Mechanical ventilation, a lifesaving intervention for patients with acute respiratory distress syndrome (ARDS), also unfortunately contributes to excessive mechanical stress and impaired lung physiological and structural integrity. We have elsewhere established the pivotal role of increased nicotinamide phosphoribosyltransferase (NAMPT) transcription and secretion as well as its direct binding to the toll-like receptor 4 (TLR4) in the progression of this devastating syndrome; however, regulation of this critical gene in ventilator-induced lung injury (VILI) is not well characterized. On the basis of an emerging role for epigenetics in enrichment of VILI and CpG sites within the NAMPT promoter and 5'UTR, we hypothesized that NAMPT expression and downstream transcriptional events are influenced by epigenetic mechanisms. Concomitantly, excessive mechanical stress of human pulmonary artery endothelial cells or lipopolysaccharide (LPS) treatment led to both reduced DNA methylation levels in the NAMPT promoter and increased gene transcription. Histone deacetylase inhibition by trichostatin A or Sirt-1-silencing RNA attenuates LPS-induced NAMPT expression. Furthermore, recombinant NAMPT administration induced TLR4-dependent global H3K9 hypoacetylation. These studies suggest a complex epigenetic regulatory network of NAMPT in VILI and ARDS and open novel strategies for combating VILI and ARDS.

Mémoire numérisé par la Direction des bibliothèques de l'Université de Montréal.

<p>Identifying metabolic vulnerabilities of cancer cells remains a subject of investigation for the identification of potential metabolically based therapies for cancer. It is well known that proliferating cells become largely dependent on glucose and glutamine for their growth. Interestingly, we find that lipid oxidizing genes are consistently downregulated across a wide variety of cancers while lipid synthesizing genes are elevated. This indicates that lipid oxidation may be refractory to cancer cell growth. Studies have shown beneficial effects of carbohydrate restriction in various forms in the treatment of cancer. For example, the use of ketogenic diets, which contain high levels of fat and protein with very low levels of carbohydrates, have shown efficacy in decreasing tumor growth in glioma, colon, prostate, and gastric cancers. A major challenge facing the use of these diets in cancer therapy is that the mechanism by which they show efficacy in cancer remains unclear. By using octanoate, the most well-known ketogenic fatty acid, we are able to drive fatty acid oxidation and ketogenesis to study these processes in proliferating cells. We found that supplementation of octanoate into complete culture medium causes a dramatic, dose-dependent and reversible suppression of proliferation across numerous cell lines and significant changes to anabolic cellular metabolism. Importantly, we have found that ketone production from octanoate had no effect on cell proliferation but that the overall cellular response to the lipid causes inhibition of cell growth.</p><p>Nutrients and metabolites are sensed by the cell at many levels and the cellular response to metabolites is critical to proliferation and survival of a cancer cell. One way in which the cell responds to glucose, the major fuel source in cancer cells, is by increasing histone acetylation to promote gene expression. Wellen et al., found that upon glucose addition there was a specific gene expression pattern characterized by the upregulation of genes involved in glucose metabolism. In this way the cell promotes glucose-derived fatty acid synthesis, a rate-limiting process for cancer cell proliferation. This is one way in which the metabolic response to nutrients is integrated into cellular signaling and the epigenome. Remarkably, we have found that lipids can promote a feed-forward mechanism of lipid metabolism by inducing histone acetylation and increasing gene expression of lipid metabolizing genes. We find that upon treatment of cells with octanoate there is an inhibition of both glucose and glutamine metabolism and that octanoate-derived carbon becomes the major fuel source in the cell. We then found that histones were hyperacetylated after octanoate treatment and remarkably, close to 90% of the carbon on histones was octanoate derived. In addition, octanoate is a weak HDAC inhibitor which further promotes octanoate-derived acetyl-CoA being deposited onto histones. A gene array from octanoate treated samples finds that fatty acid metabolism is the top pathway in our gene ontology analysis. This provides evidence that the cell responds to nutrient sources in a specific manner depending on the nature of the carbon source. Finally, we find the most negatively regulated pathway upon octanoate treatment is DNA replication. Consistently, we find that octanoate causes an accumulation of cells in G1 phase of the cell cycle and induction of apoptosis.</p><p>Here we describe a mechanism for how fatty acids are sensed and how they communicate with the nucleus to alter gene expression. We show that the cell responds to lipids via a coordinated response to promote lipid metabolism and induce histone acetylation. This feed-forward mechanism of lipid metabolism consists of a reprograming of anabolic metabolism, and promotion of gene expression changes culminating in inhibition of cell growth and apoptosis.</p> / Dissertation

Mémoire numérisé par la Direction des bibliothèques de l'Université de Montréal.

