B. Alberts, A. Johnson, J. Lewis и др. - Molecular Biology of The Cell (6th edition) (1120996), страница 72
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All four of the histones that makeup the core of the nucleosome are relatively small proteins (102–135 amino acids),and they share a structural motif, known as the histone fold, formed from three αhelices connected by two loops (Figure 4–24). In assembling a nucleosome, thehistone folds first bind to each other to form H3–H4 and H2A–H2B dimers, andthe H3–H4 dimers combine to form tetramers.
An H3–H4 tetramer then furthercombines with two H2A–H2B dimers to form the compact octamer core, aroundwhich the DNA is wound.The interface between DNA and histone is extensive: 142 hydrogen bonds areformed between DNA and the histone core in each nucleosome. Nearly half ofthese bonds form between the amino acid backbone of the histones and the sugar-phosphate backbone of the DNA.
Numerous hydrophobic interactions and saltlinkages also hold DNA and protein together in the nucleosome. More than onefifth of the amino acids in each of the core histones are either lysine or arginine(two amino acids with basic side chains), and their positive charges can effectivelyFigure 4–22 Structural organization of the nucleosome. A nucleosomecontains a protein core made of eight histone molecules. In biochemicalexperiments, the nucleosome core particle can be released from isolatedchromatin by digestion of the linker DNA with a nuclease, an enzyme thatbreaks down DNA.
(The nuclease can degrade the exposed linker DNA butcannot attack the DNA wound tightly around the nucleosome core.) Afterdissociation of the isolated nucleosome into its protein core and DNA, thelength of the DNA that was wound around the core can be determined.This length of 147 nucleotide pairs is sufficient to wrap 1.7 times around thehistone core.linker DNA“beads-on-a-string”form of chromatincore histonesof nucleosomenucleosome includes~200 nucleotidepairs of DNANUCLEASEDIGESTSLINKER DNAreleasednucleosomecore particle11 nmDISSOCIATIONWITH HIGHCONCENTRATIONOF SALToctamerichistone core147-nucleotide-pairDNA double helixDISSOCIATIONH2AH2BH3H4CHROMOSOMAL DNA AND ITS PACKAGING IN THE CHROMATIN FIBER189Figure 4–23 The structure of a nucleosomecore particle, as determined by x-raydiffraction analyses of crystals.
Eachhistone is colored according to the scheme inFigure 4–22, with the DNA double helix in lightgray. (Adapted from K. Luger et al., Nature389:251–260, 1997. With permission fromMacmillan Publishers Ltd.)DNA double helixside viewhistone H2Aedge viewhistone H2Bhistone H3histone H4neutralize the negatively charged DNA backbone. These numerous interactionsexplain in part why DNA of virtually any sequence can be bound on a histoneoctamer core. The path of the DNA around the histone core is not smooth; rather,several kinks are seen in the DNA, as expected from the nonuniform surface of the(A)H2ACNH2BNCMBoC6 m4.24/4.22H3 NCNH4Chistone foldN-terminal tail(B)N(D)NCNhistoneoctamer(C)NCCNNNNNNNFigure 4–24 The overall structural organization of the core histones.
(A) Each of the corehistones contains an N-terminal tail, which is subject to several forms of covalent modification, anda histone fold region, as indicated. (B) The structure of the histone fold, which is formed by all fourof the core histones. (C) Histones 2A and 2B form a dimer through an interaction known as the“handshake.” Histones H3 and H4 form a dimer through the same type of interaction. (D) The finalhistone octamer on DNA.
Note that all eight N-terminal tails of the histones protrude from the discshaped core structure. Their conformations are highly flexible, and they serve as binding sites forsets of other proteins.190Chapter 4: DNA, Chromosomes, and Genomescore. The bending requires a substantial compression of the minor groove of theDNA helix. Certain dinucleotides in the minor groove are especially easy to compress, and some nucleotide sequences bind the nucleosome more tightly thanothers (Figure 4–25).
This probably explains some striking, but unusual, casesof very precise positioning of nucleosomes along a stretch of DNA. However, thesequence preference of nucleosomes must be weak enough to allow other factorsto dominate, inasmuch as nucleosomes can occupy any one of a number of positions relative to the DNA sequence in most chromosomal regions.In addition to its histone fold, each of the core histones has an N-terminalamino acid “tail,” which extends out from the DNA–histone core (see Figure4–24D).
These histone tails are subject to several different types of covalent modifications that in turn control critical aspects of chromatin structure and function,as we shall discuss shortly.As a reflection of their fundamental role in DNA function through controllingchromatin structure, the histones are among the most highly conserved eukaryotic proteins. For example, the amino acid sequence of histone H4 from a peadiffers from that of a cow at only 2 of the 102 positions. This strong evolutionary conservation suggests that the functions of histones involve nearly all of theiramino acids, so that a change in any position is deleterious to the cell. But in addition to this remarkable conservation, eukaryotic organisms also produce smalleramounts of specialized variant core histones that differ in amino acid sequencefrom the main ones.
