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William Fairbrother, PhD

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William Fairbrother

Title: Associate Professor of Biology
Department: Molecular Biology, Cell Biology, & Biochemistry

William_Fairbrother@brown.edu
+1 401 863 6215, +1 401 863 6215

Download William Fairbrother's Curriculum Vitae in PDF Format

 
Overview | Research | Grants/Awards | Teaching | Publications

My lab studies RNA splicing. A third of all hereditary disease mutations affect RNA splicing. Using deep sequencing and array based synthesis, we are measuring the effects of thousands of mutations and SNPs on splicing, spliceosome assembly and RNA protein binding. In the lab there is a strong emphasis on developing hybrid approaches to science, combining genome analysis and computational biology with experimentation.

Biography

I majored in chemistry at Oberlin College then worked briefly as a freelance journalist before starting graduate school at Columbia University in the Department of Biological Sciences. My postdoctoral research at MIT was performed in Phil Sharp's Lab with Chris Burge as a joint postdoc advisor. Here at Brown, I have focused on using high throughput and computational methods to define elements important in gene expression. This work has convinced us that the disruption of pre-mRNA splicing is a common causal mechanism for many disease mutations. We have recently become interested in developing methods for analyzing clinical sequencing experiments and are active with the Mendelian Genetics Research Group in Harvard.
On a personal note, I am married to Dr Andrea Arena (Asst. Prof, Department of Family Medicine) and we have two wonderful boys!

Institutions

Columbia University

Research Description

Fairbrother on Pubmed
I believe that large scale computational analysis in conjunction with functional assays will continue to be an effective way to answer questions about gene expression. Below, I have included a more detailed description of directions we are taking.
DISCOVERING RARE INTERMEDIATES OF SPLICING IN DEEP SEQUENCING DATA
The basic multi-step biochemical mechanism of pre-mRNA splicing was determined more than two decades ago using in vitro experiments on minimal RNA substrates and extensive genetic characterization in yeast - pre-mRNA was shown to proceed through a branched RNA intermediate (i.e. the lariat) to a fully spliced message{Sharp, 1994 #1363}. The degree to which these types of biochemical assays can model splicing in vivo is unclear. Splicing occurs co-transcriptionally, often conditionally on multi-intron transcripts {Hirose, 2000 #1360}. In vitro, the branched lariat RNA is fairly abundant and the precise branchpoint can be readily mapped by a primer extension assay. In vivo, lariats are transient and difficult to characterize and therefore, few branchpoints have been identified {Vogel, 1997 #1337;Gao, 2008 #1350}. My lab has recently developed a high throughput method of mapping branchpoints in deep sequencing data and used this approach to discover more than two thousand lariats in vivo (accepted Nature Structural & Molecular Biology, NSMB-BC28404B). This novel genomic method allows for a system level approach to determining the role of this important intermediate in splice site selection. Our data, consistent with some observations{Gooding, 2006 #1352}, demonstrates that the branchsite location is an important determinant in splice site selection. Indeed, the branchpoints upstream from alternatively spliced exons are often in a suboptimal location. Alternative 3 prime splice site (3'ss) selection is often restricted by branchpoint formation on or downstream of the proximal "AG". In addition, exons that were skipped are associated with unusually distal branchpoints, implying a mechanism to weaken 3'ss definition that may be necessary to create a skippable exon. We seek to explore the effects branchpoint selection can have on splice site utilization.

RNA SPLICING Alternative splicing plays a major role in creating the complexity and diversity observed in higher eukaryotic proteomes. The goal of the splicing group in the lab is to map regulatory elements around alternatively spliced exons. Unlike location studies, which map all the genomic targets of a particular driver, the focus here is on creating, within limited regions of the genome, complete high-resolution maps of targets for all the relevant drivers. The ultimate goal is to define modules (i.e. particular arrangements of cis-elements) that regulate splice site selection. With RNA, protein binding events can be further modulated by secondary structure. We have mapped binding sites for the U1snRNP the SR protein, SF2/ASF, and for the hnRNP protein, PTB, around 4000 alternatively spliced exons. In the PTB paper we demonstrate how features of RNA structure modulate protein accessibility. The lab has made a video that illustrates how this techniques works. Comparing these mappings shows very little overlap between the repressor PTB and the activator ASF - perhaps reflecting their antagonistic function. Protein interactome maps indicate that PTB associates with about 20 other RNA binding proteins possibly creating RNPs with their own distinct specificity and function. Repeating the PTB binding assays after perturbing the levels of these interacting protein should identify scenarios of combinatorial binding or competition.

