Near promoters, both nucleosomes and CpG sites form characteristic spatial patterns. Previously, nucleosome depleted regions were observed upstream of transcription start sites and nucleosome occupancy was reported to correlate both with CpG density and the level of CpG methylation. Several studies imply a causal link where CpG methylation might induce nucleosome formation, whereas others argue the opposite, i.e. that nucleosome occupancy might influence CpG methylation. Correlations are indeed evident between nucleosomes, CpG density and CpG methylation - at least near promoter sites. It is however less established whether there is an immediate causal relation between nucleosome occupancy and the presence of CpG sites - or if nucleosome occupancy could be influenced by other factors. In this work, we test for such causality in human genomes by analyzing the three quantities both near and away from promoter sites. For data from the human genome we compare promoter regions with given CpG densities with
The role of genomic sequence in directing the packaging of eukaryotic genomes into chromatin has been the subject of considerable recent debate. A new paper from Tillo and Hughes shows that the intrinsic thermodynamic preference of a given sequence in the yeast genome for the histone octamer can largely be captured with a simple model, and in fact is mostly explained by %GC. Thus, the rules for predicting nucleosome occupancy from genomic sequence are much less complicated than has been claimed. See research article http://www.biomedcentral.com/1471-2105/10/442
Nucleosomes inhibit DNA repair in vitro, suggesting that chromatin remodeling activities might be required for efficient repair in vivo. To investigate how structural and dynamic properties of nucleosomes affect damage recognition and processing, we investigated repair of UV lesions by photolyase on a nucleosome positioned at one end of a 226-bp-long DNA fragment. Repair was slow in the nucleosome but efficient outside. No disruption or movement of the nucleosome was observed after UV irradiation and during repair. However, incubation with the nucleosome remodeling complex SWI/SNF and ATP altered the conformation of nucleosomal DNA as judged by UV photo-footprinting and promoted more homogeneous repair. Incubation with yISW2 and ATP moved the nucleosome to a more central position, thereby altering the repair pattern. This is the first demonstration that two different chromatin remodeling complexes can act on UV-damaged nucleosomes and modulate repair. Similar activities might relieve the inhibitory
Nucleosomes are the fundamental packing units of the eukaryotic genome. Understanding the dynamic structure of a nucleosome is a key to the elucidation of genome packaging in eukaryotes, which is tied to the mechanisms of gene regulation. CpG methylation of DNA is an epigenetic modification associated with the inactivation of transcription and the formation of a repressive chromatin structure. Unraveling the changes in the structure of nucleosomes upon CpG methylation is an essential step toward the understanding of the mechanisms of gene repression and silencing by CpG methylation. Here we report single-molecule and ensemble fluorescence studies showing how the structure of a nucleosome is affected by CpG methylation. The results indicate that CpG methylation induces tighter wrapping of DNA around the histone core accompanied by a topology change. These findings suggest that changes in the physical properties of nucleosomes induced upon CpG methylation may contribute directly to the formation of a
Nucleosomes are elementary units of chromatin compaction, which play crucial role in genome functioning. X-ray crystallographic studies of the nucleosome core consistently revealed a compact structure that has approximately 147 DNA base pairs wrapped in a
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TY - JOUR. T1 - A Multi-Layer Method to Study Genome-Scale Positions of Nucleosomes. AU - Lo Bosco, Giosue. AU - Di Gesu, Vito. AU - Corona, Davide. AU - Di Gesù, Vito. AU - Pinello, Luca. AU - Lo Bosco, Giosuè. AU - Yuan, Guo-Cheng. AU - Pinello, Luca. PY - 2009. Y1 - 2009. N2 - The basic unit of eukaryotic chromatin is the nucleosome, consisting of about 150 bp of DNA wrapped arounda protein core made of histone proteins. Nucleosomes position is modulated in vivo to regulate fundamentalnuclear processes. To measure nucleosome positions on a genomic scale both theoretical and experimentalapproaches have been recently reported. We have developed a new method, Multi-Layer Model (MLM), forthe analysis of nucleosome position data obtained with microarray-based approach. The MLM is a featureextraction method in which the input data is processed by a classifier to distinguish between several kinds ofpatterns. We applied our method to simulated-synthetic and experimental nucleosome position data ...
