Removal of Promoter Nucleosomes by Disassembly Rather Than Sliding In Vivo

Boeger, Hinrich; Griesenbeck, Joachim; Strattan, J. Seth; Kornberg, Roger D.

doi:10.1016/j.molcel.2004.05.013

Cited by 234 publications

(200 citation statements)

References 29 publications

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“…Because some previous studies of PHO5 chromatin structure and activation were conducted with versions of the PHO5 gene that did not contain the region in which the intergenic transcript originates (20,21), an effect of intergenic transcription on the capability of the PHO5 gene to be turned on or off was not expected to be absolute. Indeed, it seemed reasonable to expect that the effect, if any, might be reminiscent of that observed upon mutation of the histone acetyltransferase GCN5, which affects the kinetics, but not the final level, of activated PHO5 transcription (15).…”

Section: Resultsmentioning

confidence: 99%

A role for noncoding transcription in activation of the yeast PHO5 gene

Uhler

Hertel

Svejstrup

2007

Proc. Natl. Acad. Sci. U.S.A.

148

151

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Noncoding, or intergenic, transcription by RNA polymerase II (RNA-PII) is remarkably widespread in eukaryotic organisms, but the effects of such transcription remain poorly understood. Here we show that noncoding transcription plays a role in activation, but not repression, of the Saccharomyces cerevisiae PHO5 gene. Histone eviction from the PHO5 promoter during activation occurs with normal kinetics even in the absence of the PHO5 TATA box, showing that transcription of the gene itself is not required for promoter remodeling. Nevertheless, we find that mutations that impair transcript elongation by RNAPII affect the kinetics of histone eviction from the PHO5 promoter. Most dramatically, inactivation of RNAPII itself abolishes eviction completely. Under repressing conditions, an Ϸ2.4-kb noncoding exosome-degraded transcript is detected that originates near the PHO5 termination site and is transcribed in the antisense direction. Abrogation of this transcript delays chromatin remodeling and subsequent RNAPII recruitment to PHO5 upon activation. We propose that noncoding transcription through positioned nucleosomes can enhance chromatin plasticity so that chromatin remodeling and activation of traversed genes occur in a timely manner.elongation ͉ intergenic transcription ͉ RNA polymerase II I n addition to transcribing all protein-encoding genes, RNA polymerase II (RNAPII) also transcribes a large group of less known and poorly understood untranslated RNAs. Recent genome-wide studies in several species reveal that such noncoding transcription is much more extensive than previously thought and that it occurs across intergenic regions, introns, and exons (see, for example, refs. 1 and 2). Recently, genome-wide studies in yeast have identified many cases of intergenic transcripts associated with promoters (3-5), raising the question of whether and how intergenic transcription across a promoter is used as a means of regulating that gene's transcription.During our studies on elongation and RNA processing factors in yeast, we discovered an intergenic transcript across the PHO5 promoter. This finding led us to investigate whether noncoding transcription might play a role in regulating this gene. PHO5 encodes an acid phosphatase that is regulated by phosphate availability (6). In high phosphate, four positioned nucleosomes are associated with the PHO5 promoter region (7). During phosphate starvation, the Pho4 activator translocates to the nucleus (8) and binds to PHO5 upstream activation sequences (UASp1 and UASp2) along with the Pho2 activator (9-11). This leads to eviction of the four positioned nucleosomes, making a 600-bp region effectively fully accessible (7,(12)(13)(14). Promoter remodeling is facilitated by, although not always absolutely dependent on, several transcription factor complexes including SAGA, Swi/Snf complex, INO80, and the Asf1 chaperone (14-18). High phosphate causes Pho4 accumulation in the cytoplasm, nucleosome reassembly on the promoter, and transcriptional repression of the gene.Here we show tha...

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Section: Resultsmentioning

confidence: 99%

A role for noncoding transcription in activation of the yeast PHO5 gene

Uhler

Hertel

Svejstrup

2007

Proc. Natl. Acad. Sci. U.S.A.

148

151

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“…Recruitment is mediated either by activator proteins bound at promoter regions (17)(18)(19)(20)(21) or by elongating Pol II (and associated factors) at highly transcribed genes (21-24). We presume that the nucleosome-remodeling complexes and/or histone chaperones responsible for rapid histone exchange differ from those used during DNA replication.…”

Section: Relative Ip Efficiencymentioning

confidence: 99%

Splitting of H3–H4 tetramers at transcriptionally active genes undergoing dynamic histone exchange

Katan-Khaykovich

Struhl

2011

Proc. Natl. Acad. Sci. U.S.A.

