Gene promoters dictate histone occupancy within genes

Perales, Roberto; Erickson, Benjamin; Zhang, Lian; Kim, Hyunmin; Valiquett, Elan; Bentley, David L.

doi:10.1038/emboj.2013.194

Cited by 38 publications

(57 citation statements)

References 64 publications

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“…It is speculated that these effects of Spt6 are mediated through alterations in chromatin. Consistent with this hypothesis, Spt6 is a histone chaperone capable of assembling nucleosomes on naked DNA templates in the presence of topoisomerase I (22) and is involved in preventing loss of histones through transcribed regions (25,27,(40)(41)(42)(43).…”

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confidence: 56%

“…Spt6 participates in shaping the chromatin structure of Pol II-transcribed genes. Mutation of SPT6 can lead to depletion of histones H3 and H4 in actively transcribed regions and the inability to di-and trimethylate lysine 36 on his-tone H3 (14,27,40,41,43,59). Therefore, we asked whether changes in chromatin structure might account for the observed effect of Spt6 on Pol I transcription initiation.…”

Section: Spt6 Associates With Rdna and Is Essential For Rrna Synthesismentioning

confidence: 99%

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Spt6 Is Essential for rRNA Synthesis by RNA Polymerase I

Engel

French

Viktorovskaya

et al. 2015

Molecular and Cellular Biology

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b Spt6 (suppressor of Ty6) has many roles in transcription initiation and elongation by RNA polymerase (Pol) II. These effects are mediated through interactions with histones, transcription factors, and the RNA polymerase. Two lines of evidence suggest that Spt6 also plays a role in rRNA synthesis. First, Spt6 physically associates with a Pol I subunit (Rpa43). Second, Spt6 interacts physically and genetically with Spt4/5, which directly affects Pol I transcription. Utilizing a temperature-sensitive allele, spt6-1004, we show that Spt6 is essential for Pol I occupancy of the ribosomal DNA (rDNA) and rRNA synthesis. Our data demonstrate that protein levels of an essential Pol I initiation factor, Rrn3, are reduced when Spt6 is inactivated, leading to low levels of Pol I-Rrn3 complex. Overexpression of RRN3 rescues Pol I-Rrn3 complex formation; however, rRNA synthesis is not restored. These data suggest that Spt6 is involved in either recruiting the Pol I-Rrn3 complex to the rDNA or stabilizing the preinitiation complex. The findings presented here identify an unexpected, essential role for Spt6 in synthesis of rRNA. Three eukaryotic RNA polymerases (Pols), Pol I, Pol II, and Pol III, have critical and yet distinct roles in gene expression. Pol II synthesizes mainly mRNAs, which serve as the templates for translation and give rise to the diverse collection of cellular proteins. Pols I and III are responsible for producing the stable RNA components of the translation machinery, rRNA and tRNA, respectively. In Saccharomyces cerevisiae (yeast), Pol I transcribes the ribosomal DNA (rDNA) to generate the 35S rRNA precursor within a subcompartment of the nucleus called the nucleolus. This precursor is co-and posttranscriptionally processed into the mature 25S, 18S, and 5.8S rRNAs and assembled into ribosomes. Pol III synthesizes all tRNAs and the 5S rRNA. The highly repetitive nature of the rDNA (ϳ200 tandem copies of the rDNA in yeast) helps cells meet the exceptional demand for protein synthesis and, therefore, for ribosomes. However, only about half of the rDNA repeats are actively transcribed at any given time (1, 2).There is an intimate connection between ribosome biogenesis, protein synthesis, and cell growth capacity. It was observed over 100 years ago that cancer cells have enlarged nucleoli compared to those of normal host cells (3). We now know that the rate of rRNA synthesis is increased in many forms of cancer (4, 5). A number of laboratories have recently shown that selective inhibition of Pol I transcription is an effective method for impairing tumor cell growth (6-8). Taken together, both the old insights and the new insights agree that Pol I is emerging as a promising chemotherapeutic target.Despite the central role Pol I plays during cell growth, a detailed understanding of its regulation is lacking. However, a collection of trans-acting factors have been shown to influence Pol I at the initiation or elongation step in transcription. One such complex is suppressors of Ty4 and -5 (Spt4/5), which was prev...

