Epigenetics & Chromatin Biology

THERE ARE SEVERAL TYPES OF AETHERS I.E. THE ABORIGINAL CIRCULAR, THEN SQUARE THEN RECTANGULAR THEN THE HEXAGONAL AETHERS THAT WE SEE ALL AROUND US AND THE BOUNDARY LAYER THE PENTAGONAL AETHERS, WHICH PATRICK FLANAGAN POINTED OUT TO ME AS BEING WHERE DIFFERENTIATION STARTS.  THIS IS WHERE THE MAGIC HAPPENS.  ALL THINGS THAT HAVE A SKIN ARE INVOLVED WITH THE BOUNDARY LAYER AETHER. 

BLESSINGS,
MIKE

There is increasing evidence that abnormalities in epigenetic mechanisms of gene expression contribute to the development of multiple sclerosis (MS). Advances in epigenetics have given rise to a new class of drugs, epigenetic drugs. Although many classes of epigenetic drugs are being investigated, at present most attention is being paid to two classes of epigenetic drugs: drugs that inhibit DNA methyltransferase (DNMTi) and drugs that inhibit histone deacetylase (HDACi). This paper discusses the potential use of epigenetic drugs in the treatment of MS, focusing on DNMTi and HDACi. Preclinical drug trials of DNMTi and HDACi for the treatment of MS are showing promising results. Epigenetic drugs could improve the clinical management of patients with MS.

We aim to demonstrate the applicability of Peirce's iconic logic in the context of current topological explanations in the philosophy of science. We hold that the logical system of Existential Graphs is similar to contemporary topological approaches, thereby recognizing Peirce's iconic logic (Beta Graphs) as a valid method of scientific representation. We base our thesis on the nexus between iconic logic and the so-called NonReduction Theorem. We illustrate our assumptions with examples derived from biology (protein folding).

Plants interact with their environment by modifying gene expression patterns. One mechanism for this interaction
involves epigenetic modifications that affect a number of aspects of plant growth and development. Thus, the
epigenome is highly dynamic in response to environmental cues and developmental changes. Flowering is
controlled by a set of genes that are affected by environmental conditions through an alteration in their expression
pattern. This ensures the production of flowers even when plants are growing under adverse conditions, and thereby
enhances transgenerational seed production. In this review recent findings on the epigenetic changes associated
with flowering in Arabidopsis thaliana grown under abiotic stress conditions such as cold, drought, and high salinity
are discussed. These epigenetic modifications include DNA methylation, histone modifications, and the production
of micro RNAs (miRNAs) that mediate epigenetic modifications. The roles played by the phytohormones abscisic
acid (ABA) and auxin in chromatin remodelling are also discussed. It is shown that there is a crucial relationship
between the epigenetic modifications associated with floral initiation and development and modifications
associated with stress tolerance. This relationship is demonstrated by the common epigenetic pathways through
which plants control both flowering and stress tolerance, and can be used to identify new epigenomic players.

Recent studies suggest that individual subunits of chromatin-remodeling complexes produce biologically specific meaning in different cell types through combinatorial assembly. Here we show that granulocyte development requires SMARCD2, a subunit of ATP-dependent SWI/SNF (BAF) chromatin-remodeling complexes. Smarcd2-deficient mice fail to generate functionally mature neutrophils and eosinophils, a phenotype reminiscent of neutrophil-specific granule deficiency (SGD) in humans, for which loss-of-function mutations in CEBPE (encoding CEBPɛ) have been reported. SMARCD2-containing SWI/SNF complexes are necessary for CEBPɛ transcription factor recruitment to the promoter of neutrophilic secondary granule genes and for granulocyte differentiation. The homologous SMARCD1 protein (63% identical at the amino acid level) cannot replace the role of SMARCD2 in granulocyte development. We find that SMARCD2 functional specificity is conferred by its divergent coiled-coil 1 and SWIB domains. Strikingly, both CEBPE and SMARCD2 loss-of-function mutations identified in patients with SGD abolish the interaction with SWI/SNF and thereby secondary granule gene expression, thus providing a molecular basis for this disease.

The p53 protein is crucial for adapting programs of gene expression in response to stress. Recently, we revealed that this occurs partly through the formation of stress-specific p53 binding patterns. However, the mechanisms that generate these binding patterns remain largely unknown. It is not established whether the selective binding of p53 is achieved through modulation of its binding affinity to certain response elements (REs) or via a chromatin-dependent mechanism. To shed light on this issue, we used a microsphere assay for protein-DNA binding to measure p53 binding patterns on naked DNA. In parallel, we measured p53 binding patterns within chromatin using chromatin immunoprecipitation and DNase I coupled to ligationmediated polymerase chain reaction footprinting. Through this experimental approach, we revealed that UVB and Nutlin-3 doses, which lead to different cellular outcomes, induce similar p53 binding patterns on naked DNA. Conversely, the same treatments lead to stress-specific p53 binding patterns on chromatin. We show further that altering chromatin remodeling using an histone acetyltransferase inhibitor reduces p53 binding to REs. Altogether, our results reveal that the formation of p53 binding patterns is not due to the modulation of sequencespecific p53 binding affinity. Rather, we propose that chromatin and chromatin remodeling are required in this process.

