Professional Documents
Culture Documents
Histone Code
Histone Code
Histone Code
69. Y. Habu, T. Kakutani, J. Paszkowski, Curr. Opin. Genet. 79. C. Cogoni et al., EMBO J. 15, 3153 (1996). 89. P. SanMiguel et al., Science 274, 765 (1996).
Dev. 11, 215 (2001). 80. G. Faugeron, Curr. Opin. Microbiol. 3, 144 (2000). 90. R. Mauricio, Nature Rev. Genet. 2, 370 (2001).
70. M. Wassenegger, Plant Mol. Biol. 43, 203 (2000). 81. L. Jackson-Grusby et al., Nature Genet. 27, 31 (2001). 91. P. Cubas, C. Vincent, E. Coen, Nature 401, 157 (1999).
71. M. A. Matzke, A. J. Matzke, J. M. Kooter, Science 293, 82. J. P. Vielle-Calzada, R. Baskar, U. Grossniklaus, Nature 92. R. Martienssen, Curr. Opin. Genet. Dev. 8, 240
1080 (2001).
404, 91 (2000). (1998).
72. J. Bender, Trends Biochem. Sci. 23, 252 (1998).
73. E. U. Selker, Cell 97, 157 (1999). 83. P. S. Springer, D. R. Holding, A. Groover, C. Yordan, 93. Z. J. Chen, C. S. Pikaard, Genes Dev. 11, 2124 (1997).
74. M. N. Raizada, M. I. Benito, V. Walbot, Plant J. 25, 79 R. A. Martienssen, Development 127, 1815 (2000). 94. L. Comai et al., Plant Cell 12, 1551 (2000).
(2001). 84. J. P. Vielle-Calzada et al., Genes Dev. 13, 2971 (1999). 95. H. S. Lee, Z. J. Chen, Proc. Natl. Acad. Sci. U.S.A. 98,
75. R. F. Ketting, T. H. Haverkamp, H. G. van Luenen, R. H. 85. R. Vinkenoog et al., Plant Cell 12, 2271 (2000). 6753 (2001).
Plasterk, Cell 99, 133 (1999). 86. S. Adams, R. Vinkenoog, M. Spielman, H. G. Dickinson, 96. We thank E. Selker, E. Richards, V. Chandler, S. Kaep-
76. H. Tabara et al., Cell 99, 123 (1999). R. J. Scott, Development 127, 2493 (2000). pler, S. Jacobsen, and J. Bender for communicating
77. B. H. Ramsahoye et al., Proc. Natl. Acad. Sci. U.S.A. 87. M. Byrne, M. Timmermans, C. Kidner, R. Martienssen, results prior to publication, two anonymous referees
97, 5237 (2000). Curr. Opin. Plant Biol. 4, 38 (2001). for suggestions for improvement, and our colleagues
78. P. Svoboda, P. Stein, H. Hayashi, R. M. Schultz, De- 88. E. B. Cambareri, R. Aisner, J. Carbon, Mol. Cell. Biol. for many interesting discussions. R.M. and V.C. re-
velopment 127, 4147 (2000). 18, 5465 (1998). ceive grant support from the NSF (DBI 1057338).
REVIEW
Chromatin, the physiological template of all eukaryotic genetic information, is transcriptionally inert are highly condensed
subject to a diverse array of posttranslational modifications that largely in the interphase nucleus and remain cytolog-
impinge on histone amino termini, thereby regulating access to the underly- ically visible as heterochromatic foci or as the
ing DNA. Distinct histone amino-terminal modifications can generate syner- “Barr body,” which is the inactive X chromo-
gistic or antagonistic interaction affinities for chromatin-associated proteins, some in female mammalian cells (2). The
which in turn dictate dynamic transitions between transcriptionally active or distinct levels of chromatin organization are
transcriptionally silent chromatin states. The combinatorial nature of histone dependent on the dynamic higher order struc-
amino-terminal modifications thus reveals a “histone code” that considerably turing of nucleosomes, which represent the
extends the information potential of the genetic code. We propose that this basic repeating unit of chromatin. In each
epigenetic marking system represents a fundamental regulatory mechanism nucleosome, roughly two superhelical turns
that has an impact on most, if not all, chromatin-templated processes, with of DNA wrap around an octamer of core
far-reaching consequences for cell fate decisions and both normal and patho- histone proteins formed by four histone part-
logical development. ners: an H3-H4 tetramer and two H2A-H2B
dimers (3). Histones are small basic proteins
Genomic DNA is the ultimate template of our nisms for how such a code is “read” and consisting of a globular domain and a more
heredity. Yet despite the justifiable excitement translated into biological functions. flexible and charged NH2-terminus (histone
over the human genome, many challenges re- Throughout this review, we have chosen “tail”) that protrudes from the nucleosome. It
main in understanding the regulation and trans- epigenetic phenomena and underlying mecha- remains unclear how nucleosomal arrays con-
duction of genetic information (1). It is unclear, nisms in two general categories: chromatin- taining linker histone (H1) then twist and fold
for example, why the number of protein-coding based events leading to either gene activation or this chromatin fiber into increasingly more
genes in humans, now estimated at ⬃35,000, gene silencing. In particular, we center our dis- compacted filaments leading to defined high-
only doubles that of the fruit fly Drosophila cussion on examples where differences in “on- er order structures.
