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Chromatin-Based Transcriptional Punctuation Downloaded from genesdev.cshlp.org on September 26, 2021 - Published by Cold Spring Harbor Laboratory Press PERSPECTIVE Chromatin-based transcriptional punctuation Paul B. Talbert1 and Steven Henikoff Howard Hughes Medical Institute, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, USA The long polycistronic transcription units of trypano- motifs for initiation and termination of transcription, somes do not appear to be demarcated by the usual DNA which suggests a very different strategy for transcrip- motifs that punctuate transcription in familiar eukar- tional regulation from what is found in more familiar yotes. In this issue of Genes & Development, Siegel and organisms, including animals, fungi, and plants. These ob- colleagues (pp. 1063–1076) describe a system for the de- servations have led to the notion that a different system is marcation of trypanosome transcription units based on responsible for transcriptional regulation (Clayton 2002). the deposition and turnover of histone variants rather As described by Siegel et al. (2009) in this issue of Genes than on the binding of transcription factors. Replication- & Development, the punctuation of transcription appears independent incorporation of histone variants and de- to be governed by the incorporation of histone variants. stabilization of nucleosomes is an emerging theme at This discovery has important implications for more famil- promoters of more familiar eukaryotes, and it now iar organisms, where histone variant incorporation has appears that this system is an evolutionarily conserved taken a back seat to DNA-binding proteins in specifying mode of transcriptional punctuation. where transcription starts and stops. Trypanosome histone variants and transcription Eukaryotes have evolved remarkably diverse cellular Eukaryotic transcription takes place in the context of forms encoded by genomes that are regulated by a com- nucleosomes that wrap DNA, thereby achieving a greater mon set of chromatin proteins. Studies that catalog the compaction of the genome while restricting access of diversity of mechanisms for eukaryotic gene expression the transcriptional machinery. The bulk of nucleosomes focus on only a few well-studied model organisms, and are composed of octamers of two molecules each of the ‘‘from yeast to man’’ is a phrase that is often used to four ‘‘canonical’’ core histones—H3, H4, H2B, and H2A— indicate generality in eukaryotic biology. However, our which are among the most highly conserved proteins in favorite model organisms thrive in man-made environ- eukaryotes. Each of these histones, however, also exists ments, and only when a ‘‘freaky’’ eukaryote has an impact in variant forms that can carry out specialized functions. on human health or wealth does it become a popular Functionally distinct variants are uncommon for H4 and organism for intensive study. In this regard, trypano- H2B but are universal, or nearly so, for H3 and H2A somes belong to a highly distinctive eukaryotic lineage (Malik and Henikoff 2003). Considerable work in yeast that has become a model organism because of its enor- and multicellular eukaryotes in recent years has estab- mous impact on human health. They are well-known to lished the common functions that are mediated by us because of the human misery they cause as blood- nucleosomes bearing H3 and H2A variants. H3.3 medi- borne parasites, including Trypanosoma brucei, which ates nucleosome replacement and marks active chroma- causes African sleeping sickness that is transmitted by tin (Waterborg 1993; Ahmad and Henikoff 2002), CenH3 tsetse flies, and others that cause Chagas’ disease and functions in chromosome segregation (Amor et al. 2004), leishmaniasis. H2A.X participates in DNA repair (Loizou et al. 2006), The intensive study of trypanosome biology aimed at and H2AZ is associated with promoters (Raisner et al. dealing with these scourges has also uncovered remark- 2005) and maintains accessible chromatin that prevents able features of their genomic organization and chroma- silencing in yeast (Meneghini et al. 2003) and DNA tin biology. Notably, gene transcription is polycistronic, methylation in plants (Zilberman et al. 2008). Histone with 59 and 39 ends that appear to lack the usual sequence variants in unicellular protists, however, do not fit so neatly into these common functional categories. No- [Keywords: Trypanosoma brucei; histone variants; histone modification; where has this been more of a puzzle than in trypano- genome-wide ChIP-seq; transcription initiation; transcription termination] 1Corresponding author. somes. Trypanosomes have two forms of each of the four E-MAIL [email protected]; FAX (206) 667-5889. histones, all of which are considerably diverged from the