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Encyclopedia of Physical Science and Technology EN002G-104 May 17, 2001 20:53

824 Chromatin Structure and Modification

deficiency in gene activation; most remarkably, the same access and cleavage by DNAse I, but it is also clear that the
locus was commonly found mutated in both screens. The histones remain in some contact with the DNA. Whatever
cognate gene—SWI2/SNF2—was subsequently found in the nature of the remodeled entity, energy derived from
work from I. Herskowitz’s laboratory to be required for the ATP hydrolysis is required for its generation.
transcriptional upregulation of a number of budding yeast What relevance does such action of SWI/SNF in vitro
genes. have to transcriptional control in vivo? The best explana-
Inalandmarksetofexperiments,thelabofF.Winstonin tion we can offer comes from studies in mammalian sys-
1992 demonstrated that the action of SWI2/SNF2 in gene tems. Thus, work by G. Hager and colleagues on transcrip-
activation is mediated via alleviating the repressive effect tional control of the MMTV promoter (Section IV.A.1)
on gene expression of chromatin structure. These studies focused on the function of the DNAse I hypersensitive
used the classical genetic notion of epistasis—i.e., the ca- site that is induced by the liganded glucocorticoid receptor
pacity of mutations in one locus to mask a mutation in a concomitant with transcriptional activation. An important
different locus—to uncover genetic interactions between clue came from a comparative analysis of MMTV tran-
SWI2/SNF2 and the genes for histones: it was shown that scription on copies of the viral genome that have been
the inability of certain genes in the yeast genome to be integrated into the chromosome (and thus assume native
activated when SWI2/SNF2 is mutant can be “healed” by chromatin organization) vs. such DNA that has transiently
making mutations in histone genes (for example, by low- introduced into the cell by a technique called transfection
ering the histone content of the nucleus). Most strikingly, (the DNA remains extrachromosomal and does not assem-
subsequent analysis by I. Herskowitz, C. Peterson, and M. ble physiological chromatin; it is lost from the cell after
Osley demonstrated that even less drastic measures—for only a few rounds of cell division). It was known that
example, point mutations in histone H4 that impair the ca- full-scale activated transcription on the MMTV promoter
pacity of H2A–H2B to bind the (H3/H4) tetramer—will required an activator called NF1; remarkably, NF1 action
also make SWI2/SNF2 unnecessary. Thus, those genes in was only dependent on GR and its ligand when the target
yeast that require SWI2/SNF2 to become transcriptionally promoter was chromatinized: on transiently transfected
active lose that requirement when chromatin structure is DNA, NF1 was able to bind to DNA without any abetting
destabilized by making mutations in histone genes. action from the receptor.
The most immediate prediction of these remarkable An explanation for this interesting synergy was pro-
experiments—consider the extraordinary fact that the en- videdinafamousstudybyT.ArcherandG.Hagerin1992:
tirety of chromatin within the yeast nucleus can be altered they proposed that the MMTV promoter adopts a nonran-
by genetic means—is that the product of the SWI2/SNF2 dom chromatin organization in vivo, such that the binding
gene somehow alters chromatin structure over target gene site of NF1 is occluded by a nucleosome. In contrast to
promoters. A great number of studies have yielded data NF1, GR can directly bind to chromatin over the MMTV
fully compatible with that notion (the laboratories are too promoter, and then somehow remodels histone–DNA con-
many to list, but, in addition to those already mentioned tacts adjacent to its binding sites. This remodeling (man-
include those of G. Crabtree, W. H¨orz, R. Kingston, C. ifested as a DNAse I hypersensitive site) facilitates NF1
Peterson, J. Workman). access and potentiates transcriptional activation (Fig. 12).
Several important facts emerged regarding SWI2/SNF2. This two-step (“bimodal”) mechanism for GR action led
Biochemically, it was found to be an ATPase (i.e., it hy- to several predictions: the receptor had to be shown as
drolyses ribo-ATP to release ADP and phosphate)—this competent for binding to nucleosomes, and also for the
was an important observation, because it illuminated a recruitment of a chromatin remodeling engine. In fact,
possible requirement for energy in chromatin remodeling. GR and several other members of the nuclear hormone re-
In vivo, it was discovered as one of the core components ceptor superfamily can bind to nucleosomes in vitro—this
of a multisubunit complex designated as SWI/SNF (pro- is quite an achievement, considering the extensive steric
nounced “switch-sniff”). In vitro assays with nucleosomal hindrance exerted by the nucleosome ( an example of such
templates and transcriptional regulators demonstrated that binding to nucleosomes by the thyroid hormone receptor
SWI/SNF can remodel histone–DNA contacts such that is shown in Fig. 13). In addition, T. Archer and colleagues
subsequent access by these regulators to the remodeled demonstrated that a human homolog of the budding yeast
nucleosomal template is increased. For example, a TATA SWI/SNF complex is required for transcriptional activa-
box buried within a nucleosome became more accessi- tion of MMTV by GR. A central conclusion of this analy-
ble to TBP after transcriptional activator-dependent ac- sis is that bona fide transcriptional control of this promoter
tion on that nucleosome. The exact structural nature of the cannot be recapitulated on naked DNA, and that the infras-
“remodeled” nucleosome is unclear; it is known that the tructure of chromatin is integrated into the transcriptional
histone–DNA contacts are loosened sufficiently to allow regulatory pathways affecting MMTV.