. Consistent with this model, intrinsic histone acetylase activity has been found in various factors that play a role in activated transcription, including yeast and human GCN5 (Brownell et al., The transforming proteins encoded by adenovirus and several other small DNA tumor viruses disturb host cell growth control by interacting with cellular factors that Summary normally function to repress cell proliferation. Adenovirus E1A transforming activity resides in two distinct do-PCAF histone acetylase plays a role in regulation of mains, the targets of which include p300/CBP and the transcription, cell cycle progression, and differentiaretinoblastoma protein family (reviewed in Moran, 1993; tion. Here, we show that PCAF is found in a complex Nevins, 1994; Eckner, 1996). While the RB pathway has consisting of more than 20 distinct polypeptides. Strikbeen well studied, the p300/CBP pathway had not been ingly, some polypeptides are identical to TBP-assoclarified until our lab cloned the novel histone acetylase ciated factors (TAFs), which are subunits of TFIID. PCAF (Yang et al., 1996). Significantly, binding of E1A Like TFIID, histone fold-containing factors are present to p300/CBP disturbs access of PCAF acetylase to within the PCAF complex. The histone H3-and H2B-p300/CBP . In support of relevance like subunits within the PCAF complex are identical to of this competition, PCAF and E1A compete in regulation those within TFIID, namely, hTAF II 31 and hTAF II 20/15, of cell cycle progression, differentiation, and transcriptional activation: exogenous expression of PCAF in HeLa respectively. The PCAF complex has a novel histone cells inhibits cell cycle progression and counteracts the H4-like subunit with similarity to hTAF II 80 that intermitogenic activity of E1A . Exogenous acts with the histone H3-like domain of hTAFII31.

Background: The compaction of DNA in chromatin in eukaryotes allowed the expansion of genome size and
coincided with significant evolutionary diversification. However, chromatin generally represses DNA function, and
mechanisms coevolved to regulate chromatin structure and its impact on DNA. This included the selection of specific
nucleosome positions to modulate accessibility to the DNA molecule. Trypanosoma brucei, a member of the Excavates
supergroup, falls in an ancient evolutionary branch of eukaryotes and provides valuable insight into the organization
of chromatin in early genomes.
Results: We have mapped nucleosome positions in T. brucei and identified important differences compared to other
eukaryotes: The RNA polymerase II initiation regions in T. brucei do not exhibit pronounced nucleosome depletion,
and show little evidence for defined −1 and +1 nucleosomes. In contrast, a well‑positioned nucleosome is present
directly on the splice acceptor sites within the polycistronic transcription units. The RNA polyadenylation sites were
depleted of nucleosomes, with a single well‑positioned nucleosome present immediately downstream of the pre‑
dicted sites. The regions flanking the silent variant surface glycoprotein (VSG) gene cassettes showed extensive arrays
of well‑positioned nucleosomes, which may repress cryptic transcription initiation. The silent VSG genes themselves
exhibited a less regular nucleosomal pattern in both bloodstream and procyclic form trypanosomes. The DNA replication origins, when present within silent VSG gene cassettes, displayed a defined nucleosomal organization compared
with replication origins in other chromosomal core regions.
Conclusions: Our results indicate that some organizational features of chromatin are evolutionarily ancient, and may
already have been present in the last eukaryotic common ancestor.

The concept of chromatin as a complex of nucleic acid and proteins
in the cell nucleus was developed by cytologists and biochemists in the late 19th century. It was the starting point for biochemical research on DNA and nuclear proteins. Although interest in chromatin declined rapidly at the beginning of the 20th century, a few decades later a new focus on chromatin emerged, which was not only related to its structure, but also to its function in gene regulatory processes in the development
of higher organisms. Since the late 20th century, research on chromatin modifications has also been conducted under the label of epigenetics. This article highlights the major phases of chromatin research until the present time and introduces major investigators and their scientific and philosophical outlooks.

Imperatively Hidden Objects/Factors (IHO/F) refers to relevant items, which we cannot perceive and measure yet. Nevertheless, they have an impact on our predicted outcome. We have created model that allows for the integration and discovery for the still unknown. If researchers would take the time to understand it, they'd design their experimental studies in a much different way because their scientific objective would shift toward feature discovery to enhance feature selection to make even better predictions with supervised machine learning algorithms.

