‘Junk DNA’

From ScienceDaily: Researchers have shown that when parts of a genome known as enhancers are missing, the heart works abnormally, a finding that bolsters the importance of DNA segments once considered “junk” because they do not code for specific proteins. … “The cardiac changes that we observed in knockout mice lacking these enhancers highlight the role of noncoding sequences in processes that are important in human disease,” said study co-senior author Axel Visel, senior staff scientist and one of three lead researchers at the Mammalian Functional Genomics Laboratory, part of Berkeley Lab’s Environmental Genomics and Systems Biology (EGSB) Division. “Identifying and interpreting sequence changes affecting noncoding sequences is increasingly a challenge in human genetics. The genome-wide catalog of heart enhancers Read More ›

From ScienceDaily: Several years ago, biologists discovered a new type of genetic material known as long noncoding RNA. This RNA does not code for proteins and is copied from sections of the genome once believed to be “junk DNA.” Since then, scientists have found evidence that long noncoding RNA, or lncRNA, plays roles in many cellular processes, including guiding cell fate during embryonic development. However, it has been unknown exactly how lncRNA exerts this influence. Inspired by historical work showing that structure plays a role in the function of other classes of RNA such as transfer RNA, MIT biologists have now deciphered the structure of one type of lncRNA and used that information to figure out how it interacts with Read More ›

From ScienceDaily: Although variants are scattered throughout the genome, scientists have largely ignored the stretches of repetitive genetic code once dismissively known as “junk” DNA in their search for differences that influence human health and disease. A new study shows that variation in these overlooked repetitive regions may also affect human health. These regions can affect the stability of the genome and the proper function of the chromosomes that package genetic material, leading to an increased risk of cancer, birth defects and infertility. The results appear online in the journal Genome Research. … “What we found in this study is probably the tip of the iceberg,” Sullivan said. “There could be all sorts of functional consequences to having variation within Read More ›

  Over on this thread we’ve had a lively discussion, primarily about common descent.  However, one of the key side discussions has focused on the information required to build an organism. Remarkably, some have argued that essentially nothing is required except a parts list on a digital storage medium.  Yes, you heard right.  Given the right sequence of digital characters (represented by nucleotides in the DNA molecule), each part will correctly self-assemble, the various parts will make their way automatically to the correct place within the cell, they will then automatically assemble into larger protein complexes and molecular machines to perform work, the various cells will automatically assemble themselves into larger structures, such as limbs and organs, and eventually everything will Read More ›

From The Scientist: In 2002, a group of plant researchers studying legumes at the Max Planck Institute for Plant Breeding Research in Cologne, Germany, discovered that a 679-nucleotide RNA believed to function in a noncoding capacity was in fact a protein-coding messenger RNA (mRNA).1 It had been classified as a long (or large) noncoding RNA (lncRNA) by virtue of being more than 200 nucleotides in length. The RNA, transcribed from a gene called early nodulin 40 (ENOD40), contained short open reading frames (ORFs)—putative protein-coding sequences bookended by start and stop codons—but the ORFs were so short that they had previously been overlooked. When the Cologne collaborators examined the RNA more closely, however, they found that two of the ORFs did Read More ›

Not that you’d ever guess from the story at Scienmag, but It took nearly a half trillion tries before researchers at The University of Texas at Austin witnessed a rare event and perhaps solved an evolutionary puzzle about how introns, non-coding sequences of DNA located within genes, multiply in a genome. The results, published today in the Proceedings of the National Academy of Sciences, address fundamental questions about the evolution of new species and could expand our understanding of gene expression and the causes of diseases such as cancer. … For a long time, scientists have known that much of the DNA within any given organism’s genome does not code for functional molecules or protein. However, recent research has found that Read More ›

From ScienceDaily: What used to be dismissed by many as “junk DNA” is back with a vengeance as growing data points to the importance of non-coding RNAs (ncRNAs) — genome’s messages that do not code for proteins — in development and disease. But our progress in understanding these molecules has been slow because of the lack of technologies that allow the systematic mapping of their functions. Yes, that’s what they said. ncRNAs come in multiple flavours: there’s rRNA, tRNA, snRNA, snoRNA, piRNA, miRNA, and lncRNA, to name a few, where prefixes reflect the RNA’s place in the cell or some aspect of its function. But the truth is that no one really knows the extent to which these ncRNAs control Read More ›