Nucleosome-free regions (NFRs) in the 5′ and 3′ ends of genes are general A-770041 sites of transcription initiation for mRNA and noncoding RNA (ncRNA). spanning gene-coding areas and transcriptional regulatory areas. Gene-coding areas generally possess high nucleosome occupancy with arrays of well-phased nucleosomes increasing through the 5′ end of the gene. On the A-770041 other hand transcriptional regulatory areas such as for example promoters enhancers and terminators possess low nucleosome occupancy and frequently include a nucleosome-free area (NFR). NFRs also called nucleosome-depleted areas (NDRs) typically represent areas with an elevated option of micrococcal nuclease (MNase) digestive function. Thus the word NFR identifies a insufficiency in experimentally established canonical nucleosomes and will not always imply an A-770041 entire insufficient histones. To day predominately two main classes of NFRs 5 and 3′-NFRs have already been characterized. In cis as yet not known. ...
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The Chromatin Accessibility Complex (CHRAC) and ATP-utilizing chromatin assembly and remodeling factor (ACF) of Drosophila melanogaster are chromatin remodeling complexes that slide nucleosomes (Becker and Horz, 2002). Both originate from the association of the ATPase ISWI and a large subunit ACF1. CHRAC contains two additional histone-fold subunits, CHRAC-14 and CHRAC-16 (Corona et al., 2000), but its nucleosome sliding activity is essentially similar to ACF in vitro (Hartlepp et al., 2005). CHRAC/ACF are implicated in several developmental processes. Mutations of ACF1, which disrupt both complexes, mildly perturb embryogenesis and oogenesis (Boerner et al., 2016; Chioda et al., 2010), and compromise Polycomb silencing and heterochromatin formation (Fyodorov et al., 2004). Through their nucleosome sliding activity CHRAC/ACF contribute to the genome-wide formation of regular nucleosome arrays. Altered nucleosome spacing and regularity in their absence correlates with leakiness of the ...
Eukaryotic DNA is packaged in chromatin, whose repeating subunit, the nucleosome, consists of an octamer of histone proteins wrapped by about 147bp of DNA. This packaging affects the accessibility of DNA and hence any process that occurs on DNA, such as replication, repair, and transcription. An early observation from genome-wide nucleosome mapping in yeast was that genes had a surprisingly characteristic structure, which has motivated studies to understand what determines this architecture. Both sequence and trans acting factors are known to influence chromatin packaging, but the relative contributions of cis and trans determinants of nucleosome positioning is debated. Here we present data using genetic approaches to examine the contributions of cis and trans acting factors on nucleosome positioning in budding yeast. We developed the use of yeast artificial chromosomes to exploit quantitative differences in the chromatin structures of different yeast species. This allows us to place approximately 150kb
The organization of eukaryotic genomes into nucleosome arrays restricts DNA sequence accessibility to many nuclear factors. Thus most DNA-based processes require opening (or "re-closing") of these arrays. One major class of enzymes, the "chromatin/nucleosome remodeling" factors, uses ATP hydrolysis to alter the canonical histone-DNA contacts. The term "nucleosome remodeling" can be defined and monitored in different ways (Flaus and Owen-Hughes, 2004). The simplest configuration to study one aspect of nucleosome remodeling is to use a purely reconstituted system consisting of mononucleosomes and an ATP-dependent nucleosome remodeler in the so-called "nucleosome sliding" or "nucleosome mobilization" assay. This technique was initially developed by Carl Wu and Peter Becker laboratories (Hamiche et al., 1999; Langst et al., 1999) by taking advantage of two nucleosome properties: Nucleosomal histones can moderately move on DNA under rather mild temperature and salt conditions (Beard, 1978; Meersseman ...
Nucleosomes are important for gene regulation because their arrangement on the genome can control which proteins bind to DNA. Currently, few human nucleosomes are thought to be consistently positioned across cells; however, this has been difficult to assess due to the limited resolution of existing data. We performed paired-end sequencing of micrococcal nuclease-digested chromatin (MNase-seq) from seven lymphoblastoid cell lines and mapped over 3.6 billion MNase-seq fragments to the human genome to create the highest-resolution map of nucleosome occupancy to date in a human cell type. In contrast to previous results, we find that most nucleosomes have more consistent positioning than expected by chance and a substantial fraction (8.7%) of nucleosomes have moderate to strong positioning. In aggregate, nucleosome sequences have 10 bp periodic patterns in dinucleotide frequency and DNase I sensitivity; and, across cells, nucleosomes frequently have translational offsets that are multiples of 10 bp. ...