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Nucleosome deposition occurs on newly synthesized DNA during DNA replication and on transcriptionally active genes via nucleosome-remodeling complexes recruited by activator proteins and elongating RNA polymerase II. It has been long believed that histone deposition involves stable H3-H4 tetramers, such that newly deposited nucleosomes do not contain H3 and H4 molecules with their associated histone modifications from preexisting nucleosomes. However, biochemical analyses and recent experiments in mammalian cells have raised the idea that preexisting H3-H4 tetramers might split into dimers, resulting in mixed nucleosomes composed of "old" and "new" histones. It is unknown to what extent different genomic loci might utilize such a mechanism and under which circumstances. Here, we address whether tetramer splitting occurs in a locus-specific manner by using sequential chromatin immunoprecipitation of mononucleosomes from yeast cells containing two differentially tagged versions of H3 that are expressed "old" and "new" histones. At many genomic loci, we observe little or no nucleosomal cooccupancy of old and new H3, indicating that tetramer splitting is generally infrequent. However, cooccupancy is detected at highly active genes, which have a high rate of histone exchange. Thus, DNA replication largely results in nucleosomes bearing exclusively old or new H3-H4, thereby precluding the acquisition of new histone modifications based on preexisting modifications within the same nucleosome. In contrast, tetramer splitting, dimer exchange, and nucleosomes with mixed H3-H4 tetramers occur at highly active genes, presumably linked to rapid histone exchange associated with robust transcription.T he packaging of eukaryotic DNA into chromatin influences many DNA-associated processes, including transcriptional regulation. Within the chromatin fiber, each basic nucleosome unit bears important chemical and structural information. The mechanisms by which nucleosomes are assembled on DNA during replication, transcription, DNA repair, etc., can thus impact not only the integrity of chromatin structure but also patterns of gene expression and epigenetic inheritance. The H3-H4 tetramer core of each nucleosome is the more stable component and contains most of the relatively persistent and functionally important histone methylation marks. Much attention has therefore been given to the questions of how the H3-H4 tetramers are formed and maintained on chromatin.Early studies attempted to distinguish between a conservative assembly model, by which old and new histones form separate tetramers on replicating DNA, and a semiconservative assembly mechanism, by which existing tetramers are split into H3-H4 dimers, followed by association of new H3-H4 dimers to complete each nucleosome core (1-3). In the semiconservative model, the resulting tetramers would bear a mixture of old and new histones, allowing transmission of epigenetic information within the basic nucleosome unit. Though mechanistically attractive, the mixed tetramer model receiv...

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“…1): (i) sliding, or moving the histone octamer to a new position, which exposes DNA 10-12 ; (ii) ejection, or completely displacing the octamer to expose DNA [13][14][15][16] ; (iii) removal of H2A-H2B dimers, leaving only the central H3-H4 tetramer, which exposes DNA and destabilizes the nucleosome 17,18 ; and (iv) dimer replacement-for example, exchanging the resident H2A-H2B dimers for dimers NIH Public Access…”

Section: Remodelers Slide Eject and Restructure Nucleosomesmentioning

confidence: 99%

“…Studies of the yeast PHO5 gene suggest that nucleosomes are removed from the promoter upon activation 15,16 . Interestingly, genomewide analyses show that promoters are intrinsically nucleosome deficient and become more deficient during activation 73,74 .…”

Section: Nucleosome Ejection: Pulling the Rug From Under Your Neighbor?mentioning

confidence: 99%

Chromatin remodeling: insights and intrigue from single-molecule studies

Cairns

2007

Nat Struct Mol Biol

226

208

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Chromatin remodelers are ATP-hydrolyzing machines specialized to restructure, mobilize or eject nucleosomes, allowing regulated exposure of DNA in chromatin. Recently, remodelers have been analyzed using single-molecule techniques in real time, revealing them to be complex DNA-pumping machines. The results both support and challenge aspects of current models of remodeling, supporting the idea that the remodeler translocates or pumps DNA loops into and around the nucleosome, while also challenging earlier concepts about loop formation, the character of the loop and how it propagates. Several complex behaviors were observed, such as reverse translocation and long translocation bursts of the remodeler, without appreciable DNA twist. This review presents and discusses revised models for nucleosome sliding and ejection that integrate this new information with the earlier biochemical studies.Many processes involving chromosomes are guided by DNA-binding proteins, and the access of these proteins to DNA is regulated by chromatin. Nucleosomes, the primary repeating unit of chromatin, package DNA by wrapping 147 base pairs (bp) around an octamer of histone proteins in ∼1.7 helical turns 1-3 . This packaging provides topological order but occludes one face of the DNA, which slows or prevents the recognition of DNA sequences by DNA-binding proteins. To maintain topological order, and also to allow rapid and regulated access to the DNA, cells have evolved a set of chromatin-remodeling machines that alter nucleosome position, presence and structure.Remodelers can be separated into several families on the basis of their composition and activities: SWI/SNF, ISWI, NURD/Mi-2/CHD and the 'split ATPases' INO80 and SWR1 (which bear an insertion within their ATPase domains). Rad54 may represent an additional family, as it perturbs chromatin in vitro, but it apparently lacks specific nucleosome-interacting domains 4,5 . The participation of remodelers in various chromosomal processes has been the subject of many reviews 6-9 . The present work focuses solely on remodeler mechanisms, and primarily on the function of their conserved catalytic subunit, a superfamily 2 (SF2) ATPdependent DNA translocase. Recently, single-molecule approaches have been used to examine several remodelers, providing many new insights into their behavior. Here I discuss these recent studies, compare them with previous biochemical studies and suggest refinements to existing models to account for some of the observations. Remodelers slide, eject and restructure nucleosomesRemodelers can affect nucleosomes in at least four ways ( Fig. 1): (i) sliding, or moving the histone octamer to a new position, which exposes DNA 10-12 ; (ii) ejection, or completely displacing the octamer to expose DNA [13][14][15][16] ; (iii) removal of H2A-H2B dimers, leaving only the central H3-H4 tetramer, which exposes DNA and destabilizes the nucleosome 17,18 ; and (iv) dimer replacement-for example, exchanging the resident H2A-H2B dimers for dimers NIH Public Access

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Removal of Promoter Nucleosomes by Disassembly Rather Than Sliding In Vivo

Cited by 234 publications

References 29 publications

A role for noncoding transcription in activation of the yeast PHO5 gene

A role for noncoding transcription in activation of the yeast PHO5 gene

Splitting of H3–H4 tetramers at transcriptionally active genes undergoing dynamic histone exchange

Chromatin remodeling: insights and intrigue from single-molecule studies

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