My lab uses a combination of computational biology and high throughput genomics techniques to identify functional elements in the genome. I am particularly interested in sequence elements that regulate RNA splicing. Specific projects that move beyond identifying splicing signals include 1) understanding how particular arrangements of sequence elements are read by the splicing machinery, 2) identifying mutations/polymorphisms that disrupt splicing in the human population, and 3) investigating the evolution of gene expression signals.

Biography

I majored in chemistry at Oberlin College then worked briefly as a freelance journalist and in several other jobs in New York City before starting graduate school at Columbia University working in the Chasin lab where I learned library/selection approaches in somatic cell genetic systems. I then moved to Boston for a postdoc at MIT in Phil Sharp's Lab. My interest in computational methods brought me in close contact with Chris Burge's Lab and as a collaborative project we developed the first computational screen for enhancer sequences.

Institutions

Columbia University

Research Description

I believe that large scale computational analysis in conjunction with functional assays will continue to be an effective way to answer questions about the genome gene expression and the evolution of pre-mRNA processing signals. Below, I have included a more detailed description of directions we are taking.


CURRENT RESEARCH


Alternative splicing plays a major role in creating the complexity and diversity observed in higher eukaryotic proteomes. The goal of this splicing group in the lab is to develop novel high throughput methods of mapping 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. In this regard, the goal of this proposal is more similar to Davidson and colleagues' work of mapping the regulatory circuitry in sea urchin promoter regions. 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.

In addition to developing physical methods for mapping regulatory circuitry we are also defining elements computationally. We are currently incorporating spatial information in computational motif finding. We apply this algorithm to identify RNA elements that modulate splicing.

Develop a high-throughput screen to map RNA-protein complexes in the vicinity of alternatively spliced exons
Motivation: In vivo high throughput factor location methods identify broad regions of occupancy for a candidate factor. Understanding switches in gene expression that are achieved by combinatorial mechanism requires identifying factor binding sites at a resolution that discriminates overlapping binding sites from adjacent binding sites from isolated binding sites.
a) Where do ribonucleoprotein complexes (RNPs) form on alternatively spliced pre-mRNAs? We will develop an unbiased assay for surveying transient protein-RNA complexes at 10 nucleotide resolution on 2.4 Mb of pre-mRNA. Which of these complexes is dependant on phosphorylation? Do any complexes specifically form in response to DNA damaging agents or in extracts from neuronally differentiated tissue?
b) Where do the RNPs associated with early splice site recognition actually form on a pre-mRNA? We will co-immunoprecipitate RNA ligands of several selected members of the so-called enhancer (E) complex. Which complexes are dependant on post-transcriptional modifications and how is their binding affected by co-regulators?
c) Where does the negative regulator of splicing, PTB, bind pre-mRNA substrates? We will map binding sites across 58 PTB regulated transcripts. PTB has been hypothesized to inhibit splicing by competing with U2AF at the polypyrimide tract and looping out exons. We will check the map for distributions consistent with these models and validate these predictions below.

Test the activity of RNA functional elements identified in the binding and computational screens
Motivation: Technical issues in vivo and in vitro limit the study of RNA-protein specificity.
a) Which elements idenfied above or computationally have activity in vivo? Armed with candidate elements from computational and in vitro binding analysis of alternatively spliced sites, we will test whether these elements have enhancer, silencer, or no activity in a transfected splicing reporter minigene in variety of tissue culture cell lines.

Computationally predict the activity of functional elements utilizing genomic distribution
Motivation: Splicing enhancers have complex non-uniform distributions around splice sites that are often suggestive of their function.
a) Can we identify novel splicing elements based on their genomic distribution?
b) Are constitutive splicing elements distributed differently in alternatively spliced substrates?


We currently write UCSC custom genome browser tracks that displays the chromosomal positions that we find to enriched in the bound fraction of the binding assays described above..

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

International Society for Computational Biology

Funded Research

Arthur Salomon Award (December 2005)

Teaching Experience

Genetics Bio47
Independant Research Bio 195/196
Bio 2200 Advanced Topics in Molecular Biology and Biochemistry (co-taught with Rebecca Page)

Courses Taught

• genetics (bio047)

Selected Publications

• Fairbrother W, Lipscombe D. "Repressing the neuron within." Bioessays. 2008 Jan; 30(1):1-4.(2008)
• Tantin D, Gemberling M, Callister C, Fairbrother W. "High-throughput biochemical analysis of in vivo location data reveals novel distinct classes of POU5F1(Oct4)/DNA complexes." Genome Research 2008 Mar 13.(2008)
• Nicole Pfarr, Dirk Prawitt, Michael Kirschfink, Claudia Schroff, Markus Knuf, Pirmin Habermehl, Wilma Mannhardt, Fred Zepp, William Fairbrother, Michael Loos, Christopher B. Burge and Joachim Pohlenz " Linking C5 deficiency to an exonic splicing enhancer mutation." J Immunol 174(7): 4172-4177 (2005).(2005)
• Fairbrother WG, Yeo GW, Yeh R, Goldstein P, Mawson M, Sharp PA, Burge CB. "RESCUE-ESE identifies candidate exonic splicing enhancers in vertebrate exons. Nucleic Acids Res. 32: 187-190 (2004).(2004)
• Fairbrother WG, Holste D, Burge CB, Sharp PA. "Single nucleotide polymorphism-based validation of exonic splicing enhancers" PloS Biol. 2(9): 1388-1395 (2004).(2004)
• Fairbrother WG, Yeh RF, Sharp PA, Burge CB. "Predictive identification of exonic splicing enhancers in human genes". Science, 297(5583):1007-1013 (2002).(2002)
• Fairbrother WG, Chasin L. "Human genomic sequences that inhibit splicing." Molecular Cell Biology: 20(18): 6816-6825 (2000)(2000)
• Ackermann MN, Fairbrother WG, Amin NS, Deodene CJ, Lamborg CM, Martin PT. "Tetracarbonylmolybdenum complexes of 2-(phenylazo)-pyridine ligands: Correlations of molybdenum-95 chemical shifts with electronic, infrared, and electrochemical properties." J. Organometal. Chem. 523: 145-151 (1996)(1996)
• Fairbrother WG. "Difficult R&D Interface" Chemical Business (1991)(1991)
• Fairbrother WG. "Sunny Days for Solar Cells" Chemical Business (1990)(1990)