Four histone variants mark the boundaries of polycistronic transcription units in Trypanosoma brucei

T. Nicolai Siegel; Doeke R. Hekstra; Louise E. Kemp; Luisa M. Figueiredo; Joanna E. Lowell; David Fenyo; Xuning Wang; Scott Dewell; George A.M. Cross

doi:10.1101/gad.1790409

Four histone variants mark the boundaries of polycistronic transcription units in Trypanosoma brucei

¹Laboratory of Molecular Parasitology, The Rockefeller University, New York, New York 10065, USA;
²Laboratory of Living Matter, The Rockefeller University, New York, New York 10065, USA;
³Laboratory of Mass Spectrometry and Gaseous Ion Chemistry, The Rockefeller University, New York, New York 10065, USA;
⁴Department of Information Technology, The Rockefeller University, New York, New York 10065, USA;
⁵Genomics Resource Center, The Rockefeller University, New York, New York 10065, USA

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↵6 These authors contributed equally to this work.

Abstract

Unusually for a eukaryote, genes transcribed by RNA polymerase II (pol II) in Trypanosoma brucei are arranged in polycistronic transcription units. With one exception, no pol II promoter motifs have been identified, and how transcription is initiated remains an enigma. T. brucei has four histone variants: H2AZ, H2BV, H3V, and H4V. Using chromatin immunoprecipitation (ChIP) and sequencing (ChIP-seq) to examine the genome-wide distribution of chromatin components, we show that histones H4K10ac, H2AZ, H2BV, and the bromodomain factor BDF3 are enriched up to 300-fold at probable pol II transcription start sites (TSSs). We also show that nucleosomes containing H2AZ and H2BV are less stable than canonical nucleosomes. Our analysis also identifies >60 unexpected TSS candidates and reveals the presence of long guanine runs at probable TSSs. Apparently unique to trypanosomes, additional histone variants H3V and H4V are enriched at probable pol II transcription termination sites. Our findings suggest that histone modifications and histone variants play crucial roles in transcription initiation and termination in trypanosomes and that destabilization of nucleosomes by histone variants is an evolutionarily ancient and general mechanism of transcription initiation, demonstrated in an organism in which general pol II transcription factors have been elusive.

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Footnotes

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↵7 Present address: BIO Ventures for Global Health, 1225 Eye Street, NW, Washington, DC 20005, USA.
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↵8 Corresponding author.

↵E-MAIL george.cross{at}rockefeller.edu; FAX (212) 327-7572.
Article published online ahead of print. Article and publication date are online at http://www.genesdev.org/cgi/doi/10.1101/gad.1790409.
Supplemental material is available at http://www.genesdev.org.
- Received February 10, 2009.
- Accepted March 24, 2009.