233 Biotechnologies and therapeutics chromatin as a target Andreas Reik Philip D Gregory and Fyodor D Urnov As alterations in gene expression underlie a considerable proportion of human diseases correcting such aberrant transcription in vivo is expected to provide therapeutic benefit to the patient Attempts to control endogenous mammalian genes however face a significant obstacle in the form of chromatin Aberrant gene repression can be alleviated by using small molecule inhibitors that exert nucleus wide effects on chromatin based repressors Genome wide chromatin remodeling also occurs during cloning via nuclear transfer and causes the deregulation of epigenetically controlled genes Regulation of genes in vivo can be accomplished via the use of designed transcription factors these result from a fusion of a designed DNA binding domain based on the zinc finger protein motif to a functional domain of choice Addresses Sangamo Biosciences Pt Richmond Tech Center 501 Canal Blvd Suite A100 Richmond California 94804 USA Correspondence Fyodor D Urnov e mail furnov sangamo com Current Opinion in Genetics Development 2002 12 233 242 0959 437X 02 see front matter 2002 Elsevier Science Ltd All rights reserved Abbreviations Aza C 5 azacytidine DNMT DNA methyltransferase ES embryonic stem HAT histone acetyltransferase HDAC hstone deacetylase KAP 1 KRAB repressor domain associated protein 1 LOS large offspring syndrome MBD methylated DNA binding protein MEL murine erythroid leukemia VEGF A vascular endothelial growth factor A ZFP zinc finger protein Introduction Everything that happens to the eukaryotic genome in vivo occurs on a chromatin template 1 Given the relative obscurity to which the histones were relegated for the first 25 years since the discovery by Williamson and by Hewish and Burgoyne that chromatin had a sub structure 1 their rise to dominance over genome biology documented by the many articles in this issue of Current Opinion in Genetics Development offers a case study in paradigm reversal Concomitant with an exponential increase in our understanding of genome control pathways came a growing realization that the etiology of human disease can in a very large number of cases be traced to the misregulation of particular genes This gave rise to the notion of transcriptional therapy 2 in which the genome is controlled for therapeutic purposes However exciting our growing knowledge about the genome may be its failure to be broadly useful to clinical practice was well described by Lewontin in 1991 None of the advances of 20th century medicine depend on a deep knowledge of cellular processes or on any discoveries of molecular biology Cancer is still treated by gross physical and chemical assaults on the offending tissue Cardiovascular disease is treated by surgery whose anatomical bases go back to the 19th century Of course intimate knowledge of the living cell and of basic molecular processes may be useful eventually 3 A decade later molecular biology can claim very few successes for drugs in clinical use that were designed ab initio to control a specific component of a pathway linked to disease these include the monoclonal antibody Herceptin trastuzumab 4 and the kinase inhibitor STI571 Gleevec 5 Nevertheless it is likely that the paucity of available molecular biology therapies may soon end Such optimism is founded on an unprecedented array of technical advances in whole genome analysis see article by Wyrick and Young this issue pp 130 136 high throughput drug selection and screening and the development of novel technologies to regulate genes in vivo that is based on a growing understanding of the interplay between chromatin and genome control A treatment for repression The burden of repetitive DNA carried by genomes of metazoa and selective pressure to evolve mechanisms for acute gene regulation have yielded a complex machinery for transcriptional repression see articles by Berger pp 142 148 Grewal and Elgin pp 178 187 Kouzarides pp 198 209 and Simon and Tamkun pp 210 218 in this issue It includes the histone deacetylases HDACs and methyltransferases ATPases such as the Mi 2 NRD complex 6 the Polycomb proteins and various components of repressive chromatin such as HP1 In addition higher vertebrates possess a DNA methylation based host genome defense system 7 that includes a number of DNA methyltransferases DNMTs 8 and methylated DNA binding proteins MBDs 9 The majority if not all of the aforementioned components of the chromatin based repression machinery collude with the DNMTs and the MBDs to effect gene silencing over methylated DNA loci 10 Aberrant gene repression underlies a variety of human disease most notably cancer Fortunately various steps in this repression pathway can be inhibited by potent smallmolecule agents such as the HDAC inhibitors 11 and DNMT inhibitors 12 both have been used in clinical practice to achieve a therapeutic alleviation of disease symptoms Interestingly the DNMT inhibitor 5 azacytidine Aza C was first used to treat leukemia in 1971 12 that is well before the discovery that cell cycle misregulation in cancer is at least partly effected via aberrant DNA methylation and silencing of key regulators such as 234 Chromosomes and expression mechanisms p16INK4A 13 In general there appears to be a significant gap between the finding that compound X is clinically effective in the treatment of a given disease and our understanding of how the biological properties of the molecules targeted by that compound contribute to the etiology of that disease Because a number of highly effective inhibitors of the metazoan repression machinery have been developed and are being tested in clinical practice 14 16 there is a pressing need to evaluate their utility in the context of well studied disease models to determine whether their efficacy is as a result of the presumed mode of their function or some unanticipated albeit beneficial side effect An example of this approach is provided by work studying the influence of the human protein huntingtin on Drosophila neural development 17 Earlier findings suggested that huntingtin interacts with the HAT histone acetyltransferase coactivator CBP Thompson and co workers have gone on to show that a fragment of huntingtin causes neurodegeneration in Drosophila and this effect can be overcome by treatment with HDAC inhibitors 17 this was consistent with a model in which mutated huntingtin sequesters limiting quantities of CBP p300 select
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