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Molecular and Cellular Biology, September 2007, p. 6103-6115, Vol. 27, No. 17
0270-7306/07/$08.00+0     doi:10.1128/MCB.00772-07
Copyright © 2007, American Society for Microbiology. All Rights Reserved.

Rtf1 Is a Multifunctional Component of the Paf1 Complex That Regulates Gene Expression by Directing Cotranscriptional Histone Modification{triangledown}

Marcie H. Warner, Kelli L. Roinick,{dagger} and Karen M. Arndt*

Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania 15260

Received 2 May 2007/ Returned for modification 5 June 2007/ Accepted 8 June 2007

Numerous transcription accessory proteins cause alterations in chromatin structure that promote the progression of RNA polymerase II (Pol II) along open reading frames (ORFs). The Saccharomyces cerevisiae Paf1 complex colocalizes with actively transcribing Pol II and orchestrates modifications to the chromatin template during transcription elongation. To better understand the function of the Rtf1 subunit of the Paf1 complex, we created a series of sequential deletions along the length of the protein. Genetic and biochemical assays were performed on these mutants to identify residues required for the various activities of Rtf1. Our results establish that discrete nonoverlapping segments of Rtf1 are necessary for interaction with the ATP-dependent chromatin-remodeling protein Chd1, promoting covalent modification of histones H2B and H3, recruitment to active ORFs, and association with other Paf1 complex subunits. We observed transcription-related defects when regions of Rtf1 that mediate histone modification or association with active genes were deleted, but disruption of the physical association between Rtf1 and other Paf1 complex subunits caused only subtle mutant phenotypes. Together, our results indicate that Rtf1 influences transcription and chromatin structure through several independent functional domains and that Rtf1 may function independently of its association with other members of the Paf1 complex.

* Corresponding author. Mailing address: Department of Biological Sciences, University of Pittsburgh, 269 Crawford Hall, 4249 Fifth Avenue, Pittsburgh, PA 15260. Phone: (412) 624-6963. Fax: (412) 624-4759. E-mail: arndt{at}pitt.edu

{triangledown} Published ahead of print on 18 June 2007.

{dagger} Present address: EMD Biosciences Inc., San Diego, CA 92121.

Molecular and Cellular Biology, September 2007, p. 6103-6115, Vol. 27, No. 17
0270-7306/07/$08.00+0     doi:10.1128/MCB.00772-07
Copyright © 2007, American Society for Microbiology. All Rights Reserved.



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