Chez Saccharomyces cerevisiae, la methylation de la lysine 4 de l'histone H3 (H3K4) est catalysée par le complexe à activité methyltransférase Set1, conservé au cours de l'évolution. Durant la méiose, l'absence de Set1 conduit à un retard de démarrage de la phase S, et à un défaut dans la formation des coupures double-brin de l'ADN (CDBs). Nous avons cherché à mieux caractériser ces deux conséquences phénotypiques liées à l'absence de Set1. Nous montrons que le retard de réplication est lié à la perte de méthylation de H3K4 mais qu'il ne résulte pas d'un défaut d'activité des kinases responsables de l'activation des origines de réplication ou de l'activation des voies canoniques de surveillance moléculaire liées aux dommages de l'ADN. L'importante diminution de fréquence de CDB sur la majorité des points chauds chez le mutant set1&#8710; a été corrélée à l'absence de la marque de H3K4 triméthylée. Nous avons confirmé le role de la méthylation de H3K4 sur la base de la diminution générale de la fréquence des CDBs observée en absence des différentes sous-unités du complexe associé à Set1 (COMPASS) ou chez un mutant exprimant une histone H3 non-méthylable (H3K4R). Pour tester la relation de causalité entre méthylation et CDBs, différentes sous-unités du COMPASS, telles que Set1 et Spp1, ont été fusionnées avec le domaine de fixation à l'ADN de Gal4 pour les cibler vers des régions non méthylées et dépourvues de CDB. Gal4BD-Spp1 stimule fortement la fréquence des CDBs à certains loci, y compris en contexte mutant H3K4R. Ainsi, le ciblage de Spp1 peut etre suffisant pour recruter et/ou activer la machinerie de CDB. / In Saccharomyces cerevisiae, the methylation of the lysine 4 of histone H3 (H3K4) is catalysed by the evolutionary conserved Set1 methyltransferase complex. During meiosis, the absence of Set1 leads to a delay of S-phase onset and to a defect in the formation of double-strand breaks (DSBs). Our work was intended to give some clues about these two phenotypic consequences of Set1 loss. We show that the replication delay is linked to the absence of H3K4 trimethylation but does not result from a defect of the kinases responsible for the activation of replication origins or the activation of the canonical DNA-damage checkpoints. The severe decrease of DSB levels at the majority of recombination hotspots in set1&#8710; has been correlated with the specific marking of DSB sites by H3K4 trimethylation at some loci. We have confirmed the role of H3K4 methylation by observing a general decrease in DSB frequency similar to that of set1&#8710; in mutants lacking various subunits of the Set1- associated complex (COMPASS) or expressing a nonmethylatable histone H3 (H3K4R). To test for a causal relationship between H3K4 methylation and DSB formation, we have fused different proteins of the COMPASS, such as Spp1 or Set1, with the DNA binding domain of Gal4, in order to target them to H3K4-unmethylated and DSB-cold regions. Remarkably, Gal4BD-Spp1 strongly stimulates DSB formation in naturally cold DSB regions, even in the H3K4R mutant context. Thus, the specific tethering of Spp1 to a chromosome site is sufficient to recruit and/or activate the DSB machinery.