Mono- and Stereopictres of 5.0 Angstrom coordination sphere of Arsenic atom in PDB 1eqz: X-Ray Structure of the Nucleosome Core Particle At 2.5 A Resolution
The potential locations of the secondary DNA-binding site of GH5, given the dimensions of nucleosomal DNA and the distance between the GH5 binding sites, was modeled next. DNA already associated with GH5 as part of the model of the primary DNA-binding site of GH5 as linker DNA was "ligated" to the nucleosomal DNA termini of the crystal structure of the nucleosome (Luger et al. 1997) in silico. It was possible to attach this linker DNA-GH5 construct to the nucleosomal core particle terminus in a manner consistent with the recent cross-linking evidence supplied by Zhou et al. (1998), where the putative secondary DNA-binding site contacts DNA near the nucleosomal dyad. In this orientation, the b-hairpin of GH5 extends into the nucleosome. It was clear that the secondary DNA binding site does not consist of a distinct site, but rather an interaction surface generated by the C-terminal end of helix I, the inter-helical segment connecting helix I and II, and distinct contact points in both strands of ...
Relation between different nucleosomes, Organization of Genetic Material Packaging of DNA as Nucleosomes in Eukaryotes, Genetics
We assumed that the interaction of chromatin remodeling factors with nucleosomes would involve local detachments of the nucleosomal DNA from histones during DNA transaction. Therefore, we studied the interaction of chromatin remodeling factors with nicked nucleosomes by biochemical and structural analyses. As a result, the introduction of a double-strand break (DSB) into the nucleosomal DNA allows a histone chaperone FACT to efficiently form a complex with nucleosomes. It is thus indicated that DNA cleavages on nucleosomes would cause local unwrapping of the nucleosomal DNA in the vicinity of the cleavage sites upon contacting FACT, leading to subsequent reactions for chromatin remodeling. ...
There is a growing interest in manipulating chromatin dynamics for applications in cell signalling, drug discovery and chromatin research. Progress in this area requires the identification of design rules for the chromatin system.. DNA in cells is wrapped around proteins called histones forming structures known as nucleosomes. These nucleosomes can fold into higher ordered structures, concealing DNA within them. This reduces accessibility to the DNA and adds another layer to the regulation of gene expression. This is a new target for drug discovery.. Opening of these structures to expose the DNA is influenced, among other factors, by gene expression levels. The deregulation of gene expression levels could be responsible for many diseases possibly because proteins in charge of the burial of DNA in the nucleosomes are themselves deregulated. Studying these potential changes in gene expression without altering the underlying DNA sequence is known as Epigenetics, an actively expanding research ...
The linker histones H1/H5 bind to the entry and exit points of nucleosomal DNA and protect additional ~20 bp at one end. However, it is unclear whether there is any sequence feature at the ends of nucleosomal DNA facilitating the linker histone binding. T
TY - JOUR. T1 - A topological model for chromatin transcription and a role for nucleosome linkers. AU - Grigoryev, Sergei A.. AU - Krasheninnikov, Igor A.. PY - 1983/10/3. Y1 - 1983/10/3. N2 - There is a good deal of evidence that transcribing RNA polymerase may translocate across nucleosomes without their displacement and (or) rearrangement. A topological model for RNA chain elongation on a nucleosome is considered here. A new mechanism of RNA polymerase translocation is suggested in order to avoid the steric hindrances inherent in the model. It is shown that a transcribed nucleoprotein fiber should be interrupted by protein-free DNA stretches (nucleosome linkers) to allow release of nascent RNA. Possible verificiations and consequences of the model are discussed.. AB - There is a good deal of evidence that transcribing RNA polymerase may translocate across nucleosomes without their displacement and (or) rearrangement. A topological model for RNA chain elongation on a nucleosome is considered ...