We describe a system designed to express biotinylated proteins in mammalian cells in vivo and its application to the study of protein–DNA interactions in vivo by chromatin immunoprecipitation (ChIP). The system is based on coexpression of the target protein fused to a short biotin acceptor domain together with the biotinylating enzyme BirA from Escherichia coli. The superior strength of the biotin–avidin interaction allows one to employ more stringent washing conditions in the ChIP protocol, resulting in a better signal/noise ratio.

Genomic DNA is prone to a large number of insults by a myriad of endogenous and exogenous agents. The base excision repair (BER) is the major mechanism used by cells for the removal of various DNA lesions spontaneously or environmentally induced and the maintenance of genome integrity. The presence of persistent DNA damage is not compatible with life, since abrogation of BER leads to early embryonic lethality in mice. There are several lines of evidences showing existence of a link between deficient BER, cancer proneness and ageing, thus illustrating the importance of this DNA repair pathway in human health. Although the enzymology of BER mechanisms has been largely elucidated using chemically defined DNA damage substrates and purified proteins, the complex interplay of BER with another vital process like transcription or when DNA is in its natural state (i.e. wrapped in nucleosome and assembled in chromatin fiber is largely unexplored. Cells use chromatin remodeling factors to overcome the general repression associated with the nucleosomal organization. It is broadly accepted that energy-dependent nucleosome remodeling factors disrupt histones-DNA interactions at the expense of ATP hydrolysis to favor transcription as well as DNA repair. Importantly, unlike transcription, BER is not part of a regulated developmental process but represents a maintenance system that should be efficient anytime and anywhere in the genome. In this review we will discuss how BER can deal with chromatin organization to maintain genetic information. Emphasis will be placed on the following challenging question: how BER is initiated within chromatin?

One of the most remarkable chromatin remodelling processes occurs during spermiogenesis, the post-meiotic phase of sperm development during which histones are replaced with sperm-specific protamines to repackage the genome into the highly compact chromatin structure of mature sperm. Here we identify Chromodomain helicase DNA binding protein 5 (Chd5) as a master regulator of the histone-to-protamine chromatin remodelling process. Chd5 deficiency leads to defective sperm chromatin compaction and male infertility in mice, mirroring the observation of low CHD5 expression in testes of infertile men. Chd5 orchestrates a cascade of molecular events required for histone removal and replacement, including histone 4 (H4) hyperacetylation, histone variant expression, nucleosome eviction and DNA damage repair. Chd5 deficiency also perturbs expression of transition proteins (Tnp1/Tnp2) and protamines (Prm1/2). These findings define Chd5 as a multi-faceted mediator of histoneto-protamine replacement and depict the cascade of molecular events underlying this process of extensive chromatin remodelling.

V(D)J recombination proceeds according to defined developmental programs at T-cell receptor (TCR) and immunoglobulin loci as a function of cell lineage and stage of differentiation. Although the molecular details are still lacking, such regulation is thought to occur at the level of accessibility of chromosomal recombination signal sequences to the recombinase. The unique and complex organization of the TCRa/d locus poses intriguing regulatory challenges in this regard: embedded TCRa and TCRd gene segments rearrange at distinct stages of thymocyte development, there is a highly regulated progression of primary followed by secondary rearrangements involving Ja segments, and there are important developmental constraints on V gene segment usage. The locus therefore provides a fascinating laboratory in which to explore the basic mechanisms underlying developmental control. We provide here a current view of cis-acting mechanisms that enforce the TCRa/d locus developmental program, and we emphasize the unresolved issues that command the attention of our and other laboratories.

1988; Lee et al., 1993). University of Southern California Recent observations indicate that the N-terminal tails Los Angeles, California 90033 of histones contact histones of adjacent nucleosomes † Department of Biology rather than interacting directly with the DNA (Luger et Center for Molecular Genetics al., 1997) and that transcriptional regulatory molecules, University of California, San Diego other than histones, are targets of HATs (Gu and Roeder,

Chromatin-remodeling factors regulate the establishment of transcriptional programs during plant development. Although 42 genes encoding members of the SWI2͞SNF2 family have been identified in Arabidopsis thaliana, <10 have been assigned a precise function on the basis of a mutant phenotype, and none have been shown to play a specific role during the gametophytic phase of the plant life cycle. A. thaliana chromatin-remodeling protein 11 (CHR11) encodes an imitation of switch (ISWI)-like chromatin-remodeling protein abundantly expressed during female gametogenesis and embryogenesis in Arabidopsis. To determine the function of CHR11 in wild-type plants, we introduced a hairpin construct leading to the production of double-stranded RNA, which specifically degraded the endogenous CHR11 mRNA by RNA interference (RNAi). Transcription of the RNAi-inducing hairpin RNA was driven by either a constitutive cauliflower mosaic virus 35S promoter (CaMV35S) acting at most stages of the sporophytic phase or a newly identified specific promoter acting at the onset of the female gametophytic phase (pFM1). All adult transformants that constitutively lacked sporophytic CHR11 activity showed reduced plant height and small cotyledonary embryos with limited cell expansion. In contrast, RNAi lines in which CHR11 was specifically silenced at the onset of female gametogenesis (megagametogenesis) had normal height and embryo size but had defective female gametophytes arrested before the completion of the mitotic haploid nuclear divisions. These results show that CHR11 is essential for haploid nuclear proliferation during megagametogenesis and cell expansion during the sporophytic phase, demonstrating the functional versatility of SWI2͞SNF2 chromatinremodeling factors during both generations of the plant life cycle.

