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detailed descriptions of nucleosome and acf preparation , as well as single - molecule and ensemble fret , fluorescence anisotropy , protein crosslinking , and yeast experiments are described in the online methods .
briefly , various nucleosome constructs were reconstituted using cy3-labelled histone octamers and cy5-labelled dna with a biotin moiety for surface anchoring .
dna was generated by pcr or by annealing and ligating a set of overlapping , complementary oligonucleotides ( extended data fig .
histone octamer , nucleosomes , acf1 , snf2h and acf complexes were reconstituted and purified as described previously .
crosslinking experiments were carried out using nucleosomes with a cysteine - reactive crosslinker bm ( peg)3 at the h4 tail n - terminus and reaction products were analyzed by sds - page .
a , ensemble remodelling time courses of [ wt h4 , 78 bp ] nucleosomes by 10 nm acf with 5 m atp ( filled symbols ) or without ( open symbols ) atp .
nucleosome translocation is monitored by the emission intensity of the fret acceptor cy5 under constant 532 nm illumination that excites the fret donor cy3 .
b , comparison of the average remodelling kinetics for surface - anchored [ wt h4 , 40 bp ] nucleosomes ( measured by the single - molecule assay , > 250 nucleosomes ) and freely diffusing [ wt h4 , 40 bp ] nucleosomes in solution ( measured by the ensemble assay ) .
a , histogram of fret levels for the initial position and pause positions of [ wt h4 , 40 bp ] nucleosomes upon remodelling by acf .
the histogram was fit by multiple gaussian peaks ( black line ) and the peak values were used to compute the average translocation distances between pauses .
the translocation distances can be quantified using a calibration curve of fret efficiency versus exit - side linker dna length , yielding at 7.0 bp step size between the initial position and the first pause and a 3.4 bp step size between the first pause and the second pause .
the dinucleosome constructs , [ wt h4 , 40 bp , wt h4 ] and [ wt h4 , 78 bp , wt h4 ] , are each composed of one fret - labelled nucleosome and one unlabelled nucleosome , spaced by 40 bp and 78 bp of internucleosomal linker dna , respectively .
the flanking linker dna is 3 bp on the side of the fret - labelled nucleosome and 40 bp on the side of the unlabelled nucleosome .
data are mean  s.e.m derived from at least 100 remodelling traces from three independent experiments .
c , dwell time distributions for the first translocation phase , tt1 , and the first pause phase , tp1 , for nucleosomes with different lengths of linker dna .
a , the dinucleosomes contain a distal fret - labelled nucleosome and a proximal unlabelled nucleosome connected by n bp of internucleosomal linker dna .
the flanking linker dna is 3 bp and 40 bp on the side of the fret - labelled and the unlabelled nucleosome , respectively . to facilitate the study of translocation of the fret - labelled nucleosome
, we placed 2-nt ssdna gaps at the shl2 sites of the proximal nucleosome to prevent its repositioning .
b , comparison of translocation and pause - phase exit rates for mononucleosomes ( filled bars ) and dinucleosomes ( hashed bars ) with 40 and 78 bp linker lengths .
data are mean  s.e.m derived from at least 100 individual nucleosome remodelling traces from three independent experiments .
a , wt snf2h , negc snf2h , or auton-2ra snf2h were co - expressed with acf1-flag in sf9 insect cells and purified by affinity chromatography .
b , n - term acf1 or c - term acf1 was co - expressed with snf2h - flag and purified by affinity chromatography .
the presence of both acf1 and snf2h in each case indicated that wt snf2h , negc snf2h and auton-2ra snf2h can all form complexes with acf1 and that n - term acf1 and c - term acf1 can both form complexes with snf2h .
ensemble remodelling time courses of [ wt h4 , 78 bp ] , [ wt h4 , 40 bp ] and [ wt h4 , 20 bp ] nucleosomes by 130 nm wt ( a ) or negc snf2h ( b ) at 2 mm atp
. a , remodelling of [ wt h4 , 78 bp ] and [ wt h4 , 40 bp ] nucleosomes by 40 nm ( top ) and 10 nm ( bottom ) wt acf .
b , remodelling of [ wt h4 , 78 bp ] and [ wt h4 , 40 bp ] nucleosomes by 40 nm ( top ) and 10 nm ( bottom ) auton-2ra acf .
a , domain maps of wt and c - term acf1 ( residues 1423 - 1556 deleted ) .
b , fluorescence anisotropy of tmr - labelled wt or 2ra h4-tail peptide in the presence of varying amounts of wt acf1 . in the 2ra h4-tail peptide ,
two charged arginines in the basic patch of the h4-tail peptide corresponding to the 2ra mutation in auton were replaced with alanines .
the kd for the 2ra h4-tail peptide ( 41  29 nm ) is substantially higher than that of the wt h4-tail peptide ( 3  9 nm ) .
