Genomic imprinting in mammals was discovered in theearly 1980s as a result of two types of mouse experi-ment. Nuclear transplantation was used to makeembryos that had only one of the two sets of parentalchromosomes (uniparental embryos) and other sophis-ticated genetic techniques were used to make embryosthat inherited specific chromosomes from one parentonly (uniparental disomy).In both cases,the surprisingfinding was that mammalian genes could function dif-ferently depending on whether they came from themother or the father1–6.The early 1990s then saw thediscovery of the first imprinted genes, which wereindeed expressed differently on maternal and paternalchromosomes7–9,and the realization that imprintinghad a substantial effect on human genetic disease10,11.Itwas also found that DNA methylation was a key molec-ular mechanism of imprinting; methylation marks theimprinted genes differently in egg and sperm, andinheritance of these epigenetic marks leads to differen-tial gene expression12–17.Substantial progress has been made in our under-standing of imprinting in the past few years: importantphenotypic effects of imprinted genes have been discov-ered,particularly in the control of fetal growth andbehaviour after birth; a number of cis-acting sequencesare being defined that are important for the control ofimprinted gene expression; the evolutionary under-standing of imprinting and its likely biological purposesis increasing18,19; and the study of imprinting is provid-ing general insights into the importance of epigeneticmechanisms in development.Here we review these recent developments. Webegin with a brief summary of imprinted genes,thenlook at what is known about establishment and main-tenance of imprints, and the important role of thegerm line.We review the various ‘reading mechanisms’that convert the imprint into differential gene expres-sion.We discuss the evolution of imprinting,and itsmain phenotypic effects,in healthy and diseased states.Finally, we consider the effect of imprinting on impor-tant general issues in epigenetics, such as cloning andgenome reprogramming.Imprinted genesUsing several approaches (BOX 1), around 45 imprintedgenes have so far been identified in the mouse (see theHarwell imprinting web site for up-to-date statistics onimprinted gene numbers and characteristics).Some ofthese genes have been tested in other mammals and formany (but not all),the imprinting status is conserved inhumans,in some other EUTHERIAN mammals and in amarsupial20–22(but only a few genes have been tested).What are the genetic and epigenetic features that char-acterize imprinted genes?GENOMIC IMPRINTING: PARENTALINFLUENCE ON THE GENOMEWolf Reik* and Jörn Walter‡Genomic imprinting affects several dozen mammalian genes and results in the expression of those genes from only one of the two parental chromosomes. This is brought about byepigenetic instructions — imprints — that are laid down in the parental germ cells. Imprintingis a particularly important genetic mechanism in mammals, and is thought to influence thetransfer of nutrients to the fetus and the newborn from the mother. Consistent with this view is the fact that imprinted genes tend to affect growth in the womb and behaviour after birth. Aberrant imprinting disturbs development and is the cause of various diseasesyndromes. The study of imprinting also provides new insights into epigenetic genemodification during development.EUTHERIANSMammals that give birth to liveoffspring (viviparous) andpossess an allantoic placenta.NATURE REVIEWS | GENETICS VOLUME 2 | JANUARY 2001 | 21*Laboratory ofDevelopmental Geneticsand Imprinting,Developmental GeneticsProgramme, The BabrahamInstitute, Cambridge CB24AT,UK.‡Max-Planck-Institut für MolekulareGenetik, Ihnestr.73,14195Berlin and Universität desSaarlandes, Genetik, 66041Saarbrücken,Germany.e-mails:[email protected];[email protected]© 2001 Macmillan Magazines Ltd22 | JANUARY 2001 | VOLUME 2 www.nature.com/reviews/geneticsREVIEWSgenes,so these features cannot be used in a systematicsearch for new imprinted genes.The great majority of imprinted genes examinedso far show differences in DNA methylation betweenthe parental alleles (FIG. 2), but the differentiallymethylated regions (DMRs) can have different prop-erties. For example,the differential DNA methylationin some DMRs is introduced in parental germ cellsand maintained in all developmental stages and tissues25–28. Others show considerable changes inmethylation during development and acquire tissue-specific methylation patterns29,which can be associ-ated with tissue-specific imprinted expression.SomeDMRs are methylated in the inactive gene copy,whereas others are methylated in the active one.Imprinted genes can also differ with respect to bulkchromatin structure,as well as with respect to morespecific modifications,such as histone acetylation30–36(R.Feil and R. Gregory, personal communication).Two other epigenetic features have been discoveredthat might reflect the larger-scale organization ofimprinted genes into clusters or domains.First, it hasbeen shown that the DNA in imprinted regions repli-cates asynchronously in the S phase of the cell cycle;for most imprinted regions, the paternal copy repli-cates earlier than the maternal one37,38.Because mater-nally and paternally expressed genes are interspersedin some regions, this is not likely to be a gene-specificproperty and its molecular basis is not understood.Second,different frequencies of meiotic recombina-tion are found in or near to imprinted clusters,withan elevated recombination rate during male meio-sis39,40. How these regional epigenetic features arelinked with methylation and chromatin structure isnot known.The precise nature of the primary imprint and itsfate during development is still a mystery,but it is likelythat all the above epigenetic modifications are relevantto imprinting. However, at present there is no direct evi-dence that histone or other chromatin modificationshave roles in imprinting that are independent of DNAmethylation.Indeed,the importance of DNA methyla-tion,at least in the maintenance of imprints, has beenclearly established genetically17.For the most part,wetherefore equate ‘imprints’with ‘methylation imprints’or ‘differential methylation’ to simplify the discussion.Imprinted expression is then a result of the ‘reading’ofthe imprint in somatic tissues.The life cycle of imprintsGenomic imprints