Figure 3. Chromosomal distribution of three groups of MNase-seq reads in lengths of ,152, 147 ± 5, and ,142 bp. A, Distribution of MNase-seq reads (data from leaf tissue) along chromosome 4 of Arabidopsis. The two horizontal bars represent the positions of the pericentromeric region and a knob located in the short arm of the chromosome (both are highly heterochromatic; Fransz et al., 2000). B, Distribution of MNase-seq reads along chromosome 4 of rice. The short arm and pericentromeric region of the long arm, both highly heterochromatic (Cheng et al., 2001), are marked by two horizontal bars. The x axes show DNA positions along the chromosomes. The y axes represent the normalized DNA fragment count ratio ("Materials and Methods") of a specific group within 100-kb windows. Heterochromatic regions are enriched with reads ,152 bp in both species. ...
Chromatin is composed of units that repeat. Each of these units are composed of 200 base pairs of DNA, and two copies each of the four histones H2A, H2B, H3, and H4. This unit is called the histone octomer, and the repeating units are referred to as nucleosomes. The five main histones present in chromatin are H2A, H2B, H3, H4, and H1, but H1 is not part of the histone octomer. Each histone also has a flexible amino tail that have various lysine and arginine residues and extends beyond the core. These tails are very important because covalent modifications of them alter the DNA affinity of the histones. When chromatin is digested, it yields only 145 base pairs of DNA binding to the histone octomer, and this smaller unit is called the nucleosome core particle. The DNA that connects these nucleosome core particles in undigested chromatin is referred to as linker DNA. This is where H1 binds ...
Functional genomic elements are marked by characteristic DNA and histone modification signatures. How combinatorial chromatin modification states are recognized by epigenetic reader proteins and how this is linked to their biological function is largely unknown. Here we provide a detailed molecular analysis of chromatin recognition by the lysine demethylase KDM2A. Using biochemical approaches we identify a nucleosome interaction module within KDM2A consisting of a CXXC type zinc finger, a PHD domain and a newly identified Heterochromatin Protein 1 (HP1) interaction motif that mediates direct binding between KDM2A and HP1. This nucleosome interaction module enables KDM2A to decode nucleosomal H3K9me3 modification in addition to CpG methylation signals. The multivalent engagement with DNA and HP1 results in a nucleosome binding circuit in which KDM2A can be recruited to H3K9me3-modified chromatin through HP1, and HP1 can be recruited to unmodified chromatin by KDM2A. A KDM2A mutant deficient in ...
Project Description: The Kner and De La Fuente Labs are interested in using a novel 3D superresolution fluorescence microscopy approach to study nucleosome organization and the role of specific proteins in chromatin organization. The project involves the engineering of a new superresolution microscope, imaging of chromosomes, and biological questions that are important for in reproduction.. REU Student Role and Responsibility: The REU student will assist a graduate student in developing the microscope and in imaging experiments on samples form the De La Fuente lab. The student will assist in developing software to run the microscope and process the images, will help run the microscope to collect data, and will help prepare the samples for imaging.. Expected Outcome for REU student: The student will be trained in cutting-edge microscopy techniques and exposed to important questions in modern biology. Superresolution imaging of the nucleus is a hot topic. This project is expected to result in at ...
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Structure of transcribed chromatin is a sensor of DNA damage.. Early detection and repair of damaged DNA is essential for cell functioning and survival. Although multiple cellular systems are involved in the repair of single-strand DNA breaks (SSBs), it remains unknown how SSBs present in the nontemplate strand (NT-SSBs) of DNA organized in chromatin are detected. The effect of NT-SSBs on transcription through chromatin by RNA polymerase II was studied. NT-SSBs localized in the promoter-proximal region of nucleosomal DNA and hidden in the nucleosome structure can induce a nearly quantitative arrest of RNA polymerase downstream of the break, whereas more promoter-distal SSBs moderately facilitate transcription. The location of the arrest sites on nucleosomal DNA suggests that formation of small intranucleosomal DNA loops causes the arrest. This mechanism likely involves relief of unconstrained DNA supercoiling accumulated during transcription through chromatin by NT-SSBs. These data suggest the ...
We found that the H3.5 nucleosome is quite unstable, as compared to the H3.3 nucleosome in vitro (Fig. 1). Consistently, the mobility of H3.5 is remarkably faster than that of H3.3 in living cells (Fig. 5). In humans, the expression level of another histone H3 variant, H3T, is also high in the testis, but low in somatic cells [6, 8, 9]. The nucleosome containing H3T is quite unstable in vitro and in living cells [26]. Nucleosome instability was also reported with a mouse testis-specific H2A variant, H2AL2 [38]. Therefore, instability may be a common characteristic of the testis-specific nucleosomes. The unstable nature of the H3.5 nucleosome may be suitable for further replacement with transition proteins and protamines. H3.5 incorporation may also regulate the transcription of the genes required during the early stages of spermatogenesis. However, H3.3 appears to be more relevant for regulating transcription during spermatogenesis, as its incorporation is correlated with the gene expression ...