HUMAN GENETICS One of the most fundamental goals of genetics is to connect variations in genomic sequence to a phenotype or trait. In the context of human disease, an analysis of hereditary disease alleles illustrate the types of variations that have been associated with disease. Conservative estimates list splicing defects as responsible for about 15% of all diseases. In reality, researchers have found that many mutations classified as "missense" are also exacerbated by splicing defects. In addition to disease alleles, there is the more subtle class of disease causing variations that have been identified by genome wide association studies (GWAs). GWAs return regions that are associated with disease. The causal variant is presumed to be amongst the several hundred polymorphisms that are in linkage disequilibrium with the associated SNP. Our lab seeks to predict which disease allele and which associated SNP causes a splicing defect. If the causal variant is known there is an emerging class of oligo therapies that can be used therapeutically to reverse splicing defects (see example).

GENOMICS Interrogation of deep sequencing datasets to understand alternative splicing and identify splicing intermediates in vivo. Using a variety of wetlab and drylab techniques we are identifying transient intermediates of splicing in vivo. Surprising insights about global mechanisms of splicing have come form this analysis. We plan to expand this to study splicing in the nervous system and characterize special mechanisms that seem to employed predominantly in the specialized subset of cells.

STEM CELLS As part of our efforts to understand the regulatory circuitry of the core set of promoters that are important in maintaining pluripotency in stem cells, we have developed and published a high throughput method to screen large genomic regions for DNA protein complexes. This pilot approach for developing a high throughput, high-resolution nucleic acid binding assay has been further developed so we are now studying binding events in complex extract rather than binding with purified protein. Here we find several interesting features of the transcriptional circuitry that may be important to understanding stem cells and stem cell reprogramming events. We find pervasive competiton between Oct4 and FoxO1 for genomic targets upstream of genes that maintain "stemness". We find find that the paralog Oct1 modulates Oct4 specificity in ES cells and we demonstrate that features learned from the high throughput in vitro binding assay can be used to successsfully predict in vivo binding events. Our future directions will be to extend these findings on a genomic scale in ES cells and to complete the characterization of the pluripotency transcriptional control network.

Awards

NO LONGER SUPPORTED - please see CV for a most recent list of Honors and Awards

CCMB Scholarship Innovator Award 2007

Richard Salomon Award, "Discovering Combinatorial Codes in Splicing" (2005-2006)

Informatics Postdoctoral Fellowship, PhRMA Foundation (2003-2005)

James Howard McGregor Teaching Award, Columbia University (2000)

BP Research Experience Fellowship, Oberlin College (Summer 1989)

Affiliations

NO LONGER SUPPORTED - please see CV for a most recent list of Profesional Affiliations
RNA Society
International Society for Computational Biology
Board Member - Barrington Land Trust

Funded Research

Arthur Salomon Award (December 2005)


FEDERAL FUNDING
1R21HG004524-01A1 (Fairbrother, PI) 04/26/2010-01/31/2012
NIH/NHGRI $275,000
Role: Principal Investigator
Discovering and Validating Functional Elements in the Genome
This is a technology development grant that describes a high throughput nucleic acid protein interaction assay. The major goals are optimizing the experimental assay/microarray detection and developing a computational suite of tools to analyzing binding.

NSF 1020552 (Fairbrother, PI) 08/01/10-07/31/12
NSF/MCB- Genes and Genome Systems $218,426.00
Role: Principal Investigator
CIS-regulatory Circuitry of Polypyrimidine Binding Proteins

1R01GM095612-01 "A Discovery Tool for Variations that Affect Splicing", $1,250,000, 12/01/2010 - 11/30/2015, NIH/NIGM,
The goal of this grant is to discover cases of allelic differences in RNA protein interactions and function.

Teaching Experience

Genetics Bio47
Independant Research Bio 195/196
Bio 2200 Advanced Topics in Molecular Biology and Biochemistry (co-taught with Rebecca Page)
Biol2030 - Foundations in the Life Sciences.
Biol2010 - Quantitative Biology
I have developed a computational biology workshop that I have taught within Biol2010 and Biol2030

Courses Taught

  • Foundations for Advanced Study in Experimental Biology (BIOL2030)
  • genetics (bio047)