The activity of a single gene is influenced by the composition of the chromatin in which it is embedded. Nucleosome turnover, conformational dynamics, and covalent histone modifications each induce changes in the structure of chromatin and its affinity for regulatory proteins. The dynamics of histone modifications and the persistence of modification patterns for long periods are still largely unknown. In this study, we present a stochastic mathematical model that describes the molecular mechanisms of histone modification pattern formation along a single gene, with non-phenomenological, physical parameters. We find that diffusion and recruitment properties of histone modifying enzymes together with chromatin connectivity allow for a rich repertoire of stochastic histone modification dynamics and pattern formation. We demonstrate that histone modification patterns at a single gene can be established or removed within a few minutes through diffusion and weak recruitment mechanisms of histone modification
ALATZAS, ANASTASIOS; SREBREVA, LJUBA and FOUNDOULI, ATHINA. Distribution of linker histone variants during plant cell differentiation in the developmental zones of the maize root, dedifferentiation in callus culture after auxin treatment. Biol. Res. [online]. 2008, vol.41, n.2, pp.205-215. ISSN 0716-9760. http://dx.doi.org/10.4067/S0716-97602008000200010.. Although several linker histone variants have been studied in both animal and plant organisms, little is known about their distribution during processes that involve alterations in chromatin function, such as differentiation, dedifferentiation and hormone treatment. In this study, we identified linker histone variants by using specific anti-histone Hl antibodies. Each variants ratio to total Hl in the three developmental zones of maize (Zea mays L.) root and in callus cultures derived from them was estimated in order to define possible alterations either during plant cell differentiation or during their dedifferentiation. We also evaluated ...
Background: Despite their well-established functional roles, histone modifications have received less attention than DNA methylation in the cancer field. In order to evaluate their importance in colorectal cancer (CRC), we generated the first genome-wide histone modification profiles in paired normal colon mucosa and tumor samples. Methods: Chromatin immunoprecipitation and microarray hybridization (ChIP-chip) was used to identify promoters enriched for histone H3 trimethylated on lysine 4 (H3K4me3) and lysine 27 (H3K27me3) in paired normal colon mucosa and tumor samples from two CRC patients and for the CRC cell line HT29. Results: By comparing histone modification patterns in normal mucosa and tumors, we found that alterations predicted to have major functional consequences were quite rare. Furthermore, when normal or tumor tissue samples were compared to HT29, high similarities were observed for H3K4me3. However, the differences found for H3K27me3, which is important in determining cellular ...
Re histone modification profiles, which only take place inside the minority in the studied cells, but with the improved Daprodustat sensitivity of reshearing
Re histone modification profiles, which only occur inside the minority from the studied cells, but together with the increased sensitivity of reshearing these
Histones are the major protein component of nucleosomes, and de novo histone synthesis is essential for packaging newly replicated DNA into chromatin. As a result, histone gene expression is exquisitely and functionally coupled with DNA replication. Vastly divergent organisms such as yeast, fly and human all demonstrate the phylogenetically conserved propensity to maintain clustering of histone genes at one or more genomic loci. Although specific mechanisms are unclear, clustering is presumed to be important for common stringent transcriptional control of these genes at the G1/S phase transition. In this study, we describe a genomic duplication of the human histone gene cluster located at chromosome 1q21, which effectively doubles the previously known size and gene number of that cluster. The duplication persists in all examined tissues and cell lines, and the duplicated genes are transcriptionally active. Levels of messenger RNAs for duplicated histone H4 genes are high relative to those for non
This EMBO Workshop features histone variants, which are part of an interconnected "epigenetic" network including DNA methylation, posttranslational histone modifications, chromatin remodeling, regulatory RNAs and nuclear organization. Worldwide research on histone variants over the last years has revealed their important function in gene regulation, cell cycle progression, DNA damage repair, genome stability, cell differentiation and organism development. Additionally, recent studies have highlighted the role of mutations or deregulation of expression of histone variants and their binding partners in diverse diseases, most notably cancer.. This EMBO Workshop will provide a comprehensive representation of all of these histone variant-related processes, with a balanced portrayal of different model organisms, including rare variants in parasites and evolutionary aspects, as well as presentations of the different variant families, such as linker histone variants. Specialists of variant deposition ...
