Do chromatin loops provide epigenetic gene expression states?

Control of gene expression involves the concerted action of multiple regulatory elements some of which can act over large genomic distances. Physical interaction among these elements can lead to looping of the chromatin fiber. Although posttranslational modifications of chromatin are thought to play a role in the conveyance of epigenetic information, it is largely unknown whether higher order chromatin organization such as looping contributes to epigenetic memory. A related unresolved question is whether chromatin loops are the cause or the effect of transcriptional regulation. Recent work on diverse organisms suggests a memory function for long-range chromatin interactions. It is proposed that higher order folding of the chromatin fiber can serve to maintain active and repressed states of gene expression.

Introduction

The eukaryotic genome is packaged in a highly organized fashion to fit within the spatial constraints of the cell nucleus and at the same time allow for access of regulatory factors to the underlying sequences. The first layer of packaging involves the winding of 147 base pairs of DNA around an octamer of core histone proteins to form a nucleosome, the crystal structure of which has been solved [1]. A string of nucleosomes without any further folding presents itself as an 11 nm fiber under the electron microscope. The next layer of packaging involves the helical stacking of nucleosomes to form a chromatin fiber with a diameter of ∼30 nm of which the structural organization is beginning to be unraveled [2]. While the architecture of chromatin folding at the next higher level is much more obscure, it has become clear that the chromatin fiber is flexible and allows for movement inside of the nucleus [3].

In simple terms, chromatin fiber flexibility allows for physical interactions between distant regulatory sites in the genome in a manner involving contacts in cis and in trans (Figure 1). The term chromatin loop describes interactions in cis with the intervening sequence looped out. However, it is conceivable that trans interactions might turn out to be as important. Fluorescence in situ hybridization (FISH) and chromosome conformation capture (3C) and its derivatives have provided strong evidence that distant enhancers can loop to the promoters they control [4, 5, 6, 7]. Importantly, chromatin loops can be found at both active and repressed genes and are not limited to enhancer–promoter interactions but can also involve insulator elements. Genetic loci at which chromatin loops have been found and the diverse roles loops might play have been extensively reviewed recently [8, 9, 10, 11, 12]. Moreover, with the advent of new technologies that detect a broader spectrum of chromatin contacts, interactions in trans are being increasingly appreciated, although their functions remain largely obscure [13]. A functionally relevant trans interaction is discussed below in the context of polycomb-mediated chromatin interactions. Here we limit our discussion to a specific aspect of chromatin looping, namely the possible role of long-range chromatin interactions in epigenetic memory.

Our topic necessitates a brief description of the term epigenetics and how it will be used here. An epigenetic trait is defined as a stably heritable phenotype resulting from changes in a chromosome without alterations in the DNA sequence [14]. The term ‘heritable’ is most often used in the context of transgenerational inheritance or inheritance from mother to daughter cell, that is, a form of memory that persists through mitosis or meiosis. However, frequently, the term epigenetic memory is employed when considering events that do not necessarily involve cell division, such as the memory of recent transcriptional activity. In the case of the inducible GAL1 gene in yeast, it has been proposed that changes in chromatin organization and subnuclear localization might mediate this form of transcriptional memory [15, 16] (Figure 2, see below). However, additional work, including elegant heterokaryon experiments, indicates that this memory function can be imparted by information contained within the cytoplasm and can be maintained over several cell division cycles [17, 18••].

A form of transcriptional memory in mammalian cells, also referred to as transiently poised state or dynamic bookmarking has been linked to the persistence of general transcription factors. For example, a recent study in T cells showed that following repression, the prolonged presence of the histone acetyltransferase p300 and RNA polymerase II facilitates rapid re-induction of immediate early genes by stimuli that by themselves are ineffective without prior transcription [19^•]. Thus, possible mechanisms that mark genes for rapid activation might include chromatin modifications, transcription factors, and cytoplasmic proteins. In view of these possibilities, the above definition of epigenetics is somewhat arbitrarily confined, although it follows conventional and perhaps pragmatic thinking of epigenetics in the context of proteins associated with chromatin. In the following sections we specifically consider not only some recent but also older work from different systems suggesting that higher order chromatin organization might play a role epigenetic memory.