Methylation of arginine residues within histone H3 has been linked to active transcription. This modification appears on the estrogen-regulated pS2 promoter when the CARM1 methyltransferase is recruited during transcriptional activation. Here we describe a process, deimination, that converts histone arginine to citrulline and antagonizes arginine methylation. We show that peptidyl arginine deiminase 4 (PADI4) specifically deiminates, arginine residues R2, R8, R17, and R26 in the H3 tail. Deimination by PADI4 prevents arginine methylation by CARM1. Dimethylation of arginines prevents deimination by PADI4 although monomethylation still allows deimination to take place. In vivo targeting experiments on an endogenous promoter demonstrate that PADI4 can repress hormone receptor-mediated gene induction. Consistent with a repressive role for PADI4, this enzyme is recruited to the pS2 promoter following hormone induction when the gene is transcriptionally downregulated. The recruitment of PADI4 coincides with deimination of the histone H3 N-terminal tail. These results define deimination as a novel mechanism for antagonizing the transcriptional induction mediated by arginine methylation.

The DNA of each cell is wrapped around histone octamers, forming so-called 'nucleosomal core particles'. These histone proteins have tails that project from the nucleosome and many residues in these tails can be post-translationally modified, influencing all DNA-based processes, including chromatin compaction, nucleosome dynamics, and transcription. In contrast to those present in histone tails, modifications in the core regions of the histones had remained largely uncharacterised until recently, when some of these modifications began to be analysed in detail. Overall, recent work has shown that histone core modifications can not only directly regulate transcription, but also influence processes such as DNA repair, replication, stemness, and changes in cell state. In this review, we focus on the most recent developments in our understanding of histone modifications, particularly those on the lateral surface of the nucleosome. This region is in direct contact with the DNA and is formed by the histone cores. We suggest that these lateral surface modifications represent a key insight into chromatin regulation in the cell. Therefore, lateral surface modifications form a key area of interest and a focal point of ongoing study in epigenetics.

The nuclear hormone receptor co-activator CARM1 has the potential to methylate histone H3 at arginine residues in vitro. The methyltransferase activity of CARM1 is necessary for its co-activator functions in transient transfection assays. However, the role of this methyltransferase in vivo is unclear, given that methylation of arginines is not easily detectable on histones. We have raised an antibody that specifically recognizes methylated arginine 17 (R17) of histone H3, the major site of methylation by CARM1. Using this antibody we show that methylated R17 exists in vivo. Chromatin immunoprecipitation analysis shows that R17 methylation on histone H3 is dramatically upregulated when the estrogen receptor-regulated pS2 gene is activated. Coincident with the appearance of methylated R17, CARM1 is found associated with the histones on the pS2 gene. Together these results demonstrate that CARM1 is recruited to an active promoter and that CARM1-mediated R17 methylation on histone H3 takes place in vivo during this active state.

These results reveal an ordered and interdependent deposition of acetylation and arginine methylation during estrogen-regulated transcription and provide support for a combinatorial role of histone modifications in gene expression.

Histone lysine methylation can have positive or negative effects on transcription, depending on the precise methylation site. According to the "histone code" hypothesis these methylation marks can be read by proteins that bind them specifically and then regulate downstream events. Hetero-chromatin protein 1 (HP1), an essential component of heterochromatin, binds specifically to methylated Lys 9 of histone H3 (K9/H3). The linker histone H1.4 is methylated on Lys 26 (K26/H1.4), but the role of this methylation in downstream events remains unknown. Here we identify HP1 as a protein specifically recognizing and binding to methylated K26/ H1.4. We demonstrate that the Chromo domain of HP1 is mediating this binding and that phosphorylation of Ser 27 on H1.4 (S27/ H1.4) prevents HP1 from binding. We suggest that methylation of K26/H1.4 could have a role in tethering HP1 to chromatin and that this could also explain how HP1 is targeted to those regions of chromatin where it does not colocalize with methylated K9/H3. Our results provide the first experimental evidence for a "phospho switch" model in which neighboring phosphorylation reverts the effect of histone lysine methylation.In eukaryotic cells the DNA is packaged into chromatin. The building block of chromatin is the nucleosomal core particle containing a histone octamer (two each of the core histones H2A, H2B, H3, and H4) around which 147 bp of DNA are wrapped (1). Linker histone H1 binds to the DNA between the nucleosomal core particles and stabilizes higher order chromatin structure (2).The N-terminal tails of the core histones protrude from the nucleosomal surface and are subject to multiple covalent modifications including methylation, phosphorylation, and acetylation. These modifications have the potential to regulate chromatin architecture and thereby can affect all aspects of DNA processing. According to the so called "histone code" hypothesis these modifications could be read by proteins that bind to specific modifications and then can regulate downstream events (3, 4).Methylation of lysines has positive as well as negative effects on transcription, depending on the methylation site. The methylation of lysine 9 of histone H3 (K9/H3) and lysine 27 of histone H3 (K27/H3) has generally been implicated in transcriptional repression. Methylated K9/H3 is specifically recognized and bound by Heterochromatin protein 1 (HP1) 3 (5-8). HP1 has a role in heterochromatin organization, maintenance, and in gene repression. In mammals three HP1 isoforms HP1␣, HP1␤(⌴31), and HP1␥(M32) have been identified. The HP1 proteins are very similar in their amino acid sequence, they contain a conserved N-terminal Chromo domain (CD), a more variable hinge region and a conserved C-terminal Chromoshadow domain (CSD). This modular organization of HP1 allows several proteins to bind simultaneously to HP1. The CD binds specifically to methylated K9/H3; the hinge region can bind to RNA, DNA, and chromatin, whereas the CSD is involved in self-association and interacts, e.g. with the DNA m...

