Variations on the topic of the "histone code"

Histones are the fundamental structural proteins intimately associated with eukaryotic DNA to form a highly ordered and condensed nucleoproteic complex termed chromatin. They are the targets of various posttranslational modifications including acetylation, methylation, phosphorylation and ubiquitination that modulate the structure/function of chromatin. The combinatorial nature of histone modifications is hypothesized to define a "histone code" that considerably extends the information potential of the genetic code, giving rise to epigenetic information. Moreover, most core histones consist of several nonallelic variants that can mark specific loci and could play an important role in establishment and maintenance of epigenetic memory. Here we will briefly present our current knowledge about histone posttranslational modifications and their implications in the regulation of epigenetic information. We will next describe core histone variants, insisting on their mode of incorporation into chromatin to discuss their epigenetic function and inheritance.     

The Regulation and Function of Histone Methylation

Histones are wrapped around by genomic DNA to form nucleosomes which are the basic units of chromatin. In eukaryotes histones undergo various covalent modifications such as methylation, phosphorylation, acetylation, ubiquitination and ribosylation. Histone modifications play a fundamental role in the epigenetic regulation of gene expression in multicellular eukaryotes. Histone methylation is one of the most important modifications occurring on Lysine (K) and Arginine (R) residues of histones, dynamically regulated by histone methyltransferases and demethylases. Identifications of such histone modification enzymes and to study how they work are the most fundamental questions needs to be answered. Uncovering the regulation and functions of the various histone methylation enzymes will help us to better understand the epigenetic code. This review summarizes the regulation of histone methyltransferases activity, the recruitment of methyltransferases and the distribution patterns and function of histone methylations.     

Lysine methylation: beyond histones

Posttranslational modifications (PTMs) of histone proteins, such as acetylation, methylation, phosphorylation, and ubiquitylation, play essential roles in regulating chromatin dynamics. Combinations of different modifications on the histone proteins, termed 'histone code' in many cases, extend the information potential of the genetic code by regulating DNA at the epigenetic level. Many PTMs occur on non-histone proteins as well as histones, regulating protein-protein interactions, stability, localization, and/or enzymatic activities of proteins involved in diverse cellular processes. Although protein phosphorylation, ubiquitylation, and acetylation have been extensively studied, only a few proteins other than histones have been reported that can be modified by lysine methylation. This review summarizes the current progress on lysine methylation of non-histone proteins, and we propose that lysine methylation, like phosphorylation and acetylation, is a common PTM that regulates proteins in diverse cellular processes.     

An epigenetic code for DNA damage repair pathways?

Exposure of living cells to intracellular or external mutagens results in DNA damage. Accumulation of DNA damage can lead to serious consequences because of the deleterious mutation rate resulting in genomic instability, cellular senescence, and cell death. To counteract genotoxic stress, cells have developed several strategies to detect defects in DNA structure. The eukaryotic genomic DNA is packaged through histone and nonhistone proteins into a highly condensed structure termed chromatin. Therefore the cellular enzymatic machineries responsible for DNA replication, recombination, and repair must circumvent this natural barrier in order to gain access to the DNA. Several studies have demonstrated that histone/chromatin modifications such as acetylation, methylation, and phosphorylation play crucial roles in DNA repair processes. This review will summarize the recent data that suggest a regulatory role of the epigenetic code in DNA repair processes. We will mainly focus on different covalent reversible modifications of histones as an initial step in early response to DNA damage and subsequent DNA repair. Special focus on a potential epigenetic histone code for these processes will be given in the last section. We also discuss new technologies and strategies to elucidate the putative epigenetic code for each of the DNA repair processes discussed.     

The Epigenetic Reprogramming Roadmap in Generation of iPSCs from Somatic Cells

Reprogramming of somatic cells to induced pluripotent stem cells(iPSCs) is a comprehensive epigenetic process involving genome-wide modifications of histones and DNA methylation. This process is often incomplete, which subsequently affects i PSC reprograming,pluripotency, and differentiation capacity. Here, we review the epigenetic changes with a focus on histone modification(methylation and acetylation) and DNA modification(methylation) during i PSC induction. We look at changes in specific epigenetic signatures, aberrations and epigenetic memory during reprogramming and small molecules influencing the epigenetic reprogramming of somatic cells. Finally,we discuss how to improve i PSC generation and pluripotency through epigenetic manipulations.     

