Chromatin structure can strongly facilitate enhancer action over a distance

Rubtsov, Mikhail A.; Polikanov, Y.S.; Бондаренко, В. А.; Wang, Yuh‐Hwa; Studitsky, Vasily M.

doi:10.1073/pnas.0603819103

Cited by 42 publications

(49 citation statements)

References 55 publications

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“…Linker histones alter the trajectory of linker DNAs to promote greater interactions between alternate nucleosomes; divalent ions induce bending of a portion of linker DNAs, effectively reducing the number of linker DNA crossings at the chromatin axis; and internucleosomal interactions may laterally stabilize a compact state of chromatin, causing the chromatin fibers to become more compact and stiff. The increased fiber stiffness has the potential to inhibit communication between gene regulatory regions that form chromatin loops for active transcription (46) and is consistent with the recent structural analysis of the 16-kb heterochromatin region separating the differentially regulated FOA and ␤-globin genes (47). The fibers in the presence of divalent ions are predicted to contain ϳ20% bent linker DNAs, bringing some consecutive nucleosomes closer.…”

Section: Discussionsupporting

confidence: 80%

Evidence for heteromorphic chromatin fibers from analysis of nucleosome interactions

Grigoryev

Arya

Correll

et al. 2009

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

245

358

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The architecture of the chromatin fiber, which determines DNA accessibility for transcription and other template-directed biological processes, remains unknown. Here we investigate the internal organization of the 30-nm chromatin fiber, combining Monte Carlo simulations of nucleosome chain folding with EM-assisted nucleosome interaction capture (EMANIC). We show that at physiological concentrations of monovalent ions, linker histones lead to a tight 2-start zigzag dominated by interactions between alternate nucleosomes (i ؎ 2) and sealed by histone N-tails. Divalent ions further compact the fiber by promoting bending in some linker DNAs and hence raising sequential nucleosome interactions (i ؎ 1). Remarkably, both straight and bent linker DNA conformations are retained in the fully compact chromatin fiber as inferred from both EMANIC and modeling. This conformational variability is energetically favorable as it helps accommodate DNA crossings within the fiber axis. Our results thus show that the 2-start zigzag topology and the type of linker DNA bending that defines solenoid models may be simultaneously present in a structurally heteromorphic chromatin fiber with uniform 30 nm diameter. Our data also suggest that dynamic linker DNA bending by linker histones and divalent cations in vivo may mediate the transition between tight nucleosome packing within discrete 30-nm fibers and self-associated higher-order chromosomal forms.chromatin structure ͉ electron microscopy ͉ mesoscopic modeling ͉ Monte Carlo simulations ͉ linker histone T he DNA in eukaryotic chromatin is packed and functionally regulated by histones and nonhistone architectural proteins (1). The primary packing level is represented by an array of repeating units, the nucleosomes, where the DNA is wound around histone octamers (2). Further compaction is achieved through a hierarchy of folding levels, including the 30-nm chromatin fiber (secondary level) and more compact and self-associating tertiary and quaternary forms whose structures are unknown (3-6). Because DNA conformation in chromatin and nucleosome packing are intimately connected to DNA/protein recognition and gene regulation, there has been intense interest in understanding chromatin structure, energetics, and dynamics. Some experimental studies have suggested that nucleosomal arrays fold in a zigzag arrangement with relatively straight linkers and a 2-start nucleosome interaction pattern that brings each nucleosome in proximity to its second nearest neighbor (7-10) consistent with chromatin fibers observed in situ (11). Other evidence suggests that chromatin condensed with linker histones and divalent cations such as Mg 2ϩ can form either zigzag structures with various nucleosome topologies (12, 13) or solenoid-like arrangements. The latter class of structures has bent DNA linkers and predominant interactions between either nearest neighbor nucleosomes (14, 15) and/or between every fifth or sixth nucleosome along the chain (16,17).The picture has became more complex recently with our heighte...

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Section: Discussionsupporting

confidence: 80%

Evidence for heteromorphic chromatin fibers from analysis of nucleosome interactions

Grigoryev

Arya

Correll

et al. 2009

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

245

358

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“…Additional challenges faced by eukaryotic enhancers include constant competition between binding of sequence-specific proteins and chromatin formation at the enhancers and promoters and the need to communicate over chromatin-covered DNA. The molecular mechanisms of action of eukaryotic enhancers are not well studied, primarily because of the limitations of the in vitro systems poorly supporting distant enhancer action (3,26,47).…”

