Intra- and Inter-nucleosomal Protein-DNA Interactions of the Core Histone Tail Domains in a Model System

The core histone tail domains are key regulators of eukaryotic chromatin structure and function and alterations in the tail-directed folding of chromatin fibers and higher order structures are the probable outcome of much of the post-translational modifications occurring in these domains. The functions of the tail domains are likely to involve complex intra- and inter-nucleosomal histone-DNA interactions, yet little is known about either the structures or interactions of these domains. Here we introduce a method for examining inter-nucleosome interactions of the tail domains in a model dinucleosome and determine the propensity of each of the four N-terminal tail domains to mediate such interactions in this system. Using a strong nucleosome “positioning” sequence, we reconstituted a nucleosome containing a single histone site specifically modified with a photoinducible cross-linker within the histone tail domain, and a second nucleosome containing a radiolabeled DNA template. These and the inter-nucleosomal histone-DNA interactions the N-terminal of and of and histone-DNA interactions within the The of intra- to inter-nucleosome interactions we of a histone to the dinucleosome the of the and with the DNA The core histone tail domains are key regulators of eukaryotic chromatin structure and function and alterations in the tail-directed folding of chromatin fibers and higher order structures are the probable outcome of much of the post-translational modifications occurring in these domains. The functions of the tail domains are likely to involve complex intra- and inter-nucleosomal histone-DNA interactions, yet little is known about either the structures or interactions of these domains. Here we introduce a method for examining inter-nucleosome interactions of the tail domains in a model dinucleosome and determine the propensity of each of the four N-terminal tail domains to mediate such interactions in this system. Using a strong nucleosome “positioning” sequence, we reconstituted a nucleosome containing a single histone site specifically modified with a photoinducible cross-linker within the histone tail domain, and a second nucleosome containing a radiolabeled DNA template. These and the inter-nucleosomal histone-DNA interactions the N-terminal of and of and histone-DNA interactions within the The of intra- to inter-nucleosome interactions we of a histone to the dinucleosome the of the and with the DNA the of eukaryotic chromatin known the the nucleosome core is of of each of the core and and of of the core histone is a the nucleosome core DNA is is the histone within each and to these domains The of these domains and interactions with DNA nucleosome a of nucleosome in in a single histone of are chromatin fibers of about in these fibers are higher order structures of the of the core is within the N-terminal tail to These domains are and DNA in and in chromatin these domains in interactions in the chromatin the of the and structures and interactions in chromatin The tail domains are for or the structure of the nucleosome core and of the in in the and DNA within the nucleosome the tail domains are for folding of chromatin fibers and are for of fibers higher order structures of folding and the functions and the tail to the for folding the for the tail and the for folding of the chromatin the mediate interactions chromatin folding is of these interactions inter-nucleosomal the complex of structures and interactions of the tail domains in chromatin higher chromatin histone to each nucleosome of these to the of the nucleosome with and to to reconstituted in the of DNA about the histone and the of tail the DNA within the chromatin the core histone of nucleosome to chromatin fibers the of of the interactions of the core histone tail domains within post-translational either or chromatin structure to or or modifications within these domains are to to the of the modifications for the of such the to the modifications chromatin structure of in a of and alterations in the of in a histone tail in is of a or of the tail with DNA in to of chromatin the to a of interactions and post-translational modifications such to of in the tail domains. modifications are likely to in tail structures a of the post-translational modifications of the histone to of chromatin of the structures and interactions of the tail we introduce a dinucleosome for of core histone of intra- and inter-nucleosomal interactions the histone tail domains and DNA a of folding of the DNA in a of the tail domains the DNA of the nucleosome the and to in the of inter-nucleosomal interactions a of a histone the of and with the DNA for and containing a to and to the of the nucleosome DNA and and and to nucleosome and The nucleosome is and nucleosome is of the the site a of with a of The and DNA each in of or with or with and in the with DNA in the of each of and for or and for The with and the and and the in and each dinucleosome nucleosome or of either with or The DNA and the DNA each of either with in the of of and each of and and for for for for The a and in of and and and and for and and and a and The core and in and and the these in in we the of within each and containing of and and or and containing of in of and with of in the of for The for with The for and the each of of and of of of to the for The with in and with in containing the to the of and the The containing with of for and the to of The and of and