HDACs and p300 directly interact with core histones regardless of the acetylation level.

<p>Flag-tagged HDAC1 and p300 were immobilized on M2 beads. The purified hyper-acetylated or untreated HeLa core histones were incubated with immobilized HDAC1 (<b>A</b>) and p300 (<b>B</b>). Bound histones were detected by Western blotting with the anti-histone H3 and anti-acetyl histone H3 antibodies. The experiments were repeated three times.</p

Histone Deacetylase 1 and p300 Can Directly Associate with Chromatin and Compete for Binding in a Mutually Exclusive Manner

<div><p>Lysine acetyltransferases (KATs) and histone deacetylases (HDACs) are important epigenetic modifiers and dynamically cycled on active gene promoters to regulate transcription. Although HDACs are recruited to gene promoters and DNA hypersensitive sites through interactions with DNA binding factors, HDAC activities are also found globally in intergenic regions where DNA binding factors are not present. It is suggested that HDACs are recruited to those regions through other distinct, yet undefined mechanisms. Here we show that HDACs can be directly recruited to chromatin in the absence of other factors through direct interactions with both DNA and core histone subunits. HDACs interact with DNA in a non-sequence specific manner. HDAC1 and p300 directly bind to the overlapping regions of the histone H3 tail and compete for histone binding. Previously we show that p300 can acetylate HDAC1 to attenuate deacetylase activity. Here we have further mapped two distinct regions of HDAC1 that interact with p300. Interestingly, these regions of HDAC1 also associate with histone H3. More importantly, p300 and HDAC1 compete for chromatin binding both in vitro and in vivo. Therefore, the mutually exclusive associations of HDAC1/p300, p300/histone, and HDAC1/histone on chromatin contribute to the dynamic regulation of histone acetylation by balancing HDAC or KAT activity present at histones to reorganize chromatin structure and regulate transcription.</p></div

HDACs physically associate with DNA fragments.

<p>(<b>A</b>) Schematic representation of DNA pull-down assay. The biotin-labelled DNA was immobilized on streptavidin-bound Dynabeads and incubated with Flag-tagged proteins. DNA associated protein was detected by Western blotting. (<b>B</b>) and (<b>C</b>) Recruitment of HDACs by MMTV promoter sequence. The purified Flag-tagged HDAC1 (<b>B</b>) or HDAC2, 3 (<b>C</b>), LSD1, and CoREST were incubated with MMTV promoter DNA fragments. Proteins bound to DNA were separated in SDS-PAGE and detected by Western blotting. Beads: Flag-tagged HDAC1, HDAC2, and LSD1 were incubated with Dynabeads as a negative control. (<b>D</b>) Non-sequence-specific binding of HDAC1 to DNA. The purified Flag-tagged HDAC1 was incubated with 601 DNA fragments, or with MMTV promoter DNA fragments in the presence of dIdC. Beads: Flag-tagged HDAC1 was incubated with Dynabeads as a negative control. The proteins associated with DNA were detected by Western blotting. Each experiment was repeated at least three times.</p

HDAC1 and p300 are recruited by the C-terminal tail of histone H3.

<p>(<b>A</b>) Schematic representation of the GST-H3 mutant constructs. B and C. Glutathione sepharose beads immobilized GST H3 proteins were incubated with Flag-tagged HDAC1 (<b>B</b>) and p300 (<b>C</b>) and bound fractions were detected by Western blotting. The experiments were repeated three times.</p

HDACs directly interact with the reconstituted mononucleosomes.

<p>(<b>A</b>) Schematic representation of mononucleosome pull-down assay using streptavidin-coupled Dynabeads. The biotin labelled monoucleosome was immobilized on streptavidin-bound Dynabeads (Invitrogen). The purified Flag-tagged proteins were incubated with the reconstituted mononucleosome on streptavidin-bound Dynabeads and the bound fraction was subjected to SDS-PAGE and detected by Western blotting. (<b>B</b>) Reconstitution of mononucleosomes (recon). Mononuleosome particles were reconstituted using the salt dialysis method with core histones and biotin-labelled DNA fragments. The DNA fragments are 601 DNA, a well characterized non-natural strong nucleosome-positioning sequence <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0094523#pone.0094523-Lowary1" target="_blank">[21]</a>, and MMTV promoter region. Reconstituted mononucleosomes were then separated on native PAGE and stained by ethidium bromide. * Mononucleosome. (<b>C</b>) Recruitment of HDAC1 by 601 recon or MMTV recon. The purified Flag-tagged HDAC1 was incubated with the reconstituted mononucleosome. After extensive washes, proteins bound to the Dynabeads were separated in SDS-PAGE and detected by Western blotting with the anti-Flag antibody. Beads: Flag-tagged HDAC1 was incubated with Dynabeads as a negative control. (<b>D</b>) Recruitment of other HDACs by MMTV recon. The purified Flag-tagged HDAC1, 2, 3, and CoREST were incubated with the reconstituted MMTV mononucleosome. After extensive washes, proteins bound to the Dynabeads were separated in SDS-PAGE and detected by Western blotting with the anti-Flag antibody. Each experiment was repeated three times.</p

Promising Nitrogen-Rich Porous Carbons Derived from One-Step Calcium Chloride Activation of Biomass-Based Waste for High Performance Supercapacitors