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confidence: 56%

Section: Spt6 Associates With Rdna and Is Essential For Rrna Synthesismentioning

confidence: 99%

Spt6 Is Essential for rRNA Synthesis by RNA Polymerase I

Engel

French

Viktorovskaya

et al. 2015

Molecular and Cellular Biology

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“…Increasing levels of Tyr1 phosphorylation toward the 3= end then stabilizes Spt6-Pol II CTD interaction via the tSH2 domain. A recent study showed preferential loss of histones from the 5= ends of the transcribed genes in Spt6-depleted cells (16). We speculate that Spt6 recruitment by Ser2 phosphorylation is important for regulating histone occupancy near the 5= ends.…”

Section: Discussionmentioning

confidence: 99%

“…Depletion of Spt6 in yeast (Saccharomyces cerevisiae) causes a widespread reduction in histone H3 primarily from the 5= ends of transcribed genes, indicating the importance of Spt6 in maintaining histone occupancy (16). One of the effects of losing Spt6 function is altered gene expression and activation of intragenic cryptic transcription (17)(18)(19).…”

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confidence: 99%

Histone Deacetylases and Phosphorylated Polymerase II C-Terminal Domain Recruit Spt6 for Cotranscriptional Histone Reassembly

Burugula

Jeronimo

Pathak

et al. 2014

Molecular and Cellular Biology

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Spt6 is a multifunctional histone chaperone involved in the maintenance of chromatin structure during elongation by RNA polymerase II (Pol II). Spt6 has a tandem SH2 (tSH2) domain within its C terminus that recognizes Pol II C-terminal domain (CTD) peptides phosphorylated on Ser2, Ser5, or Try1 in vitro. Deleting the tSH2 domain, however, only has a partial effect on Spt6 occupancy in vivo, suggesting that more complex mechanisms are involved in the Spt6 recruitment. Our results show that the Ser2 kinases Bur1 and Ctk1, but not the Ser5 kinase Kin28, cooperate in recruiting Spt6, genomewide. Interestingly, the Ser2 kinases promote the association of Spt6 in early transcribed regions and not toward the 3= ends of genes, where phosphorylated Ser2 reaches its maximum level. In addition, our results uncover an unexpected role for histone deacetylases (Rpd3 and Hos2) in promoting Spt6 interaction with elongating Pol II. Finally, our data suggest that phosphorylation of the Pol II CTD on Tyr1 promotes the association of Spt6 with the 3= ends of transcribed genes, independently of Ser2 phosphorylation. Collectively, our results show that a complex network of interactions, involving the Spt6 tSH2 domain, CTD phosphorylation, and histone deacetylases, coordinate the recruitment of Spt6 to transcribed genes in vivo. D ynamic reorganization of chromatin structure is important for the regulation of transcription by RNA polymerase II (Pol II). Several ATP-dependent chromatin remodelers, histone-modifying enzymes, and histone chaperones promote the disruption of chromatin structure to allow transcription by Pol II and to restore chromatin structure in the wake of transcription (1, 2). Spt6 is a highly conserved and multifunctional protein shown to regulate multiple steps of transcription, including initiation (3, 4) and elongation (5, 6). In addition, it is important for other DNAdependent processes such as recombination (7,8), mRNA export (9), and viral replication (10).Spt6 interacts with histones H3 and H4 (11) and functions as a histone chaperone to regulate cotranscriptional nucleosome reassembly and to modulate chromatin structure, including histone modifications (11-15). Depletion of Spt6 in yeast (Saccharomyces cerevisiae) causes a widespread reduction in histone H3 primarily from the 5= ends of transcribed genes, indicating the importance of Spt6 in maintaining histone occupancy (16). One of the effects of losing Spt6 function is altered gene expression and activation of intragenic cryptic transcription (17-19). Aberrant transcription is also associated with histone deacetylase (HDAC) mutants. Impairing the function of the HDAC Rpd3-small (Rpd3S) and Hos2-Set3 complexes leads to cryptic and antisense transcription genome-wide (20, 21). It is not clear whether Spt6 and HDACs collaborate to suppress spurious transcription.Spt6 localization to transcribed regions strongly correlates with Pol II occupancy (15,22). It possesses a tandem Src homology 2 domain (tSH2) that interacts with phosphorylated Pol II C-terminal doma...

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“…A similar promoter modulation of downstream histone positioning was recently shown in yeast. 60 This suggests that promoter occupancy regulates events that occur on chromatin domains that largely exceed the promoter region. How is this achieved?…”

Section: Discussionmentioning

confidence: 99%