We aim to demonstrate the applicability of Peirce’s iconic logic in the context of current topological explanations in the philosophy of science. We hold that the logical system of Existential Graphs is similar to contemporary topological approaches, thereby recognizing Peirce’s iconic logic (Beta Graphs) as a valid method of scientific representation. We base our thesis on the nexus between iconic logic and the so-called NonReduction Theorem. We illustrate our assumptions with examples derived from biology (protein folding).

Genomic DNA is prone to a large number of insults by a myriad of endogenous and exogenous agents. The base excision repair (BER) is the major mechanism used by cells for the removal of various DNA lesions spontaneously or environmentally induced and the maintenance of genome integrity. The presence of persistent DNA damage is not compatible with life, since abrogation of BER leads to early embryonic lethality in mice. There are several lines of evidences showing existence of a link between deficient BER, cancer proneness and ageing, thus illustrating the importance of this DNA repair pathway in human health. Although the enzymology of BER mechanisms has been largely elucidated using chemically defined DNA damage substrates and purified proteins, the complex interplay of BER with another vital process like transcription or when DNA is in its natural state (i.e. wrapped in nucleosome and assembled in chromatin fiber is largely unexplored. Cells use chromatin remodeling factors to over...

Epigenomic data sets provide critical information about the dynamic role of chromatin states
in gene regulation, but a key question of how chromatin state segmentations vary under
different conditions across the genome has remained unaddressed. Here we present
ChromDiff, a group-wise chromatin state comparison method that generates an information theoretic representation of epigenomes and corrects for external covariate factors to better isolate relevant chromatin state changes. By applying ChromDiff to the 127 epigenomes from the Roadmap Epigenomics and ENCODE projects, we provide novel group-wise comparative analyses across sex, tissue type, state and developmental age. Remarkably, we find that distinct sets of epigenomic features are maximally discriminative for different group-wise comparisons, in each case revealing distinct enriched pathways, many of which do not show gene expression differences. Our methodology should be broadly applicable for epigenomic comparisons and provides a powerful new tool for studying chromatin state differences at the genome scale.

Epigenomics is the collective study of all epigenetic modifications that can affect the genome, the most pivotal of which are DNA methylation (DNAm), histone modifications (e.g., acetylation, citrullination and phosphorylation) and nucleosome remodeling. The latter refers to the dynamic reorganization in the spatial arrangement of chromatin by means of repositioning the nucleosomes, which are short segments of DNA, consisting of approximately 200 base pairs, coiled around eight histone proteins. The resulting alterations in the structure of these bead-like complexes may favor or oppose transcription, determining the course of disease pathogenesis [1], such as coronavirus disease 2019 (COVID-19). Known to correlate inversely with gene expression, DNAm might be associated with increased susceptibility of the pulmonary tissue to COVID-19 [2] and a higher predisposition to this viral disease in patients with pancreatic [3] and prostate cancer [4]. A lesser known epigenetic mechanism, 'X inactivation' is thought to be connected with the function of innate immunity against COVID-19, particularly in male patients [5]. Furthermore, immunity is also influenced by the extensively diverse histone modifications, especially histone citrullination [6]. Nucleosome remodeling, mediated by contextually important proteins such as SMARCA4 and SMAD3, is another epigenetic mechanism that can affect the course of disease, assuming a patient-wise unfavorable role in the case of COVID-19 [7]. The footprint of epigenomics can even be traced back to prenatal life, when developmentally crucial genes such as PEG10 and ECE1, can be affected by DNAm in response to maternal COVID-19 [8], indicating the overall significance of epigenetics in the recent viral pandemic. COVID-19: unwelcome infection facilitated by epigenetic modifications A consequence of SARS coronavirus 2 (SARS-CoV-2) infection, COVID-19 is perhaps the greatest health issue of the century, affecting more than 45 million individuals, with a global death toll exceeding one million [7]. The recent, less-anticipated advent of novel SARS-CoV-2 variants with altered Spike proteins, including the strain with 'Spike N453Y' mutation reported in Netherlands and Denmark; and the more overwhelming variants with 'Spike D614G' and 'N501Y' mutations spreading in England, has caused concerns regarding the efficacy of the recently approved vaccines in the future. The N501Y variant, in particular, has been suggested to be 56% more transmissible, owing to the enhanced binding affinity of the Spike protein to its polypeptide receptor, ACE2, on the host cell [9]; a finding with potential epigenetic implications. Containing a positive-sense ssRNA, SARS-CoV-2 is an enveloped β-coronavirus coated with Spike protein on its surface, which relies on the interaction between this protein and the transmembrane ACE2 on the host cell for viral entry. The epigenetic modifications, especially DNAm, regulating the expression of ACE2 had been known well before the emergence of SARS-CoV-2 [2]. Nonetheless, the rising prominence of epigenomics in the expansive research field of COVID-19 is not solely due to the role of ACE2 in the pathophysiology of the disease, as 332 human proteins have recently been identified to interact with SARS-CoV-2 proteins in several ways. A noteworthy example is HDAC2, which is involved in the initiation of immune responses against viruses [10]. HDAC2 contains a cleavage site that can be targeted by NSP5, Epigenomics

