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- Chromatin Assembly Kit
- Nucleosome Assembly Control DNA
- Recombinant Histones
- Histone Modifying Enzymes
- Histone Modification Antibodies
Chromatin, the material into which genomic DNA is packaged in eukaryotes, is a very dynamic structure. The smallest subunit of chromatin is the nucleosome, consisting of 147 base pairs of DNA wrapped around an octamer of core histone proteins. The histone octamer is composed of a central heterotetramer of histones H3 and H4, flanked by two heterodimers of histones H2A and H2B. Each nucleosome is separated by 10 to 60 bp of linker DNA. The resulting nucleosomal array constitutes a chromatin fiber of about 10 nm in diameter. This arrangement is folded into more condensed fibers (about 30 nm) that are stabilized by binding of a linker histone (Histone H1) to each nucleosome core. Such 30 nm fibers are then condensed in vivo to form thicker interphase fibers or the most highly compacted metaphase chromosome structures1.
But, the role of histones and nucleosomes is not limited to the compaction of the chromatin. Epigenetic modifications such as phosphorylation, acetylation, methylation and ubiquitination at specific amino acid residues on the histone tails influence higher-order chromatin structure that regulates the nuclear processes of transcription, chromosome packaging and DNA damage repair2. Many of these specific histone modifications are conserved throughout eukaryotes. While the biological significance of some histone modifications remains to be understood, some have been demonstrated to correlate very closely with specific cellular states like transcriptional activity3,4. Transcriptionally active chromatin is referred to as euchromatin, while transcriptionally inactive chromatin is called heterochromatin.
Mononucleosomes refers to a single monomer of the nucleosome array. Due to the number of potential binding interactions that are possible on the histone tails, histone globular domain and the nucleosomal DNA, mononucleosomes can offer a simplified substrate for chromatin analysis.
Active Motif offers Nucleosome Assembly Control DNA which can be used for in vitro assembly of mononucleosomes. The 187 bp double stranded DNA can be added to your core histones for formation of a control mononucleosome with a known DNA sequence. The Nucleosome Assembly Control DNA can also be used to monitor how chromatin interacting proteins or compounds effect mononucleosome assembly kinetics.
Understanding the position of nucleosomes can help provide information about chromatin context and gene regulation. Traditional methods used to look at nucleosome positioning include nuclease digestions methods, such as MNase-Seq or DNase-Seq, which rely on the fact that a nucleosome bound to DNA will protect the DNA from enzymatic digestions. However, these techniques destroy the physical linkages between binding sites and therefore are designed to look at average distribution across a panel of remodeled nucleosomes and not to determine the status of a single DNA molecule5,6.
Formaldehyde-Assisted Isolation of Regulatory Elements (FAIRE-Seq) is a method used to enrich for nucleosome depleted DNA using formaldehyde fixation and phenol-chloroform extraction7. The nucleosome depleted DNA can be sequenced to identify regions that correspond with transcriptional start sites, enhancers and promoters.
While understanding nucleosome positioning has great value, the ability to study nucleosome occupancy in the context of other epigenetic modifications provides a powerful tool for researchers to use in studying the different states of chromatin and its effect on gene regulation. Active Motif is the first company to offer a method to study both nucleosome occupancy and DNA methylation within the same DNA strand. NOMe-Seq (Nucleosome Occupancy and Methylome Sequencing) is a published method that was developed by the Peter A. Jones lab which can be used for gene-specific analysis of both nucleosome occupancy and DNA methylation levels on the same DNA strand of the gene of interest8,9,10. It provides a temporal relationship between nucleosomes, transcription factor binding and DNA methylation.
The assembly of genomic DNA and histones into chromatin is a fundamental process that affects a broad range of genome-dependent processes including DNA replication, DNA repair and gene expression. In general, there are ATP-dependent and ATP-independent methods for reconstituting or assembling chromatin in vitro, but only the ATP-dependent process generates an extended array of ordered nucleosomes. Active Motif's Chromatin Assembly Kit utilizes an ATP-dependent method which enables you to study your DNA sequence of interest in a native chromatin environment. The simple, easy-to-follow protocol generates assembled chromatin in hours with few manipulations, providing you with material that is ideal for downstream applications such as in vitro ChIP, transcription and histone modification assays. To study specific histone modifications within a chromatin context, Active Motif's Recombinant Histones with site and degree-specific modifications can be used as substrates for chromatin assembly.
Histones with specific methylation states are an essential tool for investigating which methylation patterns are key to complex functional questions about chromatin-associated proteins, nucleosome remodeling, transcriptional regulation, replication and DNA repair.
In addition to methylation specific recombinant histones, Active Motif also offers histones with site-specific acetylation or phosphorylation modifications. Histone acetylation and phosphorylation are post-translational modifications that affect nucleosome structure and therefore the ability of transcription factors to access the DNA and regulate gene expression. Click on our link to get a complete list of our Recombinant Histones and Modified Histones.
- Peterson, C.L. & Laniel, M.A. (2004) Curr Biol 14:R546-551.
- Bartova, E. et al. (2008) J. Histochemistry & Cytochemistry 56:711-721.
- Kirmizis, A. et al. (2004) Genes & Dev. 18:1592-1605.
- Squazzo, S. et al. (2006) Genome res. 16:890-900.
- Fragoso, G. et al. (1995) Genes Dev., 9:1933-1947.
- Bouazoune, K. et al. (2009) Nucl. Acids Res., 37:5279-5294.
- Giresi, P.G. and Lieg, J.D. (2009) Methods, 48:233-239.
- You, J.S. et al. (2011) Proc. Natl. Acad. Sci., 108:14497-14502.
- Wolff, E.M. et al. (2010) PLoS Genetics, 6(4):e1000917.
- Kelly, T.K. et al. (2010) Mol. Cell, 39:901-911.