Chromatin domain boundaries: insulators and beyond

The eukaryotic genome is organized into functionally and structurally distinct domains, representing regulatory unitsfor gene expression and chromosome behavior. DNA sequences that mark the border between adjacent domains are theinsulators or boundary elements, which are required in maintenance of the function of different domains. Some insula-tors need others enable to play insulation activity. Chromatin domains are defined by distinct sets of post-translationallymodified histones. Recent studies show that these histone modifications are also involved in establishment of sharpchromatin boundaries in order to prevent the spreading of distinct domains. Additionally, in some loci, the high-orderchromatin structures for long-range looping interactions also have boundary activities, suggesting a correlation betweeninsulators and chromatin loop domains. In this review, we will discuss recent progress in the field of chromatin domainboundaries.

Reading and Interpreting the Histone Acylation Code

Decades of research has explored the epigenetic control of gene expression and the impact of histone post-translational modifications （PTMs）, such as acetylation, on chromatin remodel- ing. Indeed, the writers, readers, and erasers of lysine acetylation are increasingly well understood. Recent studies have added crotonylation, butyrylation, and propionylation to the types of acylations by which histones are modified, and identified the YEATS protein domain as a critical reader of crotonylation. Now, Haitao Li, David Allis, and their col- leagues expand the scope of protein domains capable of read- ing crotonyl-lysine （Kcr） to include double PHD finger （DPF） domains. Importantly, the mechanism through which these domains recognize Kcr is quite distinct from their recognition by the YEATS domain [1]. In this highlight, we discuss recognition of acylated histones by the bromodomain （BRD）, the YEATS domain, and PHD fingers. We contrast the structural basis for their recognition of histones modified by acetylation and more recently discovered histone crotonylation [2-6].

Histone modifications dictate specific biological readouts

The basic unit of chromatin is the nucleosomal core particle, containing 147 bp of DNA that wraps twice around an octamer of core histones. The core histones bear a highly dynamic N-terminal amino acid tail around 20-35 residues in length and rich in basic amino acids. These tails extending from the surface of nucleosome play an important role in folding of nucleosomal arrays into higher order chromatin structure, which plays an important role in eukaryotic gene regulation. The amino terminal tails protruding from the nuclesomes get modified by the addition of small groups such as methyl, acetyl and phosphoryl groups. In this review, we focus on these complex modi- fication patterns and their biological functions. Moreover, these modifications seem to be part of a complex scheme where distinct histone modifications act in a sequential manner or in combination to form a ＂histone code＂ read by other proteins to control the structure and/or function of the chromatin fiber. Errors in this histone code may be involved in many human diseases especially cancer, the nature of which could be therapeutically exploited. Increasing evidence suggests that many proteins bear multiple, distinct modifications, and the ability of one modification to antagonize or synergize the deposition of another can have significant biological consequences.

Acidic domains differentially read histone H3 lysine 4 methylation status and are widely present in chromatin-associated proteins

Histone methylation is believed to provide binding sites for specific reader proteins, which translate histone code into biological function. Here we show that a family of acidic domain-containing proteins including nucleophosmin （NPM 1）, pp32, SET/TAF 113, nucleolin （NCL） and upstream binding factor （UBF） are novel H3K4me2-binding proteins. These proteins exhibit a unique pattern of interaction with methylated H3K4, as their binding is stimulated by H3K4me2 and inhibited by H3K4mel and H3K4me3. These proteins contain one or more acidic domains consisting mainly of aspartic and/or glutamic residues that are necessary for preferential binding of H3K4me2. Furthermore, we demonstrate that the acidic domain with sufficient length alone is capable of binding H3K4me2 in vitro and in vivo. NPM1, NCL and UBF require their acidic domains for association with and transcriptional activation ofrDNA genes. Interestingly, by defining acidic domain as a sequence with at least 20 acidic residues in 50 continuous amino acids, we identified 655 acidic domain-containing protein coding genes in the human genome and Gene Ontology （GO） analysis showed that many of the acidic domain proteins have chromatin-related functions. Our data suggest that acidic domain is a novel histone binding motif that can differentially read the status of H3K4 methylation and is broadly present in chromatin-associated proteins.