From ScienceDaily: A gene that scientific dogma insists is inactive in adults actually plays a vital role in preventing the underlying cause of most heart attacks and strokes, researchers have determined. The discovery opens a new avenue for battling those deadly conditions, and it raises the tantalizing prospect that doctors could use the gene to prevent or delay at least some of the effects of aging. … The gene, Oct4, plays a key role in the development of all living organisms, but scientists have, until now, thought it was permanently inactivated after embryonic development. Some controversial studies have suggested it might have another function later in life, but the UVA researchers are the first to provide conclusive evidence of that: Read More ›

A reader sent this link to a free 2013 paper in Genome Biol Evol wherein we read: Although once said to be “junk,” or “parasitic,” DNA (Doolittle and Sapienza 1980; Orgel and Crick 1980), a recent large and rapid accumulation of evidence indicates that transposable elements (TEs) have been a significant factor in the evolution of a wide range of eukaryotic taxa (Bennetzen 2000; Kazazian 2004; Biémont and Vieira 2006; Feschotte and Pritham 2007; Bohne et al. 2008; Hua-Van et al. 2011). We have proposed TEs as powerful facilitators of evolution (Oliver and Greene 2009), formalized this proposal into the TE-Thrust hypothesis (Oliver and Greene 2011), and more recently, expanded and strengthened this hypothesis (Oliver and Greene 2012). More. But Read More ›

From ScienceDaily: Key gene in development of celiac disease has been found in ‘junk’ DNA 40% of the population carry the main risk factor for celiac disease but only 1% develop the disease. A newly found gene that influences its development has been found in what until recently has been known as ‘junk’ DNA. Celiac disease is a chronic, immunological disease that is manifested as intolerance to gluten proteins present in wheats to an inflammatory reaction in the small intestine that hampers the absorption of nutrients. The only treatment is a strict, life-long, gluten-free diet. … This study confirms the importance of the regions of the genome previously regarded as ‘junk’ in the development of common complaints such as celiac Read More ›

An earlier story here today mentioned Dan Graur: Plagiarism in science texts, not just journals? (Maybe, with enough publicity, a public explanation will be forthcoming…) From Jerry Coyne’s Why Evolution Is True blog, we learn the twelve truths of Darwinian evolutionary biology, and some other stuff as well: Dan Graur, who is Professor of Biology and Biochemistry at the University of Houston, describes himself on Tw*tter as “A Very Angry Evolutionary Biologist, a Very Angry Liberal, and an Even Angrier Art Lover”. His Tumblr says he ‘has a very low threshold for hooey, hype, hypocrisy, postmodernism, bad statistics, ignorance of population genetics and evolutionary biology masquerading as -omics, and hatred of any kind.’ Anyway, yesterday he tw**eted a link to Read More ›

Yeah, the dumpster, not the Thrift. Oh, and ID is wrong. From key proponent of junk DNA, University of Houston’s (human genome is mostly junk) Dan Graur, RUBBISH DNA: THE FUNCTIONLESS FRACTION OF THE HUMAN GENOME Abstract: Because genomes are products of natural processes rather than “intelligent design,” all genomes contain functional and nonfunctional parts. The fraction of the genome that has no biological function is called “rubbish DNA.” Rubbish DNA consists of “junk DNA,” i.e., the fraction of the genome on which selection does not operate, and “garbage DNA,” i.e., sequences that lower the fitness of the organism, but exist in the genome because purifying selection is neither omnipotent nor instantaneous. In this chapter, I (1) review the concepts of Read More ›

Further to: Blocking “junk” DNA can prevent stroke damage (so it obviously does something, right?): In a book review in a Darwin lobby journal, “A deeper confusion,” (of The Deeper Genome and Junk DNA: A Journey Through the Dark Matter of the Genome), we read a note of concern: If taken uncritically, these texts can be expected to generate even more confusion in a field that already has a serious problem when it comes to communicating the best understanding of the science to the public. Hmmm. Anything, “taken uncritically,” can be expected to do that. So… ah, now we come to it: They will also certainly provide ammunition for intelligent design proponents and other creationists. The debunking of junk DNA and Read More ›

From ScienceDaily: Blocking a type of RNA produced by what used to be called ‘junk DNA’ can prevent a significant portion of the neural destruction that follows a stroke, a new study in rats demonstrates. … The research also links two mysteries: Why does the majority of damage follow the restoration of blood supply? And what is the role of the vast majority of the human genome, which was once considered junk because it does not pattern for the RNA that makes proteins? Note the expression: “once considered” junk. Someone tell science writer Carl Zimmer. And junk DNA spear carrier Dan Graur (“If ENCODE [little “junk DNA” found] is right, then Evolution is wrong.”). No, wait… Anyway, “Stroke influences the Read More ›