Professor of Oncological Sciences
B.A. Rice University
Ph.D. University of Washington
Barbara Graves' Lab Page
Barbara Graves' PubMed Literature Search
Molecular Biology Program
Biological Chemistry Program
Transcriptional Regulation, Transcription Mechanisms, Protein Biochemistry, autoinhibition and specificity of ETS transcription factors
The Graves Laboratory focuses on mechanistic questions in the area of transcriptional regulation. We use biochemical and genomics approaches to investigate how sequence-specific DNA binding transcription factors regulate gene expression in normal and diseased states. Current projects explore signaling pathways, DNA binding properties, and protein-protein interactions within the ETS family of regulatory transcription factors. Disease areas include prostate cancer and leukemia.
Regulation of gene expression requires the targeting of regulatory transcription factors to their site of action in the genome. Molecular complementarity between a regulatory protein and its DNA binding site provides the primary targeting mechanism. A constellation of electrostatic and hydrophobic interactions between matching surfaces of the DNA helix and the protein establish high-affinity and sequence-specific binding. The effectiveness of this macromolecular match-making is challenged by the complexities of eukaryotes. There are hundreds of regulatory transcription factors that function by binding DNA sequences within promoter regions. Almost all of these proteins are encoded by multi-gene families. Members of a family display the same structural fold for binding DNA and recognize similar DNA sequences. My laboratory investigates the regulatory pathways that provide specificity for transcription factors that belong to multi-gene families.
Our investigations are currently focused on the ETS gene family that dramatically illustrates the specificity problem. ETS genes are present in all metazoan phyla with 28 homologs in the human genome. Most human cell types express at least 16 ETS genes. The ETS domain, a highly conserved 85-amino acid region, defines the family and directs DNA binding to the core recognition sequence 5'-GGAA/T-3'. With such a high degree of conservation, we ask how specific biology is performed by each ETS protein. Using biochemical approaches we have discovered auto-regulatory circuits, identified transcriptional co-factors, and determined the mechanism of action of post-translational modifications that distinguish ETS proteins. We are performing genome-wide searches for transcriptional targets of ETS proteins to determine the rules for specificity using the latest technology for high-through put sequencing.
We use these biochemical and genomics approaches to investigate the role of the ETS family in human cancers. Nuclear oncogenes are most often transcription factors that cause inappropriate gene expression. The ETS family illustrates this oncogenic potential. The genes that encode several ETS proteins, ERG, FLI and ETV6, are altered by chromosome translocations that associate with specific human cancers. Classes of sarcoma, leukemia, and prostate cancer are driven by these altered ETS genes. ETS proteins are also targets of Ras-dependent signaling, a growth control pathway frequently mutated to be superactivated in human cancers. Using genomics approaches we are identifying the target genes of these oncogenic ETS factors. We are also investigating critical roles of ETS factors in chromatin remodeling by identifying co-factors that associate with these oncogenic ETS factors.
- Desjardins G, Okon M, Graves BJ, McIntosh LP. 2016. Conformational Dynamics and the Binding of Specific and Nonspecific DNA by the Autoinhibited Transcription Factor Ets-1. Biochemistry. 55:4105-18.
- De S, Okon M, Graves BJ, McIntosh LP. 2016. Autoinhibition of ETV6 DNA Binding Is Established by the Stability of Its Inhibitory Helix. J Mol Biol. 428:1515-30.
- Huang F, Ramakrishnan S, Pokhrel S, Pflueger C, Parnell TJ, Kasten MM, Currie SL, Bhachech N, Horikoshi M, Graves BJ, Cairns BR, Bhaskara S, Chandrasekharan MB. 2015. Interaction of the Jhd2 Histone H3 Lys-4 Demethylase with Chromatin Is Controlled by Histone H2A Surfaces and Restricted by H2B Ubiquitination. J Biol Chem. 290:28760-77.
- Desjardins G, Meeker CA, Bhachech N, Currie, SL, Graves, BJ, McIntosh LP. 2014. Synergy of aromatic residues and phosphoserines within the intrinsically disordered DNA-binding inhibitory elements of Ets-1. Proc Natl Acad Sci U S A. 111:11019-24.
- De S, Chan AC, Coyne HJ 3rd, Bhachech N, Hermsdorf U, Okon M, Murphy ME, Graves BJ, McIntosh LP. 2014. Steric mechanism of auto-inhibitory regulation of specific and non-specific DNA binding by the ETS transcriptional repressor ETV6. J Mol Biol. 426:1390-406.
- Coyne HJ 3rd, De S, Okon M, Green SM, Bhachech N, Graves BJ, McIntosh LP. 2012. Autoinhibition of ETV6. TEL. DNA binding: appended helices sterically block the ETS domain. J Mol Biol. 421:67-84.
- Hollenhorst PC, Ferris MW, Hull MA, Chae H, Kim S, Graves BJ. 2011. Oncogenic ETS proteins mimic activated RAS/MAPK signaling in prostate cells. Genes Dev. 25:2147-57.
- Oler AJ, Alla RK, Roberts DN, Wong A, Hollenhorst PC, Chandler KJ, Cassiday PA, Nelson CA, Hagedorn CH, Graves BJ, Cairns BR. 2010. Human RNA polymerase III transcriptomes and relationships to Pol II promoter chromatin and enhancer-binding factors. Nat Struct Mol Biol. 17:620-8.
- Nelson ML, Kang HS, Lee GM, Blaszczak AG, Lau DK, McIntosh LP, Graves BJ. 2010. Ras signaling requires dynamic properties of Ets1 for phosphorylation-enhanced binding to coactivator CBP. Proc Natl Acad Sci U S A. 107:10026-31.
- Hollenhorst PC, McIntosh LP, Graves BJ. 2010. Genomic and biochemical insights into the specificity of ETS transcription factors. Ann Rev Biochem. 80:437-71.
- Green SM, Coyne HJ, McIntosh LP, Graves BJ 2010. DNA binding by the ETS protein TEL. ETV6. is regulated by autoinhibition and self-association. J Biol Chem. 285:18496-504.
- Hollenhorst PC, Chandler KJ, Poulsen RL, Johnson WE, Speck NA, Graves BJ. 2009. DNA specificity determinants associate with distinct transcription factor functions. PLoS Genet. 5:e1000778.
- Pufall MA, Lee GM, Nelson ML, Kang HS, Velyvis A, Kay LE, McIntosh LP, Graves BJ. 2005. Variable control of Ets-1 DNA binding by multiple phosphates in an unstructured region. Science. 309:142-5.
- Pufall MA, Graves BJ. 2002. Autoinhibitory domains: modular effectors of cellular regulation. Ann. Rev. Cell Develop. 18:421-462.