Category Archives: Transhuman News

Published: Sept. 18, 2013 at 2:44 PM

STATE COLLEGE, Pa., Sept. 18 (UPI) -- Two U.S. scientists said they discovered more on origin of genomic dark matter, non-coding RNA, which comprises more than 95 percent of the human genome.

B. Franklin Pugh, the Willaman chair in Molecular Biology at Penn State University, and Bryan Venters, who is on faculty at Vanderbilt University, discovered essentially all coding and non-coding RNA originates at the same types of locations along the human genome, Penn State said Wednesday in a release.

The scientists said their findings could help pinpoint exactly where complex-disease traits reside, since genetic origins of many diseases are outside of the coding region of the genome.

Pugh and Venters set out to identify the precise location of the beginnings of transcription, the first step in the expression of genes into proteins but they determined where proteins that initiate transcription of non-coding RNA were located along human chromosomes.

"So rather than look for the RNA product of transcription we looked for the 'initiation machine' that makes the RNA," Pugh said. "This 'machine' assembles RNA polymerase, which goes on to make RNA, which goes on to make a protein."

Pugh and Venters determined non-coding initiation machines recognized the same DNA sequences as the ones at coding genes, indicating they have a specific origin and their production is regulated, Pugh said.

"These non-coding RNAs have been called the 'dark matter' of the genome because, just like the dark matter of the universe, they are massive in terms of coverage ... . However, they are difficult to detect and no one knows exactly what they all are doing or why they are there," Pugh said. "Now at least we know that they are real, and not just 'noise' or 'junk.'"

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Scientists uncover milestone in genome's 'dark matter'

Public release date: 18-Sep-2013 [ | E-mail | Share ]

Contact: Craig Boerner craig.boerner@vanderbilt.edu 615-322-4747 Vanderbilt University Medical Center

Using technology he helped develop, Vanderbilt University scientist Bryan Venters, Ph.D., has shed new light on the "dark matter" of the genome and has begun to explore a possible new approach to treating cancer.

"Clarity is everything," said Venters, assistant professor of Molecular Physiology and Biophysics who further developed the high-resolution technology as a postdoctoral fellow in the lab of Frank Pugh, Ph.D., at Pennsylvania State University before moving to Vanderbilt in January.

Venters and Pugh are co-authors of a paper published this week in the journal Nature that describes their finding.

Much of the DNA of the human genome has been called "dark matter" because only a tiny fraction, about 3 percent, makes up the approximately 20,000 protein-coding genes that are transcribed into RNA copies, and then translated into proteins.

Other parts of the genome are transcribed into non-coding RNA, presumably to perform other functions, but until recently the origin of this non-coding RNA was unknown.

Now, with a technique called ChIP-exo developed at Penn State that identifies protein-DNA interactions at near base-pair resolution, Venters and Pugh have shown that so-called transcription initiation complexes drive much of the non-coding transcription occurring throughout the genome.

In a model leukemia cell line, they discovered about 150,000 complexes along non-coding stretches of the DNA the most ever discovered. This suggests, they concluded, that "pervasive non-coding transcription is promoter-specific, regulated, and not that much different from coding transcription (of genes)."

Venters compared the technique to the highly sensitive satellite cameras that enable web-based map applications to zoom in from a continental view to street level, "and tell house from house."

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Study helps bring genome's 'dark matter' into light

Public release date: 18-Sep-2013 [ | E-mail | Share ]

Contact: Leah Ramsay lramsay@jhu.edu 202-642-9640 Johns Hopkins Medicine

The National Human Genome Research Institute has selected the Johns Hopkins Berman Institute of Bioethics to establish a "Center of Excellence" to study the ethical, legal and social implications (ELSI) of genomic research. The Berman Institute will receive three years of funding to build on its multidisciplinary expertise in the ethics of human genomics and public health, bringing the fields together in the largely unexplored but crucial study of genomics as applied to infectious disease. The center will be known as GUIDE: Genomic Uses in Infectious Disease & Epidemics.

Pandemic scares in recent years, from SARS to influenza to MERS, necessitate this research, says Gail Geller, a co-principal investigator for GUIDE and faculty member at the Berman Institute. "Infectious diseases account for a significant proportion of illness and death worldwide, across all aspects of society," Geller notes. Recent research has suggested that a person's genes can play a significant role in the severity of viral infection, and even a predisposition to death from flu.

"It is important to begin to map out and address the ELSI issues involved in the use of genomic information for major public health areas like infectious disease, as the science in this area is moving quickly," says Jeffrey Kahn, co-principal investigator with Geller and deputy director at the Berman Institute.

As an exploratory Center for Excellence in ELSI Research (CEER), the GUIDE Center will bring together a multidisciplinary team of Hopkins' global leaders in diverse fields including genomics, immunology and infectious disease, bioethics, epidemiology, public health preparedness, education, and health policy, in keeping with the intention that CEERs create opportunities for trans-disciplinary research. This team will initially explore public health genomics in two case studies of human-to-human infectious disease: pandemic influenza and Hepatitis C.

The research team will examine how the genome affects a person's response to a flu vaccine as well as to the virus. "Although vaccinations are generally safe and highly effective interventions for disease prevention, understanding more about the genetics of an individual's response may help us design vaccines that maximize protective efficacy while minimizing the potential for adverse events," says Ruth Karron, a co-investigator in the CEER and director of the Johns Hopkins Center for Immunization Research. She says that in the future, genomic information could result in the production and use of vaccines with more refined understanding of effects on particular subpopulations, which will necessitate decisions about prioritization, privacy, opt-out policies and genotyping for flu-resistant first responders.

The project will also assess the ELSI issues arising from recent Hepatitis C studies, including research conducted by GUIDE co-investigators Chloe Thio and Priya Duggal, showing that individuals with a specific variation of the gene IFNl3 had five times better response to treatment and three times better chance of clearing the virus spontaneously, without treatment. These discoveries raise important questions about disclosure of genetic status as well as the use of expensive therapies in those individuals carrying the mutation. Currently Hepatitis C is found in virtually every region of the world, with an estimated 123 million people chronically infected.

"Hepatitis C is a timely and crucial case study in the necessity of clear ethical guidance for rapidly advancing public health genomics," says Geller. "Should individuals with the IFNl3 variation receive different treatments and priority? Should reporting the IFNl3 variation be mandatory?" Kahn adds that "These are among the questions the Berman Institute's CEER will address in our Hepatitis C case study, with the goal of producing an ethical framework that can apply more widely to genomics in the context of infectious disease."

At the conclusion of the three-year grant period, GUIDE will apply to transition from an exploratory to a specialized CEER, a designation that would come with an additional five years of funding from the National Human Genome Research Institute.

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Personal genome, public health