Current models of transcriptional activation involve multiple steps. a , An idealized pathway is shown that begins with chromatin, in which nucleosomes exist in a characteristic beads-on-a-string array. This contrasts to transcriptionally inert chromatin, a highly compacted structure in which DNA is tightly packaged not just through wrapping around nucleosomes but through additional higher-order structures that entail linker histones and other proteins such as heterochromatin protein 1 (not shown). b , The activation pathway is initiated by one or more transcriptional activators that bind to their cognate sites in the regulatory region of the gene. These factors recruit a series of chromatin co-activators that can covalently modify nucleosomes at specific histone residues (not identified) and mobilize nucleosomes through ATP-requiring reactions. c , The resulting intermediate contains chromatin that is characterized by distinct covalent modifications, such as acetylation (Ac) and methylation ...
03/2013: Eric joined the lab for his PhD thesis study. Welcome back, Eric! . 01/2013: Zhengs 3UTR paper was in revision in Nature. Fingers Crossed! . 01/2013: BCM News and Epigenie Headline about our recent work on nucleosome dynamics. . 12/2012: Kaifus variomics paper with Xuewen Pan lab was accepted to Cell Reports. . 12/2012: Liguo and HJs CPAT RNA coding potential prediction paper was accepted to Nucleic Acids Research. . 11/2012: Kaifus nucleosome methodology paper DANPOS was accepted to Genome Research. . 10/2012: Kaifus promoter nucleosome paper was accepted to Genome Research. . 09/2012: A NIH R01 grant was funded. We will work with Dr. Issa at Temple Univ. to understand DNA methylation in Cancer. . 08/2012: A mouse ES nucleosome paper from Kaestner lab at Upenn was accepted to Cell. Kaifu and Wei used DANPOS to analyze the data and were listed as co-authors. . 08/2011: Dr. Benjamin Rodriguez will join us as a Postdoc Associate. Ben has PhD in Integrated Biomedical Science from the ...
There are three major forms of life on Earth, bacteria, archaea and eukaryotes (Figure 3). RNA polymerase in bacteria is less complex than RNA polymerase in eukaryotes. Some of the increased complexity of RNA polymerase in eukaryotes reflects differences between DNA in eukaryotes and DNA in bacteria. Two important differences are that eukaryotes organize their DNA into nucleosomes and have more complex mechanisms for regulation of gene transcription.[5] Nucleosomes are a complex of DNA and histone proteins (Figure 4). In order for transcription to occur, DNA must be released from being tightly coiled in nucleosomes. Bacteria do not have nucleosomes. Another complication of eukaryotic gene expression regulation is that gene sequences controlling transcription are often distant from the DNA site where transcription starts. The RNA polymerase of bacteria is relatively small with a core of five protein subunits and one additional protein that recognizes the start points for transcription[6]. In ...
epigenetic -is the study of inherited changes in phenotype (appearance) or gene expression caused by mechanisms other than changes in the underlying DNA sequence, hence the name epi- (Greek: επί- over, above) -genetics. These changes may remain through cell divisions for the remainder of the cells life and may also last for multiple generations. However, there is no change in the underlying DNA sequence of the organism;[1] instead, non-genetic factors cause the organisms genes to behave (or "express themselves") differently.[2] Wikipedia ...
Abstract. Abstract 3387Objective:. The formation of neutrophil extracellular traps (NETs) and the exposure of nucleosomes on these NETs contribute to coagulat
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This protocol describes the reconstitution of nucleosomes containing differentially isotope-labeled sister histones. At the same time,...
