Часть 1 (1120999), страница 70
Текст из файла (страница 70)
Nearly halfof these bonds form between the amino acid backbone of the histones and thephosphodiester backbone of the DNA. Numerous hydrophobic interactions andsalt linkages also hold DNA and protein together in the nucleosome. For example, more than one-fifth of the amino acids in each of the core histones are eitherlysine or arginine (two amino acids with basic side chains), and their positiveIt-^,^^-^r *(woctamerich i s t o n ec o r e+ilJH2Aside view€ t h i s t o n eH 2 Abottom view@ h i s t o n eH 2 B@ h i s t o n eH 3Oh i s t o n eH 4r"ill".'"?..&ll rir ..:;;;i:rsLH2B147-nucleotide-pairD N Ad o u b l eh e l i xJt'H3ar6H4Figure4-24 The structureof a nucleosomecore particle,as determined by x-raydiffraction analysesof crystals.Eachhistoneis coloredaccordingto the schemein Figure4-23,with the DNAdoublehelixinlight gray.(From K. Luger et al.,Nature389:251-260,1997.With permissionfromMacmillanPublishersLtd.)CHROMOSOMALDNAAND IT5PACKAGINGINTHECHROMATINFIBER213(A)H2A4la6tH2BH3NnH4m*"'-'N - t e r m i n atla i l**ffih i s t o n ef o l dFigure4-25 The overallstructuralorganizationof the core histones.(A)Eachof the corehistonescontainsan N-terminaltail,which is subjecttoseveralformsof covalentmodification,and a histonefold region,as(B)Thestructureof the histonefold,whichis formedby allfourindicated.(C)Histonesof the corehistones.24 and 28 form a dimerthroughaninteractionknownasthe "handshakei'HistonesH3 and H4 form a dimerthroughthe sametype of interaction.charges can effectively neutralize the negatively charged DNA backbone.
Thesenumerous interactions explain in part why DNA of virtually any sequencecan bebound on a histone octamer core. The path of the DNA around the histone coreis not smooth; rather, several kinks are seen in the DNA, as expected from thenonuniform surface of the core.The bending requires a substantial compressionof the minor groove of the DNA helix. Certain dinucleotides in the minor grooveare especiallyeasyto compress,and some nucleotide sequencesbind the nucleosome more tightly than others (Figure 4-27).
This probably explains somestriking, but unusual, casesof very precise positioning of nucleosomes along astretch of DNA. For most of the DNA sequencesfound in chromosomes, however, the sequence preference of nucleosomes must be small enough to allowother factors to dominate, inasmuch as nucleosomes can occupy any one of anumber of positions relative to the DNA sequence in most chromosomalregions.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 Figure4-26). 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 controlling chromatin structure, the histones are among the most highly conservedeucaryotic proteins.
For example, the amino acid sequenceof histone H4 from apea and from a cow differ at only 2 of the 102 positions. This strong evolutionaryconservation suggeststhat the functions of histones involve nearly all of theiramino acids, so that a change in any position is deleterious to the cell. This suggestion has been tested directly in yeast cells, in which it is possible to mutate agiven histone gene in uitro andintroduce it into the yeast genome in place of thenormal gene. As might be expected, most changes in histone sequences arelethal; the few that are not lethal cause changes in the normal pattern of geneexpression,as well as other abnormalities.Despite the high conservation of the core histones, eucaryotic organismsalso produce smaller amounts of specializedvariant core histones that differ inamino acid sequence from the main ones.
As we shall see,these variants, combined with a surprisingly large variety of covalent modifications that can beadded to the histones in nucleosomes, make possible the many different chromatin structures that are required for DNA function in higher eucaryotes.c214Chapter4: DNA,Chromosomes,and GenomesFigure4-26 The assemblyof a histoneoctamer on DNA.The histoneH3-H4dimerand the H2A-H2Bdimerareformed from the handshakeinteraction.An H3-H4tetramerformsand bindstothe DNA.Two H2A-H2Bdimersarethenadded,to completethe nucleosome.Thehistonesarecoloredas in Figures4-24and4-25.
Notethat all eight N-terminaltailsof the histonesprotrudefrom thedisc-shapedcorestructure.Theirconformationsarehighlyflexible.lnsidethe cell,the nucleosomeassemblyreactionsshownherearemediatedby histonechaperoneproteins,some specificfor H3-H4 and othersspecificfor H2A-H28.(Adaptedfromfiguresby J.Waterborg.)H 3 - H 4d i m e rIH3-H4 tetramertwo dimersbind to H3-H4tetramer/3G-Cpreferred here(minor groove outside)TT,and TA dinucleotidespreferred here( m i n o rg r o o v ei n s i d e )histone coreof nucleosome(histoneoctamer)D N Ao fnucteosomeFigure4-27 The bending of DNA in anucleosome.The DNAhelixmakes1.7tight turnsaroundthe histoneoctamer.Thisdiagramillustrateshow theminorgrooveis compressedon theinsideof the turn.Owingto certainstructuralfeaturesof the DNAmolecule,the indicateddinucleotidesarepreferentiallyaccommodatedin suchanarrowminorgroove,which helpstoexplainwhy certainDNAsequenceswillbind moretightlythan othersto thenucleosomecore.CHROMOSOMALDNAAND ITSPACKAGINGINTHECHROMATINFIBERw r a p p e on u c r e o s o m eexistsfor 250millisecondsu n w r a p p e dn u c l e o s o m eexistsfor 10-50millisecondsrewrappednucleosome215Figure4-28 Dynamicnucleosomes.showthat the DNAKineticmeasurementsis surprisinglyin an isolatednucleosomedynamic,rapidlyuncoilingand thencore.rewrappingaroundits nucleosomeAs indicated,this makesmostof its boundto otherDNADNAsequenceaccessiblebindingproteins.(Datafrom G.