of and and nucleosome reconstituted a DNA and the second reconstituted a a of or of with of of and of with for each of in of DNA and histone the of in containing in The nucleosome a The or of or each of and of and of for in a of the of of and of for The for and of and to for to to a to and of to and with of and of The the of a a The with a for The with of of of and for of and The in of and of the with in a of for to with and for the The with and a containing and for and of the interactions of the core histone tail we a model dinucleosome in nucleosome and a radiolabeled DNA the second histone with a within the tail the the reconstituted we for the of the DNA and the in with a and to of the nucleosome this nucleosome to with and a of 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interactions of the core histone tail domains much of this with either single or with chromatin inter-nucleosomal tail interactions or to of inter-nucleosomal to histone of a tail with DNA of the interactions, for histone or N-terminal yet these and the are for of the chromatin the tail to the of the chromatin and the of the tail to with a to with the of the in nucleosome These are with these to the DNA of nucleosome in is or the DNA to or these with the to the structure of the chromatin nucleosome to or These are with the the are the of DNA the in a or of of a a or structure in the of of of of to a structure with the a chromatin chromatin of to the of the of the histone tail domains in we or of the in the of inter-nucleosome interactions to in the of inter-nucleosome interactions with the of to of the dinucleosome is the of the dinucleosome the interactions of histone with DNA in such a in inter-nucleosome is in in for of the chromatin of the tail domains in inter-nucleosomal interactions in chromatin this we in the nucleosome to histone nucleosome in interactions in structures of nucleosome or of histone inter-nucleosomal histone interactions these the of eukaryotic chromatin known the the nucleosome core is of of each of the core and and of of the core histone is a the nucleosome core DNA is is the histone within each and to these domains The of these domains and interactions with DNA nucleosome a of nucleosome in in a single histone of are chromatin fibers of about in these fibers are higher order structures of the of the core is within the N-terminal tail to These domains are and DNA in and in chromatin these domains in interactions in the chromatin the of the and structures and interactions in chromatin The tail domains are for or the structure of the nucleosome core and of the in in the and DNA within the nucleosome the tail domains are for folding of chromatin fibers and are for of fibers higher order structures of folding and the functions and the tail to the for folding the for the tail and the for folding of the chromatin the mediate interactions chromatin folding is of these interactions inter-nucleosomal the complex of structures and interactions of the tail domains in chromatin higher chromatin histone to each nucleosome of these to the of the nucleosome with and to to reconstituted in the of DNA about the histone and the of tail the DNA within the chromatin the core histone of nucleosome to chromatin fibers the of of the interactions of the core histone tail domains within post-translational either or chromatin structure to or or modifications within these domains are to to the of the modifications for the of such the to the modifications chromatin structure of in a of and alterations in the of in a histone tail in is of a or of the tail with DNA in to of chromatin the to a of interactions and post-translational modifications such to of in the tail domains. modifications are likely to in tail structures a of the post-translational modifications of the histone to of chromatin of the structures and interactions of the tail domains. 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with in containing the to the of and the The containing with of for and the to of The and of and of and and nucleosome reconstituted a DNA and the second reconstituted a a of or of with of of and of with for each of in of DNA and histone the of in containing in The nucleosome a The or of or each of and of and of for in a of the of of and of for The for and of and to for to to a to and of to and with of and of The the of a a The with a for The with of of of and for of and The in of and of the with in a of for to with and for the The with and a containing and for and DNA for and containing a to and to the of the nucleosome DNA and and and to nucleosome and The nucleosome is and nucleosome is of the the site a of with a of The and DNA each in of or with or with and in the with DNA in the of each of and for or and for The with and the and and the in and each dinucleosome nucleosome or of either with or The DNA and the DNA each of either with in the of of and each of and and for for for for The a and in of and and and and for and and and a and The core and in and and the these in in we the of within each and containing of and and or and containing of in of and with of in the of for The for with The for and the each of of and of of of to the for The with in and with in containing the to the of and the The containing with of for and the to of The and of and of and and nucleosome reconstituted a DNA and the second reconstituted a a of or of with of of and of with for each of in of DNA and histone the of in containing in The nucleosome a The or of or each of and of and of for in a of the of of and