melanogaster. Is DNA alone then responsible off ” transcriptional states are reflected by dif- Central to our current thinking is that
for generating the full range of information that ferences in histone modifications that are either chromatin structure plays an important regu-
ultimately results in a complex eukaryotic or- “euchromatic” (on) or “heterochromatic” (off ) latory role and that multiple signaling path-
ganism, such as ourselves? (Fig. 1A). We also point out that, despite many ways converge on histones (4). Although
We favor the view that epigenetics, im- elegant genetic and biochemical insights into histone proteins themselves come in generic
posed at the level of DNA-packaging proteins chromatin function and gene regulation in the or specialized forms (5), exquisite variation is
(histones), is a critical feature of a genome- budding yeast Saccharomyces cerevisiae, some provided by covalent modifications (acetyla-
wide mechanism of information storage and of the heterochromatic mechanisms (e.g., HP1- tion, phosphorylation, methylation) of the hi-
retrieval that is only beginning to be under- based gene silencing) discussed here do not stone tail domains, which allow regulatable
stood. We propose that a “histone code” ex- exist in an obvious form in this organism. Thus, contacts with the underlying DNA. The en-
ists that may considerably extend the infor- we will need to pursue other model systems, zymes transducing these histone tail modifi-
mation potential of the genetic (DNA) code. such as Schizosaccharomyces pombe, Caeno- cations are highly specific for particular ami-
We review emerging evidence that histone rhabditis elegans, Drosophila, and mice, to no acid positions (6, 7), thereby extending
proteins and their associated covalent modi- “crack” the histone code. the information content of the genome past
fications contribute to a mechanism that can the genetic (DNA) code. This hypothesis pre-
alter chromatin structure, thereby leading to Chromatin Template and Histone dicts that (i) distinct modifications of the
inherited differences in transcriptional “on- Code
off ” states or to the stable propagation of In the nuclei of all eukaryotic cells, genomic 1
Research Institute of Molecular Pathology (IMP) at
chromosomes by defining a specialized high- DNA is highly folded, constrained, and com- the Vienna Biocenter, Dr. Bohrgasse 7, A-1030 Vi-
enna, Austria. E-mail: jenuwein@nt.imp.univie.ac.at
er order structure at centromeres. Under the pacted by histone and nonhistone proteins in 2
Department of Biochemistry and Molecular Genetics,
assumption that a histone code exists, at least a dynamic polymer called chromatin. For University of Virginia Health Science Center, Char-
in some form, we discuss potential mecha- example, chromosomal regions that remain lottesville, VA 22908, USA. E-mail: allis@virginia.edu
VIEWPOINT
In diverse organisms, small RNAs derived from cleavage of double-strand- ent ribonuclease complex, RISC (RNA-induced
ed RNA can trigger epigenetic gene silencing in the cytoplasm and at the silencing complex), which cleaves the homolo-
genome level. Small RNAs can guide posttranscriptional degradation of gous single-stranded mRNAs. RISC from Dro-
complementary messenger RNAs and, in plants, transcriptional gene si- sophila extracts cofractionates with siRNAs
lencing by methylation of homologous DNA sequences. RNA silencing is a that guide sequence-specific mRNA cleavage
potent means to counteract foreign sequences and could play an impor- (12). RISC cuts the mRNA approximately in
tant role in plant and animal development. the middle of the region paired with antisense
siRNA (14) (Fig. 1), after which the mRNA is
RNA silencing is a new field of research that sult from the same highly conserved mecha- further degraded. Although most protein com-
has coalesced during the last decade from inde- nism, indicating an ancient origin (5–10). The ponents of RISC have not yet been identified,
pendent studies on various organisms. Scien- basic process involves a dsRNA that is pro- they might include an endonuclease, an exonu-
tists who study plants and fungi have known cessed into shorter units that guide recogni- clease, a helicase, and a homology-searching
since the late 1980s that interactions between tion and targeted cleavage of homologous activity (6, 10). A candidate for a 3⬘,5⬘-exonu-
homologous DNA and/or RNA sequences can mRNA. dsRNAs that trigger PTGS/RNAi clease is C. elegans MUT7, an RNase D–like
silence genes and induce DNA methylation (1). can be made in the nucleus or cytoplasm in a protein recovered in a screen for RNAi mutants
The discovery of RNA interference (RNAi) in number of ways, including transcription (10). Another component of RISC is a protein
Caenorhabditis elegans in 1998 (2) focused through inverted DNA repeats, simultaneous of the PAZ/Piwi family (17), which could in-
attention on double-stranded RNA (dsRNA) as synthesis of sense and antisense RNAs, viral teract with Dicer through their common PAZ
an elicitor of gene silencing, and indeed, many replication, and the activity of cellular or viral domains (18) to incorporate the siRNA into
gene-silencing effects in plants are now known RNA– dependent RNA polymerases (RdRP) RISC (17). Genes encoding members of the
to be mediated by dsRNA (3). RNAi is usually on single-stranded RNA templates (Fig. 1). In PAZ/Piwi family (Arabidopsis: AGO1; N.
