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Wrong William Fairbrother?

William G. Fairbrother

Associate Professor

Brown University

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Brown University


Providence, Rhode Island,02912

United States

Company Description

Located in historic Providence, Rhode Island and founded in 1764, Brown University is the seventh-­oldest college in the United States. Brown is an independent, coeducational Ivy League institution comprising undergraduate and graduate programs, plus the Alper...more

Background Information

Employment History

Associate Professor - Biology Department

Bio Med Molecular






Web References(14 Total References)

Researchers ID Disease-Causing Mutations in the Exome That Alter Gene Splicing | Articles | ClinicalOMICs

clinicalomics.com [cached]

"Our validation technologies-our means of analyzing variance-is actually very low throughput," said William Fairbrother, Ph.D., a biology professor at Brown University.
To help identify disease-causing variants in the genome, Dr. Fairbrother and his colleagues created MaPSy (Massively Parallel Splicing Assay), a tool that works by producing artificial "minigenes" that either contain disease-causing mutations or the corresponding "normal" versions of the sequence. "That's by pretty stringent criteria-we demand that there's at least 1.5-fold difference in the representation of an allele to call it a splicing mutation," Dr. Fairbrother noted. "It [also] has to happen in two different systems. So we might be undercounting that number." Some exons, the researchers found, had a higher proportion of splicing-associated mutations than others. "Some [exons] were robust and everything worked great, but others were sort of borderline-so if there was no mutation, everything was fine and you'd splice normally, but many mutations would disrupt splicing," Dr. Fairbrother said. In addition, he added, there were certain features of those exons made them easier to disrupt than others. "It was [generally] things that made the exon a worse substrate for splicing," he said. A few years ago, Dr. Fairbrother and his colleagues created Spliceman, a freely available web-based tool for predicting how likely mutations in DNA sequences are to cause splicing errors. Currently, the team is looking for ways to improve MaPSy. One of their goals, Dr. Fairbrother noted, is to synthesize longer regions of DNA-presently, the system can only test mutation in exons that are less than 100 nucleotides long. They also hope to expand that assay to test more mutations at once. "In this study, we tested 5,000 mutations," he said.

National Ataxia Foundation - National Ataxia Foundation Research

www.ataxia.org [cached]

William G. Fairbrother, Ph.D.
Research NAF Research 2014 William G. Fairbrother, Ph.D. Brown University, Providence, RI

Technology - Genetic Variation and RNA binding proteins: tools and techniques to detect functional polymorphisms (Case 2251)

brown.technologypublisher.com [cached]

William Fairbrother, PhD, Associate Professor of Biology
Department of Bio Med Molecular, Cellular Biology Biochemistry Brown University William Fairbrother


Using a technology he invented, Brown researcher William Fairbrother (pictured center) and colleagues have discovered new molecular interactions in the process that will help regenerative medicine researchers better understand pluripotency.
In a study, Fairbrother's team showed that different proteins called transcription factors compete and cooperate in the cells to produce complex bindings along crucial sequences of DNA. This game of molecular "capture the flag," played in teams and amid shifting alliances, appears to be a necessary part of what determines whether stem cells retain their pluripotency and whether specialized, or differentiated, cells can regain it. In recent years scientists have reported spectacular successes in turning fully differentiated cells back into pluripotent stem cells, a process called reprogramming. But the animals derived from these cells often suffer higher rates of tumors and other problems, Fairbrother said. The reason may be because the complex details of the reprogramming process haven't been fully understood. He said there are many misconceptions about how reprogramming transcription factors interact with DNA. "Most people think of a protein binding to DNA as a single, surgical thing where you have this isolated binding event," Fairbrother said. "But in fact we show that sometimes these binding events occur over hundreds of nucleotides so they seem more like great greasy globs of proteins that are forming. In addition, the proteins interact with each other, diversifying their function by appearing in complexes with different partners at different places." By employing a high-throughput, high-resolution binding assay that he's dubbed MEGAShift, Fairbrother and his colleagues, who include pathology researchers from the University of Utah School of Medicine, were able to analyze the interactions of several key transcription factors in a region of 316,000 letters of DNA with a resolution as low as 10 base pairs. Through hundreds of thousands of array measurements, lead authors Luciana Ferraris (pictured left) and Allan Stewart, Fairbrother, Alec DeSimone (pictured right), and the other authors learned of previously unspotted patterns of protein interactions. Fairbrother said. "Who binds next to a protein is a determinant of who ends up binding to a sequence," Fairbrother said. With support from the National Institutes of Health, Fairbrother's group is also applying MEGAShift to other questions, including how protein-protein interactions affect the formation of RNA-protein complexes, which can be even more complicated than binding DNA.


"Something like 85 percent of the mutations in the Human Gene Mutation Database are presumed to affect how proteins are coded, but what this work shows is that 22 percent of those are affecting the splicing process," says William Fairbrother, assistant professor of biology at Brown University.
Add that to the 15 percent already believed to affect splicing of mRNA, and nearly one in three mutations in the HGMD may owe at least part of their harmful results-hundreds of hereditary diseases-to the way in which they cause splicing errors. "Splicing mutations are already known to be a large fraction, but we're saying they are even more," Fairbrother says. "A processing defect may be able to be detected and fixed much more easily and safely than a protein coding defect," Fairbrother says. Fairbrother and the study's lead author, computer science graduate student Kian Huat Lim developed a new computer to analyze the human genome and data on splicing operations.

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