RNA



Structure of the histone mRNA hairpin required for cell cycle regulation of histone gene expression


KATIA  ZANIER a1, INGRID  LUYTEN a1, CATRIONA  CROMBIE a2, BERNDT  MÜLLER a2, DANIEL  SCHÜMPERLI a3, JENS P.  LINGE a1p1, MICHAEL  NILGES a1p1 and MICHAEL  SATTLER a1c1
a1 Structural and Computational Biology, European Molecular Biology Laboratory, Heidelberg, Germany
a2 Department of Molecular and Cell Biology, Institute of Medical Sciences, University of Aberdeen, Aberdeen AB25 2ZD, Scotland, United Kingdom
a3 Institute of Cell Biology, University of Bern, 3012 Bern, Switzerland

Abstract

Expression of replication-dependent histone genes requires a conserved hairpin RNA element in the 3′ untranslated regions of poly(A)-less histone mRNAs. The 3′ hairpin element is recognized by the hairpin-binding protein or stem-loop-binding protein (HBP/SLBP). This protein–RNA interaction is important for the endonucleolytic cleavage generating the mature mRNA 3′ end. The 3′ hairpin and presumably HBP/SLBP are also required for nucleo-cytoplasmic transport, translation, and stability of histone mRNAs. RNA 3′ processing and mRNA stability are both regulated during the cell cycle. Here, we have determined the three-dimensional structure of a 24-mer RNA comprising a mammalian histone RNA hairpin using heteronuclear multidimensional NMR spectroscopy. The hairpin adopts a novel UUUC tetraloop conformation that is stabilized by base stacking involving the first and third loop uridines and a closing U-A base pair, and by hydrogen bonding between the first and third uridines in the tetraloop. The HBP interaction of hairpin RNA variants was analyzed in band shift experiments. Particularly important interactions for HBP recognition are mediated by the closing U-A base pair and the first and third loop uridines, whose Watson–Crick functional groups are exposed towards the major groove of the RNA hairpin. The results obtained provide novel structural insight into the interaction of the histone 3′ hairpin with HBP, and thus the regulation of histone mRNA metabolism.

(Received August 23 2001)
(Revised September 18 2001)
(Accepted October 22 2001)


Key Words: hairpin; hairpin-binding protein; histone gene expression; isotope labeling; NMR; stem-loop-binding protein; structure.

Correspondence:
c1 Reprint requests to: Michael Sattler, European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany; e-mail: sattler@EMBL-Heidelberg.de.
p1 Present address: Unité de Bioinformatique Structurale, Institut Pasteur, 25–28 rue du docteur Roux, F-75015 Paris, France.