›

With respect to “A “junk DNA” jumping gene is critical for embryo cell development, philosopher of biology Paul Nelson writes to say, In personal correspondence over the past couple of years with a tenured geneticist at a major university who is a “junk DNA” proponent, I’ve pointed out that “x has no function” propositions in biology have just about the worst track record one can imagine. Namely, the propositions lead nowhere (empirically), and sit in a forlorn dim corner with other such propositions, waiting to be overturned by research. One doesn’t need to be an ID proponent to see that natural scientific curiosity will have investigators poking at apparent junk, wondering what it might be doing. As expressed beautifully in Read More ›