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.

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...

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.

In any biological system with memory, the state of the system depends on its history. Epigenetic memory maintains gene expression states through cell generations without a change in DNA sequence and in the absence of initiating signals. It is immensely powerful in biological systems - it adds long-term stability to gene expression states and increases the robustness of gene regulatory networks. The Polycomb group (PcG) and Trithorax group (TrxG) proteins can confer long-term, mitotically heritable memory by sustaining silent and active gene expression states, respectively. Several recent studies have advanced our understanding of the molecular mechanisms of this epigenetic memory during DNA replication and mitosis.

During the regeneration of Drosophila imaginal discs, cellular identities can switch fate in a process known as transdetermination. For leg-to-wing transdetermination, the underlying mechanism involves morphogens such as Wingless that, when activated outside their normal context, induce ectopic expression of the wing-specific selector gene vestigial. Polycomb group (PcG) proteins maintain cellular fates by controlling the expression patterns of homeotic genes and other developmental regulators. Here we report that transdetermination events are coupled to PcG regulation. We show that the frequency of transdetermination is enhanced in PcG mutant flies. Downregulation of PcG function, as monitored by the reactivation of a silent PcG-regulated reporter gene, is observed in transdetermined cells. This downregulation is directly controlled by the Jun amino-terminal kinase (JNK) signalling pathway, which is activated in cells undergoing regeneration. Accordingly, transdetermination frequency is reduced in a JNK mutant background. This regulatory interaction also occurs in mammalian cells, indicating that the role of this signalling cascade in remodelling cellular fates may be conserved.