Robert W West, PhD
- Associate Professor of Biochemistry and Molecular Biology
Research Programs and Affiliations
- Biochemistry and Molecular Biology
Education & Fellowships
- Postdoctoral Fellow: Harvard University, (mentor: Mark Ptashne)
- PhD: University of California at Davis, 1981, (mentor: Ray Rodriguez)
Regulation of Gene Expression; Genomics & Proteomics; Personalized Medicine
HealthLinkOnAir Radio Interview10/9/11 What Is Personalized Medicine?
Regulation of Gene Expression.
Research conducted in the West lab from 1984 to 2002 involved studies on transcriptional regulation in the budding yeast Saccharomyces cerevisiae. The model gene system used originally involved the adjacent and divergently transcribed GAL1 and GAL10 genes, which are controlled by the availability of the sugars galactose (induces) and glucose (represses). Regulation is mediated via both activator (mainly Gal4) and repressor (mainly Mig1) proteins that bind to control sites between GAL1 and GAL10 in a region designated as the GAL upstream activating sequence or UASG. Classical yeast genetic methods were used in attempt to tease out additional factors responsible for controlling GAL1 and GAL10 transcription. This largely involved a cascade of suppressor searches, indicated in Figure A below. Thus, to understand the function of UASG, an attenuated version of UASG was employed in a suppressor screen that eventually led to the identification of the suppressor tsf3/sin4. Sin4 was ultimately identified as a component of the 25-subunit Mediator protein, a primary yeast coactivator/corepressor protein. To understand the function of Sin4, a suppressor search was conducted that identified the suppressor rlr1. Rlr1 was subsequently identified as a component of the TREX complex that plays a major role in coordinating and integrating the processes of transcription elongation, mRNA processing, and mRNA export. To understand the function of Rlr1, a multicopy suppressor search was conducted that identified the suppressor SUB2. While Sub2 was originally characterized as a component of the mRNA splicing apparatus, it was subsequently identified as a member of the TREX complex along with Rlr1. A model summarizing our view of the role of Rlr1 and Sub2, in conjunction with other yeast regulatory proteins, is presented in Figure B below (West & Milgrom, 2002). In summary, the suppressor walk unwittingly progressed from the characterization of regulatory proteins acting upstream of the gene to those acting increasingly downstream, underscoring the connectedness between the various control processes that govern gene expression. Each regulatory protein turned out to be a global regulator of yeast gene transcription rather than GAL gene-specific, and each is phylogenetically conserved from yeast to man. These studies, in parallel with similar approaches and discoveries by other yeast researchers, helped elucidate key components of the gene regulatory machinery and clarify mechanisms of transcriptional control in eukaryotic cells.
FIGURE A (adapted from R. Young, MIT). Components of the transcription initiation machinery in gene expression- connecting the dots. A "suppressor walk" which began with UASG, led to sin4, then to rlr1, and finally to SUB2, thereby demonstrating the intrinsic coupling of stages of gene expression, starting from gene-specific regulators (UASG-binding proteins) and leading to mRNA biogenesis/export functions (Rlr1 and Sub2; for further details see Figure B). Surprisingly, TAF9, a subunit of both TFIID and SAGA, may be another integral component involved in this overall connectedness, perhaps coupling stages of transcription initiation with those of elongation (for further details see Figure 1 and Milgrom et al., 2005).
FIGURE B (from West & Milgrom, 2002) Hypothetical scheme where Rlr1, Hpr1, and Sub2 ("TREX complex” subunits) facilitate the coupling of transcription and mRNP biogenesis/export. Rlr1, perhaps recruited to RNA polymerase II (PolII or “II”) by Mediator (not shown), recruits Sub2 to the transcription elongation complex. Sub2, in turn, facilitates the association (Npl3, Yra1) or dissociation (Mud2, Rrp6) of various RNA-binding proteins affiliated with mRNP biogenesis/export. Rlr1 may act as a protein chaperone by facilitating interactions among RNA-binding proteins, perhaps via polar zipper interactions involving mixed charge clusters (KEKE repeats) at its C-terminus (green zigzag line). Hpr1 may be involved in DNA chaperone-like functions. Cbc1/Cbc2, cap-binding complex. Gray wavy line, nascent mRNA; yellow zigzag line, PolII CTD (C-terminal domain); broken black line, DNA template; thick horizontal arrow, direction of transcription.
Genomics and Proteomics.
Beginning in 2002 I began devoting my research effort, in conjunction with colleagues in the Biochemistry department, to the establishment and operation of proteomics and genomics core facilities located in the Biochemistry and Molecular Biology Department (see Lab/Professional Web Site links at top, or "Research Facilities" on side-bar). These facilities allow faculty and students in the department, as well as other departments at Upstate Medical University, Syracuse University, and the SUNY School of Environmental Science and Forestry, the ability to perform research using technology relevant to studies of genomes and proteomes. Further information can be obtained from web links for the respective core facilities. The outcome of a collaboration with Dr. Winston Shen in our department, involving the use of our genomic core facilities to perform synthetic genetic array (SGA) analysis, demonstrated a specific and previously uncharacterized role for TAF9, likely in the context of the transcription factor SAGA (see Figure A above), in transcription elongation as well as initiation (see Figure 1 below).
Figure 1 (from Milgrom et al, 2005). Genome-wide synthetic interactions involving TAF9. Genes for transcription factors are classified into three major groups: Mediator, chromatin-modifying complexes, and regulators of transcription elongation. Yellow ovals denote sets of genes that encode transcription factors that have been demonstrated to biochemically associate with TAFs. Genes marked in red indicate strong genetic interactions; those marked in blue indicate conditional synthetic interactions. Underlined genes are present in multiple categories. Asterisks denote two essential genes identified by a conventional synthetic lethality screen. Solid lines denote functional connections involving specific transcription factors associated with particular cellular processes.
West Jr., R.W., Kruger, B., Thomas, S., Ma, J., and Milgrom, E. (2000). RLR1 (THO2), required for expressing lacZ fusions in yeast, is conserved from yeast to humans and is a suppressor of SIN4. Gene, 243: 195-205.
West Jr., R.W. and Milgrom, E. (2002) DEAD-box RNA helicase Sub2 is required for expression of lacZ fusions in Saccharomyces cerevisiae and is a dosage-dependent suppressor of RLR1 (THO2). Gene, 288: 19-27.
Sambade, M., Alba, M., Smardon, A., West, Jr., R.W. and Kane. P.M. (2005) A Genomic Screen for Yeast vma (Vacuolar Membrane ATPase) Mutants. Genetics, 170: 1539-1551..
Milgrom, E., West Jr., R.W., Gao, C., and Shen, W.C. (2005) TFIID and SAGA functions probed by genome-wide synthetic genetic array (SGA) analysis using a Saccharomyces cerevisiae taf9-ts allele. Genetics, 171: 959-973.
Electron Microscopy reconstruction of the yeast vacuolar ATPase. Ribbon models for individual protein subunits have been fit to the electron density.
From the lab of Stephan Wilkens, PhD.