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Molecular and Cellular Biology, July 2009, p. 4002-4013, Vol. 29, No. 14
0270-7306/09/$08.00+0     doi:10.1128/MCB.00189-09
Copyright © 2009, American Society for Microbiology. All Rights Reserved.

Chromatin Structure Is Implicated in "Late" Elongation Checkpoints on the U2 snRNA and β-Actin Genes{triangledown} ,§

Sylvain Egloff, Hadeel Al-Rawaf, Dawn O'Reilly, and Shona Murphy*

Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford OX1 3RE, United Kingdom

Received 10 February 2009/ Returned for modification 19 March 2009/ Accepted 7 May 2009

The negative elongation factor NELF is a key component of an early elongation checkpoint generally located within 100 bp of the transcription start site of protein-coding genes. Negotiation of this checkpoint and conversion to productive elongation require phosphorylation of the carboxy-terminal domain of RNA polymerase II (pol II), NELF, and DRB sensitivity-inducing factor (DSIF) by positive transcription elongation factor b (P-TEFb). P-TEFb is dispensable for transcription of the noncoding U2 snRNA genes, suggesting that a NELF-dependent checkpoint is absent. However, we find that NELF at the end of the 800-bp U2 gene transcription unit and RNA interference-mediated knockdown of NELF causes a termination defect. NELF is also associated 800 bp downstream of the transcription start site of the β-actin gene, where a "late" P-TEFb-dependent checkpoint occurs. Interestingly, both genes have an extended nucleosome-depleted region up to the NELF-dependent control point. In both cases, transcription through this region is P-TEFb independent, implicating chromatin in the formation of the terminator/checkpoint. Furthermore, CTCF colocalizes with NELF on the U2 and β-actin genes, raising the possibility that it helps the positioning and/or function of the NELF-dependent control point on these genes.

* Corresponding author. Mailing address: Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford OX1 3RE, United Kingdom. Phone: 44 1865 275616. Fax: 44 1865 277556. E-mail: shona.murphy{at}path.ox.ac.uk

{triangledown} Published ahead of print on 18 May 2009.

§ Supplemental material for this article may be found at http://mcb.asm.org/.

Molecular and Cellular Biology, July 2009, p. 4002-4013, Vol. 29, No. 14
0270-7306/09/$08.00+0     doi:10.1128/MCB.00189-09
Copyright © 2009, American Society for Microbiology. All Rights Reserved.





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