After publication of our recent article [1], it has been brought to our attention that the incorrect wording was used to acknowledge our EU funding source. The correct statement should read:. "The research leading to these results has received funding from the European Union Seventh Framework Programme (FP7/2007-2013) under grant agreement n° 261382." ...
In contrast to many other genes containing a CpG island, the testis-specific H2B (TH2B) histone gene exhibits tissue-specific methylation patterns in correlation with gene activity. Characterization of the methylation patterns within a 20-kb segment containing the TH2A and TH2B genes in comparison with that in a somatic histone cluster revealed that: (i) the germ cell-specific unmethylated domain of the TH2A and TH2B genes is defined as a small region surrounding the CpG islands of the TH2A and TH2B genes and (ii) somatic histone genes are unmethylated in both liver and germ cells, like other genes containing CpG islands, whereas flanking sequences are methylated. Transfection of in vitro-methylated TH2B, somatic H2B, and mouse metallothionein I constructs into F9 embryonal carcinoma cells revealed that the CpG islands of the TH2A and TH2B genes were demethylated like those of the somatic H2A and H2B genes and the metallothionein I gene. The demethylation of those CpG islands became ...
Variability in the quality of antibodies to histone post-translational modifications (PTMs) is a widely recognized hindrance in epigenetics research. Here, we produced recombinant antibodies to the trimethylated lysine residues of histone H3 with high specificity and affinity and no lot-to-lot varia …
Post-translational histone modifications have a critical role in regulating transcription, the cell cycle, DNA replication andDNA damage repair1 . The identification of new histone modifications critical for transcriptional regulation at initiation, elongation or termination is of particular interest. Here we report a new layer of regulation in transcriptional elongation that is conserved from yeast to mammals. This regulation is based on the phosphorylation of a highly conserved tyrosine residue, Tyr 57, in histone H2A and is mediated by the unsuspected tyrosine kinase activity of casein kinase 2 (CK2). Mutation of Tyr 57 in H2Ain yeast or inhibition of CK2 activityimpairs transcriptional elongation in yeast as well asin mammalian cells. Genome-wide binding analysis reveals that CK2a, the catalytic subunit of CK2, binds across RNA-polymerase-II-transcribed coding genes and active enhancers.Mutation of Tyr 57 causes a loss of H2Bmono-ubiquitination as well as H3K4me3 and H3K79me3, histone marks ...
Circadian clocks are biochemical mechanisms that allow eukaryotic and some prokaryotic organisms to coordinate their physiology with daily environmental changes. It enables organisms to increase their fitness by taking advantage of beneficial environmental conditions while also avoiding or restricting certain sensitive processes during harsh conditions. Similarly, post-translational histone modifications allow eukaryotic organisms to regulate gene expression in response to environmental or developmental factors. Some post-translational modifications of histones are associated with active transcription while others are associated with repressed transcription depending upon the location, type and degree of modification. Trimethylation of lysine 4 on the N-terminal tail of histone H3 (H3K4me3) near a genes promoter has been linked to active transcription of that gene in several organisms. The purpose of the current study was to investigate whether the amount of H3K4me3 at promoters of three specific genes
It is becoming increasingly evident that the cellular response towards DNA damage is affected by the structure of the chromatin region surrounding the damage site [1], while at the same time the chromatin structure is affected by the damage response [2]. DNA double-strand breaks (DSBs) elicit a response in an Mbp-large chromatin region surrounding the break that involves alterations in several post-translational modifications (PTMs). Phosphorylation of histone variant H2AX at serine 139 (S139) to yield γ-H2AX is a hallmark step in the cellular response to DSB. The γ-H2AX chromatin domains, which can be visualized as ionizing radiation induced foci (IRIF), delineate regions where a large variety of signalling and repair proteins accumulate [3].. Immunofluorescence detection of PTMs demonstrated alterations in several modifications in the γ-H2AX domain following DSB induction that are associated with regulation of chromatin accessibility, recruitment of DNA damage response factors, and ...
The identification of demethylase enzymes has revealed that histone methylation can be dynamically regulated in a manner similar to that of histone acetylation and phosphorylation. In S. cerevisiae, the enzymes that place histone methylation marks are well characterized and coordinate mainly the addition of these modifications during the process of active transcription (25). Previously, only one histone demethylase enzyme, Jhd1, was identified in budding yeast. Jhd1 is a JmjC-domain-containing protein that catalyzes the demethylation of H3K36me2 and H3K36me1 modification states (36). Given that Jhd1 does not target H3K36me3 in yeast, it remained possible that this methylation state was irreversible.. Here, we identify Rph1 as being a histone demethylase with activity towards histone H3K36me3 and H3K36me2 modification states. Deletion of RPH1 does not affect global histone H3K36 methylation profiles, and deletion strains are viable, displaying no obvious morphological or cellular defects. This ...