During cell activation the tightly compacted DNA is made available to DNA-binding proteins allowing the induction of gene transcription. In the resting cell, DNA is packaged into chromatin whose fundamental subunit is the nucleosome, composed of an octamer of four core histones (H) 3, 4, 2A and 2B. During the induction of gene transcription, modification of histones, by acetylation, methylation etc., results in unwinding of the DNA, permitting access of large DNAbinding proteins, such as RNA polymerase II, and subsequent induction of gene transcription. This investigation initially examined the effects of pro-inflammatory stimuli LPS and TNF-a on the production of IL-8 in a macrophage cell line (U937 cells) and in two T-cell lines (Jurkat and HUT-78 cells) as a marker of NF-KB-directed inflammatory gene expression. The ability of dexamethasone (Dex) and triamcinolone acetonide (TA) (synthetic glucocorticoid agonists) to suppress expression of the inflammatory cytokine IL-8 and to regulate histone acetylation was also investigated in these cells. LPS and TNF-a caused an increase in IL-8 expression, which was further enhanced by the histone deacetylases inhibitor trichostatin A (TSA), suggesting a role for histone acetylation in IL-8 production in these cells. Dex and TA, repressed LPS- and TNF-a -induced IL-8 expression in all three cell lines. This effect of both Dex and TA was attenuated by TSA in all cell lines studied, where the effect of TSA was greater in TA stimulated cells. Stimulation of all cell lines with LPS and TNF-a induced acetylation of H4 lysine residues (K5, 8, 12 and 16), the highest elevation of which was for K8 and K12. Also demonstrate is a K5 and K16 specificity of acetylation by glucocorticoids, apparent in all cell lines studied. Dex and, to a greater extent, TA suppressed LPS- and TNFa-induced K8 and K12 acetylation. TSA attenuated the inhibitory effect of the glucocorticoids for all three cell lines. An inCrease in HDAC activity with GCs was observed and ChiP assay showed these events occur on the native IL-8 promoter via histone acetylation. Further studies investigated whether there were any links between histone acetylation and the regulation of apoptosis. It was showed that TSA induced apoptosis in cells previously stimulated with the inducer of oxidative stress hydrogen peroxide (H20 2). Studies into the activation of caspase 3 in LPS- and TNF-a stimulated cells revealed that the combinatory effect of Dex or TA with TSA Significantly enhanced expression of the marker in all three cell lines. In resting cells, Dex, and TA, in the presence of TSA downregulated caspase 3 expression. These findings support the notion that glucocorticoid actions on apoptosis is mediated, at least in part, through an action on histone acetylation. Finally, histone acetylation was investigated in vivo in two rat models of inflammation and in human subjects with inflammatory bowel disease (IBD). The results showed an increase in histone H4 acetylation lysine specificity of acetylation on K8 and K12 in inflamed tissue and Peyer's patches in animal models and in IBD patients. Whereas H3 acetylation was not elevated to the same extent in tissue and was restricted to the mantle zone of Peyer's patches. In general, the present studies on histone acetylation and inflammation (in animal models and IBD patients) underlined the possibility of a general mechanism linking activation of the transcription factor NFKB with histone acetylation. The ultimate objective of this work is to aid in the understanding of the mechanisms of how deregulation of chromosome structure leads to progression of the disease state. This knowledge may aid in the development of new therapeutic approaches or improved glucocorticoids.

In this study, the role of histone-like proteins in gene regulation in uropathogenic Escherichia coli isolate 536 was monitored. The histone-like nucleoid structuring protein H-NS is a global regulator in Escherichia coli that has been intensively studied in non-pathogenic strains. No comprehensive study on the role of H-NS and it’s homolog StpA on gene expression in a pathogenic E. coli strain has been carried out so far. Moreover, we identified a third, so far uncharacterized member of the H-NS-like protein family in uropathogenic E. coli isolate 536, which was designated Hlp (H-NS-like protein). Hlp is a 134-amino acid protein, which shares 58 % sequence identity with H-NS. The gene coding for the Hlp protein, hlp, is found in several uropathogenic E. coli variants, but not in non-pathogenic E. coli K-12. In UPEC strains 536 and CFT073, Hlp is encoded on a possibly horizontally acquired 23-kb genomic region inserted into the serU locus. Studies on hlp transcription revealed, that the gene is transcribed monocistronically from a single promoter and that expression is repressed by H-NS. Purified Hlp protein was binding to its own and to the hns promoter, thereby mediating negative auto- and crossregulation. Furthermore, Hlp and H-NS were directly interacting, resulting in the formation of stable heteromers. Complementation studies with hns mutant strains in a