The tails of histone proteins are central players for all chromatin-mediated processes. Whereas the N-terminal histone tails have been studied extensively, little is known about the function of the H2A C-terminus. Here, we show that the H2A Cterminal tail plays a pivotal role in regulating chromatin structure and dynamics. We find that cells expressing C-terminally truncated H2A show increased stress sensitivity. Moreover, both the complete and the partial deletion of the tail result in increased histone exchange kinetics and nucleosome mobility in vivo and in vitro. Importantly, our experiments reveal that the H2A C-terminus is required for efficient nucleosome translocation by ISWI-type chromatin remodelers and acts as a novel recognition module for linker histone H1. Thus, we suggest that the H2A C-terminal tail has a bipartite function: stabilisation of the nucleosomal core particle, as well as mediation of the protein interactions that control chromatin dynamics and conformation.

Post-translational modifications (PTMs) of histones constitute a major chromatin indexing mechanism, and their proper characterization is of highest biological importance. So far, PTM-specific antibodies have been the standard reagent for studying histone PTMs despite caveats such as lot-to-lot variability of specificity and binding affinity. Herein, we successfully employed naturally occurring and engineered histone modification interacting domains for detection and identification of histone PTMs and ChIP-like enrichment of different types of chromatin. Our results demonstrate that histone interacting domains are robust and highly specific reagents that can replace or complement histone modification antibodies. These domains can be produced recombinantly in Escherichia coli at low cost and constant quality. Protein design of reading domains allows for generation of novel specificities, addition of affinity tags, and preparation of PTM binding pocket variants as matching negative controls, which is not possible with antibodies.

Background: Alzheimer’s disease (AD) is a neurodegenerative disorder characterized by amyloid-β (Aβ) plaque formation, tau pathology, neurodegeneration and inflammatory processes. Monocytes are involved in inflammation in AD and are recruited to the diseased brain. Recently it has been shown that aberrant epigenetic processes including acetylation are associated with the development of AD. The aim of the present study was to examine acetylation of histone H4 at lysine 12 (H4K12) in monocytes in two transgenic AD mouse models (the triple transgenic 3xTg and a model overexpressing amyloid-precursor protein APP with the Swedish-Dutch-Iowa mutations), and to compare with monocytes isolated from human patients with mild cognitive impairment (MCI) and AD. Methods: Mouse and human monocytes were selectively isolated with a positive (PluriSelect) respectively with a negative selection method (Miltenyi). Histones were extracted and acetylation of H4K12 was analyzed by a quantification fluorometric kit. Moreover, monocyte cytokine release was measured and cell death analyzed by FACS using incorporation of 7-AAD. Results: Our data show a significant increase of monocytic H4K12 acetylation in both transgenic AD mouse models early during development of the plaque deposition in the brain. In line with these data we found significantly elevated acetylation of H4K12 in human patients with MCI but not in patients with AD. Further we observed that the monocytes of AD mice and of AD patients were significantly more vulnerable to cell damage (as seen by 7-AAD incorporation in FACS analysis) and displayed an enhanced release of pro-inflammatory cytokines (MIP2 and TNFα). Conclusion: Our findings indicate that epigenetic changes in peripheral monocytes are an early event in AD-pathology. Thus H4K12 acetylation may be considered as a novel biomarker for early changes in AD development.

