In June 2006, about 90 scientists came together at the Wellcome Trust Conference Centre in Hinxton (near Cambridge, UK), to attend the first European Science Foundation (ESF)–Wellcome Trust Conference on Signalling to Chromatin Epigenetics. This meeting addressed how cellular processes both signal and respond to chromatin. Chromatin is composed of nucleosomes that each comprise 147 base pairs of DNA wrapped around an octamer of two copies of each histone H2A, H2B, H3 and H4. Nucleosomes are folded into higher-order structures that are stabilized by linker histones. Chromatin structure can be altered by enzymes that post-translationally modify histones (for example, through phosphorylation, acetylation, methylation or ubiquitination) or by ATP-driven chromatin-remodelling complexes that alter nucleosome position and/or composition. The role of chromatin in cellular processes, such as transcription, DNA-damage repair and cell differentiation, was discussed at the meeting. In this report, we summarize a few of the highlights from the broad range of topics discussed.

It is evident that chromatin has a crucial role in signalling the cellular response to DNA damage. Phosphorylation of the histone variant H2AX occurs rapidly in chromatin that flanks DNA double-strand breaks (DSBs; Fernandez-Capetillo et al, 2004). Ataxia telangiectasia mutated (ATM), ATM and Rad3-related (ATR) and DNA-dependent protein kinase catalytic subunit (DNA-PKcs) are responsible for this phosphorylation, which occurs on the conserved Ser 139 residue at the carboxyl terminus of H2AX. Loss of H2AX results in radiosensitivity, genomic instability and defects in DNA repair. It has long been suspected that phosphorylated H2AX (referred to as γ-H2AX) recruits factors that function in the repair of DNA damage and/or activation of the DNA-damage checkpoint (which delays cell-cycle progression until repair is complete) to sites of DNA damage. S. Jackson (Cambridge, UK) presented results that provide more insight into the function of γ-H2AX in the cellular response to DNA damage. To identify γ-H2AX-interacting proteins, Jackson used a phospho-peptide comprising the phosphorylated H2AX C terminus to pull down mediator of DNA-damage checkpoint 1 (MDC1) and the MRE11, RAD50 and NBS1 (MRN) complex from cellular extracts (Stucki et al, 2005). MDC1 contains a C-terminal BRCT domain, which seems to be essential for interaction with the H2AX phosphopeptide. MDC1 colocalizes with γ-H2AX ionizing-radiation-induced foci (IRIF). Mutation of the MDC1 BRCT domain (S1933Q) or expression of the H2AX phospho-acceptor mutant protein (H2AX–S136/139A) impaired the targeting of MDC1 to IRIF. Furthermore, mutation of the BRCT domain also impaired recruitment of the DNA damage-response factors NBS1, 53BP1 and phosphorylated ATM to IRIF. Jackson proposed a model in which the initial H2AX phosphorylation results from the MRN-mediated recruitment of ATM to DSBs (Fig 1). MDC1 binds to γ-H2AX, recruits more MRN–ATM complex and the new pool of ATM then starts to phosphorylate more H2AX. This cascade of reactions could propagate H2AX phosphorylation over large distances and might be responsible for the maintenance of γ-H2AX IRIF. Consistent with this, downregulation of MDC1 did not abolish γ-H2AX IRIF formation, but impaired its extent and maintenance over time. Finally, Jackson showed that γ-H2AX spreads for 1 Mb on average from critically short telomeres in senescent cells. His group is examining why and how γ-H2AX spreads from telomeres in these cells.

The levels of many transcription factors are carefully controlled in response to the environment of a cell. The recent findings that ubiquitin ligases and proteasome subcomponents are present at many promoters indicate that several transcription factors might be targeted for degradation at the site of their activity. J. Boyes (Leeds, UK) described the complex series of post-translational modifications that regulate the activity and turnover of the GATA-1 transcription factor. The acetylation of GATA-1 potentiates its DNA-binding and transcriptional activity, which is essential for terminal erythroid differentiation. However, acetylation also targets GATA-1 for ubiquitination and degradation. In addition, Boyes found that a further seven sites on GATA-1 must be phosphorylated for ubiquitination to occur. Interestingly, phosphorylation of two mitogen-activated protein kinase target sites only occurs if GATA-1 is able to bind DNA. Boyes suggested that only the active, promoter-bound form of GATA-1 is subject to rapid degradation. Consistent with this, GATA-1 ubiquitination was enhanced in response to stem-cell factor and erythropoietin signalling.

The first ESF–Wellcome Trust Conference on Signalling to Chromatin Epigenetics brought together researchers from several fields to discuss how cells signal to and from chromatin. A key finding presented at the meeting was that the rapid turnover of histone modifications, such as phosphorylation and acetylation, can be important for transcription and cell differentiation. The identification of a growing family of histone demethylases indicates that histone methylation, which is often considered to be a stable mark, can also be dynamic and subject to turnover. These findings highlight a technical challenge that we all face: to accurately decipher the histone code, not only must we look in the right ‘place', we must also look at the right time. Another key finding was that interchromosomal interactions might be a common feature of co-regulated genes, particularly those with expression levels on different chromosomes that must be coordinated or reciprocated in response to common signals. If such interchromosomal sharing of regulatory elements occurs frequently in the genome, we need to consider the consequences for illegitimate crosstalk. This meeting highlighted how common epigenetic mechanisms can emerge from the comparison of the many diverse processes that signal to and from chromatin.