It has long been demonstrated that KOH and ZnCl₂ can be used as efficient chemical activation agents to prepare porous carbons. Herein, we develop a green activation method, that is, one-step calcium chloride (CaCl₂) activation sugar cane bagasse with urea, for the preparation of nitrogen-rich porous carbons (NPCs). The nitrogen contents, specific surface areas, pore sizes, and specific capacitances of the obtained NPCs can be effectively tuned by adjusting the ratio of carbon precursor (sugar cane bagasse), nitrogen source (urea), and activation agent (CaCl₂). The synthesized three-dimensional oriented and interlinked porous nitrogen-rich carbons (3D-NPCs) contain not only abundant porosities which can impose an advantage for ion buffering and accommodation, but also high nitrogen content in the carbons which can obviously increase the pseudocapacitance. Therefore, for the typical sample, obtained from pyrolysis of the mixture of sugar cane bagasse, urea, and CaCl₂ in a mass ratio of 1:2:2 at 800 °C for 2 h under N₂ atmosphere, shows a high specific capacitance, excellent rate capability (with 323 and 213 F g^–1 at the discharge/charge current densities of 1 and 30 A g^–1, respectively), and outstanding cycle performance (a negligible capacitance loss after 10 000 cycles at 5 A g^–1)

HDACs directly interact with all core histone subunits.

<p>(<b>A</b>) All histone subunits interact with HDAC1. Flag-tagged HDAC1 was incubated with the purified glutathione sepharose beads immobilized GST-H3, H4, H2A, or H2B in a pull-down assay and histone associated HDAC1 was detected by Western blotting. * indicates the protein of interest in Coomassie blue staining. (<b>B</b>) Histone subunits interact with other Class I HDACs. Flag-tagged HDAC 2 and 3 were incubated with the purified GST-histone H3, H4, H2A, or H2B and detected by Western blotting. * indicates the protein of interest in Coomassie blue staining. (<b>C</b>) Histone H3 interacts with Class II HDACs. The purified GST-histone H3 was incubated with Flag-tagged HDAC4, 5 and 6. Proteins bound to GST-H3 were separated in SDS-PAGE and detected by Western blotting. (<b>D</b>) Histone H3 tail 1-57 interacts with HDAC1 regardless of HDAC1 acetylation. Flag-tagged HDAC1 acetylation mimic mutant 6Q, single mutation of HDAC1 H141A and wild type HDAC1 were incubated with the purified GST-histone H3 1-57. Associated proteins were detected by Western blotting. Each experiment was repeated at least three times.</p

Autocatalytic Production of 5‑Hydroxymethylfurfural from Fructose-Based Carbohydrates in a Biphasic System and Its Purification

An efficient autocatalytic process for the production of 5-hydroxymethylfurfural (HMF) from fructose-based carbohydrates has been investigated without the addition of any external catalysts in a methyl isobutyl ketone/water biphasic system, leading to elevated HMF yield through continuous extraction of HMF from an aqueous solution. The results show that both the reaction temperature and time have significant effects on fructose conversion and HMF yield; 96.8% of fructose can be converted into 73.6% of HMF with a small amount of levulinic acid and formic acid formed at a point of compromise between the reaction temperature and time (160 °C for 2 h). In addition, this autocatalytic system is suitable for other fructose-based feedstocks, such as sucrose and inulin, to achieve acceptable HMF yield. Moreover, a simple and efficient purification strategy for as-prepared HMF, viz., the NaOH neutralization method, has also been tested, achieving more than 99% of HMF recovery with more than 98% of purity correspondingly

Catalytic Fractionation of Raw Biomass to Biochemicals and Organosolv Lignin in a Methyl Isobutyl Ketone/H₂O Biphasic System

A biphasic system, consisting of methyl isobutyl ketone and H₂O, has been achieved for a highly integrated one-pot catalytic transformation and delignification process of lignocellulosic biomass. Using SO₃H-functionalized ionic liquids as catalysts, 85.8% of bagasse can be fractionated into 71.4% water-soluble chemicals at 76.3% lignin extraction ratio, under the optimized conditions. The practicability of this biphasic system for other typical biomass sources has also been tested with high efficiency, viz., 79.6 to 91.9% lignin extraction ratio of corncob, corn stalk, rice husk, and rice straw with 56.6 to 72.8% water-soluble chemicals yield at 64.8 to 81.3% feed conversion

Hydrodesulfurization of 4,6-Dimethyldibenzothiophene over CoMo Catalysts Supported on γ‑Alumina with Different Morphology

Nanostructured γ-alumina with two different morphologies (rod-like and cube-like) was used as support for CoMo hydrodesulfurization catalyst. Both γ-aluminas were prepared by thermal decomposition of ammonium aluminum carbonate hydroxide precursor, which was synthesized by a convenient hydrothermal method at two pH values. Fourier transform infrared spectroscopy of prydine adsorption, thermogravimetric analysis, and ²⁷Al magic angle spinning (MAS) NMR showed that the rod-like γ-alumina exhibited a lower acidity than the cube-like γ-alumina. The result of X-ray diffraction and temperature-programmed reduction indicated that CoMo oxidic catalysts supported on the rod-like γ-alumina presented higher reducibility compared to those of cube-like γ-alumina, because more β-CoMoO₄ was formed on the surface of the rod-like γ-alumina than that of the cube-like γ-alumina. After sulfidation, a large stack with slightly longer MoS₂ slabs was formed on the rod-like γ-alumina supports, thereby creating a catalyst with higher hydrodesulfurization activity and hydrogenation selectivity. The morphology of γ-alumina has an influence on the activity and selectivity of the as-synthesized CoMo catalyst