Histone N-terminal tails are extensively modified by a plethora of post-translational modifications, including histone methylation. Histone methylation has been implicated in multiple biological processes including heterochromatin formation, Xinactivation, genomic imprinting and silencing of homeotic genes. Methylation occurs on both lysine (K) and arginine (R) residues. Multiple K residues on the tails of histone H3 and H4 have been shown to be sites for methylation (mono-, di, and tri-methylation). Methylation at these sites has been linked to transcriptional activation and repression, as well as DNA damage response, indicating a widespread role for histone methylation in various aspects of chromatin biology. Unlike other histone modifications such as acetylation, methylation has long been considered a "permanent" modification. Our identification of the first histone demethylase LSD1 disproved this dogma, and suggested that histone methylation is dynamically regulated by both histone ...
The main goal of this project is to develop a simple, yet powerful and versatile technology for detection and imaging of epigenetic histone modifications and hi...
Aberrant gene expression is a common feature of cancer cells, which is caused by a combination of gene mutations and aberrant regulation of gene expression by epigenetic mechanisms, including DNA methylation, microRNAs and histone modifications. Histone modifications play a crucial role in many cellular processes during embryonic development, cell proliferation and cellular differentiation [2]. In cancer, aberrant expression of histone modifications has been described frequently [1]. Therefore, we investigated the nuclear expression of three well-studied histone modifications in colon cancer.. In this study, we found that nuclear expression of histone trimethylation on H3K4, H3K9 and H4K20 has prognostic value in early-stage colon cancer. Changes in expression of key histone modifications are found in early-stage tumors, which would be expected because tumor cells require instant changes in gene expression and chromatin structure in order to promote cell proliferation and tumor cell survival. ...
The field of cancer epigenetics has received much attention in recent years. However, the relationship of cancer epigenetics with cancer etiology is not clear. Recent studies suggest the involvement of altered DNA methylation and histone modifications in the emergence of epigenetically reprogrammed cells with specific tumor-related phenotypes at premalignant stages of tumor development. In this study, we used a methyl-deficient model of rodent hepatocarcinogenesis to examine the roles of DNA, histone H3 lysine 9 and histone H4 lysine 20 methylation, and the level of the expression of Suv39h1 and Suv4-20h2 histone methyltransferases in the carcinogenic process. We demonstrated that the development of liver tumors was characterized by progressive demethylation of DNA repeats, decrease in histone H4 lysine 20 trimethylation, and a gradual decrease in the expression of Suv4-20h2 histone methyltransferase. A prominent increase in the trimethylation of histone H3 lysine 9 and in the expression of ...
Introduction Hepatic steatosis is a major risk factor for the development of severe liver damage, including fibrosis, cirrhosis and hepatocellular carcinoma. It often exists as a co-morbidity factor with diabetes type I/II and with other manifestations of the metabolic syndrome. Recent studies highlight the importance of an epigenetic basis for the development of steatosis based on macroH2A1. MacroH2A1 is a histone variant of histone H2A, which possesses an additional protein domain called macro. When incorporated into the chromatin of hepatocytes, macroH2A1 regulates gene expression. Two alternatively spliced isoforms of macroH2A1 exist, which have been shown to be markers of breast, skin and lung cancer. Whole-body knock out of macroH2A1 in mice induces glucose intolerance and changes in genes regulating hepatic lipid metabolism. However, overt hepatic steatosis was not observed and the significance of these findings is unclear. We hypothesised that macroH2A1 could be involved in the ...