Section: Enhancer Action In Chromatinmentioning

confidence: 99%

Distant Activation of Transcription: Mechanisms of Enhancer Action

Kulaeva

Nizovtseva

Polikanov

et al. 2012

Molecular and Cellular Biology

Self Cite

112

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Enhancers are regulatory DNA sequences that activate transcription over long distances. Recent studies revealed a widespread role of distant activation in eukaryotic gene regulation and in development of various human diseases, including cancer. Genomic and gene-targeted studies of enhancer action revealed novel mechanisms of transcriptional activation over a distance. They include formation of stable, inactive DNA-protein complexes at the enhancer and target promoter before activation, facilitated distant communication by looping of the spacer chromatin-covered DNA, and promoter activation by mechanisms that are different from classic recruiting. These studies suggest the similarity between the looping mechanisms involved in enhancer action on DNA in bacteria and in chromatin of higher organisms. E nhancers (Es) are short (20-to 400-bp) DNA sequences that can activate transcription from target promoters (P) in trans and over various distances (more than 100 kb) (7). Enhancers operate in pro-and eukaryotes; in the majority of cases, action of Es involves direct E-P interaction through proteins bound at the E and P, accompanied by formation of an intervening chromatin loop (7,24,38). Recent genomic studies using various versions of the 3C approach revealed widespread use of gene regulation by enhancers (see reference 32 for a review). In parallel, genomic studies identified specific signatures (histone modifications and associated proteins) of enhancers that greatly facilitated analysis of the databases (32).At the same time, understanding of mechanistic aspects of enhancer action trails behind, primarily due to the lack of in vitro systems faithfully recapitulating distant activation. The enhancer field remains driven by the concept of recruiting that was proposed to explain short-distance activation of transcription in prokaryotes (Fig. 1A) (44). During recruiting, an activator protein increases the local concentration of another protein/protein complex (e.g., RNA polymerase [RNAP]) in the vicinity of its binding site. The local increase of protein concentration results in relief of a step limiting the rate of initiation (usually binding of RNAP to a promoter nearby) and induces transcription. During distant action, even if a protein complex was recruited to the enhancer, its concentration at the target would not necessarily be increased because E/P do not typically colocalize. Furthermore, enhancers typically activate preformed complexes already recruited to DNA ( Fig. 1B; also see below). Thus, the concept of recruiting cannot explain some principal aspects of enhancer action; instead, the presence of preformed enhancer targets raises questions about efficient E-P communication and activation of transcription (Fig. 1B). In this review, we focus primarily on mechanistic aspects of enhancer action; other recent studies were covered in several excellent reviews (7,24,32,38). ENHANCER ACTION ON DNAIn prokaryotes, there are two types of transcriptional enhancers using tracking and looping mechanisms for enhancer-...

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“…We speculate that chromatin assembly and DNA supercoiling of the episomal DNA may differ following gene transfer of minicircles and after adenoviral transfer. Since chromatin assembly and DNA supercoiling affect interactions between promoter and enhancers, 44 this may explain differences in transgene expression. Whereas mature hepatocytes in adults divide at low frequency, cell division in PC occurs more frequently in children.…”

Section: Adenoviral and Hydrodynamic Transfermentioning

confidence: 99%

Direct comparison of hepatocyte-specific expression cassettes following adenoviral and nonviral hydrodynamic gene transfer

et al. 2008

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Hepatocytes are a key target for treatment of inborn errors of metabolism, dyslipidemia and coagulation disorders. The development of potent expression cassettes is a critical target to improve the therapeutic index of gene transfer vectors.Here we evaluated 22 hepatocyte-specific expression cassettes containing a human apo A-I transgene following hydrodynamic transfer of plasmids or adenoviral transfer with E1E3E4-deleted vectors in C57BL/6 mice. The DC172 promoter consisting of a 890 bp human a 1 -antitrypsin promoter and two copies of the 160 bp a 1 -microglobulin enhancer results in superior expression levels compared to constructs containing the 1.5 kb human a 1 -antitrypsin promoter, the 790 bp synthetic liver-specific promoter or the DC190 promoter containing a 520 bp human albumin promoter and two copies of the 99 bp prothrombin enhancer. The most potent expression cassette consists of the DC172 promoter upstream of the transgene and two copies of the hepatic control region-1. Minicircles containing this expression cassette induce persistent physiological human apo A-I or human factor IX levels after hydrodynamic transfer. In conclusion, in this comparative study of 22 hepatocyte-specific expression cassettes, the DC172 promoter in combination with two copies of the hepatic control region-1 induces the highest expression levels following hydrodynamic and adenoviral transfer.

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Chromatin structure can strongly facilitate enhancer action over a distance

Cited by 42 publications

References 55 publications

Evidence for heteromorphic chromatin fibers from analysis of nucleosome interactions

Evidence for heteromorphic chromatin fibers from analysis of nucleosome interactions

Distant Activation of Transcription: Mechanisms of Enhancer Action

Direct comparison of hepatocyte-specific expression cassettes following adenoviral and nonviral hydrodynamic gene transfer

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