Review
Interpreting the language of histone and DNA modifications

https://doi.org/10.1016/j.bbagrm.2014.03.001Get rights and content

Highlights

  • Histone PTMs and DNA modifications coordinately regulate chromatin function.

  • Newly revealed modifications add distinct elements of regulatory control on the chromatin template.

  • Aided by new technologies, a newfound appreciation for the complexities of DNA and histone recognition is emerging.

Abstract

A major mechanism regulating the accessibility and function of eukaryotic genomes are the covalent modifications to DNA and histone proteins that dependably package our genetic information inside the nucleus of every cell. Formally postulated over a decade ago, it is becoming increasingly clear that post-translational modifications (PTMs) on histones act singly and in combination to form a language or ‘code’ that is read by specialized proteins to facilitate downstream functions in chromatin. Underappreciated at the time was the level of complexity harbored both within histone PTMs and their combinations, as well as within the proteins that read and interpret the language. In addition to histone PTMs, newly-identified DNA modifications that can recruit specific effector proteins have raised further awareness that histone PTMs operate within a broader language of epigenetic modifications to orchestrate the dynamic functions associated with chromatin. Here, we highlight key recent advances in our understanding of the epigenetic language encompassing histone and DNA modifications and foreshadow challenges that lie ahead as we continue our quest to decipher the fundamental mechanisms of chromatin regulation. This article is part of a Special Issue entitled: Molecular mechanisms of histone modification function.

Introduction

Eukaryotic DNA is tightly packaged within the nucleus of each cell and must be faithfully regulated, copied, and transmitted during cell division. DNA packaging amounts to an amazing feat, often requiring several meters of DNA to be compacted into the confines of a 2–10 micron nucleus. This high level of compaction presents a potential problem, as the underlying DNA must remain accessible to the vast protein machineries that utilize it for critical biological functions. Thus, a fundamental question being addressed by many labs has been how these diverse genomic functions, such as gene transcription, DNA repair, replication, and recombination, occur at the appropriate place and time to promote cellular growth, differentiation, and proper organismal development.

Key contributors to DNA packaging are the highly basic histone proteins, which wrap ~ 147 base pairs of DNA around an octamer of histones (2 copies each of H3, H4, H2A and H2B) to form the nucleosome core particle [1], [2]. This repeating nucleosomal subunit is the fundamental building block of chromatin. Chromatin is organized into distinct domains, such as euchromatin and heterochromatin, which are defined by the level of compaction and associated genomic functions. For example, euchromatin has relatively loose compaction and is typically transcriptionally permissive, whereas heterochromatin (facultative or constitutive) is more condensed and typically transcriptionally repressive [3], [4], [5]. The degree to which chromatin is organized and packaged is highly influenced by numerous factors, including the actions of linker histone H1 that regulate the formation of higher-order chromatin states [6], histone variants that can be substituted for canonical histones in the nucleosome core particle [7], chromatin remodelers that use the power of ATP hydrolysis to slide and evict histones [8], histone chaperones that facilitate deposition and eviction of histones [9], [10], and small chemical modifications to histones and DNA [11], [12], [13], [14], [15], whose interwoven functions are the primary focus of this review.

A major mechanism by which chromatin structure and function is regulated is through the actions of histone post-translational modifications (PTMs). An astonishing number of PTMs, including lysine acetylation, lysine and arginine methylation, arginine citrullination, lysine ubiquitination, lysine sumoylation, ADP-ribosylation, proline isomerization, and serine/threonine/tyrosine phosphorylation occur on histones [11], [15] (Table 1). While the majority are found in the flexible N- and C-terminal ‘tail’ domains that protrude away from the nucleosome core particle, a significant number also occur in the histone fold or globular domains that regulate histone–histone and histone–DNA interactions [16], [17].

A long-standing question in the field has been how histone PTMs function in chromatin regulation. While it has been half a century since Vincent Allfrey first described the presence of acetylation and methylation on histones [18], and Lubomir Hnilica documented histone phosphorylation [19], the functional significance of these modifications remained elusive for many years. Fundamental breakthroughs in our understanding of histone PTM function (many of which occurred in recent years) have been made through the identification of the protein machineries that incorporate (write), remove (erase), and bind (read) histone PTMs. Two landmark discoveries in this regard were the identifications in 1996 of p55/Gcn5 and HDAC1/Rpd3 as transcription-associated histone acetyltransferases [20] and deacetylases [21], respectively — thereby linking dynamic histone modification activity directly to the transcription process. These findings changed the landscape of how the transcription and chromatin fields viewed histone PTMs and have resulted in a fast-paced and exciting field that shows no signs of slowing down.