Histone variants play further important roles in DNA packaging and controlling gene expression. However, our understanding about their composition and their functions is limited. Integrating proteomic and genomic approaches, we performed a comprehensive analysis of the epigenetic landscapes containing the four histone variants H3.1, H3.3, H2A.Z, and macroH2A. These histones were FLAG-tagged in HeLa cells and purified using chromatin immunoprecipitation (ChIP). By adopting ChIP followed by mass spectrometry (ChIP-MS), we quantified histone post-translational modifications (PTMs) and histone variant nucleosomal ratios in highly purified mononucleosomes. Subsequent ChIP followed by next-generation sequencing (ChIP-seq) was used to map the genome-wide localization of the analyzed histone variants and define their chromatin domains. Finally, we included in our study large datasets contained in the ENCODE database. We newly identified a group of regulatory regions enriched in H3.1 and the histone variant
We describe the chromosomal location of GC-rich regions, 28S and 5S rDNA, core histone genes, and telomeric sequences in the veneroid bivalve species Venerupis aurea and Tapes (Venerupis) rhomboides,
Changes in chromatin structure play a large role in the regulation of transcription in eukaryotes (1). The nucleosome is the primary building block of chromatin, and is made up of four core histone proteins (H2A, H2B, H3 and H4) (2). Acetylation of core histones regulates gene expression (2). Histone H3 is primarily acetylated at lysines 9, 14, 18, and 23 (3,4). Acetylation at lysine 9 appears to have a dominant role in histone deposition and chromatin assembly in some organisms (3,4). Phosphorylation at Ser10 of histone H3 is tightly correlated with chromosome condensation during both mitosis and meiosis (5 ...
Tight regulation of histone relative stoichiometry and overall levels is fundamental to the preservation of genome integrity in all eukaryotes. Abnormal histone levels induce defects in mitotic chromosome segregation, chromatin structure, and transcription and lead to loss of viability (Meeks-Wagner and Hartwell 1986; Han et al. 1987; Clark-Adams et al. 1988; Kim et al. 1988; Norris et al. 1988). Defects in chromatin structure caused by inactivation of nucleosome assembly factors cause high rates of chromosomal rearrangements and spontaneous DNA damage and elicit checkpoint activation (Myung et al. 2003; Ye et al. 2003; Ramey et al. 2004).. This study provides genetic and biochemical evidence that Trf4 and Trf5 make a redundant contribution to genome stability in yeast through control of histone mRNA levels during S phase. We show that the mRNAs coding for the four core histones, but not other cell cycle-regulated transcripts tested, accumulate to abnormally high levels in S phase in a trf4-ts ...
Background Histone variants establish structural and functional diversity of chromatin by affecting nucleosome stability and histone-protein interactions. H3.3 is an H3 histone variant that is incorporated into chromatin outside of S-phase in various eukaryotes. In animals, H3.3 is associated with active transcription and possibly maintenance of transcriptional memory. Plant H3 variants, which evolved independently of their animal counterparts, are much less well understood. Results We profile the H3.3 distribution in Arabidopsis at mono-nucleosomal resolution using native chromatin immunoprecipitation. This results in the precise mapping of H3.3-containing nucleosomes, which are not only enriched in gene bodies as previously reported, but also at a subset of promoter regions and downstream of the 3′ ends of active genes. While H3.3 presence within transcribed regions is strongly associated with transcriptional activity, H3.3 at promoters is often independent of transcription. In particular, ...
Histone binding pocket. (A) Potential histone peptide binding site. Superposition of the Smyd3 and SET7/9 (PDB code 1O9S) structures was performed as in Figure
Histones are basic nuclear proteins that are responsible for the nucleosome structure of the chromosomal fiber in eukaryotes. Nucleosomes consist of approximately 146 bp of DNA wrapped around a histone octamer composed of pairs of each of the four core histones (H2A, H2B, H3, and H4). The chromatin fiber is further compacted through the interaction of a linker histone, H1, with the DNA between the nucleosomes to form higher order chromatin structures. This gene encodes a replication-independent histone that is a member of the histone H1 family. [provided by RefSeq, Oct 2015 ...