Resistance to chemotherapy, biological and targeted therapies is an important clinical problem. Resistance can arise and/or be selected for multiple mechanisms of action. Unfortunately, acquired resistance to antitumor agents or regimens is nearly inevitable in all patients with metastatic disease. Until recently, it was believed that this resistance was unalterable and irreversible, rendering retreatment with the same or similar drugs futile in most cases. However, the introduction of epigenetic therapies, including HDAC inhibitors and DNA methyltransferase inhibitors (DNMTIs), has provided oncologists with new strategies to potentially overcome this resistance. For example, if chemoresistance is the product of multiple non-genetic alterations, which develop and accumulate over time in response to treatment, then the ability to epigenetically modify the tumor to reconfigure it back to its baseline non-resistant state, holds tremendous promise for the treatment of advanced, metastatic cancer. This minireview aims (1) to explore the potential mechanisms by which a group of small molecule agents including HDACs (entinostat and vorinostat), DNA hypomethylating agents such as the DNMTIs (decitabine (DEC), 5-azacytidine (5-AZA)) and redox modulators (RRx-001) may reprogram the tumors from a refractory to non-refractory state, (2) highlight some recent findings in this area, and (3) discuss the therapeutic potential of resensitization approaches with formerly failed chemotherapies.

PCAF is a histone acetyltransferase that associates with p300/CBP and competes with E1A for access to them. While exogenous expression of PCAF potentiates both MyoD-directed transcription and myogenic differentiation, PCAF inactivation by anti-PCAF antibody microinjection prevents differentiation. MyoD interacts directly with both p300/CBP and PCAF, forming a multimeric protein complex on the promoter elements. Viral transforming factors that interfere with muscle differentiation disrupt this complex without affecting the MyoD–DNA interaction, indicating functional significance of the complex formation. Exogenous expression of PCAF or p300 promotes p21 expression and terminal cell-cycle arrest. Both of these activities are dependent on the histone acetyltransferase activity of PCAF, but not on that of p300. These results indicate that recruitment of histone acetyltransferase activity of PCAF by MyoD, through p300/CBP, is crucial for activation of the myogenic program.

p300/CBP is a transcriptional adaptor that integrates signals from many sequence-specific activators via direct interactions. Various cellular and viral factors target p300/CBP to modulate transcription and/or cell cycle progression. One such factor, the cellular p300/CBP associated factor (PCAF), possesses intrinsic histone acetyltransferase activity. Here, we demonstrate that p300/CBP is not only a transcriptional adaptor but also a histone acetyltransferase. p300/CBP represents a novel class of acetyltransferases in that it does not have the conserved motif found among various other acetyltransferases. p300/CBP acetylates all four core histones in nucleosomes. These observations suggest that p300/CBP acetylates nucleosomes in concert with PCAF.

CRISPR/Cas technologies have rapidly become routine in many laboratories. Despite this, the efficiency of CRISPR/Cas9 functioning cannot entirely be predicted, and it is not fully understood which factors contribute to this variability. Recent studies indicate that heterochromatin can negatively affect Cas9 binding and functioning. Investigating chromatin factors indicates that 5-cytosine methylation does not directly block Cas9 binding. Nucleosomes, however, can completely block Cas9 access to DNA in cell-free assays and present a substantial hurdle in vivo. In addition to being associated with an open chromatin state, active transcription can directly stimulate DNA cleavage by influencing Cas9 release rates in a strand-specific manner. With these insights and a better understanding of genome-wide chromatin and transcription states, CRISPR/Cas9 effectiveness and reliability can be improved.

In a cell, the chromatin state is controlled by the highly regulated interplay of epigenetic mechanisms ranging from DNA methylation and incorporation of different histone variants to posttranslational modification of histones and ATP-dependent chromatin remodeling. These changes alter the structure of the chromatin to either facilitate or restrict the access of transcription machinery to DNA. These epigenetic modifications function to exquisitely orchestrate the expression of different genes, and together constitute the epigenome of a cell. In the skin, different epigenetic regulators form a regulatory network that operates to guarantee skin stem cell maintenance while controlling differentiation to multiple skin structures. In this review, we will discuss recent findings on epigenetic mechanisms of skin control and their relationship to skin pathologies.

Aflatoxin B1 (AFB1) is currently the most commonly studied mycotoxin due to its great toxicity, its distribution in a wide variety of foods such as grains and cereals and its involvement in the development of + (HCC). HCC is one of the main types of liver cancer, and has become a serious public health problem, due to its high incidence mainly in Southeast Asia and Africa. Studies show that AFB1 acts in synergy with other risk factors such as hepatitis B and C virus (HBV and HCV) leading to the development of HCC through genetic and epigenetic modifications. The genetic modifications begin in the liver through the biomorphic AFB1, the AFB1-exo-8.9-Epoxy active, which interacts with DNA to form adducts of AFB1-DNA. These adducts induce mutation in codon 249, mediated by a transversion of G to T in the p53 tumor suppressor gene, causing HCC. Thus, this review provides an overview of the evidence for AFB1-induced epigenetic alterations and the potential mechanisms involved in the development of HCC, focusing on a critical analysis of the importance of severe legislation in the detection of aflatoxins.

