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Histone Deacetylase

Histone Deacetylases (HDACs) are enzymes that remove acetyl groups from lysine residues on histone proteins, leading to chromatin condensation and transcriptional repression.
They play a crucial role in regulating gene expression and are implicated in various biological processes, such as cell cycle control, differentiation, and development.
HDACs have emerged as important therapeutic targets for conditions like cancer, neurodegenerative disorders, and inflammatory diseases.
Researchers can optimize their HDAC studies using PubCompare.ai, an AI-driven platform that enhances reproducibility and accuracy by providing AI-powered comparisons to locate the best protocols and products from literature, preprints, and patents.
This cutting-edg technology can help take HDAC research to the next levle.

Most cited protocols related to «Histone Deacetylase»

1
Molecular Docking of Quinoxaline Derivatives on HDAC
Cited 6 times
A molecular docking study of the newly synthesized quinoxaline derivatives at the histone deacetylase (HDAC) receptor was performed, and the co-crystallized inhibitor, trichostatin A (TSA), was used as a reference standard. Using MOE 2019.0102 drug design software (Inc, 2016 ), the binding mode of the compound against histone deacetylase (ID: 1C3R) was predicted (Finnin et al., 1999 (link)). The crystal structure of the target receptor (HDAC) was downloaded from Protein Data Bank (http://www.rcsb.org/, PDB code: 1C3R, resolution of 2.00 Å) (Finnin et al., 1999 (link)). The protein structure was prepared for docking studies by the default method (Alnajjar et al., 2020 (link); Soltan et al., 2021 (link); Soltane et al., 2021 (link); Zaki et al., 2020 (link)). The deacetylase and deacetylase-TSA structures show an active site consisting of a tubular pocket, a zinc-binding site (which is the metal cofactor required for HDAC activity), and two Asp-His charge-relay systems, and explain the mechanism of HDAC inhibition (Finnin et al., 1999 (link)). Validation of the docking procedure was carried out by applying the docking process for the co-crystallized ligand (Elmaaty et al., 2021a (link); Elmaaty et al., 2021b (link); Kandeil et al., 2021 (link)). All of the newly synthesized quinoxaline derivatives were prepared and imported in the same database together with the co-crystallized inhibitor (TSA) and generally docked. After completion of the docking process, the obtained poses for each were carefully studied, and the ones having the best scores and binding modes with the protein pocket residues were selected.
Ma C., Taghour M.S., Belal A., Mehany A.B., Mostafa N., Nabeeh A., Eissa I.H, & Al-Karmalawy A.A. (2021). Design and Synthesis of New Quinoxaline Derivatives as Potential Histone Deacetylase Inhibitors Targeting Hepatocellular Carcinoma: In Silico, In Vitro, and SAR Studies. Frontiers in Chemistry, 9, 725135.
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Publication 2021
Binding Proteins Binding Sites derivatives Histone Deacetylase Ligands Metals Pharmaceutical Preparations Proteins Psychological Inhibition Quinoxalines trichostatin A Zinc
2
Optimized ChIP-seq Peak Identification
Cited 6 times
We downloaded ChIP-seq reads from the Gene Expression Omnibus (31 (link)) and aligned them to the human (GRCh37/hg19) or mouse (GRCm38/mm10) genomes using Bowtie (32 (link)). Unique reads mapped to a single genomic location from the best stratum (allowing up to three mismatches) were kept for peak identification. When replicates existed, peaks were called on pooled reads from all replicates. We called peaks using the MACS algorithm (version 1.4) (33 (link)), the SICER algorithm (version 1.1) (34 (link)) or the spp pipeline (35 (link)) (modified from version 1.10 by Anshul Kundaje) with IDR guidelines (36 ). We used SICER for ChIP-seq data of HMs and histone deacetylases, MACS for samples with < 10 million pooled reads and spp with IDR for the rest of the ChIP-seq samples (Supplementary Table S1). The importance of IDR in determining optimal peak calling parameters has been described previously (37 (link)). During our analysis, we also randomly picked regions with the distribution of their sizes matched to that of REST peaks as controls.
Rockowitz S, & Zheng D. (2015). Significant expansion of the REST/NRSF cistrome in human versus mouse embryonic stem cells: potential implications for neural development. Nucleic Acids Research, 43(12), 5730-5743.