Trimethylation of histone H3 lysine 4 (H3K4me3) accumulates at promoters in a gene activity-dependent manner. The Set1 complex is responsible for most H3K4me3 in somatic cells and contains the conserved subunit Cfp1, which is implicated in targeting the Set1 complex to CpG islands in mammals. In mouse embryonic stem cells, Cfp1 is necessary for H3K4me3 accumulation at constitutively active gene promoters, but is not required to maintain steady-state transcription of the associated gene. Here we show that Cfp1 is instrumental for targeting H3K4me3 to promoters upon rapid transcriptional induction in response to external stimuli. Surprisingly, H3K4me3 accumulation is not required to ensure appropriate transcriptional output but rather plays gene-specific roles. We also show that Cfp1-dependent H3K4me3 deposition contributes to H3K9 acetylation genome-wide, suggesting that Cfp1-dependent H3K4me3 regulates overall H3K9 acetylation dynamics and is necessary for histone acetyl transferase recruitment. Finally
TY - JOUR. T1 - Systems level analysis of Histone H3 posttranslational modifications (PTMs) reveals features of PTM crosstalk in chromatin regulation. AU - Schwämmle, Veit. AU - Sidoli, Simone. AU - Ruminowicz, Chrystian. AU - Wu, Xudong. AU - Lee, Chung Fan. AU - Helin, Kristian. AU - Jensen, Ole N.. PY - 2016/8. Y1 - 2016/8. N2 - Histones are abundant chromatin constituents carrying numerous post-translational modifications (PTMs). Such PTMs mediate a variety of biological functions, including recruitment of enzymatic readers, writers and erasers that modulate DNA replication, transcription and repair. Individual histone molecules contain multiple coexisting PTMs, some of which exhibit crosstalk, i.e. coordinated or mutually exclusive activities. Here, we present an integrated experimental and computational systems level molecular characterization of histone PTMs and PTM crosstalk. Using wild type and engineered mouse embryonic stem cells (mESCs) knocked out in components of the Polycomb ...
The analysis of the recently available ChIP-seq data on 8 histone modification marks and 13 TF binding sites in mES cells confirmed the distinct chromatin signatures associated with promoters and enhancers. We did not observe any significant correlation between the histone modification patterns and the binding of the 13 TFs probably because none of these factors are involved in chromatin modification. The unexpected correlations between several histone marks and the binding strength of TFs (Table S3 in Additional file 2) still needs further validation and determination of the underlying molecular mechanisms.. Histone modifications reflect the epigenetic state of a cell, which provides useful information to map the functional activities of regulatory elements. In this study, we present a new computational model called Chromia that integrates sequence motif and chromatin signatures to predict target loci of TFs. We have demonstrated that the performance of our method is superior to many other ...
Post-translational histone modifications play important roles in chromatin functions, ranging from DNA damage and repair, DNA recombination, chromatin structure...
Histones are basic nuclear proteins that are responsible for the nucleosome structure of the chromosomal fiber in eukaryotes. Two molecules of each of the four core histones (H2A, H2B, H3, and H4) form an octamer, around which approximately 146 bp of DNA is wrapped in repeating units, called nucleosomes. The linker histone, H1, interacts with linker DNA between nucleosomes and functions in the compaction of chromatin into higher order structures. The protein has antibacterial and antifungal antimicrobial activity. This gene is intronless and encodes a replication-dependent histone that is a member of the histone H2B family. Transcripts from this gene lack polyA tails but instead contain a palindromic termination element. This gene is found in the large histone gene cluster on chromosome 6. [provided by RefSeq, Aug 2015 ...
Packaging DNA into chromatin is dynamic, reversible, and essential for eukaryotic cell viability. The principal packaging unit of chromatin is the nucleosome, consisting of an octamer of two copies each of the four canonical histones (H2A, H2B, H3, and H4) wrapped in 146 bp of DNA (1). Histone proteins are decorated with posttranslational modifications, including lysine acetylation, which influence chromatin architecture by altering nucleosome contacts or by affecting interactions with nonhistone proteins (2). During DNA-dependent processes, nucleosomes disassemble to grant access to specific regions of DNA and reassemble in a way that preserves the local chromatin landscape. By virtue of their highly basic charge, histones are prone to both aggregation and promiscuous interactions when they are not associated with DNA, such as when they are newly synthesized or during nucleosome turnover. To prevent these deleterious effects, a network of histone chaperones regulates each step of chromatin ...
Histone acetyltransferases serve many biological roles inside the cell. Chromatin is a combination of proteins and DNA found in the nucleus, and it undergoes many structural changes as different cellular events such as DNA replication, DNA repair, and transcription occur.[22] Chromatin in the cell can be found in two states: condensed and uncondensed. The latter, known as euchromatin, is transcriptionally active, whereas the former, known as heterochromatin, is transcriptionally inactive.[22][23] Histones comprise the protein portion of chromatin. There are five different histone proteins: H1, H2A, H2B, H3, and H4. A core histone is formed when two of each histone subtype, excluding H1, form a quaternary complex. This octameric complex, in association with the 147 base pairs of DNA coiled around it, forms the nucleosome.[3] Histone H1 locks the nucleosome complex together, and it is the last protein to bind in the complex.. Histones tend to be positively charged proteins with N-terminal tails ...