MeCP2 forms defined complexes with nucleosomes in vitro. Gels in (A, B, C and E) were stained in ethidium bromide, the gel in D was stained with Coomassie blue.
acting as spools around which DNA winds, and play a role in gene regulation. Without histones, the unwound DNA in chromosomes would be very long; each human cell has about 1.8 meters of DNA, but wound on the histones it has about 90 micrometers (0.09 mm) of chromatin, which, when duplicated and condensed during mitosis, result in about 120 micrometers of chromosomes.[3] DNA is wrapped around nucleosomes with approximately 50 base pairs of DNA between subsequent nucleosomes (also referred to as linker DNA). The assembled histones and DNA is called chromatin. During mitosis and meiosis, the condensed chromosomes are assembled through interactions between nucleosomes and other regulatory proteins. ...
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H3.3 nucleosome splitting events are better markers for active transcription than H3.3 nucleosome occupancy.(A) Split H3.3 nucleosomes were enriched in the top
Chromatin is the major regulator of gene expression and genome maintenance. Proteins that bind the nucleosome, the repetitive unit of chromatin, and the Histon...
My lab will be exploring proteins that interact with the nucleosome-a nuclear structure made of DNA coiled around a core of proteins. The nucleosome is a lively signaling hub that regulates DNA-related processes from replication and repair to gene expression-all processes that go awry in cancer development. As a postdoc, I elucidated how a protein complex binds to the nucleosome and acts to block gene expression. To expand on this research, we will now perform novel techniques in chemical biology, biochemistry, and structural studies to screen for the nucleosome "interactome," a network of proteins that interact with the nucleosome and modify gene expression. We aim to characterize how certain proteins recognize and bind to the nucleosome by carefully examining the architecture of the nucleosome surface. This work could potentially unearth key regulators of genome activity, especially those with pathogenic roles in human cancers.. ...
The accessibility of the DNA is a primary determinant of gene expression, and is therefore of great interest to molecular geneticists. A central question is how nucleosomes are distributed around the regions at which transcription starts. The selection of the start site, or gene promoter, is the first crucial step in the conversion of genetic information into the bricks and mortar of all cells, the proteins. It turns out that these promoter sites are marked by the presence of a nucleosome-free zone flanked by a specific pattern of nucleosomes. The biological function of these gaps seems to be to provide accessible docking sites for the transcriptional machinery, which comprises a multi-protein complex consisting of many subunits ...
Heavy metals have the potential to engage in strong bonding interactions and can thus function in essential as well as toxic or therapeutic capacities. We conducted crystallographic analyses of heavy cation binding to the nucleosome core particle and found that Co(2+) and Ni(2+) preferentially associate with the DNA major groove, in a sequence- and conformation-dependent manner. Conversely, Rb(+) and Cs(+) are found to bind only opportunistically to minor groove elements of the DNA, in particular at narrow AT dinucleotide sites. Furthermore, relative to Mn(2+) the aggressive coordination of Co(2+) and Ni(2+) to guanine bases is observed to induce a shift in histone-DNA register around the nucleosome center by stabilizing DNA stretching over one region accompanied by expulsion of two bases at an opposing location. These softer transition metals also associate with multiple histone protein sites, including inter-nucleosomal cross-linking, and display a proclivity for coordination to histidine. ...
Nucleosome-remodeling factor, a complex which catalyzes ATP-dependent nucleosome sliding and facilitates transcription of chromatin. Members: by similarity to mice ...
2gcj: The structure of the yFACT Pob3-M domain, its interaction with the DNA replication factor RPA, and a potential role in nucleosome deposition.
Single molecule DNA unzipping reveals a novel model for the regulation of transcription factors and nucleosome positioning via nucleosome remodeling in yeast.
Background Core component of nucleosome. Nucleosomes wrap and compact DNA into chromatin, limiting DNA accessibility to the cellular machineries which require DNA as a template. Histones thereby play a central role in...
SWISS-MODEL Template Library (SMTL) entry for 1p34.1. Crystallographic Studies of Nucleosome Core Particles containing Histone Sin Mutants
A behind-the-scenes look at how researchers solved the high-resolution crystal structure of the nucleosome core particle raises the age-old question of assigning credit in science.. 6 Comments. ...
AlphaLISA Acceptor beads conjugated to Anti-H3K36me2 antibody, for use in AlphaLISA epigenetic assays using histone or nucleosome substrates.
Chromatin remodelers can either organize or disrupt nucleosomal arrays, yet the mechanisms specifying these opposing actions are not clear. Here, we show that the outcome of nucleosome sliding by Chd1 changes dramatically ...