Article is online at http://www.genesdev.org/cgi/doi/10.1101/gad.1806409. Freely available online through the Genes & Development Open Access canonical histones of plants and animals (Alsford and option. Horn 2004; Siegel et al. 2009). GENES & DEVELOPMENT 23:1037–1041 Ó 2009 by Cold Spring Harbor Laboratory Press ISSN 0890-9369/09; www.genesdev.org 1037 Downloaded from genesdev.cshlp.org on September 26, 2021 - Published by Cold Spring Harbor Laboratory Press Talbert and Henikoff The two forms of H2A in T. brucei are markedly divergent from other H2As but appear to correspond to the canonical H2A and its universal variant, H2AZ. Previous work has shown that T. brucei H2AZ is co- incident in distribution and specifically coimmunopreci- pitates with the H2B variant H2BV, with which it is presumed to dimerize (Lowell et al. 2005). H2BV has only 38% identity to its more conventional H2B counterpart and, together with H2AZ, it is required for viability, indicating that H2AZ/H2BV nucleosomes have a func- tion distinct from H2A/H2B nucleosomes. Siegel et al. (2009) describe a previously uncharacter- Figure 1. Schematic diagram of a portion of a T. brucei chro- ized variant of H4 in T. brucei, designated H4V, which is mosome. Polycistronic transcription of co-oriented protein- 85% identical to its H4 counterpart. The unusual occur- coding genes occurs from divergent SSRs and terminates at rence of variants of H4 and H2B in trypanosomes is convergent SSRs, which are often inhabited by tRNA genes. striking, but no less so than the complement of only Incorporation of H2AZ/H2BV/H3K4me/H4K10ac nucleosomes two forms of H3 variants, both highly divergent from occurs at putative transcription initiation sites and incorpora- tion of H2A/H2B/H3V/H4V nucleosomes occurs at putative canonical H3. Multicellular eukaryotes commonly have transcription termination sites (Clayton 2002; Mandava et al. three forms of H3. In addition to the canonical form that 2008; Siegel et al. 2009). is incorporated exclusively during replication, a nearly identical variant known as H3.3 incorporates in replace- ment nucleosomes that are assembled throughout the some genomes, however, lack recognizable pol II pro- cell cycle, including during replication (Ahmad and moter elements (Clayton 2002). General transcription Henikoff 2002). H3.3 is incorporated after transcription factors that act on protein-encoding genes have been (Schwartz and Ahmad 2005) and is enriched at the 59 end difficult to find, and most known families of locus- of genes and also in regulatory elements, where nucleo- specific transcription factors appear to be absent from some remodeling complexes may be responsible for its the genome (Iyer et al. 2008). turnover (Henikoff 2008). Although the replication- In order to gain insight into whether chromatin struc- dependent H3 is commonly called canonical, ascomycetes ture and histone variants play a role in transcription such as yeast and some unicellular organisms such as the initiation, Siegel et al. (2009) used chromatin immuno- algae Cyanidioschyzon and Chlamydomonas have only precipitation (ChIP) to tagged or untagged histone var- a single form of packaging H3 that corresponds function- iants or modifications followed by Solexa sequencing of ally to replication-independent H3.3. Replication-specific the nucleosomal DNA (ChIP-seq) to map the locations of forms of canonical H3 appear to have evolved recurrently histone variants on the assembled genome sequence. in eukaryotic evolution, presumably by divergence from Using an antibody to H4 acetylated on Lys 10 (H4K10ac), H3.3-like forms (Waterborg and Robertson 1996; Malik they found twin peaks of H4K10ac enrichment at every and Henikoff 2003). A third near-universal but much less SSR with divergently oriented transcription units, and no conserved H3 variant, called CENP-A or CenH3, specifies peaks at convergent SSRs. They also found 61 single the centromere and is essential for kinetochore assembly peaks not at SSRs, most of which were downstream from (Amor et al. 2004). The two T. brucei H3s, designated H3 pol III-transcribed tRNA genes that interrupted what and H3V, are ;60% identical. Neither variant corre- otherwise appeared to be a single polycistronic pol II sponds to replication-coupled H3 nor, surprisingly, to transcription unit. All but three other tRNA genes were CenH3, which is missing from trypanosome genomes found in convergent SSRs, leading Siegel et al. (2009) to (Lowell and Cross 2004). propose that all peaks of H4K10ac enrichment correspond Trypanosomes are highly unusual for eukaryotes in to transcription start sites either at divergent SSRs or be- having polycistronic transcription units of up to 100 tween adjacent co-oriented transcription units, many of genes, similar to bacterial
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