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Publication 2015
Chromatin Immunoprecipitation Sequencing Gene Expression Genome Histone Deacetylase Homo sapiens Mice, Laboratory
3
Protein Expression Analysis by Western Blotting
Cited 5 times
Cell lysis and western blotting were performed as described (Rizzo et al., 2008 (link)). Antibodies were as follows: Notch-1 (C-20; Santa Cruz Biotechnology, Santa Cruz, CA, USA), ERα (G-20; Santa Cruz Biotechnology), RBP-Jk (CBF1, D-20; Santa Cruz Biotechnology), MAML1 (AB5975; Chemicon International, Temecula, CA, USA), Notch-1IC (ab8925; Abcam, Cambridge, MA, USA), IKKα (Imgenex, San Diego, CA, USA), p300 (N-15; Santa Cruz Biotechnology), GAPDH (MAB374; Chemicon International), histone deacetylase (H-51; Santa Cruz Biotechnology) and β-actin (Sigma-Aldrich, St Louis, MO, USA).
Hao L., Rizzo P., Osipo C., Pannuti A., Wyatt D., Cheung L.K., Sonenshein G., Osborne B, & Miele L. (2009). Notch-1 activates estrogen receptor-α-dependent transcription via IKKα in breast cancer cells. Oncogene, 29(2), 201-213.
Publication 2009
Actins Antibodies Cells Conserved Helix-Loop-Helix Ubiquitous Kinase EP300 protein, human GAPDH protein, human Histone Deacetylase MAML1 protein, human RBPJ protein, human
4
Cell Lines Characterization and Treatment
Cited 4 times
HH, H9, Hut78, MJ and Hut102 patient-derived CTCL cell lines were previously described [55 (link), 56 (link)] and were purchased from the American Tissue Culture Collection (ATCC). H9 is a clonal derivative of Hut78 cell line [57 (link)]. MyLa, PB2B, Mac2A, SZ4, SeAx, Sez4 were a generous gift from professors K. Kaltoft and N. Ødum (Copenhagen, Denmark) and were initially described elsewhere [31 (link), 58 (link)–61 (link)]. Detailed summary of cell lines is provided in Supplementary Table 1. MJ, Hut78 cells were serially passaged in IMDM media (Invitrogen) containing 20% and 10% fetal bovine serum, respectively (FBS) (Invitrogen). HH, H9, Hut102, MyLa, Mac2A and SZ4 cells were grown in RPMI media containing 10% FBS. Finally, Sez4 and SeAx cells were grown in RPMI media containing 10% FBS, 5 ng/mL of recombinant human IL-2 and IL-4 (R&D Systems, Minneapolis, MN). All cells were grown in 5% CO2, 95% air humidified incubator at 37°C.
To inhibit histone deacetylase (HDAC) activity cells were treated with 0-40 μM of Suberoylanilide Hydroxamic Acid (SAHA also known as Vorinostat, Santa Cruz, Dallas, TX) or 0-4μM Romidepsin (Adooq Bioscience, Irvine CA). Cells were also treated with 0-40μM of Bexarotene (Santa Cruz Biotechnology, Dallas, TX).
Netchiporouk E., Gantchev J., Tsang M., Thibault P., Watters A.K., Hughes J.D., Ghazawi F.M., Woetmann A., Ødum N., Sasseville D, & Litvinov I.V. (2017). Analysis of CTCL cell lines reveals important differences between mycosis fungoides/Sézary syndrome vs. HTLV-1+ leukemic cell lines. Oncotarget, 8(56), 95981-95998.
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Publication 2017
aldesleukin Bexarotene Cardiac Arrest Cell Lines Cells Clone Cells Histone Deacetylase Lymphoma, T-Cell, Cutaneous Patients romidepsin Vorinostat
5
Chromatin Remodeling in Achilles Tendon
Cited 4 times
Freshly harvested Achilles tendons were immediately isolated from all surrounding tissue with the peritenon left intact. RNA was isolated as previously described (10 (link)) from three separate pools of 12–24 combined Achilles tendons from un-injured (UI) mice and from each experimental and control group (Table S1). Briefly, tendon pools in RNALater were flash frozen with liquid N2, fragmented by hammer impact at −196 °C in a Bessman Tissue Pulverizer, recovered, and extracted in 1mL of Trizol by vortexing for 60 seconds. RNA was purified with an RNeasy MiniKit (Qiagen).Consistent with an anabolic response to injury, yields per tendon were: UI ~ 305 ng, post-injury 3d ~805 ng, post-injury 14d and 14dTM ~1800ng, and post-injury 28d and 28dTM ~ 800ng. A260:A280 for all preparations was >1.90. cDNA was synthesized with 0.5ug of mRNA (RT2 First Strand Kit, Qiagen). Chromatin modification enzyme transcript abundances were determined with SYBR qt-PCR array plates (PAMM-085Z, Qiagen) with 84 genes divided into the following functional groups: 6 DNA/Histone Demethylases (DHD), 3 DNA Methyltransferases (DM); 17 Histone Acetyltransferases (HA); 11 Histone Deacetylases (HD), 16 Histone Methyltransferases (HM), 7 Histone Phosphorylation (HP), 9 Histone Ubiquitinases (HU), and 15 SET Domain Proteins with HM activity (SET). The coefficient of variation for triplicate array assays was <3%. The same cDNA preparations were used for Taqman qt-PCR of single genes (Table S2), with primers from Thermo-Lifetech and the coefficient of variation was < 7%.