As discussed later, these variants, combined with the surprisingly large number of covalent modifications that can be added to the histones innucleosomes, give rise to a variety of chromatin structures in cells.Nucleosomes Have a Dynamic Structure, and Are FrequentlySubjected to Changes Catalyzed by ATP-Dependent ChromatinRemodeling ComplexesFor many years biologists thought that, once formed in a particular position onDNA, a nucleosome would remain fixed in place because of the very tight association between its core histones and DNA. If true, this would pose problems forgenetic readout mechanisms, which in principle require easy access to manyspecific DNA sequences.
It would also hinder the rapid passage of the DNA transcription and replication machinery through chromatin. But kinetic experimentsshow that the DNA in an isolated nucleosome unwraps from each end at a rate ofabout four times per second, remaining exposed for 10 to 50 milliseconds beforethe partially unwrapped structure recloses. Thus, most of the DNA in an isolatednucleosome is in principle available for binding other proteins.For the chromatin in a cell, a further loosening of DNA–histone contacts isclearly required, because eukaryotic cells contain a large variety of ATP-dependent chromatin remodeling complexes.
These complexes include a subunit thathydrolyzes ATP (an ATPase evolutionarily related to the DNA helicases discussedin Chapter 5). This subunit binds both to the protein core of the nucleosome andto the double-stranded DNA that winds around it. By using the energy of ATPhydrolysis to move this DNA relative to the core, the protein complex changes thestructure of a nucleosome temporarily, making the DNA less tightly bound to thehistone core. Through repeated cycles of ATP hydrolysis that pull the nucleosomecore along the DNA double helix, the remodeling complexes can catalyze nucleosome sliding.
In this way, they can reposition nucleosomes to expose specificregions of DNA, thereby making them available to other proteins in the cell (Figure 4–26). In addition, by cooperating with a variety of other proteins that bind tohistones and serve as histone chaperones, some remodeling complexes are able toremove either all or part of the nucleosome core from a nucleosome—catalyzingeither an exchange of its H2A–H2B histones, or the complete removal of the octameric core from the DNA (Figure 4–27). As a result of such processes, measurements reveal that a typical nucleosome is replaced on the DNA every one or twohours inside the cell.G-C preferred here(minor groove outside)AA, TT, and TA dinucleotidespreferred here(minor groove inside)histone coreof nucleosome(histone octamer)DNA ofnucleosomeFigure 4–25 The bending of DNA in anucleosome.
The DNA helix makes1.7 tight turns around the histone octamer.This diagram illustrates how the minorgroove is compressed on the inside of theturn. Owing to structural features of theDNA molecule, the indicated dinucleotidesare preferentially accommodated in sucha narrow minor groove, which helps toexplain why certain DNA sequenceswill bind more tightly than others to thenucleosome core.MBoC6 m4.27/4.24CHROMOSOMAL DNA AND ITS PACKAGING IN THE CHROMATIN FIBER191Cells contain dozens of different ATP-dependent chromatin remodeling complexes that are specialized for different roles.
Most are large protein complexesthat can contain 10 or more subunits, some of which bind to specific modifications on histones (see Figure 4–26C). The activity of these complexes is carefullycontrolled by the cell. As genes are turned on and off, chromatin remodeling complexes are brought to specific regions of DNA where they act locally to influencechromatin structure (discussed in Chapter 7; see also Figure 4–40, below).Although some DNA sequences bind more tightly than others to the nucleosome core (see Figure 4–25), the most important influence on nucleosome positioning appears to be the presence of other tightly bound proteins on the DNA.Some bound proteins favor the formation of a nucleosome adjacent to them.Others create obstacles that force the nucleosomes to move elsewhere.
The exactpositions of nucleosomes along a stretch of DNA therefore depend mainly on thepresence and nature of other proteins bound to the DNA. And due to the presenceof ATP-dependent chromatin remodeling complexes, the arrangement of nucleosomes on DNA can be highly dynamic, changing rapidly according to the needsof the cell.Nucleosomes Are Usually Packed Together into a CompactChromatin FiberAlthough enormously long strings of nucleosomes form on the chromosomalDNA, chromatin in a living cell probably rarely adopts the extended “beads-on-astring” form. Instead, the nucleosomes are packed on top of one another, generating arrays in which the DNA is even more highly condensed.
Thus, when nucleiare very gently lysed onto an electron microscope grid, much of the chromatin isseen to be in the form of a fiber with a diameter of about 30 nm, which is considerably wider than chromatin in the “beads-on-a-string” form (see Figure 4–21).ATP-dependentchromatin remodelingcomplexATPADPCATALYSIS OFNUCLEOSOME SLIDING(A)(B)(C)10 nmFigure 4–26 The nucleosome slidingcatalyzed by ATP-dependent chromatinremodeling complexes. (A) Using theenergy of ATP hydrolysis, the remodelingcomplex is thought to push on the DNAof its bound nucleosome and loosen itsattachment to the nucleosome core.
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