Epigenetic regulation consists of a multitude of different modifications that determine active and inactive states of chromatin. Conditions such as cell differentiation or exposure to environmental stress require concerted changes in gene expression. To interpret epigenomics data, a spectrum of different interconnected datasets is needed, ranging from the genome sequence and positions of histones, together with their modifications and variants, to the transcriptional output of genomic regions. Here we present a tool, Podbat (Positioning database and analysis tool), that incorporates data from various sources and allows detailed dissection of the entire range of chromatin modifications simultaneously. Podbat can be used to analyze, visualize, store and share epigenomics data. Among other functions, Podbat allows data-driven determination of genome regions of differential protein occupancy or RNA expression using Hidden Markov Models. Comparisons between datasets are facilitated to enable the study of the comprehensive chromatin modification system simultaneously, irrespective of data-generating technique. Any organism with a sequenced genome can be accommodated. We exemplify the power of Podbat by reanalyzing all to-date published genome-wide data for the histone variant H2A.Z in fission yeast together with other histone marks and also phenotypic response data from several sources. This meta-analysis led to the unexpected finding of H2A.Z incorporation in the coding regions of genes encoding proteins involved in the regulation of meiosis and genotoxic stress responses. This incorporation was partly independent of the H2A.Z-incorporating remodeller Swr1. We verified an Swr1-independent role for H2A.Z following genotoxic stress in vivo. Podbat is open source software freely downloadable from www.podbat.org, distributed under the GNU LGPL license. User manuals, test data and instructions are available at the website, as well as a repository for third party-developed plug-in modules. Podbat requires Java version 1.6 or higher.

Chromatin-remodeling factors regulate the establishment of transcriptional programs during plant development. Although 42 genes encoding members of the SWI2͞SNF2 family have been identified in Arabidopsis thaliana, <10 have been assigned a precise function on the basis of a mutant phenotype, and none have been shown to play a specific role during the gametophytic phase of the plant life cycle. A. thaliana chromatin-remodeling protein 11 (CHR11) encodes an imitation of switch (ISWI)-like chromatin-remodeling protein abundantly expressed during female gametogenesis and embryogenesis in Arabidopsis. To determine the function of CHR11 in wild-type plants, we introduced a hairpin construct leading to the production of double-stranded RNA, which specifically degraded the endogenous CHR11 mRNA by RNA interference (RNAi). Transcription of the RNAi-inducing hairpin RNA was driven by either a constitutive cauliflower mosaic virus 35S promoter (CaMV35S) acting at most stages of the sporophytic phase or a newly identified specific promoter acting at the onset of the female gametophytic phase (pFM1). All adult transformants that constitutively lacked sporophytic CHR11 activity showed reduced plant height and small cotyledonary embryos with limited cell expansion. In contrast, RNAi lines in which CHR11 was specifically silenced at the onset of female gametogenesis (megagametogenesis) had normal height and embryo size but had defective female gametophytes arrested before the completion of the mitotic haploid nuclear divisions. These results show that CHR11 is essential for haploid nuclear proliferation during megagametogenesis and cell expansion during the sporophytic phase, demonstrating the functional versatility of SWI2͞SNF2 chromatinremodeling factors during both generations of the plant life cycle.

. Consistent with this model, intrinsic histone acetylase activity has been found in various factors that play a role in activated transcription, including yeast and human GCN5 (Brownell et al., The transforming proteins encoded by adenovirus and several other small DNA tumor viruses disturb host cell growth control by interacting with cellular factors that Summary normally function to repress cell proliferation. Adenovirus E1A transforming activity resides in two distinct do-PCAF histone acetylase plays a role in regulation of mains, the targets of which include p300/CBP and the transcription, cell cycle progression, and differentiaretinoblastoma protein family (reviewed in Moran, 1993; tion. Here, we show that PCAF is found in a complex Nevins, 1994; Eckner, 1996). While the RB pathway has consisting of more than 20 distinct polypeptides. Strikbeen well studied, the p300/CBP pathway had not been ingly, some polypeptides are identical to TBP-assoclarified until our lab cloned the novel histone acetylase ciated factors (TAFs), which are subunits of TFIID. PCAF (Yang et al., 1996). Significantly, binding of E1A Like TFIID, histone fold-containing factors are present to p300/CBP disturbs access of PCAF acetylase to within the PCAF complex. The histone H3-and H2B-p300/CBP . In support of relevance like subunits within the PCAF complex are identical to of this competition, PCAF and E1A compete in regulation those within TFIID, namely, hTAF II 31 and hTAF II 20/15, of cell cycle progression, differentiation, and transcriptional activation: exogenous expression of PCAF in HeLa respectively. The PCAF complex has a novel histone cells inhibits cell cycle progression and counteracts the H4-like subunit with similarity to hTAF II 80 that intermitogenic activity of E1A . Exogenous acts with the histone H3-like domain of hTAFII31.