Changes in transcript abundance (ΔCt=Ct for transcript of interest minus Ct for the housekeeping gene B2m) were used to calculate the fold change (2^-ΔΔCt) from UI levels for each experimental group. A 1-way ANOVA with Tukey’s post-hoc test was conducted using GraphPad Prism 5 (La Jolla, CA) on the ΔCt values to determine the significance (p<0.05) in expression of genes in the injured relative to UI groups. Statistical evaluation was not possible on data from single tissue pool controls (anesthesia only, anesthesia with needle injury only, and treadmill only), although it should be recognized that the data obtained with any pool represents the average expression in 12–24 tendons.
Trella K.J., Li J., Stylianou E., Wang V.M., Frank J.M., Galante J., Sandy J.D., Plaas A, & Wysocki R. (2016). Genome-wide analysis identifies differential promoter methylation of Leprel2, Foxf1, Mmp25, Igfbp6 and Peg12 in murine tendinopathy. Journal of orthopaedic research : official publication of the Orthopaedic Research Society, 35(5), 947-955.
Publication 2016
Acetyltransferase, Histone Androgens, Synthetic Anesthesia Biological Assay Chromatin DNA, Complementary DNA Modification Methylases Enzymes Freezing Gene Expression Genes Genes, Housekeeping Histone Deacetylase Histone Demethylases Histones Injuries Methyltransferase, Histone Mus Needles Neoplasm Metastasis neuro-oncological ventral antigen 2, human Oligonucleotide Primers Phosphorylation prisma Proteins RNA, Messenger SET Domain Tendon, Achilles Tendons Tissues trizol

Most recents protocols related to «Histone Deacetylase»

1
Epigenetic Screening Library Assay
An epigenetics screening library was purchased from Cayman Chemical (Ann Arbor, MI, USA). The library consists of 148 small-molecule epigenetic compounds that are known to modulate the activity of a variety of epigenetic ‘writers and erasers’ and ‘reader’ proteins such as DNA/histone methyltransferases, DNA/histone demethylases, histone acetyltransferases, histone deacetylases, and acetylated histone binding proteins. All compounds were provided as 10 mM stocks in dimethyl sulfoxide (DMSO). An aliquot of each compound was further diluted to 0.1 mM in serum-free RPMI 1640 medium. HT-29/DEFB1-luc cells were seeded at 2 × 104 cells/well in 50 μL of complete RPMI 1640 medium in white 96-well plates overnight and treated with individual epigenetic compounds at the final concentration of 20 μM for 24 h, followed by luciferase assay. To measure cell viability, 5 μL alamarBlue Reagent (Thermo Fisher Scientific, Waltham, MA, USA) was added to individual wells and incubated for 4 h prior to cell lysis and luciferase assay. The cell viability was measured on FLx80 Microplate Fluorescence Reader (BioTek Instruments, Winooski, VT, USA) at 545 nm excitation and 590 nm emission, followed by luciferase assay on L-Max II Luminescence Microplate Reader (Molecular Devices). The luciferase activity of each compound was normalized to its cell viability. The strictly standardized mean difference (SSMD) [25 (link)] was calculated for each compound, and the positive hits were identified with a normalized SSMD value of no less than 3.0 [25 (link)].
Lyu W., Deng Z, & Zhang G. (2023). High-Throughput Screening for Epigenetic Compounds That Induce Human β-Defensin 1 Synthesis. Antibiotics, 12(2), 186.