K-12 background revealed that the Hlp protein had in vivo activity, being able to complement the lack of H-NS in terms of motility, growth, and repression of the proU, bgl, and clyA genes. When analyzing the role of the histone-like proteins in expression of virulence-associated genes by using DNA arrays and classical phenotypic assays, most of the observed effects were mediated by the H-NS protein alone. Expression profiling revealed that transcript level of more than 500 genes was affected by an hns mutation, resulting in increased expression of alpha-hemolysin, fimbriae and iron-uptake systems, as well as genes involved in stress adaptation. Furthermore, several other putative virulence factors were found to be part of the H-NS regulon. On the other hand, no effect of StpA alone was observed. An hns stpA double mutant, however, exhibited a distinct gene expression pattern that differed in great parts from that of the hns single mutant. This suggests a direct interaction between the two homologs and the existence of distinct regulons of H-NS and an H-NS/StpA heteromeric complex. Although the H-NS protein has – either as homomer or in complex with StpA – a marked impact on gene expression in pathogenic E. coli strains, its effect on urovirulence is ambiguous. At a high infection dose, hns mutants accelerate lethality in murine UTI and sepsis models relative to the wild type, probably due to increased production of alpha-hemolysin. At lower infectious dose, however, mutants lacking H-NS are attenuated through their impaired growth rate, which can only partially be compensated by the higher expression of numerous virulence factors. As seen with StpA, an hlp single mutant did not exhibit a notable phenotype under standard growth conditions. A severe growth defect of hns hlp double mutants at low temperatures, however, suggests a biological relevance of H-NS/Hlp heteromers under certain circumstances. Furthermore, these mutants expressed more capsular polysaccharide and curli fimbriae, thereby indicating a distinct role of H-NS and Hlp in regulation of these surface structures. The H-NS paralogs Hlp and StpA also modulated H-NS-mediated regulation of fimbrial adhesins, and are oppositely required for normal growth at low or high temperatures, respectively. Finally, expression levels of the three histone-like proteins H-NS, StpA and Hlp itself varied with different temperatures, thereby suggesting a flexible composition of the nucleoid-associated protein pool. Hence, we propose that the biological role of Hlp and StpA does not rely on a distinct function of the single protein, but rather on their interaction with the global regulator H-NS. / In dieser Studie wurde die Rolle von Histon-ähnlichen Proteinen bei der Genregulation im uropathogenen Escherichia coli (UPEC) Isolat 536 untersucht. Das Histon-ähnliche Protein H-NS (engl. histone-like nucleoid structuring protein) ist ein globaler Regulator in E. coli, der in apathogenen Stämmen eingehend untersucht worden ist. Im Gegensatz dazu liegen noch keine umfassenden Studien zur Rolle von H-NS und des homologen Proteins StpA in einem pathogenen E. coli Stamm vor. Zudem konnten wir ein drittes, bis jetzt noch nicht charakterisiertes Mitglied der Familie von H-NS-ähnlichen Protein im uropathogenen E. coli Isolat 536 identifizieren, das Hlp benannt wurde (für H-NS-like protein). Hlp ist ein aus 134 Aminosäuren bestehendes Protein, dessen Sequenz zu 58 % identisch mit der des H-NS Proteins ist. Das Gen, das für das Hlp Protein kodiert, hlp, konnte in zahlreichen uropathogenen und Fäkalisolaten nachgewiesen werden, jedoch nicht im apathogenen E. coli K-12. In den UPEC Isolaten 536 und CFT073 ist das hlp Gen auf einer 23-kb großen genomischen Insel lokalisiert, die in den serU Lokus inseriert ist und möglicherweise über horizontalen Gentransfer erworben wurde. Untersuchungen zur Transkription des hlp Gens ergaben, dass das Gen monocistronisch von einem einzigen Promotor transkribiert, und dessen Expression durch H-NS reprimiert wird. Rekombinantes Hlp Protein war befähigt, sowohl an seinen eigenen, als auch an den hns Promotor zu binden, was zu negativer Auto- und Kreuzregulation führte. Zudem konnte gezeigt werden, dass Hlp und H-NS direkt miteinander interagieren, was zu stabilen Heteromeren führte. Komplementierungsstudien in hns Mutanten einiger K-12 Stämme ergaben, dass das Hlp Protein über in vivo Aktivität verfügt, was es befähigte, die Abwesenheit von H-NS bei zahlreichen Phänotypen wie z.B. Motilität, Wachstum, und Repression der proU, bgl und clyA Gene zu komplementieren. Die Rolle der Histon-ähnlichen Proteine bei der Expression von Virulenz-assoziierten Genen wurde mittels DNA Array Technologie, sowie klassischen phänotypischen Tests analysiert. Dabei wurden die meisten der beobachteten Effekte einzig durch das H-NS Protein bedingt. Die Expressionsstudien ergaben, dass über 500 Gene von einer hns Mutation beeinflusst wurden, was eine verstärkte Expression des alpha-Hämolysins, mehrerer Fimbrien und Eisenaufnahmesysteme sowie von Genen, die in Stress-Antworten involviert sind, bedingte. Des Weiteren konnten zahlreiche