During the development of multicellular organisms, cells become different from one another by changing their genetic program in response to transient stimuli. Long after the stimulus is gone, "cellular memory" mechanisms enable cells to remember their chosen fate over many cell divisions. The Polycomb and Trithorax groups of proteins, respectively, work to maintain repressed or active transcription states of developmentally important genes through many rounds of cell division. Here we review current ideas on the protein and DNA components of this transcriptional memory system and how they interact dynamically with each other to orchestrate cellular memory for several hundred genes.

A crucial aim upon completion of whole genome sequences is the functional analysis of all predicted genes. We have applied a high-throughput RNA-interference (RNAi) screen of 19,470 double-stranded (ds) RNAs in cultured cells to characterize the function of nearly all (91%) predicted Drosophila genes in cell growth and viability. We found 438 dsRNAs that identified essential genes, among which 80% lacked mutant alleles. A quantitative assay of cell number was applied to identify genes of known and uncharacterized functions. In particular, we demonstrate a role for the homolog of a mammalian acute myeloid leukemia gene (AML1) in cell survival. Such a systematic screen for cell phenotypes, such as cell viability, can thus be effective in characterizing functionally related genes on a genome-wide scale.

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DEVELOPMENT 223Polycomb/Trithorax group response elements (PRE/TREs) are fascinating chromosomal pieces. Just a few hundred base pairs long, these elements can remember and maintain the active or silent transcriptional state of their associated genes for many cell generations, long after the initial determining activators and repressors have disappeared. Recently, substantial progress has been made towards understanding the nuts and bolts of PRE/TRE function at the molecular level and in experimentally mapping PRE/TRE sites across whole genomes. Here we examine the insights, controversies and new questions that have been generated by this recent flood of data. IntroductionDuring the 1990s, studies of the regulation of homeotic genes in the Drosophila Bithorax complex (BX-C) uncovered very different behaviour for two classes of cis-regulatory DNA element: initiator elements and maintenance elements (or Polycomb/Trithorax group response elements, PRE/TREs) (Busturia et al., 1989;Chan et al., 1994;Chiang et al., 1995;Simon et al., 1993;Simon et al., 1990) (reviewed by Maeda and Karch, 2006). One can think of these two types of elements as 'shift workers' that use very different strategies to regulate the expression patterns of the same genes at different stages of embryonic development. In the first three hours of development, the initiator elements are in control: the output of each homeotic gene depends on the local concentrations of segmentation gene products (these are activators and repressors that are present in different concentrations at different positions of the embryo). However, a few hours after these homeotic gene patterns have been established, the segmentation gene products decay, and thus the positional information they provide is lost. The transcriptional history of each gene is subsequently maintained throughout the rest of development, and into adulthood, by the ubiquitously expressed Polycomb group (PcG) and Trithorax group proteins (TrxG), which work antagonistically via the PRE/TRE elements to maintain active (TrxG) or silenced (PcG) transcriptional states (Moehrle and Paro, 1994). Although the effects of mutations in the PcG and TrxG genes are seen only after the segmentation gene products decay, the PcG and TrxG proteins themselves appear to associate with PRE/TREs much earlier, so that PRE/TREs are 'preloaded' with PcG and TrxG proteins, ready to maintain the transcriptional states that are set by the transiently acting segmentation gene products (Orlando et al., 1998).The maintenance of transcriptional memory at PRE/TREs is 'epigenetic'. This term has suffered much overuse and abuse in recent years, but we use here the classical definition given by Ptashne and Gann (Ptashne and Gann, 2002) (p100): "a change in the state of expression of a gene that does not involve a mutation, but that is nevertheless inherited (after cell division) in the absence of the signal (or event) that initiated that change". In the case of PRE/TREs, the information required to turn gene activity off or on after ea...

The amyloid precursor protein (APP) plays a central role in Alzheimer's disease, but its physiological function and that of its mammalian paralogs, the amyloid precursor-like proteins 1 and 2 (APLPs), is still poorly understood. APP has been proposed to form dimers, a process that could promote cell adhesion via trans-dimerization. We investigated the dimerization and cell adhesion properties of APP/APLPs and provide evidence that all three paralogs are capable of forming homo-and heterocomplexes. Moreover, we show that trans-interaction of APP family proteins promotes cell-cell adhesion in a homo-and heterotypic fashion and that endogenous APLP2 is required for cell-cell adhesion in mouse embryonic fibroblasts. We further demonstrate interaction of all the three APP family members in mouse brain, genetic interdependence, and molecular interaction of APP and APLPs in synaptically enriched membrane compartments. Together, our results provide evidence that homo-and heterocomplexes of APP/APLPs promote trans-cellular adhesion in vivo.

Polycomb/Trithorax response elements (PRE/TREs) maintain transcriptional decisions to ensure correct cell identity during development and differentiation. There are thought to be over 100 PRE/TREs in the Drosophila genome, but only very few have been identified due to the lack of a defining consensus sequence. Here we report the definition of sequence criteria that distinguish PRE/TREs from non-PRE/TREs. Using this approach for genome-wide PRE/TRE prediction, we identify 167 candidate PRE/TREs, which map to genes involved in development and cell proliferation. We show that candidate PRE/TREs are bound and regulated by Polycomb proteins in vivo, thus demonstrating the validity of PRE/TRE prediction. Using the larger data set thus generated, we identify three sequence motifs that are conserved in PRE/TRE sequences.

The Polycomb (Pc) gene of Drosophila melanogaster is a member of a large class of genes (Pc group) required for the segment-specific repression of homeotic selector genes. Mutations in Pc-group genes show strong posterior transformations in homozygous embryos resulting from an ectopic expression of homeotic genes in segments where they are not supposed to be active. Genetic evidence uggests thatPc is part of a cellular memory mechanism responsble for the transmission of the homeotic expression pattern through developmental time. We have determined the nucleotide sequence for the genomic DNA of the Pc gene and for cDNAs corresponding to the 2.5-kilobase Pc mRNA. The deduced sequence of the Pc protein exhibits a homology to the heterochromatinassociated protein HP1 encoded by the suppressor of position effect variegation gene Su(var) 205. The homology is confined to a 37-amino acid domain in the N-terminal part of the two proteins. Our minas extend to the molecule level the genetically identified parallels between the Pc-group genes and the modifiers of position effect variegation. This sggess that Pc could use analogous mechanisms at the level ofthe higher order chromatin structure for the stable transmission ofa determined state, as has been proposed for the donal propagation of heterochromatin domains.

Recent transcriptome analyses show that substantial proportions of eukaryotic genomes can be copied into RNAs, many of which do not encode protein sequences. However, cells have developed mechanisms to control and counteract the high transcriptional activity of RNA polymerases in order to achieve cell-specific gene activity or to prevent the expression of deleterious sequences. Here we compare how two silencing modes - the Polycomb system and heterochromatin - are targeted, established and maintained at different chromosomal locations and how DNA-binding proteins and non-coding RNAs connect these epigenetically stable and heritable structures to the sequence information of the DNA.