Recombinant Histone H3K36me3 (MLA) protein, methylated lysine analog for analysis of transcription regulation, DNA repair, DNA replication and chromosomal stability
Histones are modified at specific positions on their conserved amino‐terminal tails, and these modifications play central roles in gene regulation (Jenuwein and Allis, 2001; Turner, 2002). For example, acetylation at lysine 14 of histone H3 (H3K14Ac) or methylation of lysine 4 (H3K4Me) is associated with gene activation. In contrast, the lack of acetylation as well as the methylation of lysine 9 of histone H3 (H3K9Me) is correlated with gene repression (Jenuwein and Allis, 2001; Turner, 2002). These two types of modifications are performed by histone acetyltransferases (HATs) and histone methyltransferases (HMTases). These modifying enzymes are members of large multiprotein complexes with other subunits likely serving roles in targeting or regulation. The primary substrates for these enzymes are the amino‐terminal tails of the histone proteins. Modified tails function as binding platforms for transcriptional regulatory factors. For example, the histone H3 tail methylated at lysine 9 is ...
Histone peptide arrays are essential screening tools to evaluate the specificity and cross-reactivity of antibodies against histones H2A, H2B, H3, H4, and their post-translational modifications.The arrays are designed on PVDF membranes for a simple Western blot-like assay.
HIV-1 latency is maintained by several mechanisms. a , Transcription factors (TFs), including nuclear factor-κB (NF-κB) and nuclear factor of activated T cells (NFAT), are sequestered in the cytoplasm, which leads to transcriptional silencing. Bryostatin and prostratin induce activation of NF-κB, leading to its translocation to the nucleus where it activates HIV-1 transcription. b , The HIV-1 long terminal repeat (LTR) is flanked by the Nuc-0 and Nuc-1 nucleosomes that, when latent, can encode repressive post-translational histone modifications. Histone deacetylases (HDACs), which are recruited by transcription factors (such as YY1 and CBF-1), remove the acetyl groups from chromatin. Histone methyltransferases (HMTs), such as SUV39H1, G9a and EZH2, deposit methyl groups onto histones. HDACs and HMTs enforce the repressive state. Both HDAC inhibitors and HMT inhibitors can induce transcription from quiescent LTR promoters. HIV-1 DNA can also be methylated, although recent evidence suggests ...
Author Summary Eukaryotic DNA is packaged into chromatin through its association with histone proteins. The linker histone H1 sits at the base of the nucleosome near the DNA entry and exit sites to stabilize two full turns of DNA. In particular, histone H1 participates in nucleosome spacing and formation of the higher-order chromatin structure. In addition, H1 seems to be actively involved in the regulation of gene expression. Histone H1 in mammals is a family of closely related, single-gene encoded proteins, including five somatic subtypes (from H1.1 to H1.5) and a terminally differentiated expressed isoform (H1.0). It is not well known whether the different variants have distinct roles or if they regulate specific promoters. We have explored this by inducible knock-down of each of the H1 variants in breast cancer cells. A different subset of genes is altered in each H1 knock-down, and depletion has different effects on cell survival. Interestingly, H1.2 and H1.4 depletion specifically caused arrest of
Role of H1 Linker Histones and Chromatin Remodeling Factors in Chromatin Structure, DNA Methylation, the Histone Code, Gene Expression and Development in Mice and Drosophila. Recent studies show that posttranslational modifications of core histones (H2A, H2B, H3, H4) (the Histone Code) play a very important role in control of gene expression. The H1 linker histones are more diverse than the core histones. Mice contain 8 H1 histone subtypes including differentiation-specific and tissue-specific subtypes, whereas Drosophila has only one type of H1. H1s are thought to be responsible for the final level of packaging DNA into the compact chromatin structure but we know very little about their role in gene expression and development. We are studying the functional roles of H1 linker histones by inactivating (knocking-out) specific H1 genes in mice and the single H1 in Drosophila. We are also reintroducing mutant H1 linker histones into H1 depleted mouse cells and flies, to perform structure-function ...
