Interaction of yeast RNA-binding proteins Nrd1 and Nab3 with RNA polymerase II terminator elements

  1. Kristina L. Carroll1,
  2. Rodolfo Ghirlando2,
  3. Jessica M. Ames1, and
  4. Jeffry L. Corden1
  1. 1Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA
  2. 2Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892-0540, USA

Abstract

Yeast RNA-binding proteins Nrd1 and Nab3 direct transcription termination of sn/snoRNA transcripts, some mRNA transcripts, and a class of intergenic and anti-sense transcripts. Recognition of Nrd1- and Nab3-binding sites is a critical first step in the termination and subsequent processing or degradation of these transcripts. In this article, we describe the purification and characterization of an Nrd1–Nab3 heterodimer. This Nrd1–Nab3 complex binds specifically to RNA sequences derived from a snoRNA terminator. The relative binding to mutant terminators correlates with the in vivo termination efficiency of these mutations, indicating that the primary specificity determinant in nonpoly(A) termination is Nrd1–Nab3 binding. In addition, several snoRNA terminators contain multiple Nrd1- and Nab3-binding sites and we show that multiple heterodimers bind cooperatively to one of these terminators in vitro.

Keywords

Footnotes

  • Reprint requests to: Jeffry L. Corden, Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, 725 N. Wolfe Street, Baltimore, MD 21205, USA; e-mail: jcorden{at}jhmi.edu; fax: (410) 502-6718.

  • Article published online ahead of print. Article and publication date are at http://www.rnajournal.org/cgi/doi/10.1261/rna.338407.

    • Received October 9, 2006.
    • Accepted December 6, 2006.
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