Higher-order structure of chromatin: evidence from photochemically detected linear dichroism

Sen, Dipankar; Mitra, Sekhar; Crothers, Donald M.

doi:10.1021/bi00359a052

Cited by 36 publications

(29 citation statements)

References 33 publications

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“…To avoid steric clashes the model also incorporates a nucleosome tilt of 17°in relation to the fiber axis. This value corresponds well to the range (13°to 38°) measured for chromatin isolated from a number of different species by using both electric (28,29) and photochemical dichroism (30,31). The proposed nucleosome packing arrangement can easily be extended to the 44-nm fiber because the concomitant increase in volume and mass per unit length would result in an essentially constant nucleosome density.…”

Section: Discussion Chromatin Fibers Form Two Discrete Structural Clasupporting

confidence: 82%

“…During the past three decades evidence from EM (14-23), x-ray and neutron scattering (24)(25)(26)(27), electric and photochemical dichroism (28)(29)(30)(31), sedimentation analysis (32)(33)(34)(35), nuclease digestion (6,9,36), and x-ray crystallography (4,5,37,38) has led to the proposal of a number of different models for the 30-nm fiber. These models fall into two main classes: the one-start helix or solenoid models, and the two-start helix models.…”

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confidence: 99%

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EM measurements define the dimensions of the “30-nm” chromatin fiber: Evidence for a compact, interdigitated structure

Robinson

Fairall

Huynh

et al. 2006

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

449

512

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Chromatin structure plays a fundamental role in the regulation of nuclear processes such as DNA transcription, replication, recombination, and repair. Despite considerable efforts during three decades, the structure of the 30-nm chromatin fiber remains controversial. To define fiber dimensions accurately, we have produced very long and regularly folded 30-nm fibers from in vitro reconstituted nucleosome arrays containing the linker histone and with increasing nucleosome repeat lengths (10 to 70 bp of linker DNA). EM measurements show that the dimensions of these fully folded fibers do not increase linearly with increasing linker length, a finding that is inconsistent with two-start helix models. Instead, we find that there are two distinct classes of fiber structure, both with unexpectedly high nucleosome density: arrays with 10 to 40 bp of linker DNA all produce fibers with a diameter of 33 nm and 11 nucleosomes per 11 nm, whereas arrays with 50 to 70 bp of linker DNA all produce 44-nm-wide fibers with 15 nucleosomes per 11 nm. Using the physical constraints imposed by these measurements, we have built a model in which tight nucleosome packing is achieved through the interdigitation of nucleosomes from adjacent helical gyres. Importantly, the model closely matches raw image projections of folded chromatin arrays recorded in the solution state by using electron cryo-microscopy.chromatin structure ͉ electron microscopy ͉ linker histone ͉ reconstitution E ukaryotic chromosomes have a compact structure in which linear nucleosome arrays are first folded into a fiber of around 30-nm diameter (1, 2). The fundamental repeating unit of chromatin, the nucleosome core particle, organizes 147 bp of DNA in 1.7 left-handed superhelical turns around an octamer of the four core histones (H2A, H2B, H3, and H4) (3-5). Linker histone (H1͞H5) binding organizes an additional 20 bp of DNA to complete the nucleosome containing 167 bp of DNA (6, 7). Such binding determines the geometry of the DNA entering and exiting the nucleosome core particle (8). In nucleosome arrays, adjacent nucleosomes are separated by linker DNA, varying in length between 0 and 80 bp in a tissue-and species-specific manner (9, 10). In vitro, linear nucleosome arrays fold into the ''30-nm'' fiber upon increasing ionic strength (11) in a process that depends on both the integrity of the core histone N-terminal tails (12, 13) and the presence of the linker histone (14,15).During the past three decades evidence from EM (14-23), x-ray and neutron scattering (24-27), electric and photochemical dichroism (28-31), sedimentation analysis (32-35), nuclease digestion (6, 9, 36), and x-ray crystallography (4, 5, 37, 38) has led to the proposal of a number of different models for the 30-nm fiber. These models fall into two main classes: the one-start helix or solenoid models, and the two-start helix models. The solenoid models are comprised of simple one-start helices in which successive nucleosomes are adjacent in the filament and connected by linker DNA that bends into t...

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Section: Discussion Chromatin Fibers Form Two Discrete Structural Clasupporting

confidence: 82%

mentioning

confidence: 99%

EM measurements define the dimensions of the “30-nm” chromatin fiber: Evidence for a compact, interdigitated structure

Robinson

Fairall

Huynh

et al. 2006

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

449

512

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“…At this compaction all structures have a ~ 110 Å separation between helix gyres and a low helical pitch (5.3–11.4°). These measurements are wholly consistent with values determined from photochemical dichroism studies 10 and the X‐ray diffraction patterns of partially oriented chromatin samples 11, 12.…”

