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A UV-crosslinkable interaction in human U6 snRNA

Published online by Cambridge University Press:  01 May 1998

JING-SONG SUN ,
SABA VALADKHAN  and
JAMES L. MANLEY
JING-SONG SUN
Affiliation:
Department of Biological Sciences, Sherman Fairchild Center of Life Science, Columbia University, New York, New York 10027, USA
SABA VALADKHAN
Affiliation:
Department of Biological Sciences, Sherman Fairchild Center of Life Science, Columbia University, New York, New York 10027, USA
JAMES L. MANLEY
Affiliation:
Department of Biological Sciences, Sherman Fairchild Center of Life Science, Columbia University, New York, New York 10027, USA

Abstract

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U6 snRNA is the most conserved of all the snRNAs involved in pre-mRNA splicing, and likely plays an important role in splicing catalysis. Using a U6 snRNA fragment encompassing residues 25–99, we have identified a strong, UV-sensitive tertiary intramolecular interaction. A 5′ deletion that removed sequences up to nt 37 only slightly reduced crosslinking, but further deletion of 11 bases, eliminating the nearly invariant ACAGAGA sequence, essentially abolished crosslinking, as did deletion of sequences 3′ of 82A. The crosslinked residues were mapped to 44G in the ACAGAGA sequence and to 81C, the nucleotide at the base of the U6 intramolecular helix, opposite the G of the invariant AGC trinucleotide. This interaction is striking in that it has the potential to juxtapose invariant regions of U6 believed to play critical roles in splicing catalysis.

Keywords

pre-mRNA splicingtertiary interactionsnRNA structure
Type
LETTER TO THE EDITOR
Information
RNA , Volume 4 , Issue 5 , May 1998 , pp. 489 - 497
Copyright
1998 RNA Society