( errors report the 95% confidence interval , n = 3 three independent titration experiments ) .
when excess unlabelled h4-tail peptide was added to compete the tmr - labelled peptide off acf1 , the fluorescence anisotropy was reduced to the background level in the absence of acf1 .
c , fluorescence anisotropy of tmr - labelled h4-tail peptide in the presence of varying amounts of wt or c - term acf1 .
the measured kd for c - term acf1 is 2  7 nm , which is similar to that for wt acf1 ( 3  9 nm ) .
( errors report the 95% confidence interval , n = 3 independent titration experiments ) .
d , ensemble remodelling time courses of [ wt h4 , 78 bp ] , [ wt h4 , 40 bp ] , and [ h41 - 19 , 78 bp ] nucleosomes by 40 nm wt ( balck / gray lines ) and c - term acf ( purple / light purple symbols ) at 5 m atp .
electrophoretic mobility of dsdna ( 225 bp , 8 nm ) in the presence or absence of 22 nm wt or n - term acf1 . as a comparison ,
lanes 2 and 4 show acf1 samples without the dsdna . a , left : sds page analysis of samples containing acf alone or acf with nucleosomes ( 20 bp linker dna ) that do not possess the cysteine - reactive crosslinker on the h4 tail .
both samples yield two distinct bands corresponding to the acf1 and snf2h subunits ( 180 kda and 122 kda , respectively ) .
additionally , histone bands at low molecular weights are present in the lane for the sample containing nucleosomes . right : corresponding immunoblot using -h4 antibody . in the presence of nucleosomes without crosslinker ,
b , top : incubation of acf and nucleosomes that contain a crosslinker at the h4 tail yield acf1-h4 and snf2h - h4 crosslinking bands .
these bands are absent for acf without addition of nucleosomes (  - nucleosomes  ) or upon addition of nucleosomes without a crosslinker .
bottom : -histone h4 immunoblotting reveals specific acf1-h4 and snf2h - h4 bands that are absent for acf without addition of nucleosomes (  - nucleosomes  ) or upon addition of nucleosomes without a crosslinker .
the 601 nucleosome positioning sequence is shown in green ( 601 * represents the introduction of 2-nt gaps at nucleotides 53 and 54 in the top and bottom strands of the 601 positioning sequence , respectively ) .
for mononucleosome dna constructs , the ssdna spacer used to circumvent surface effects in single - molecule fret measurements is underlined .
were used in single - molecule and bulk remodelling experiments . for ensemble remodelling experiments with mononucleosomes ,
only 3 bp of linker dna on the other side displayed quantitatively similar crosslinking behaviour .
iswi - family remodelling enzymes regulate access to genomic dna by mobilizing nucleosomes1 . 
 these atp - dependent chromatin remodellers promote heterochromatin formation and transcriptional silencing1 by generating regularly - spaced nucleosome arrays2 - 5 . 
 the nucleosome - spacing activity arises from regulation of nucleosome translocation by the length of extranucleosomal linker dna6 - 10 , but the underlying mechanism remains unclear . here , we studied nucleosome remodelling by human acf , an iswi enzyme comprised of a catalytic subunit , snf2h , and an accessory subunit , acf12,11 - 13 . 
 we found that acf senses linker dna length through an interplay between its accessory and catalytic subunits mediated by the histone h4 tail of the nucleosome . 
 mutation of auton , an auto - inhibitory domain within snf2h that bears sequence homology to the h4 tail14 , abolished the linker - length sensitivity in remodelling . 
 addition of exogenous h4-tail peptide or deletion of the nucleosomal h4 tail also diminished the linker - length sensitivity . 
 moreover , the accessory subunit acf1 bound the h4-tail peptide and dna in a manner that depended on its n - terminal domain , and lengthening the linker dna in the nucleosome reduced the proximity between acf1 and the h4 tail . 
 deletion of the n - terminal portion of acf1 ( or its homologue in yeast ) abolished linker - length sensitivity in nucleosome remodeling and led to severe growth defects in vivo . taken together , our results suggest a mechanism for nucleosome spacing where linker dna sensing by acf1 is allosterically transmitted to snf2h through the h4 tail of the nucleosome . for nucleosomes with short linker dna , acf1 preferentially binds to the h4 tail , allowing auton to inhibit the atpase activity of snf2h . 
 as the linker dna lengthens , acf1 shifts its binding preference to the linker dna , freeing the h4 tail to compete auton off the atpase and thereby activating acf .