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Publication 2023
Acetyltransferase, Histone Alamar Blue Binding Proteins Biological Assay Caimans cDNA Library Cells Cell Survival DEFB1 protein, human Epigenetic Process Fluorescence Histone Deacetylase Histone Demethylases Histones HSP40 Heat-Shock Proteins HT29 Cells Luciferases Luminescence Medical Devices Methyltransferase, Histone Serum Sulfoxide, Dimethyl
2
Optimizing Recombinant KSHV Production
To establish efficient recombinant virus-producing cells, tetracycline/doxycycline (Dox)-inducible (Tet-On) RTA/ORF50-expressing iSLK cells [47 (link),48 (link),49 (link)] or iVero cells [50 (link)] were used as recombinant KSHV-producing cells. For maintenance, iSLK cells were cultured in a growth medium containing 1 μg/mL of puromycin (InvivoGen, CA, USA) and 0.25 mg/mL of G418 (Nacalai Tesque, Kyoto, Japan). iVero cells were cultured in a growth medium containing 2.5 μg/mL of puromycin. WT KSHV BAC16 (WT-BAC16) and ORF21-mutated KSHV BAC16 (21KD-BAC16 and 21del-BAC16) were transfected into iSLK and iVero cells by the calcium phosphate method [51 ]. The transfected cells were selected under 1000 μg/mL of hygromycin B (Wako, Osaka, Japan) to establish doxycycline-inducible recombinant KSHV-producing cell lines. iSLK (or iVero) cells transfected with WT-BAC16, 21KD-BAC16, and 21del-BAC16 were named iSLK-WT, iSLK-21KD, and iSLK-21del cells, respectively (or iVero-WT, iVero-21KD, and iVero-21del cells, respectively). To induce the lytic replication for recombinant KSHV production, BAC16-harboring iSLK (or iVero) cells were treated with sodium butyrate (NaB) and Dox. NaB binds to histone deacetylases (HDACs) and induces the hyperacetylation of the histones, resulting in transcriptional activation. Dual treatment of both Dox and NaB was used in this study because it induced the RTA/ORF50 expression and the lytic cycle more effectively.
Yamaguchi T., Watanabe T., Iwaisako Y, & Fujimuro M. (2023). Kaposi’s Sarcoma-Associated Herpesvirus ORF21 Enhances the Phosphorylation of MEK and the Infectivity of Progeny Virus. International Journal of Molecular Sciences, 24(2), 1238.
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Publication 2023
antibiotic G 418 Calcium Phosphates Cell Lines Cells Culture Media DNA Replication Doxycycline Histone Deacetylase Histones Human Herpesvirus 8 Hygromycin B Puromycin Sodium Butyrate Tetracycline Transcriptional Activation Virus
3
Quantifying Nuclear HDAC Activity in RAW246.7 Cells
Nuclear protein of RAW246.7 cells was extracted with nuclear and cytoplasmic extraction kit (Beyotime, Shanghai, China) according to the manufacturer’s instructions, and HDAC activities upon LPS treatment were evaluated by Histone Deacetylase Assay Kit, Fluorometric (Abnova, USA). Briefly, a total of 10–50 μg of nuclear extract was added to each well, then diluted with ddH2O until the final volume was 85 μL (for background reading, add 85 μL ddH2O only), or added 2 μL of Trichostatin A into diluted sample for negative control. Besides, 2 μL of HeLa nuclear extract was diluted with 83 μL ddH2O for positive control. After incubating with HDAC Fluorometric substrate at 37 °C for 30 min, 10 μL of Lysine Developer was added to stop the reaction. The plate was incubated at room temperature for 30 min, the fluorescence intensity of the wells was measured on a fluorometric plate reader with excitation set at 350–380 nm and emission detection set at 440–460 nm.
Gong L., Shen Y., Wang S., Wang X., Ji H., Wu X., Hu L, & Zhu L. (2023). Nuclear SPHK2/S1P induces oxidative stress and NLRP3 inflammasome activation via promoting p53 acetylation in lipopolysaccharide-induced acute lung injury. Cell Death Discovery, 9, 12.
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Publication 2023
Biological Assay Cells Cytoplasm Fluorescence Fluorometry HeLa Cells Histone Deacetylase Lysine Nuclear Protein trichostatin A
4
Colorimetric HDAC Activity Assay
The HDAC Activity Assay Kit (colorimetric) (ab1432) uses a colorimetric method to measure the activity of histone deacetylases (HDACs) according to the kit's protocol. The HDAC colorimetric substrate is a peptide that contains an acetylated lysine side chain. This peptide is incubated with a sample containing HDAC activity or inhibitory activity. If HDAC activity is present, the HDAC will deacetylate the lysine side chain of the peptide. This makes the peptide more susceptible to cleavage by an enzyme called the lysine developer. The lysine developer cleaves the peptide, releasing a chromophore. The levels of chromophore released is proportional to the amount of HDAC activity present in the sample tested. The absorbance of the chromophore was measured at 405 nm using a microplate reader. The final sample concentration was in the range of 1–4 mg/mL for egg yolk and egg yolk fat samples (CCEF and FCEF). Trichostatin A was used as the positive control.