Histone proteins have central roles in both chromatin organisation (as structural units of the nucleosome) and gene regulation (as dynamic components that have a direct impact on DNA transcription and replication). Eukaryotic DNA wraps around a histone octamer to form a nucleosome, the first order of compaction of eukaryotic chromatin. The core histone octamer is composed of a central H3-H4 tetramer and two flanking H2A-H2B dimers. Each of the core histone contains a common structural motif, called the histone fold, which facilitates the interactions between the individual core histones.. In addition to the core histones, there is a "linker histone" called H1 (or H5 in avian species). The linker histones present in all multicellular eukaryotes are the most divergent group of histones, with numerous cell type- and stage-specific variant. Linker histone H1 is an essential component of chromatin structure. H1 links nucleosomes into higher order structures. Histone H5 performs the same function as ...
In developing multi-cellular organisms, cell fate decisions are largely determined by epigenetic programs that activate and repress specific sets of genes. For eukaryotic gene regulation, the post-translational modifications of the DNA-associated histone proteins are critical in transcriptional control. Here, we describe a novel trans-tail histone code where the monomethylation of histones H4 lysine 20 (H4K20) and H3 lysine 9 (H3K9) defines specific genomic regions of transcriptionally repressed chromatin. Global analysis of this code revealed a defined unidirectional temporal sequence of methylmodifications in which monomethylated H3K9 depends on the H4K20 monomethyltransferase, PR-Set7. Importantly, we have identified a repressor protein, L3MBTL1, which is recruited to and binds monomethylated H4K20 and that this interaction is required to initiate transcriptional repression in vivo. Using expression microarray analysis, we have identified numerous cell type-specific genes involved in certain ...
Anti-human histone H2B (polyclonal antibody) raised in rabbits. Histone H2B plays a role in the packaging and maintenance of chromatin in eurkaryotic cells. CODE NUMBER: RH2B.. QUANTITY: 0.1 mL.. SPECIFICITY: Reacts with histone H2B in human nuclear fractions. No cross-reactivity with other histones: H1, H2A, H3 or H4.. IMMUNOGEN: Synthetic peptide.. SUGGESTED APPLICATIONS: Western blot, immunohistochemistry on frozen and formaldehyde treated sections. Optimal working dilutions must be determined by end user.. SPECIES REACTIVITY: Human. Binding to histone H2B from other species has not been tested, but is likely as the amino acid sequence of histone H2B has been found to be identical in all species examined.. FORMAT: Rabbit antiserum.. PRESENTATION: Liquid. No preservatives.. STORAGE/HANDLING: Maintain at -20°C in undiluted aliquots for up to 12 months. Avoid repeated freeze/thaw cycles.. For research use only; not for use in diagnostic procedures. Not for human or animal consumption.. To ...
In eukaryotic cells DNA is associated with histones and other proteins to form chromatin. The basic unit of chromatin is the nucleosome consisting of 140 bp of DNA wrapped around an octameric core of the four conserved histones H2A, H2B, H3 and H4.

The relatively unstructured and highly charged N-terminal tail domains of histones, are central to the processes that modulate chromatin structure. A diverse and elaborate array of post-translational modifications that include acetylation, phosphorylation, methylation, ubiquitination and ADP-ribosylation, occur on the N-terminal tail domains of histones. Acetylation of lysine residues within these N-terminal domains by histone acetyl-transferases (HATs), is associated with transcriptional activation. This modification results in remodeling of the nucleosome structure into an open conformation more accessible to transcription complexes. In most species, histone H3 is primarily acetylated at lysines 9, 14, 18 and 23. Acetylation at lysine 9 appears to
Epigenetics is defined as inheritable phenotypic traits that are maintained by mechanisms other than encoding in the DNA sequence. Epigenetic mechanisms are DNA methylation and oxidation of methylcytosine within DNA, small non-protein coding RNAs and a whole set of posttranslational histone modifications. Epigenetic modifications can be highly susceptible to external stimuli such as chemicals, nutrition or even stress. Yet, they may then be very stably inherited over mitotic cell division almost like a genetic mutation. These so-called epimutations have been recognized to be involved in the pathogenesis of many diseases and, as they despite their potential stability are in principle reversible, are also the target of epigenetic drugs. Six epigenetic inhibitors are already approved for the treatment of cancer. Among the histone modifications lysine methylation is an emerging target with the first inhibitors of lysine methyltransferase or demethylases in Phase I clinical trials as anticancer ...
