International ‘ENCODE’ Project Reveals Function of Human Genome

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DETROIT – Dr. Leonard Lipovich’s determination to prove genetic matter once deemed “junk” has a place in clinical medicine is bringing the Wayne State University School of Medicine to the forefront of a field occupying genome enthusiasts while also contributing to ENCODE, the global follow-up to The Human Genome Project.

Upon completion in 2003, the HGP produced an almost complete list of the 3 billion pairs of chemical letters in the DNA that embodies the human genetic code, but revealed nothing on how this blueprint works. Five years of concerted effort by more than 440 researchers in 32 labs around the world has changed that.

The group, working collaboratively in the Encyclopedia of DNA Elements (ENCODE) Project, has produced the first view of how the human genome actually does its job. Researchers across the United States, United Kingdom, Spain, Singapore and Japan performed more than 1,600 sets of experiments on 147 types of tissue with technologies standardized across the consortium.

Among them are WSU Assistant Professor of Molecular Medicine and Genetics and of Neurology Leonard Lipovich, Ph.D., and his team at WSU’s Center for Molecular Medicine and Genetics.

Two groundbreaking articles highlighting results from his lab are included in a coordinated publication released Sept. 5. It includes one main integrative paper and five other papers in the journal Nature, 18 papers in Genome Research and six papers in Genome Biology.

The experiments relied on innovative uses of next-generation sequencing technologies, which had only become available around the start of the ENCODE production effort five years ago. ENCODE generated more than 15 trillion bytes of raw data and consumed the equivalent of more than 300 years of computer time to analyze.

Dr. Lipovich’s contributions, on long non-coding ribonucleic acids, or lncRNAs, could lead to new therapeutics for cancer and other diseases.

“Long non-coding RNA genes comprise half of human genes. Most medical, therapeutic work so far has focused on normal, protein-coding genes. So, we – working as part of a multinational team of scientists – have just expanded, twofold, the set of genes that can be therapeutic targets,” he said.

During the ENCODE study, researchers found that more than 80 percent of the human genome sequence is linked to biological function. They mapped more than 4 million regulatory regions where proteins specifically interact with DNA with exquisite specificity. These findings represent a significant advance in understanding the precise and complex controls over the expression of genetic information within a cell.

The findings bring into much sharper focus the continually active genome in which proteins routinely turn genes on and off using sites that are sometimes at great distances from the genes they regulate; where sites on a chromosome interact with each other, also sometimes at great distances; where chemical modifications of DNA influence gene expression; and where various functional forms of RNA, a form of nucleic acid related to DNA, help regulate the whole system.
 

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