Li andJ.Widom, Nat.Struct.Mol.Biol.11:763-769,from Macmillan2004.With oermissionLtd.)PublishersNucleosomesHavea DynamicStructure,and Are FrequentlySubjectedto ChangesChromatinCatalyzedby ATP-DependentRemodelingComplexesFor many years biologists thought that, once formed in a particular position onDNA, a nucleosome remains fixed in place because of the very tight associationbetween its core histones and DNA. If true, this would pose problems for geneticreadout mechanisms, which in principle require rapid accessto many specificDNA sequences,as well as for the rapid passageof the DNA transcription andreplication machinery through chromatin.
But kinetic experiments show that theDNA in an isolated nucleosome unwraps from each end at rate of about 4 timesper second, remaining exposed for 10 to 50 milliseconds before the partiallyunr,trapped structure recloses.Thus, most of the DNA in an isolated nucleosomeis in principle availablefor binding other proteins (Figure 4-28).For the chromatin in a cell, a further loosening of DNA-histone contacts isclearly required, because eucaryotic cells contain a large variety of ATP-dependent chromatin remodeling complexes. The subunit in these complexes thathydrolyzes ATP is evolutionarily related to the DNA helicases (discussed inChapter 5), and it binds both to the protein core of the nucleosome and to thedouble-stranded DNA that winds around it.
By using the energy of AIP hydrolysis to move this DNA relative to the core, this subunit changes the structure of anucleosome temporarily, making the DNA less tightly bound to the histone core.Through repeated cycles of ATP hydrolysis, the remodeling complexes can catalyze nucleosomesliding, and by pulling the nucleosome core along the DNAdouble helix in this way, they make the nucleosomal DNA availableto other proteins in the cell (Figure 4-25). In addition, by cooperating with negativelyATP-dependentc h r o m a t i nr e m o d e l i n gcomplex/4J.s.FlCATALYSISOFNUCLEOSOMSLEI D I N GFigure4-29 The nucleosomeslidingcatalyzedby ATP-dependentchromatinremodelingcomplexes.Usingthethe remodelingenergyof ATPhydrolysis,complexis thoughtto pushon the DNAand loosenitsof its bound nucleosomecore.Eachattachmentto the nucleosomeandcycleof ATPbinding,ATPhydrolysis,releaseof the ADPand PiProductstherebymovesthe DNAwith respecttothe histoneoctamerin the directionofthe arrowin this diagram.lt requiresmanysuchcyclesto producetheslidingshown.(SeealsonucleosomeFigure4-468.)2'16Chapter4: DNA,Chromosomes,and GenomesFigure4-30 Nucleosomeremovaland histoneexchangecatalyzedby ATP-dependentchromatinremodelingcomplexes.Bycooperatingwith specifichistonechaperones,somechromatinremodelingcomplexescanremovethe H2A-H2Bdimersfrom a(top seriesof reactions)nucleosomeandreplacethem with dimersthat containa varianthistone,suchas the H2AZ-H2Bdimer (seeFigure4-41).Otherremodelingcomplexesareattractedto specificsiteson chromatintoremovethe histoneoctamercompletelyand/orto replaceit with a differentnucleosomecore(bottomseriesof reactions)h i s t o n ec h a p e r o n eATP-dependentchromatinremodelingcomplexi2"i+bcharged proteins that serve as histone chaperones,some remodeling complexesare able to remove either all or part of the nucleosome core from a nucleosome-catalyzing either an exchange of its HZA-H2B histones, or the completeremoval of the octameric core from the DNA (Figure 4-90).Cellscontain dozensof differentATP-dependentchromatin remodeling complexes that are specializedfor different roles.
Most are large protein complexesthat can contain 10 or more subunits. The activity of these complexesis carefullycontrolled by the cell.As genesare turned on and off, chromatin remodeling complexes are brought to specific regions of DNA where they act locally to influencechromatin structure (discussedin Chapter 7; seealso Figure 4-46, below).As pointed out previously,for most of the DNA sequencesfound in chromosomes,experimentsshow that a nucleosomecan occupy any one of a number of positions relative to the DNA sequence.The most important influence onnucleosomepositioning appearsto be the presenceof other tightly bound proteins on the DNA. Some bound proteins favor the formation of a nucleosomeadjacent to them.
others create obstacles that force the nucleosomes ro moveto positions between them. The exact positions of nucleosomes along a stretchof DNA therefore depends mainly on the presence and nature of other proteinsbound to the DNA. Due to the presenceof ATP-dependentremodeling complexes, the arrangement of nucleosomes on DNA can be highly dynamic,changing rapidly accordingto the needs of the cell.NucleosomesAre UsuallyPackedTogetherinto a CompactCh r o m a t i Fn i b erAlthough 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 anothe; generating regular arrays in which the DNA is even more highly condensed.
![](https://s.studizba.com/z.php?f=/templates/si/i/noavatar.png&w=100&h=100&t=1"){kind=avatar}