, & Ediriweera M.K. (2023). The Histone Deacetylase Inhibitory Potential of Chicken Egg Yolk Fat and Their Fatty Acid Composition. Scientifica, 2023, 6360487.
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Publication 2023
Biological Assay Colorimetry Cytokinesis Enzymes Histone Deacetylase Lysine Peptides Psychological Inhibition trichostatin A Yolks, Egg
5
Prediction of SMAD2 Lysine Acetylation
A Group-based Prediction System (GPS) online tool (http://pail.biocuckoo.org) was used to predict Lys451 in SMAD2 modified by histone acetyltransferases, with high score values suggesting better results. The amino acid sequence of the protein in FASTA format was downloaded from UniProt and uploaded to the GPS website. Deep-PLA (http://deeppla.cancerbio.info/webserver.php) predicted that Lys451 in SMAD2 is modified by histone deacetylase.
Yang S., Yang G., Wang X., Xiang J., Kang L, & Liang Z. (2023). SIRT2 alleviated renal fibrosis by deacetylating SMAD2 and SMAD3 in renal tubular epithelial cells. Cell Death & Disease, 14(9), 646.
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Publication 2023
Acetyltransferase, Histone Amino Acid Sequence Histone Deacetylase Proteins SMAD2 protein, human

Top products related to «Histone Deacetylase»

1
Histone deacetylase assay kit by Merck Group
Sourced in United States
The Histone Deacetylase Assay Kit is a laboratory equipment product designed to measure the activity of histone deacetylase (HDAC) enzymes. It provides a quantitative method for assessing HDAC activity in cell and tissue samples.
2
Trichostatin a by Merck Group
Sourced in United States, Germany, Sao Tome and Principe, Macao
Trichostatin A is a histone deacetylase (HDAC) inhibitor used in laboratory research. It functions by inhibiting HDAC enzymes, which are involved in the regulation of gene expression. Trichostatin A is commonly utilized in cell-based assays and experiments to study the effects of HDAC inhibition on various biological processes.
3
Fetal bovine serum (fbs) by Thermo Fisher Scientific
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Fetal Bovine Serum (FBS) is a cell culture supplement derived from the blood of bovine fetuses. FBS provides a source of proteins, growth factors, and other components that support the growth and maintenance of various cell types in in vitro cell culture applications.
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Dimethyl sulfoxide (dmso) by Merck Group
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DMSO is a versatile organic solvent commonly used in laboratory settings. It has a high boiling point, low viscosity, and the ability to dissolve a wide range of polar and non-polar compounds. DMSO's core function is as a solvent, allowing for the effective dissolution and handling of various chemical substances during research and experimentation.
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Epigenase hdac activity inhibition direct assay kit by Epigentek
Sourced in United States
The Epigenase HDAC Activity/Inhibition Direct Assay Kit is a lab equipment product that measures the activity or inhibition of histone deacetylases (HDACs) directly in cell or tissue extracts. The kit provides a simple, sensitive, and reliable method for assaying HDAC activity or screening HDAC inhibitors.
6
Nuclease extraction kit by Merck Group
The Nuclease extraction kit is a laboratory product designed to extract and purify nucleases from biological samples. It provides a standardized and efficient method for isolating these important enzymes, which play crucial roles in various molecular biology and biochemical applications.
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Epiquik hdac activity inhibition assay kit by Epigentek
Sourced in United States
The EpiQuik HDAC Activity/Inhibition Assay Kit is a laboratory equipment product designed to measure the activity or inhibition of histone deacetylases (HDACs) in cell extracts, tissue samples, or purified enzymes. The kit provides a quantitative colorimetric method for detecting HDAC activity or the inhibitory effects of substances on HDAC activity.
8
Trizol reagent by Thermo Fisher Scientific
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TRIzol reagent is a monophasic solution of phenol, guanidine isothiocyanate, and other proprietary components designed for the isolation of total RNA, DNA, and proteins from a variety of biological samples. The reagent maintains the integrity of the RNA while disrupting cells and dissolving cell components.
9
Hdac glo 1 2 assay by Promega
Sourced in United States
The HDAC-Glo I/II Assay is a luminescent-based assay that detects the activity of histone deacetylases (HDACs) class I and II enzymes. The assay utilizes a proluminescent HDAC substrate that, upon deacetylation, produces a light signal proportional to HDAC activity.
10
Histone deacetylase hdac activity assay kit fluorometric by Abcam
Sourced in Australia
The Histone Deacetylase (HDAC) Activity Assay Kit (Fluorometric) is a laboratory tool designed to measure the enzymatic activity of histone deacetylases. It utilizes a fluorogenic substrate to detect HDAC activity in a quantitative manner.

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