described as a posttranscriptional gene-silenc- C. elegans, dsRNAs can be injected or intro- crassa: QDE2; C. elegans: RDE1), which are
ing phenomenon in which dsRNA triggers deg- duced simply by soaking the worms in a homologous to the translation factor eIF2C,
radation of homologous mRNA in the cyto- solution containing dsRNA or feeding them have been shown to be required for PTGS/
plasm (4). However, the potential for nuclear bacteria expressing sense and antisense RNA RNAi in several mutant screens (3, 5, 8, 10).
dsRNA to enter a pathway leading to epigenetic (10). A putative RdRP was the first cellular pro-
modifications of homologous DNA sequences Genetic and biochemical approaches are be- tein shown to be required for PTGS/RNAi in
and silencing at the transcriptional level should ing used to dissect the mechanism of PTGS/ genetic screens (N. crassa: QDE1; C. elegans:
not be discounted. Although the nuclear aspects RNAi. Putative RdRPs, putative helicases, and Ego1; Arabidopsis: SGS2/SDE1) (3, 5, 8, 10),
of RNA silencing have been studied primarily members of the PAZ/Piwi family are some of but its exact role is unclear and the predicted
in plants, there are hints that similar RNA- the common proteins identified in genetic enzyme activity remains to be established. This
directed DNA or chromatin modifications screens in N. crassa, C. elegans, and Arabidop- protein might be dispensible when large
might occur in other organisms as well. Here sis (3, 5, 8, 10). Although these proteins provide amounts of dsRNA are produced from trans-
we adopt a broad definition of RNA silencing clues about dsRNA synthesis and processing, genes or when viral RdRPs are present (5).
that encompasses effects in the cytoplasm and the most detailed insight into the two-step RNA RdRP might be needed only when dsRNA is
the nucleus, and consider their possible devel- degradation process has come from biochemi- synthesized to initiate silencing—for example,
opmental roles and evolutionary origins. cal experiments with cytoplasmic extracts from from “aberrant” sense RNAs that are prema-
Drosophila (11–15) (Fig. 1). The first step in- turely terminated or processed improperly (19).
RNA Guiding Homologous RNA volves a dsRNA endonuclease [ribonuclease III RISC-cleaved mRNAs may also be used as
Degradation (RNase III)–like] activity that processes dsRNA templates and converted into dsRNA, increas-
Although they may differ in detail, RNAi in into sense and antisense RNAs 21 to 25 nucle- ing the level of siRNAs and enhancing PTGS/
animals and the related phenomena of post- otides (nt) long. These small interfering RNAs RNAi (Fig. 1).
transcriptional gene silencing (PTGS) in (siRNAs), which were first described in a plant Putative helicases are another class of en-
plants and quelling in Neurospora crassa re- system (16), are generated in Drosophila by an zyme found repeatedly in mutant screens (N.
RNase III–type protein termed Dicer. Orthologs crassa: QDE3; C. elegans: SMG-2; Chlamy-
of Dicer, which contains a helicase, dsRNA domas: MUT6; Arabidopsis: SDE3) (3, 5, 8,
1
Institute of Molecular Biology, Austrian Academy of
Sciences, A-5020 Salzburg, Austria. 2Department of
binding domains, and a PAZ domain, have 10). Those recovered so far are not highly
Developmental Genetics, Vrije Universiteit, Amster- been identified in Arabidopsis, C. elegans, related and have not yet been characterized
dam, Netherlands. mammals, and Schizosaccharomyces pombe biochemically. A DNA helicase (QDE3) and
*To whom correspondence should be addressed. E- (15). In the second step, the antisense siRNAs members of two RNA helicase superfamilies
mail: mmatzke@imb.oeaw.ac.at produced by Dicer serve as guides for a differ- (MUT6 and SMG2/SDE3, respectively) have