Dr. Karen Arndt

Genetics
K. Arndt
T.-L. Ashman
G. Campbell
D. Chapman
G. Hatfull
J. Hildebrand
L. Jacobson
S. Kalisz
J. Martens
W. Saunders
B. Stronach
S. Tonsor
R. Wood

Microbiology
J. Boyle
G. Hatfull
R. Hendrix
J. Lawrence
J. Pipas
M. Popa
R.L. Duda
S. Godfrey
V. Oke

Molecular Biology
K. Arndt
J. Franzen
P. Grabowski
G. Hatfull
R. Hendrix
L. Jen-Jacobson
J. Martens
C. Peebles
J. Pipas
J. Rosenberg
A. Schwacha
C. Walsh

Plant Biology
T.-L. Ashman
W. Carson
S. Kalisz
V. Oke
C. Partanen
S. Tonsor
B. Traw

Science Education
A. Bledsoe
K. Curto
L. Daniels
S. Godfrey
N. Kaufmann
C. LaFave
J. Newman
E. Polinko
M. Popa
L. Roberts
T. Seiflein
R. Sherwin
A. Slinskey Legg

Structural Biology
M. Grabe
J. Hempel
R. Hendrix
L. Jen-Jacobson
J. Rosenberg
A. VanDemark

Former Faculty

Photo of Dr.
Arndt

Mechanisms of Transcriptional Regulation in Yeast

Associate Professor

Dr. Arndt received her Ph.D. in 1988 with Michael Chamberlin at the University of California at Berkeley, performed her postdoctoral studies with Fred Winston at Harvard Medical School, and joined the Department in 1994.

Currently, Dr. Arndt is accepting graduate students in her laboratory. Dr. Arndt is accepting undergraduate researchers, and does sponsor students in other laboratories.

Professional Interests - Publications - Contact Information - Lab Personnel

Professional Interests of Karen Arndt

Fig. 1
Fig. 1. Diagram of a typical eukaryotic promoter. The general transcription machinery assembles at the TATA region of the promoter. Gene-specific regulatory factors, activators and repressors, generally bind upstream of the TATA box and activate or repress transcription. In vivo, the DNA template exists in the form of chromatin with both histone and non-histone proteins bound to the DNA. The general transcription factor TFIID is comprised of TBP and several TBP-associated factors.

As the first step in the complex process of gene expression, synthesis of mRNA by RNA polymerase II is subject to a multiplicity of controls. Proper regulation of transcription is essential for the normal growth and development of all organisms. The fundamental importance of transcriptional regulation to human health is evident from the large number of diseases, including cancer and AIDS, that result when cellular transcription factors are altered by mutation or when viral proteins commandeer the cellular transcription machinery. Therefore, a detailed understanding of the proteins and regulatory mechanisms that influence the activity of RNA polymerase II, the central research focus of our lab, is a vital step toward understanding the causes of a number of important human diseases.

The transcription cycle in all organisms can be divided into three fundamental steps: (1) promoter recognition and initiation of RNA synthesis; (2) elongation of the growing RNA chain; and (3) termination. We are using a combined experimental approach to study transcription initiation and elongation by RNA polymerase II. In particular, we are exploiting the vast array of genetic, biochemical, and genomic tools uniquely available in the model eukaryote, Saccharomyces cerevisiae. This simple yeast is an excellent model system for our studies because the proteins and mechanisms that regulate transcription initiation and elongation have been highly conserved through evolution.

Fig. 2
Fig. 2. Structure of yeast TBP. Amino acid substitutions at positions 109 and 159 severely reduce the DNA binding affinity of TBP and lead to promoter specific defects in transcriptional activation in vivo (Arndt et al. 1995). Using genetic approaches, proteins that restore function to these TBP mutants have been identified (Shirra et al. 1999, Liu et al. 1999). Analysis of additional TBP mutants has provided insight into the determinants of orientation-specific DNA binding by TBP (Spencer and Arndt 2002).This figure was adapted from the work of Kim et al. (Nature 365:512-520).

Fig.3
Fig. 3. RNA polymerase is subject to pause and arrest sites that hinder its progress through a transcription unit.

Transcription initiation

Transcription initiation by RNA polymerase II in eukaryotes requires the coordinated activities of a large number of proteins (Fig. 1). Central among these is the TATA box binding protein, TBP (Fig. 2), which binds directly to the promoter and nucleates the assembly of a transcriptionally competent preinitiation complex. Several studies have shown that binding of TBP to TATA elements is a highly regulated, rate-limiting step in transcription. Using our collection of yeast TBP mutants as a foundation, we are currently investigating:

The proteins and mechanisms that regulate DNA binding by TBP in vivo
How different environmental cues and signal transduction cascades facilitate or impede the binding of TBP to promoters
The interplay between gene-specific transcription factors and more generally acting regulatory proteins, such as chromatin modifiers, and the effect of this interplay on TBP function

Transcription elongation

It is now widely accepted that the synthesis of an RNA transcript is not a monotonous process with each successive nucleotide being added at a constant rate. Instead, RNA polymerases encounter a variety of transcription elongation blocks that must be overcome for efficient RNA synthesis (Fig. 3). Eukaryotes encode a number of proteins that modulate the elongation properties of RNA polymerase. Some of these are shown in Figure 4. Using genetic and biochemical approaches, we have identified a novel transcription elongation factor, Rtf1, and demonstrated that it is a member of the RNA polymerase II-associated Paf1 complex. We and others have found that the Paf1 complex associates with the coding regions of actively transcribed genes, interacts with other highly conserved transcription elongation factors, and plays a key role in chromatin-mediated regulation of transcription elongation. Rtf1 exhibits strong functional and physical interactions with the chromatin remodeling factor Chd1 and is essential for histone modifications associated with regions of active transcription. We are currently investigating:

The mechanism by which Rtf1 and associated proteins regulate elongation
The genes that are regulated by Rtf1, and how Rtf1 activity might be controlled at those genes
Other factors that regulate transcription elongation in yeast, particularly in the context of chromatin

Fig.4
Fig. 4. The transition from initiation to elongation is a pivotal step in transcription. A subset of the proteins involved in transcription elongation is shown. Phosphorylation of the carboxy-terminal domain (CTD) of Pol II correlates strongly with progression from initiation to elongation. Proteins highlighted in color were identified in a genetic screen for factors that are essential in the absence of Rtf1 function (Costa and Arndt, 2000). Rtf1 is a member of the Paf1 complex (shown in pink), which associates with RNA polymerase II on actively transcribed genes and regulates chromatin structure (Squazzo et al. 2002; Simic et al. 2003). Rtf1 is essential for methylation of histone H3 on lysine 4 (shown in red), a mark of active transcription.

Publication Archive
24 Citations
22 Abstracts
19 PDFs

Recent Publications of Karen Arndt

Rubenstein, E.M., R.R. McCartney, C. Zhang, K.M. Shokat, M.K. Shirra, K.M. Arndt, and M.C. Schmidt (2008) Access denied: Snf1 activation loop phosphorylation is controlled by availability of the phosphorylated threonine 210 to the PP1 phosphatase. J. Biol. Chem. 283:222-230

Arndt, K.M. (2007) Molecular biology: genome under surveillance. Nature 450:959-960

Chu, Y., R. Simic, M.H. Warner, K.M. Arndt, and G. Prelich (2007) Regulation of histone modification and cryptic transcription by the Bur1 and Paf1 complexes. EMBO J. 26:4646-4656

Warner, M.H., K.L. Roinick, and K.M. Arndt (2007) Rtf1 is a multifunctional component of the Paf1 complex that regulates gene expression by directing cotranscriptional histone modification. Mol. Cell Biol. 27:6103-6115 (PDF Reprint: 860 kb)

Braun, M.A., P.J. Costa, E.M. Crisucci, and K.M. Arndt (2007) Identification of Rkr1, a nuclear RING domain protein with functional connections to chromatin modification in Saccharomyces cerevisiae. Mol. Cell. Biol. 27:2800-2811 (PDF Reprint: 451 kb)

Sheldon, K.E., D.M. Mauger, and K.M. Arndt (2005) A requirement for the Saccharomyces cerevisiae Paf1 Complex in snoRNA 3' end formation. Mol. Cell 20:225-236 (PDF Reprint: 523 kb)

Arndt, K., and F. Winston (2005) An unexpected role for ubiquitylation of a transcriptional activator. Cell 120:733-734 (PDF Reprint: 48 kb)

Shirra, M.K., S.E. Rogers, D.E. Alexander, and K.M. Arndt (2005) The Snf1 protein kinase and Sit4 protein phosphatase have opposing functions in regulating TBP association with the Saccharomyces cerevisiae INO1 promoter. Genetics 169:1957-1972 (PDF Reprint: 620 kb)

Arndt, K.M., and C.M. Kane (2003) Running with RNA polymerase: eukaryotic transcript elongation. Trends Genet. 19:543-550 (PDF Reprint: 337 kb)

Simic, R., D.L. Lindstron, H.G. Tran, K.L. Roinick, P.J. Costa, A.D. Johnson, G.A. Hartzog, and K.M. Arndt (2003) Chromatin remodeling protein Chd1 interacts with transcription elongation factors and localizes to transcribed genes. EMBO J. 22:1846-4856 (PDF Reprint: 339 kb)

Spencer, J.V., and K.M. Arndt (2002) A TATA binding protein mutant with increased affinity for DNA directs transcription from a reversed TATA sequence in vivo. Mol. Cell. Biol. 22:8744-8755 (PDF Reprint: 422 kb)

Squazzo, S.L., P.J. Costa, D. Lindstrom, K.E. Kumer, R. Simic, J.L. Jennings, A.K. Link, K.M. Arndt, and G. Hartzog (2002) The Paf1 complex physically and functionally associates with transcription elongation factors in vivo. EMBO J. 21:1764-1774 (PDF Reprint: 332 kb)

Shirra, M.K., J. Patton-Vogt, A. Ulrich, O. Liuta-Tehlivets, S.D. Kohlwein, S.A. Henry, and K.M. Arndt (2001) Inhibition of acetyl coenzyme A carboxylase activity restores expression of the Ino1 gene in a snf1 mutant strain of Saccharomyces cerevisiae. Mol Cell Biol 21:5710-5722 (PDF Reprint: 422 kb)

Costa, P.J., and K.M. Arndt (2000) Synthetic lethal interactions suggest a role for the Saccharomyces cerevisiae Rtf1 Protein in transcription elongation. Genetics 156:535-547 (PDF Reprint: 462 kb)

How to Contact Karen Arndt

US Mail
University of Pittsburgh
Department of Biological Sciences
269A Crawford Hall
4249 Fifth Avenue
Pittsburgh, PA 15260

Phone, FAX, Internet
Office : (412) 624-6963
Lab : (412) 624-6992
FAX : (412) 624-4759
Email : arndt+@pitt.edu
Web :

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