The Trithorax group (TrxG) is composed of diverse, evolutionary conserved proteins that form chromatin-associated complexes accounting for epigenetic transcriptional memory. However, the molecular mechanisms by which particular loci are marked for reactivation after mitosis are only partially understood. Here, based on genetic analyses in zebrafish, we identify the multidomain protein Brpf1 as a novel TrxG member with a central role during development. brpf1 mutants display anterior transformations of pharyngeal arches due to progressive loss of anterior Hox gene expression. Brpf1 functions in association with the histone acetyltransferase Moz (Myst3), an interaction mediated by the N-terminal domain of Brpf1, and promotes histone acetylation in vivo. Brpf1 recruits Moz to distinct sites of active chromatin and remains at chromosomes during mitosis, mediated by direct histone binding of its bromodomain, which has a preference for acetylated histones, and its PWWP domain, which binds histones independently of their acetylation status. This is the first demonstration of histone binding for PWWP domains. Mutant analyses further show that the PWWP domain is absolutely essential for Brpf1 function in vivo. We conclude that Brpf1, coordinated by its particular set of domains, acts by multiple mechanisms to mediate Moz-dependent histone acetylation and to mark Hox genes for maintained expression throughout vertebrate development.KEY WORDS: Brpf1, Bromodomain, PWWP domain, Moz, Hox gene expression, Craniofacial development, Cranial neural crest, Pharyngeal arch, Anterior-posterior patterning, Homeotic transformation, Zebrafish Development 135, 1935Development 135, -1946Development 135, (2008 Here, based on the positional cloning of bimandibular zebrafish mutants, we identify the multidomain protein Brpf1 (Bromodomain and PHD finger containing 1; also known as Br140 and Peregrin) as a TrxG member and close partner of Moz. Brpf1 contains a unique combination of domains typically found in chromatin-associated factors, including PHD fingers, a bromodomain and a PWWP domain. Bromodomains interact with acetylated lysines on Nterminal tails of histones and other proteins (reviewed by Yang, 2004), and PHD fingers were recently shown to bind to methylated K4H3 Wysocka et al., 2006), whereas the histonebinding properties of PWWP domains remain to be shown. Based on its domains, Brpf1 has been proposed to be involved in chromatin remodeling (Thompson et al., 1994). However, its exact function in vertebrates is currently unknown.In this study, we show that during zebrafish development, Brpf1 is required for histone acetylation, maintenance of cranial Hox gene expression and proper determination of pharyngeal segmental identities. We demonstrate genetic and physical interaction of Brpf1 with the HAT Moz. This interaction can explain how Brpf1 promotes histone acetylation. Furthermore, in contrast to Moz, Brpf1 remains associated with the chromatin even during metaphase, contributing to transcriptional memory throughout mitosis. ...

Histones are highly covalently modified, but the functions of many of these modifications remain unknown. In particular, it is unclear how histone marks are coupled to cellular metabolism and how this coupling affects chromatin architecture. We identified histone H3 Lys14 (H3K14) as a site of propionylation and butyrylation in vivo and carried out the first systematic characterization of histone propionylation. We found that H3K14pr and H3K14bu are deposited by histone acetyltransferases, are preferentially enriched at promoters of active genes and are recognized by acylation-state-specific reader proteins. In agreement with these findings, propionyl-CoA was able to stimulate transcription in an in vitro transcription system. Notably, genome-wide H3 acylation profiles were redefined following changes to the metabolic state, and deletion of the metabolic enzyme propionyl-CoA carboxylase altered global histone propionylation levels. We propose that histone propionylation, acetylation and butyrylation may act in combination to promote high transcriptional output and to couple cellular metabolism with chromatin structure and function.

Histone modifications are central to the regulation of all DNA-dependent processes. Lys64 of histone H3 (H3K64) lies within the globular domain at a structurally important position. We identify trimethylation of H3K64 (H3K64me3) as a modification that is enriched at pericentric heterochromatin and associated with repeat sequences and transcriptionally inactive genomic regions. We show that this new mark is dynamic during the two main epigenetic reprogramming events in mammals. In primordial germ cells, H3K64me3 is present at the time of specification, but it disappears transiently during reprogramming. In early mouse embryos, it is inherited exclusively maternally; subsequently, the modification is rapidly removed, suggesting an important role for H3K64me3 turnover in development. Taken together, our findings establish H3K64me3 as a previously uncharacterized histone modification that is preferentially localized to repressive chromatin. We hypothesize that H3K64me3 helps to 'secure' nucleosomes, and perhaps the surrounding chromatin, in an appropriately repressed state during development.