Human RNA polymerase (Pol) III-transcribed genes are thought to share a simple termination signal constituted by four or more consecutive thymidine residues in the coding DNA strand, just downstream of the RNA 3′-end sequence. We found that a large set of human tRNA genes (tDNAs) do not display any T4 stretch within 50bp of 3′-flanking region. In vitro analysis of tDNAs with a distanced T4 revealed the existence of non-canonical terminators resembling degenerate T5 elements, which ensure significant termination but at the same time allow for the production of Pol III read-through pre-tRNAs with unusually long 3′ trailers. A panel of such non-canonical signals was found to direct transcription termination of unusual Pol III-synthesized viral pre-miRNA transcripts in gammaherpesvirus 68-infected cells. Genome-wide location analysis revealed that human Pol III tends to trespass into the 3′-flanking regions of tDNAs, as expected from extensive terminator read-through. The widespread occurrence of partial termination suggests that the Pol III primary transcriptome in mammals is unexpectedly enriched in 3′-trailer sequences with the potential to contribute novel functional ncRNAs.
Bibliographical noteFunding Information:
Fondazione Cariparma (2010), Italian Ministry of Education, University and Research (PRIN Program), AICCRE—Regione Emilia Romagna (to G.D.); from Conseil Régional d’Aquitaine, European Regional Development Fund, Agence Nationale de la Recherche (ANR, ‘REGPOLSTRESS’) and Ligue Contre le Cancer-Comités Gironde et Dordogne (to M.T.); the National Institutes of Health (CA103632 and P30AI054907 to L.v.D.); the Burroughs Wellcome Investigator in Infectious Diseases award and a University of Colorado Technical Transfer Office award (to K.W.D. and L.v.D.). C.P. was supported by a doctoral fellowship from the ‘Università Italo-Francese/Université Franco-Italienne’. V.P., D.R. and N.H. were supported by the University of Lausanne and Swiss National Science Foundation (NSF grant 3100A0-109941 to N.H.). Funding for open access charge: Fondazione Cariparma, Parma, Italy and Conseil Régional d’Aquitaine, France.