Tài liệu Báo cáo khoa học: The sequentiallity of nucleosomes in the 30 nm chromatin fibre pptx

The sequentiallity of nucleosomes in the 30 nm

chromatin fibre

Dontcho Z. Staynov1 and Yana G. Proykova2

1 Imperial College London, National Heart and Lung Institute, UK

2 School of Earth and Environmental Sciences, University of Portsmouth, UK

The DNA is packed on several levels as chromatin in

the eukaryotic nucleus. The first level of packing,

the highly conserved nucleosome, allows transcrip￾tion, after remodelling and ⁄ or histone modifications⁄

replacements. The nucleosome core particles have been

reconstituted and crystallized and their structure solved

in detail at 1.9 A˚ resolution [1–3]. The second level of

packing is the transcriptionally dormant 30 nm chro￾matin fibre. Understanding its structure, as well as the

processes that determine its folding and unfolding, is a

prerequisite for studying the epigenetic mechanism,

which leads to poised-for-transcription or dormant

chromatin [4]. The fibre consists of the entire chroma￾tin of the nucleated avian erythrocytes and comprises

approximately 85% of the chromatin in other cell

types [5].

The structure of chicken erythrocyte chromatin is

the most widely studied in the whole nucleus, as well

as in solution. Using small angle X-ray and neutron

scattering, it has been shown that all the high mole￾cular weight material that diffuses out of the nuclei

after micrococcal nuclease (MNase) digestion is in the

30 nm fibre conformation. It consists of a regular helix

with a diameter of approximately 33 nm and a variable

mass per unit length, which approaches 0.6 nucleo￾somesÆnm)1 with an 11 nm pitch at 80 mm salt concen￾trations. This implies that there are seven nucleosomes

per helical turn with their flat surfaces almost parallel

to the fibre axis [6–11]. The unusually small cross￾sectional radius of gyration (9.5 nm at 80 mm salt)

suggests a very compact structure with close nucleo￾some–nucleosome contacts.

There are several basic models for the structure of

the fibre that were proposed in the late 1970s and early

1980s, and some variants have been published subse￾quently [4,5,12]. They all comprise regular helices of

more or less seven nucleosomes per turn and thus

approximately satisfy the results obtained by small

angle X-ray and neutron scattering and low resolution

electron microscopy with respect to the packing of

Keywords

30 nm fibre; chromatin structure;

nucleosome

Correspondence

D. Z. Staynov, Imperial College London,

National Heart and Lung Institute, Guy

Scadding Building, Dovehouse Street,

London SW3 6LY, UK

Tel: +44 207 6223644

E-mail: [email protected]

(Received 29 March 2008, revised 20 May

2008, accepted 23 May 2008)

doi:10.1111/j.1742-4658.2008.06522.x

The folding of eukaryotic DNA into the 30 nm fibre comprises the first

level of transcriptionally dormant chromatin. Understanding its structure

and the processes of its folding and unfolding is a prerequisite for under￾standing the epigenetic regulation in cell differentiation. Although the

shape of the fibre and its dimensions and mass per unit length have been

described, the path of the internucleosomal linker DNA and the sequential￾lity of the nucleosomes in the fibre are poorly understood. In the present

study, we have chemically crosslinked adjacent nucleosomes along the

helix of chicken erythrocyte oligonucleosome fibres, digested the inter￾nucleosomal linker DNA and then examined the digestion products by

sucrose gradient sedimentation. We found that the digestion products con￾tain considerable amounts of mononucleosomes but less dinucleosomes,

which suggests that there are end-discontinuities in the fibres. This can be

explained by a nonsequential arrangement of the nucleosomes along the

fibre helix.

Abbreviations

as, acid soluble; DSP, dithiobis-(succinimidyl propionate); EDC, 1-ethyl-3(3-dimethylaminopropyl)-carbodiimide; MNase, micrococcal nuclease.

FEBS Journal 275 (2008) 3761–3771 ª 2008 The Authors Journal compilation ª 2008 FEBS 3761