of for The for and of and to for to to a to and of to and with of and of The the of a a The with a for The with of of of and for of and The in of and of the with in a of for to with and for the The with and a containing and for and of the interactions of the core histone tail we a model dinucleosome in nucleosome and a radiolabeled DNA the second histone with a within the tail the 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this of the to the inter-nucleosomal in a model containing a the of nucleosome and in nucleosome for to in and are and and and in with in are the of nucleosome DNA and and in and with is in the to N-terminal with interactions the N-terminal tail of we radiolabeled the of nucleosome and in nucleosome of the nucleosome to DNA the N-terminal tail in inter-nucleosomal interactions we the of inter-nucleosomal interactions of the in a model containing a the of nucleosome DNA and in nucleosome and for in and are in and in and the in and in and and in with containing in and is in the to and in the for interactions the N-terminal tail domains of and to DNA in a to for and to the dinucleosome the the of either the or tail in nucleosome and the of nucleosome a the nucleosome to the DNA of nucleosome of the and and These and with the DNA of the nucleosome in model dinucleosome of DNA interactions in the with a the of nucleosome and in nucleosome and to in and and and and of of with is in the to in 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nucleosome or or for of with of nucleosome in the and model dinucleosome site the the of each site in the and the The N-terminal DNA in a to DNA the tail in the model we a to a the of N-terminal tail in nucleosome the of nucleosome and the of inter-nucleosomal to DNA the tail the of and a strong the dinucleosome and intra- and inter-nucleosomal to DNA the tail of with of the is of inter-nucleosomal DNA the N-terminal tail the we the and within the nucleosome in the of a to the the of the is to a we in the of the the of and and the for this is in to a of the of the a of is with and in the to a the in is to mediate inter-nucleosome is the of the N-terminal tail and the histone domain, the of the DNA and is likely to in inter-nucleosomal DNA of containing in to DNA to either of the nucleosome with the known structure of this complex to the the of nucleosome in the dinucleosome and nucleosome a and DNA the in and the of the to this in a second we the and in the this of the to the The 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dinucleosome the N-terminal of and interactions with the DNA of a the of and histone-DNA interactions within model within of such to in chromatin to a of inter-nucleosomal interactions and a of chromatin structure of or of such within a much of folding of the a higher order structure in of the of of the in with the and to interactions of the core histone tail domains much of this with either single or with chromatin inter-nucleosomal tail interactions or to of inter-nucleosomal to histone of a tail with DNA of the interactions, for histone or N-terminal yet these and the are for of the chromatin the tail to the of the chromatin and the of the tail to with a to with the of the in nucleosome These are with these to the DNA of nucleosome in is or the DNA to or these with the to the structure of the chromatin nucleosome to or These are with the the are the of DNA the in a or of of a a or structure in the of of of of to a structure with the a chromatin chromatin of to the of the of the histone tail domains in we or of the in the of inter-nucleosome interactions to in the of inter-nucleosome interactions with the of to of the dinucleosome is the of the dinucleosome the interactions of histone with DNA in such a in inter-nucleosome is in in for of the chromatin of the tail domains in inter-nucleosomal interactions in chromatin this we in the nucleosome to histone nucleosome in interactions in structures of nucleosome or of histone inter-nucleosomal histone interactions these the histone in chromatin in model dinucleosome the N-terminal of and interactions with the DNA of a the of and histone-DNA interactions within model within of such to in chromatin to a of inter-nucleosomal interactions and a of chromatin structure of or of such within a much of folding of the a higher order structure in of the of of the in with the and to interactions of the core histone tail domains much of this with either single or with chromatin inter-nucleosomal tail interactions or to of inter-nucleosomal to histone of a tail with DNA of the interactions, for histone or N-terminal yet these and the are for of the chromatin the tail to the of the chromatin and the of the tail to with a to with the of the in nucleosome These are with these to the DNA of nucleosome in is or the DNA to or these with the to the structure of the chromatin nucleosome to or These are with the the are the of DNA the in a or of of a a or structure in the of of of of to a structure with the a chromatin chromatin of to the of the of the histone tail domains in we or of the in the of inter-nucleosome interactions to in the of inter-nucleosome interactions with the of to of the dinucleosome is the of the dinucleosome the interactions of histone with DNA in such a in inter-nucleosome is in in for of the chromatin of the tail domains in inter-nucleosomal interactions in chromatin this we in the nucleosome to histone nucleosome in interactions in structures of nucleosome or of histone inter-nucleosomal histone interactions these for the