HIstome is a freely available, specialist, electronic database dedicated to display infomation about human histone variants, sites of their post-translational modifications and about various histone modifying enzymes. HIstome data is available by browsing the contents. The database covers 5 types of histones, 8 types of their post-translational modifications and 13 classes of modifying enzymes. Current version contains information for about ~50 histone proteins and ~150 histone modifying enzymes. Many data fields are hyperlinked to other databases (e.g. UnprotKB/Swiss-Prot, HGNC, OMIM, Unigene etc.). Additionally, this database also provides sequences of promoter regions (-700 TSS +300) for all gene entries. These sequences were extracted from the UCSC genome browser. Sites of post-translational modifications of histones were manually searched from PubMed listed literature. This infobase would be of use to biology researchers, especially those interested in epigenetic regulation. We welcome ...
Hematopoietic differentiation is governed by a complex regulatory program controlling the generation of different lineages of blood cells from multipotent hematopoietic stem cells. The transcriptional program that dictates hematopoietic cell fate and differentiation requires an epigenetic memory function provided by a network of epigenetic factors regulating DNA methylation, posttranslational histone modifications, and chromatin structure. Aberrant interactions between epigenetic factors and transcription factors cause perturbations in the blood cell differentiation program that result in various types of hematopoietic disorders. To elucidate the contributions of different epigenetic factors in human hematopoiesis, high-throughput cap analysis of gene expression was used to build transcription profiles of 199 epigenetic factors in a wide range of blood cells. Our epigenetic transcriptome analysis revealed cell type- (eg, HELLS and ACTL6A), lineage- (eg, MLL), and/or leukemia- (eg, CHD2, CBX8, ...
Histone post-translational modification (PTM) is a marker for gene transcription and is involved in a range of cancers, such as breast cancer. Most importantly, different modifications of a specific site (e.g., mono-, di- and tri-methylations and acetylation at a lysine residue) are individually enriched in particu
Methylation of lysine residues on the tails of histone proteins is a major determinant of the transcription state of associated DNA coding regions. The interplay among methylation states and other histone modifications to direct transcriptional outcome is referred to as the histone code. In addition to histone methyltransferases and demethylases which function to modify the methylation state of lysine sidechains, other proteins recognize specific histone methylation marks essentially serving as code readers. While these interactions are highly specific with respect to site and methylation state of particular lysine residues, they are generally weak and therefore difficult to monitor by traditional assay techniques. Herein, we present the design and implementation of a homogeneous, miniaturizable, and sensitive assay for histone methylation-dependent interactions. We use AlphaScreen, a chemiluminescence-based technique, to monitor the interactions of chromodomains (MPP8, HP1beta and CHD1), tudor domains
The genetic information of a human diploid cell is contained within approximately 2 metres of linear DNA. The DNA molecules are compacted and organized in various ways to fit inside the cell nucleus. Various kinds of histones are involved in this compaction. One of these histones, histone H1 is the topic of the present thesis. In addition to its structural role, H1 histones have been implicated in various processes, for example gene regulation and inhibition of chromatin replication.. H1 histones, also termed linker histones, are relatively conserved proteins, and the various subtypes seem to have different and important functions even though redundancy between the subtypes has been demonstrated. Despite the sequence conservation of H1 subtypes, two sequence variations were detected within the H1.2 and H1.4 subtypes using hydrophilic interaction liquid chromatographic separation of H1 proteins from K562 and Raji cell lines in Paper I in the present thesis. The variations were confirmed by ...
Epigenetics is the study of heritable changes in gene expression that occur independent of changes in the primary DNA sequence. Chromatin structure defines the state in which genetic information is organized in the cell. The organization of this structure greatly influences the abilities of genes to be activated or silenced. In eukaryotic cells, 146 base pairs of DNA is wrapped around the histone octamer (two H2A/H2B dimers and one H3/H4 tetramer) forming the nucleosomes, the basic unit of chromatin. The nucleosome cores are connected by linker DNA sequences to further package into higher-order chromatin structures. In addition to the core histones, each histone contains an unstructured N-terminal tail. The histone tails are the sites of most of the post-translational modifications (PTMs), such as acetylation, methylation and phosphorylation. These modifications regulate the structure and function of chromatin through two general mechanisms. In the first model, histone modifications may play a ...