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NYU's Center for Comparative Functional Genomics part of $57 million MOD-ENCODE consortium

New York University

New York University biologist Fabio Piano, an associate professor at NYU's Center for Comparative Functional Genomics, was selected by National Human Genome Research Institute (NHGRI) to lead one of the teams charged with decoding the genome. NHGRI is an institute within the National Institutes of Health (NIH).

The award to Piano, a professor in NYU's Biology Department, and the nine other researchers leading genome centers across the nation, will create a consortium of scientists who will collaborate in a four-year, $57 million scientific endeavor to understand every part of the genome needed for organisms to develop and thrive, as announced by NIH today.

This four-year, multi-institutional collaborative genome project called "MOD-ENCODE" aims to identify all the functional elements (ENCODE) in the genomes of the model organisms (MOD) fruit fly and round worm Caenorhabditis elegans (C. elegans) as models to understand the functional elements and to shed light on the function of these elements in humans.

The effort will build upon the foundation laid by the ENCyclopedia of DNA Elements (ENCODE) consortium, which is preparing to build a comprehensive catalog, or "parts list," of all elements in the human genome crucial to biological function. In addition to genes that code for proteins, these functional elements include: non-protein-coding genes; regulatory elements involved in the control of gene transcription; and DNA sequences that mediate the structure and dynamics of chromosomes. For more information about NHGRI's ENCODE project, go to www.genome.gov/ENCODE.

"We are making great strides in identifying functional elements in the human genome, but we still don't know much about their biological relevance," said NHGRI Director Francis S. Collins. "This parallel effort in the fruit fly and worm genomes will provide us with information about the functional landscape of two key model organisms, which should aid our efforts to tackle such questions in humans."

Piano and his research team at NYU's Center for Comparative Functional Genomics will develop an encyclopedia of a specific part of the genome of the round worm C. elegans called the 3'UTR. 3'UTR is a section of all animal genomes where special regulatory genes called microRNAs (miRNA) bind to messenger RNA (mRNA) and regulate whether a gene is to be expressed or not. Thus, the 3'UTR is the area where regulatory sequences act as switches to ultimately turn on or off the production of protein from a specific gene. This level of regulation is especially prevalent in embryogenesis. C. elegans is the first animal species whose genome was completely sequenced and a model organism to study how embryos develop.

Piano's earlier research predicted, using computational analysis, miRNA functions of C. elegans genes. This work was in collaboration with other members of the Center for Comparative Functional Genomics at NYU. The researchers found that one-third of C. elegans miRNAs target gene sets have related functions. That is, it appears that miRNAs can control groups of genes that work in a specific biological process. At least 10 percent of C. elegans genes are predicted miRNA targets.

To confirm the computational predictions, the NYU team developed a new in vivo analysis system comparing the expression of a reporter, green fluorescent protein (GFP) carrying target 3' UTRs with controls that did not carry the target 3'UTRs. The laboratory results confirmed the role of specific 3' UTRs in suppressing gene expression even more widely than predicted by the computational analysis, suggesting that 3' UTRs contain a largely unexplored universe for gene regulation.

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EDITOR'S NOTE

New York University, located in the heart of Greenwich Village, was established in 1831 and is one of America's leading research universities and a member of the selective Association of American Universities. It is one of the largest private universities, it is a leader in attracting international students and scholars in the U.S, and it sends more students to study abroad than any other U.S. college or university. Through its 14 schools and colleges, NYU conducts research and provides education in the arts and sciences, law, medicine, business, dentistry, education, nursing, the cinematic and performing arts, music, public administration, social work, and continuing and professional studies, among other areas.

The National Institutes of Health -- "The Nation's Medical Research Agency" -- includes 27 institutes and centers, and is a component of the U.S. Department of Health and Human Services. It is the primary federal agency for conducting and supporting basic, clinical and translational medical research, and it investigates the causes, treatments, and cures for both common and rare diseases. For more, visit www.nih.gov.

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