Replication stress,a source of epigenetic aberrations in cancer?

Cancer cells accumulate widespread local and global chromatin changes and the source of this instability remains a key question. Here we hypothesize that chromatin alterations including unscheduled silencing can arise as a consequence of perturbed histone dynamics in response to replication stress. Chromatin organization is transiently disrupted during DNA replication and maintenance of epigenetic information thus relies on faithful restoration of chromatin on the new daughter strands. Acute replication stress challenges proper chromatin restoration by deregulating histone H3 lysine 9 mono‐methylation on new histones and impairing parental histone recycling. This could facilitate stochastic epigenetic silencing by laying down repressive histone marks at sites of fork stalling. Deregulation of replication in response to oncogenes and other tumor‐promoting insults is recognized as a significant source of genome instability in cancer. We propose that replication stress not only presents a threat to genome stability, but also jeopardizes chromatin integrity and increases epigenetic plasticity during tumorigenesis.     

Germline histone dynamics and epigenetics

Germ cells have the same DNA sequence as somatic cells, but the processes that act on their chromatin are different. Germline chromatin undergoes a series of dramatic remodeling events during the life cycle of an organism. Different aspects of germline chromatin have been dissected in recent years, such as differences between the sex chromosomes and autosomes in histone variants and modifications. Excitingly, histone dynamics have recently been implicated in imprinted X inactivation and genomic imprinting processes that are independent of DNA methylation. Taken together with observations of core histone retention in mature sperm of diverse animals, histones have become prime candidates for mediating germline epigenetic inheritance.     

A new insight into male genome reprogramming by histone variants and histone code

The very nature of the packed male genome, essentially containing non-histone proteins, suggests that most of the epigenetic marks which have been defined in somatic cells are not valid in mature male gametes and that new specific rules prevail for the transmission of epigenetic information in male germ cells. Recent investigations are now uncovering a male-specific genome reprogramming mechanism, which likely cooperates with and extends beyond DNA methylation, specifying different regions of the genome and which could encode a new type of epigenetic information transmitted to the egg. Here we highlight the general traits of this unconventional male-specific epigenetic code, which largely relies on the use of histone variants and specific histone modifications.     

Coordinated methyl-lysine erasure: structural and functional linkage of a Jumonji demethylase domain and a reader domain

Both components of chromatin (DNA and histones) are subjected to dynamic postsynthetic covalent modifications. Dynamic histone lysine methylation involves the activities of modifying enzymes (writers), enzymes removing modifications (erasers), and readers of the epigenetic code. Known histone lysine demethylases include flavin-dependent monoamine oxidase lysine-specific demethylase 1 and α-ketoglutarate-Fe(II)-dependent dioxygenases containing Jumonji domains. Importantly, the Jumonji domain often associates with at least one additional recognizable domain (reader) within the same polypeptide that detects the methylation status of histones and/or DNA. Here, we summarize recent developments in characterizing structural and functional properties of various histone lysine demethylases, with emphasis on a mechanism of crosstalk between a Jumonji domain and its associated reader module(s). We further discuss the role of recently identified Tet1 enzyme in oxidizing 5-methylcytosine to 5-hydroxymethylcytosine in DNA.     

Regulation beyond genome sequences: DNA and histone methylation in embryonic stem cells

Embryonic stem (ES) cells distinct themselves from other cell type populations by their pluripotent ability. The unique features of ES cells are controlled by both genetic and epigenetic factors. Studies have shown that the methylation status of DNA and histones in ES cells is quite different from that of differentiated cells and somatic stem cells. Herein, we summarized recent advances in DNA and histone methylation studies of mammalian ES cells. The methylation status of several key pluripotent regulatory genes is also discussed.     

Progressive methylation of ageing histones by Dot1 functions as a timer

Post-translational modifications of histone proteins have a crucial role in regulating gene expression. If efficiently re-established after chromosome duplication, histone modifications could help propagate gene expression patterns in dividing cells by epigenetic mechanisms. We used an integrated approach to investigate the dynamics of the conserved methylation of histone H3 Lys 79 (H3K79) by Dot1. Our results show that methylation of H3K79 progressively changes after histone deposition, which is incompatible with a rapid copy mechanism. Instead, methylation accumulates on ageing histones, providing the cell with a timer mechanism to directly couple cell-cycle length to changes in chromatin modification on the nucleosome core.