Plants interact with their environment by modifying gene expression patterns. One mechanism for this interaction involves epigenetic modifications that affect a number of aspects of plant growth and development. Thus, the epigenome is highly dynamic in response to environmental cues and developmental changes. Flowering is controlled by a set of genes that are affected by environmental conditions through an alteration in their expression pattern. This ensures the production of flowers even when plants are growing under adverse conditions, and thereby enhances transgenerational seed production. In this review recent findings on the epigenetic changes associated with flowering in Arabidopsis thaliana grown under abiotic stress conditions such as cold, drought, and high salinity are discussed. These epigenetic modifications include DNA methylation, histone modifications, and the production of micro RNAs (miRNAs) that mediate epigenetic modifications. The roles played by the phytohormones abscisic acid (ABA) and auxin in chromatin remodelling are also discussed. It is shown that there is a crucial relationship between the epigenetic modifications associated with floral initiation and development and modifications associated with stress tolerance. This relationship is demonstrated by the common epigenetic pathways through which plants control both flowering and stress tolerance, and can be used to identify new epigenomic players.

Sleep is an essential physiological process, which has been divided into rapid eye movement sleep (REMS) and non-REMS (NREMS) in higher animals. REMS is a unique phenomenon that unlike other sleep-waking states is not under voluntary control. Directly or indirectly it influences or gets influenced by most of the physiological processes controlled by the brain. It has been proposed that REMS serves housekeeping function of the brain. Extensive research has shown that during REMS at least noradrenaline (NA)-ergic neurons must cease activity and upon REMS loss, there are increased levels of NA in the brain, which then induces many of the REMS loss associated acute and chronic effects. The NA level is controlled by many bio-molecules that are regulated at the molecular and transcriptional levels. Similarly, NA can also directly or indirectly modulate the synthesis and levels of many molecules, which in turn may affect physiological processes. The burgeoning field of behavioral neuroepigenetics has gained importance in recent years and explains the regulatory mechanisms underlying several behavioral phenomena. As REMS and its loss associated changes in NA modulate several pathophysiological processes, in this review we have attempted to explain on one hand how the epigenetic mechanisms regulating the gene expression of factors like tyrosine hydroxylase (TH), monoamine oxidase (MAO), noradrenaline transporter (NAT) control NA levels and on the other hand, how NA per se can affect other molecules in neural circuitry at the epigenetic level resulting in behavioral changes in health and diseases. An understanding of these events will expose the molecular basis of REMS and its loss-associated pathophysiological changes; which are presented as a testable hypothesis for confirmation.

We have isolated a human RNA polymerase II complex that contains chromatin structure remodeling activity and histone acetyltransferase activity. This complex contains the Srb proteins, the Swi-Snf complex, and the histone acetyltransferases CBP and PCAF in addition to RNA polymerase II. Notably, the general transcription factors are absent from this complex. The complex was purified by two different methods: conventional chromatography and affinity chromatography using antibodies directed against CDK8, the human homolog of the yeast Srb10 protein. Protein interaction studies demonstrate a direct interaction between RNA polymerase II and the histone acetyltransferases p300 and PCAF. Importantly, Purification of RNAPII complexes. RNAPII complexes were purified as follows. HeLa cell nuclear extracts (2.3 g) were fractionated on a 500-ml phosphocellulose (Sigma) column which was step eluted with buffer C (20 mM Tris-HCl [pH 7.85], 0.2 mM EDTA, 10 mM ␤-mercaptoethanol, 10% [vol/vol] glycerol, 0.2 mM phenylmethylsulfonyl fluoride [PMSF]) containing 0.1 M KCl (BC100) (0.8 g of protein), 0.3 M KCl (0.5 g of protein), 0.5 M KCl (0.3 g of protein), and 1.0 M KCl (0.1 g of protein)

Histone acetyltransferases (HAT) play a critical role in transcriptional control by relieving repressive effects of chromatin, and yet how HATs themselves are regulated remains largely unknown. Here, it is shown that Twist directly binds two independent HAT domains of acetyltransferases, p300 and p300/CBP–associated factor (PCAF), and directly regulates their HAT activities. The N terminus of Twist is a primary domain interacting with both acetyltransferases, and the same domain is required for inhibition of p300-dependent transcription by Twist. Adenovirus E1A protein mimics the effects of Twist by inhibiting the HAT activities of p300 and PCAF. These findings establish a cogent argument for considering the HAT domains as a direct target for acetyltransferase regulation by both a cellular transcription factor and a viral oncoprotein.