putative Virulenzfaktoren dem H-NS-Regulon zugeordnet werden. Andererseits konnten keine Effekt durch StpA beobachtet werden. Eine hns stpA Doppelmutante wies jedoch ein eindeutiges Expressionsmuster auf, das in großen Teilen von dem der hns Einzelmutante abwich. Dies legt nahe, dass beide Proteine direkt miteinander interagieren, was das Auftreten von unterschiedlichen Regulons zur Folge hat, die entweder durch H-NS oder einem heteromeren H-NS/StpA Komplex beeinflusst werden. Obwohl das H-NS Protein – entweder als Homomer oder als Komplex mit StpA – einen sehr starken Einfluss auf die Genexpression pathogener E. coli Stämme nimmt, bleiben dessen Effekte auf die tatsächliche Virulenz im Urogenitaltrakt unklar. In einem experimentellen Mausmodell der aufsteigenden Harnwegsinfektion bewirken hns Mutanten, in hoher Dosis verabreicht, eine rasch eintretende Lethalität, was vermutlich der verstärkten Produktion von alpha-Hämolysin zuzuschreiben ist. In verringerter Dosis verabreicht, sind diese Mutanten durch ihre langsameren Wachstumsraten jedoch attenuiert, was nur teilweise durch die vestärkte Expression zahlreicher Virulenzfaktoren kompensiert werden kann. Wie schon bei StpA beobachtet, besitzt eine hlp Mutante keinen offensichtlichen Phänotyp, zumindest unter Standard-Wachstumsbedingungen. Jedoch macht sich in hns hlp Doppelmutanten ein starker Wachstumsdefekt bei erniedrigten Temperaturen bemerkbar, was eine biologische Relevanz von H-NS/Hlp Heteromeren unter bestimmten Bedingungen nahe legt. Des Weiteren exprimierten diese Mutanten erhöhte Mengen an Kapsel-Polysacchariden und Curli-Adhesin, was als Indiz für eine besondere Rolle für H NS und Hlp bei der Regulation dieser Oberflächenstrukturen dienen kann. Zudem hatten beide H-NS-Paraloge Hlp und StpA einen modulierenden Effekt bei der H-NS-vermittelten Regulation weiterer Fimbrien-Adhesine und waren in gegenläufigen Maßen für normales Wachstum bei erhöhten bzw. erniedrigten Temperaturen notwendig. Zuletzt variierte das Expressionsniveau der drei Histon-ähnlichen Proteine H-NS, StpA und Hlp bei unterschiedlichen Temperaturen, was auf eine flexible Zusammensetzung verfügbarer Nucleoid-assoziierter Proteine hindeutet. Dies alles impliziert, dass die biologische Relevanz von Hlp, und StpA gleichermaßen, nicht auf gesonderten Funktionen des einzelnen Proteins beruht, sondern vielmehr auf deren Interaktionen mit dem globalen Regulatorprotein H-NS.

Le variant d'histone CENP-A est le facteur responsable de la détermination épigéné- tique du centromère. Il permet le recrutement de nombreuses protéines centromériques, et constitue ainsi la brique fondatrice du kinétochore. Il possède un domaine amino-terminal non structuré dont la fonction précise reste encore à élucider, bien qu'il soit déjà établi chez certaines espèces que ce domaine est requis pour le bon fonctionnement du cen- tromère et conséquemment le bon déroulement de la mitose. Nous avons construit des lignées cellulaires humaines exprimant stablement diverses formes mutantes de CENP-A, qui nous ont permis de réaliser des expériences de pseudogénétique en supprimant l'ex- pression de la protéine CENP-A endogène. Nous observons une augmentation drastique du taux de défauts de ségrégation des chromosomes et de cellules plurinucléées dans des cellules exprimant uniquement le domaine globulaire de CENP-A, ce qui est en accord avec les données de la littérature et confirme l'importance du domaine amino-terminal. Un phénotype similaire est observé dans des cellules exprimant une protéine CENP-A entière mais dont le domaine amino-terminal n'est pas phosphorylable. Nos résultats montrent l'implication de la phosphorylation de la sérine de CENP-A dans le bon déroulement de la mitose, et suggèrent que la fonction mitotique du domaine amino-terminal est centrée sur cette seule phosphorylation. / The histone variant CENP-A is the epigenetic factor responsible for centromere deter- mination. It allows the recruitment of a handful of centromeric proteins, and thus acts as the primary foundation for the kinetochore. It comprises an unstructured amino-terminal domain to which no precise function has yet been assigned, although it is established in some species that the mere presence of that domain is required for proper centromere func- tion and thus successful completion of mitosis. We have established several human cell lines stably expressing GFP-tagged CENP-A constructs, allowing us to perform pseudoge- netic experiments by siRNA-mediated silencing of the endogenous CENP-A. Our results show a dramatic increase of mitotic defects and plurinuclear cells when cells express only the globular domain of CENP-A; this is in accordance with the litterature and confirms the importance of the amino-terminal tail. More importantly, a similar increase of mitotic defects is observed when cells express a full-length, but non-phosphatable, CENP-A. Our results show the involvement of the phosphatable serine 7 of CENP-A in the successful completion of mitosis, and may suggest that the role of the whole amino-terminal tail of CENP-A could be reduced to this single phosphorylation event.