In 2000, the concept of a ‘histone code’ emerged as a hypothesis to stimulate new thinking about how histone PTMs might function [22], [23]. This postulate grew out of the observation that histone H3 serine 10 (H3S10) phosphorylation could be associated with seemingly opposite functions in chromatin (i.e., chromatin decompaction in transcription and chromatin condensation in mitosis) [24], [25], [26], [27], [28]. From analysis of this and other PTMs where the associated functions were known, it was possible to infer that PTMs might work singly as well as in combination (on one or more histone tails) to mediate the distinct functions associated with them. It was envisioned that, in addition to histone PTMs having a direct physical effect on chromatin structure (as is the case for lysine acetylation negating the positive charge of this residue) [29], they might also function through the selective recruitment of effector proteins or readers that ‘dock’ onto histone PTMs to direct specific downstream events in chromatin. One of the major landmarks in deciphering this aspect of the hypothesis was the discovery of the bromodomain module as an acetyl-lysine reader motif [30]. This result paved the way for subsequent characterization of this important family of chromatin effectors [31], [32], and further suggested the existence of other, yet-to-be identified protein domains, that read histone PTMs.

A large body of data now supports the notion that histone PTMs function, at least in part, through the recruitment of effector proteins harboring specialized reader domains [33], [34]. While the ‘histone code’ hypothesis provided a retrospectively simplistic explanation of how histone PTMs function, recent advances have revealed that the context in which histone PTMs operate is much more complex than originally envisioned. In addition to combinatorial PTMs that function together both synergistically and antagonistically, there is now an appreciation for PTM asymmetry within individual nucleosomes [35], novel types of PTMs with unique functions [36], nucleosomes bearing histone variants [7], and nuclear compartmentalization events [5] that are all contributing to the final output of chromatin organization and function. Furthermore, fueled in part by the recent discovery of an active DNA demethylation pathway and proteins that read these pathway intermediates [14], [37], a new appreciation for the function of histone PTMs in coordination with DNA modifications is emerging. This review will focus on several key findings from the last few years that have helped to expand our current understanding of how histone PTMs and DNA modifications function in the context of a more integrated epigenetic language [22], [38]. Posing several key questions to the field, we also foreshadow where studies into chromatin organization and function are headed and highlight several new technologies that are taking us there.

Section snippets

Identifying and mapping histone PTMs beyond the histone tails

Technological advances in mass spectrometric (MS)-based analyses of histones have greatly facilitated our understanding of the types of PTMs that occur on histones, as well as their abundance and co-occurrence [39], [40], [41], [42], [43]. Perhaps one of the most surprising findings from early MS studies using the high resolving power of Fourier transform ion cyclotron resonance MS was the significant number of previously unknown acetylation, methylation and phosphorylation events that were

Emergence of a DNA methylation language

Classic studies have unquestionably shown that DNA sequence is a major driving force in genome function through the direct recruitment of sequence-specific binding factors to cognate DNA elements (Fig. 2). Perhaps the clearest examples lie in the control of gene expression, where many landmark studies have identified an expanding list of activators and repressors that target DNA elements to drive transcriptional states [124]. These studies have also shaped our view of how the transcription

Multivalency in DNA and histone recognition

Significant insight into chromatin regulation has come from recent studies revealing that DNA and histone modifications are functioning in a cooperative manner to re-shape chromatin organization and facilitate the recruitment of effector proteins and their macromolecular complexes to discreet locations throughout the genome. Significantly, pioneering work of Kouzarides, Mann, and colleagues using a semi-synthetic mononucleosome assembly strategy coupled with quantitative MS has begun defining

Future challenges towards understanding chromatin regulation

Similar to histone PTMs, we are still just scratching the surface of understanding how key players in the generation, removal, and interpretation of DNA modifications are regulated in the context of the epigenetic landscape. To fully grasp the depth and breadth of complexity underlying how histone and DNA modifications function together, many remaining unanswered questions must be tested experimentally. A number of immediate future challenges towards interpreting the complex epigenetic language

Concluding remarks

Progress over the past several decades has ushered in a new wave of appreciation for the role of histone modifications in diverse chromatin functions. The complexity of histone modifications in regards to the sheer number of identified PTMs, alone and in combination, is astonishing in itself. The discovery of proteins harboring multiple reader domains that interpret these combinatorial PTMs on histones to perform their chromatin functions suggests that our original one modification–one domain

Acknowledgements

We thank C. David Allis for his insightful discussions, suggestions, and critical reading of the manuscript. We also thank members of the Strahl Lab, Zu-Wen Sun, Jean Cook, and Lindsey Rizzardi for their helpful comments and suggestions, and Alexey Soshnev from the Allis lab for sharing his cartoon rendering that served as the basis for Fig. 2. We apologize to authors whose contributions could not be acknowledged due to space limitations. S.B.R. is supported by a Pathway to Independence Award

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