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Northeastern professor\u2019s book \u201cEclipsed Horizons: Unveiling the Dark Genome,\u201d highlights the so-called \u201cjunk\u201d DNA of the human genome.
Photo by Alyssa Stone\/Northeastern University<\/p>\n
Since the Human Genome Project first produced<\/a> the genetic instructions for a human being by sequencing DNA 22 years ago, scientists have been focused on roughly 2% of the genome producing proteins.<\/p>\n But what about the rest?\u00a0<\/p>\n Northeastern University professor Sudhakaran Prabakaran says this \u201cdark genome\u201d is not only actively making \u201cdark proteins,\u201d but its secrets could provide the future for the pharmaceutical industry and modern medicine.<\/p>\n \u201cIf biology and evolution are known to keep things simple and efficient, if it is just using 1% or so of the genome, why would it keep the remaining 98%? There must be some reasons for it,\u201d says Prabakaran, associate professor of biotechnology and chemistry and chemical biology at Northeastern. \u201cNow we are discovering those reasons.\u201d<\/p>\n Prabakaran is the author of the upcoming book \u201cEclipsed Horizons: Unveiling the Dark Genome,\u201d<\/a> an account of the scientific investigations into the so-called \u201cjunk\u201d or non-coding DNA of the human genome. He has also recently reviewed the scientific literature in this field in new research<\/a>.\u00a0<\/p>\n It\u2019s an expansive area to research \u2014 the human genome consists of 3.6 billion nucleotides that make up our DNA and have accumulated over our evolutionary journey. Moreover, this dark genome \u2014 and the dark proteins it encodes \u2014 has only recently become visible due to technological and computational advances.\u00a0<\/p>\n \u201cThink about the analogy of flying over the Himalayas at 30,000 feet,\u201d Prabakaran explains. \u201cWe only see the tallest peaks, but as we come down to 20,000 feet and 10,000 feet we start seeing other things in the landscape \u2014 more proteins, more regions that we know as functional or active or both.\u201d<\/p>\n But the common notion that the dark genome is inactive or inconsequential is wrong, Prabakaran says.\u00a0<\/p>\n Scientists in Prabakaran\u2019s lab have already cataloged around 250,000 new \u201cdark proteins,\u201d learning about the biological processes they are involved in and whether they are dysfunctional in various diseases. Algorithms, meanwhile, have predicted at least 2 million more.\u00a0<\/p>\n In fact, the dark genome has spawned a new focus for research.<\/p>\n \u201cWe look at just the protein aspect of it,\u201d Prabakaran says of his particular focus. \u201cSome look at repeating regions, some look at just the viruses that are encoded in those regions, some look at how modifications in those regions affect the known proteins.\u201d<\/p>\n Biotech and the pharmaceutical companies are also expressing interest, with companies investigating the dark genome and its dark proteins for therapeutic purposes.\u00a0<\/p>\n But Prabakaran says harnessing the dark genome will require a new approach in the \u201cconservative\u201d pharmaceutical industry.\u00a0<\/p>\n Prabakaran says that while billions of dollars have been spent trying to cure diseases over the last 50 years, the pharmaceutical industry has only looked at 20,000 proteins and \u2014 of those \u2014 selected 812 to investigate for treating illness. Add in a high likelihood of failure \u2014 95% of clinical trials fail by the time they reach phase three, at which point roughly $2 billion has been already spent, Prabakaran says \u2014 and you get, say, five pharmaceutical companies competing to produce the best weight-loss drug rather than five companies each working on five more revolutionary treatments.\u00a0<\/p>\n \u201cThe target space is very small and we keep looking at it again and again,\u201d Prabakaran says.<\/p>\n But Prabakaran is hopeful.\u00a0<\/p>\n![\"Portrait](\"https:\/\/www.newsbeep.com\/us\/wp-content\/uploads\/2025\/07\/071025_AS_Sudhakaran_Prabakaran_007.jpg\")
Sudhakaran Prabakaran, professor of biotechnology, chemistry and chemical biology, studies \u201cdark proteins\u201d made by the \u201cdark genome.\u201d Photo by Alyssa Stone\/Northeastern University<\/p>\n