Section: Physical Attributes Of the Proposed Structuresupporting

confidence: 86%

“…In addition to early EM images 3 a 2‐start structure is supported by Fourier analysis of images of chromatin fibres 2, chemical cross‐linking 4, the crystal structure of a tetranucleosome 5, cryo‐EM of native fibres 6, cryo‐EM structures of reconstituted fibres containing up to 24 nucleosomes 7 and cryo‐tomographic analysis of native chromatin 8, 9. Nevertheless, early studies on various native chromatin samples by photochemical dichroism 10 and X‐ray diffraction 11, 12, revealed, respectively, a small tilt of the nucleosomal disc relative to the fibre axis and narrow diffraction arcs at 110 Å. Together these observations suggested a helical structure with a low pitch, more consistent with the 1‐start model.…”

Section: Tablementioning

confidence: 99%

A metastable structure for the compact 30‐nm chromatin fibre

McGeehan

Travers

2016

FEBS Letters

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The structure of compact 30‐nm chromatin fibres is still debated. We present here a novel unified model that reconciles all experimental observations into a single framework. We propose that compact fibres are formed by the interdigitation of the two nucleosome stacks in a 2‐start crossed‐linker structure to form a single stack. This process requires that the dyad orientation of successive nucleosomes relative to the helical axis alternates. The model predicts that, as observed experimentally, the fibre‐packing density should increase in a stepwise manner with increasing linker length. This model structure can also incorporate linker DNA of varying lengths.

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“…In addition to early EM images (Woodcock et al 1984), a 2-start structure is supported by Fourier analysis of images of chromatin fibers (Williams et al 1986), chemical crosslinking (Dorigo et al 2004), the crystal structure of a tetranucleosome (Schalch et al 2005), cryo-EM of native fibers (Bednar et al 1998), cryo-EM structures of reconstituted fibers containing up to 24 nucleosomes (Song et al 2014), and cryo-tomographic analysis of native chromatin (Horowitz et al 1994;Scheffer et al 2011). Nevertheless, early studies on various native chromatin samples by photochemical dichroism (Sen et al 1986) and X-ray diffraction (Widom and Klug 1985; revealed, respectively, a small tilt of the nucleosomal disc relative to the fiber axis and narrow diffraction arcs at 110 Å. Together, these observations Fig.…”

Section: -Nm Fibermentioning

confidence: 99%

The regulatory role of DNA supercoiling in nucleoprotein complex assembly and genetic activity

Muskhelishvili

Travers

2016

Biophys Rev

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We argue that dynamic changes in DNA supercoiling in vivo determine both how DNA is packaged and how it is accessed for transcription and for other manipulations such as recombination. In both bacteria and eukaryotes, the principal generators of DNA superhelicity are DNA translocases, supplemented in bacteria by DNA gyrase. By generating gradients of superhelicity upstream and downstream of their site of activity, translocases enable the differential binding of proteins which preferentially interact with respectively more untwisted or more writhed DNA. Such preferences enable, in principle, the sequential binding of different classes of protein and so constitute an essential driver of chromatin organization.Keywords DNA supercoiling . DNA translocases . Chromatin organization . Superhelicity gradients . DNA untwisting . DNAwrithing Dynamic changes of DNA supercoiling act as a driving force behind the alterations of genetic activity and DNA compaction both in eukaryotes and prokaryotes. Both these processes involve formation of spatially organized nucleoprotein structures by DNA architectural proteins. Whereas in eukaryotes the paradigmal example is the histone octamer, in prokaryotes a similar function is attributed to a small class of highly abundant nucleoid-associated proteins. We argue that, depending on the primary sequence organization, the changes of superhelicity elicit various alterations of local DNA geometry, while these, in turn, facilitate the assembly of distinct nucleoprotein structures pertinent to genetic function. Genome-wide conversion of the superhelical energy into various three-dimensional DNA structures thus acts as an analogue code coordinating the energy supply with the genetic expression of the chromosome.Recent studies make it increasingly clear that the DNA double helix carries at least two types of encoded information and that these include the well-known genetic code and the structural information determining the form and physical properties of the double helix itself. Since both these information types are inscribed in the same DNA sequence, and yet one is discrete whereas the other is continuous, they have been respectively dubbed the digital and analog DNA codes (Marr et al. 2008;Travers et al. 2012;Muskhelishvili and Travers 2013). The potential of the DNA to adopt distinct configurations is strongly modulated by DNA supercoiling, which is increasingly recognized as one of the major forces coordinating the cellular DNA transactions in both prokaryotes (including Archaea) and eukaryotes.DNA supercoiling can be generated by the simple application of torque to the double helix (Strick et al. 1998) but, importantly, because the DNA molecule itself possesses chirality-it is, after all, a right-handed double helix-the local structures stabilized by changes in superhelical density depend on both the sign and strength of the applied torque. For example, both positive and negative torque (respectively overand underwinding of the double helix) can change the intrinsic coiling of ...

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Higher-order structure of chromatin: evidence from photochemically detected linear dichroism

Cited by 36 publications

References 33 publications

EM measurements define the dimensions of the “30-nm” chromatin fiber: Evidence for a compact, interdigitated structure

EM measurements define the dimensions of the “30-nm” chromatin fiber: Evidence for a compact, interdigitated structure

A metastable structure for the compact 30‐nm chromatin fibre

The regulatory role of DNA supercoiling in nucleoprotein complex assembly and genetic activity

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