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  1. The ENCODE project revealed that "the vast majority of the 3 billion "letters" of the human genetic code are busily toiling at an array of previously invisible tasks." and " many genes overlap one another and share stretches of molecular code, as with phone lines that carry many voices at once", Intricate Toiling Found In Nooks of DNA Once Believed to Stand Idle, Washington Post, 2007
  2. 3 million previously undetectable elements in non-coding regions carefully preserved across all mammals, whose disruptions are associated with human disease, A high-resolution map of human evolutionary constraint using 29 mammals., (summary).
  3. Nearly all of the genome is transcribed, to RNA. At a cost of 2 ATP per bp, it's unlikely this costly process would be preserved by evolution unless it served a purpose. "convincing evidence that the genome is pervasively transcribed, such that the majority of its bases can be found in primary transcripts, including non-protein-coding transcripts." Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project, Nature, 2007
  4. "mounting evidence over the past decade has suggested that the vast majority of the genome is transcribed, well beyond the boundaries of known genes, a phenomenon known as pervasive transcription."The reality of pervasive transcription, PLoS Biology, 2011
  5. "But until we did our experiments, we didn't realize that RNAs as small as 15 nucleotides, which we thought were simply cell waste, are surprisingly stable, and are repeatedly, reproducibly, and accurately produced across different tissue types. We have dubbed these as usRNAs, and we have identified thousands of them, present in a diversity that far exceeds all other longer RNAs found in our study." No Such Thing As 'Junk RNA,' Say Researchers, ScienceDaily, 2009
  6. "In fact almost every time you functionally test a non-coding RNA that looks interesting because it's differentially expressed in one system or another, you get functionally indicative data coming out.", Non-coding RNAs and eukaryotic evolution - a personal view, BMC Biol., 2010
  7. Francis Collins is head of the NIH, and formerly head of the human genome project. He has departed from his previous position on junk DNA from 4 years earlier: "The discoveries of the past decade, little known to most of the public, have completely overturned much of what used to be taught in high school biology. If you thought the DNA molecule comprised thousands of genes but far more 'junk DNA', think again.", and "The exons and introns of protein-coding genes add up together to about 30 percent of the genome. Of that 30 percent, 1.5 percent are coding exons and 28.5 percent are removable introns. What about the rest? It appears there are also long 'spacer' segments of DNA that lie between genes and that don't crowd for protein. In some instances, these regions extend across hundreds of thousands or even millions of base pairs, in which case they are referred to rather dismissively as 'gene deserts.' These regions are not just filler, however. They contain many of the signals that are needed to instruct a nearby gene about whether it should be on or off at a given developmental time in a given tissue. Furthermore, we are learning that there may be thousands of genes hanging out in these so-called deserts that don't code for protein at all. They are copied into RNA, but those RNA molecules are never translated--instead, they serve some other important functions.", and "only about 1.5 percent of the human genome is involved in coding for protein. But that doesn't mean the rest is 'junk DNA.' A number of exciting new discoveries about the human genome should remind us not to become complacent in our understanding of this marvelous instruction book. For instance, it has recently become clear that there is a whole family of RNA molecules that do not code for protein. These so-called non-coding RNAs are capable of carrying out a host of important functions, including modifying the efficiency by which other RNAs are translated. In addition, our understanding of how genes are regulated is undergoing dramatic revision, as the signals embedded in the DNA molecule and the proteins that bind to them are rapidly being elucidated. The complexity of this network of regulatory information is truly mind-blowing, and has given rise to a whole new branch of biomedical research, sometimes referred to as 'systems biology.'" Francis Collins, The Language of Life: DNA and the Revolution in Personalized Medicine, (p. 5-6, 9, 293), 2010
  8. Redundant codons are found to control transcription speed, The anti-Shine–Dalgarno sequence drives translational pausing and codon choice in bacteria
  9. Disruption of introns (spaces between genes) has been linked to genetic diseases 1, 2
  10. Mice were engineered to lack a 58,000bp segment of their DNA that had no known function. When fed a high cholesterol diet for 20 weeks, a significant number of them died, compared to the control group. How Junk DNA Affects Heart Disease, NIH, 2010
  11. Strangely, and contrary to the other items in this list, ultra-conserved elements in DNA, predicted by common descent to provide the most important function, don't. "We deleted two large non-coding intervals, 1,511 kilobases and 845 kilobases in length, from the mouse genome. Viable mice homozygous for the deletions were generated and were indistinguishable from wild-type littermates with regard to morphology, reproductive fitness, growth, longevity and a variety of parameters assaying general homeostasis" Megabase deletions of gene deserts result in viable mice, Nature, 2004
  12. Over 80 different functions of repetitive DNA are identified. "In particular, the fact that repeat elements serve either as initiators or boundaries for heterochromatin domains and provide a significant fraction of scaffolding/matrix attachment regions (S/MARs) suggests that the repetitive component of the genome plays a major architectonic role in higher order physical structuring." and "There is extensive documentation in the molecular genetic literature (some of it tabulated here) that all structural varieties of repetitive DNA play significant roles in one or more categories of genomic tasks." Why repetitive DNA is essential to genome function, Biol Rev Camb Philos Soc, 2005
  13. Long non-coding RNAs promote pluripotency (the ability of stem cells to differentiate) and neuronal differentiation, 1, 2
  14. "For years, many biochemists were skeptical that lincRNA played any important role in a cell and considered the molecules just mere "noise," perhaps vestigial protein-coding genes that had mutated to become nonfunctional. Chang's group has been instrumental in proving that lincRNAs can play a critical regulatory role: determining what proteins a cell produces and, thereby, what identity it assumes.", Researchers discover molecular determinant of cell identity, 2011
  15. ERV's regulate human transcription on a large scale: "We report the existence of 51,197 ERV-derived promoter sequences that initiate transcription within the human genome, including 1743 cases where transcription is initiated from ERV sequences that are located in gene proximal promoter or 5' untranslated regions. ... Our analysis revealed that retroviral sequences in the human genome encode tens-of-thousands of active promoters; transcribed ERV sequences correspond to 1.16% of the human genome sequence and PET tags that capture transcripts initiated from ERVs cover 22.4% of the genome. These data suggest that ERVs may regulate human transcription on a large scale." Retroviral promotors in the human genome, Bioinformatics, 2008
  16. "Codon frequencies in the human genome are clustered around 2 fractal-like attractors, strongly linked to the golden ratio 1.618." Codon populations in single-stranded whole human genome DNA Are fractal and fine-tuned by the Golden Ratio 1.618, 2010; (Layman's summary and discussion)