Mammalian neural stem cell (NSC) lines provide a useful experimental model for basic and applied research across stem cell and developmental biology, regenerative medicine and neuroscience. NSCs are clonally expandable, genetically stable, and easily transfectable - experimental attributes compatible with functional genetic analyses. However, targeted genetic manipulations have not been reported for mammalian NSC lines. Here, we deploy the CRISPR/Cas9 technology and demonstrate a variety of diverse targeted genetic modifications in both mouse and human NSC lines such as: targeted transgene insertion at safe harbour loci; biallelic knockout of neurodevelopmental genes; knock-in of epitope tags and fluorescent reporters; and engineering of glioma driver mutations at endogenous proto-oncogenes. Leveraging these new optimised methods, we explored gene editing to model the earliest stages of paediatric gliomagenesis in primary human NSCs. Our data indicate that oncogenic mutations in histone H3.3 play a role in NSC transformation and may operate through suppression of replication induced senescence. By comparing cellular responses of NSC cultures from different compartments of the developing brain, we also identify differences in susceptibility to distinct H3.3 mutations that mirror the disease etiology. Altogether, our findings indicate that CRISPR/Cas9-assisted genome editing in NSC lines is a versatile tool to explore gene function in CNS development and cancer biology. Our project resulted in the creation of valuable human cellular models of paediatric gliomagenesis, which will allow us to further our understanding of the disease and carry out cell based drug discovery projects.

Barley (Hordeum vulgare) is an economically important crop species with a large diploid genome. Around a half of the barley genome and a fifth of the genes are constrained within a low-recombining pericentromeric (LR-PC) region. I explored the LR-PC gene component with a genomic investigation of gene expression, diversity and evolution. Chromatin environments were also explored in the LR and high recombining (HR) regions by surveying the genic and genomic distributions of nine histone modifications. Firstly, regions of HR and LR were identified and compared for gene evolution, expression and diversity. LR regions of the barley genome were found to be restrictive for gene evolution and diversity, but not gene expression. I employed a bioinformatics approach to identify ancient gene pairs in barley to determine the long-term effects of residency in those regions upon gene evolution. Gene pair loss in LR regions was found to be elevated relative to the HR regions. Applying the same method to rice and Brachypodium distachyon revealed the same situation, suggesting a universal process in the grasses for loss of gene pairs in LR regions. The chromosomal distributions of transposable elements (TEs) were also explored and examined for correlations with recombination rate. Secondly, I developed a chromatin immunoprecipitation followed by Next Generation Sequencing (ChIP-seq) protocol for the investigation of histone modifications in barley seedlings. A protocol was optimised for the fixation, extraction and sonication of barley chromatin. The protocol was applied using antibodies against 13 different histone modifications. Following DNA library construction and Illumina sequencing, a bioinformatics pipeline was devised to analyse the sequence data. NGS reads were mapped to a custom assembly of the barley cultivar Morex reference genome sequence before peak calling. Genomic and genic locations were determined for the covalently modified histones. Four modifications were discarded from further study on the basis of low peak numbers or unexpected chromosomal locations. The remaining nine modifications were classified into four groups based on chromosomal distributions. Groupings were closely mirrored by peak sharing relationships between the modifications except histone H3 lysine-27 tri-methylation (H3K27me3). In addition, chromatin states representing local chromatin environments were defined in the barley genome using the peak sharing data. Mapping the states onto the genome revealed a striking chromatin structure of the gene-rich chromosome arms. A telomere-proximal region bearing high levels of H3K27me3-containing states was found adjacent to an interior gene-rich region characterised by active chromatin states lacking H3K27me3. The LTR retroelement-rich interior was found to be associated with repressive chromatin states. The histone modification status of TE classes were also probed revealing unexpected differences relating to the genomic and genic distributions of these elements. Finally, a genome browser was created to host the information publicly.