Computational identification of protein-protein interactions in model plant proteomes | Scientific Reports
Histone deacetylase HDA6 is functionally associated with AS1 in repression of KNOX genes in Arabidopsis. PLoS genetics 8, ... and histone deacetylase 6 (HDA6) (AT5G63110). Although they have a very low STRING score a previous study showed that HDA6 ... 2. k is the k-th reference genome, \({R}_{ik}\) is the BLAST search bit score of homolog of protein i in the k-th genome ... The two hyper-parameter values, C and γ, were determined to be \(lo{g}_{2}C=5\) and \(lo{g}_{2}\gamma =-\,1\) for SVMloc and \( ...
EGR1 reactivation by histone deacetylase inhibitors promotes synovial sarcoma cell death through the PTEN tumor suppressor |...
Although histone deacetylase (HDAC) inhibitors are known to suppress synovial sarcoma in vitro and in vivo, the exact mechanism ... Although histone deacetylase (HDAC) inhibitors are known to suppress synovial sarcoma in vitro and in vivo, the exact mechanism ... 2005). Significant growth suppression of synovial sarcomas by the histone deacetylase inhibitor FK228 in vitro and in vivo. ... EGR1 reactivation by histone deacetylase inhibitors promotes synovial sarcoma cell death through the PTEN tumor suppressor. *L ...
Genome-wide association study identifies a variant in HDAC9 associated with large vessel ischemic stroke | Nature Genetics
We identified a new association for large vessel stroke within HDAC9 (encoding histone deacetylase 9) on chromosome 7p21.1 ( ... They identify a SNP in HDAC9, a histone deacetylase gene, that is associated with large vessel ischemic stroke and suggest ... Histone deacetylases 5 and 9 govern responsiveness of the heart to a subset of stress signals and play redundant roles in heart ... We identified a new association for large vessel stroke within HDAC9 (encoding histone deacetylase 9) on chromosome 7p21.1 ( ...
Reciprocal H3.3 gene editing identifies K27M and G34R mechanisms in pediatric glioma including NOTCH signaling | Communications...
show that histone H3.3 K27M and G34R mutations share key oncogenic mechanisms such as activation of neurogenesis and NOTCH ... Histone H3.3 mutations are a hallmark of pediatric gliomas, but their core oncogenic mechanisms are not well-defined. To ... 5a, Supplementary Table 6). In contrast to DAPT, treatment with histone deacetylase inhibitor Panobinostat largely killed cells ... Because changes in global histone levels could somewhat impact interpretation of histone marks changes, all histone mark ...
CETSA quantitatively verifies in vivo target engagement of novel RIPK1 inhibitors in various biospecimens | Scientific Reports
Insights into neuroepigenetics through human histone deacetylase PET imaging. Sci Transl Med 8, 351ra106 (2016). ... one group applied this technology to investigate histone deacetylase isoform selectivity of a compound with human brain ... Figure 2. Development of a CETSA for human RIPK1 with HT-29 cells. (a) Chemical structure of representative tool compounds. (b ... Decision coefficient R2 for all data points is 0.9120. (b) Scatter plots of IC50 of recombinant RIPK1 binding assay with ITDRF ...
Radiation-induced tumor immune microenvironments and potential targets for combination therapy | Signal Transduction and...
... a dual-target NP using both a cisplatin prodrug and a histone deacetylase inhibitor increased DNA damage, impaired cancer cell ... are upregulated by RT and histone deacetylase inhibitor (HDACi) therapy, which increased the cytotoxicity of NK cells against ... ORCID: orcid.org/0000-0002-2044-26101,2,3,4 Show authors. Signal Transduction and Targeted Therapy volume 8, Article number: ... 2. Radiation on DCs and TAMs. DAMPs derived from irradiated cancer cells, such as CRT, ATP, HMGB1, and F-actin, can promote DC ...
Integrative genome-wide analysis of dopaminergic neuron-specific PARIS expression in Drosophila dissects recognition of...
Yang, Y. et al. Peroxisome proliferator-activated receptor γ is inhibited by histone deacetylase 4 in cortical neurons under ... Histone deacetylases (HDACs) are among the core components of this large protein complex. Considering that transcriptional ... or histone antibody (Cell signaling) as a positive control. Antibody-DNA complexes were isolated by ChIP grade protein G- ... Table 2 Top 5 "Disease" and "pathway" terms enriched by DAVID Knowledge analysis21.. Full size table. ...
p53 in ferroptosis regulation: the new weapon for the old guardian | Cell Death & Differentiation
Death by histone deacetylase inhibitor quisinostat in tongue squamous cell carcinoma via apoptosis, pyroptosis, and ferroptosis ... the histone deacetylase inhibitor quisinostat activates multiple death types of tumor cell including apoptosis, pyroptosis, and ... Sirtuins are a family of deacetylases closely associated with p53 function [80]. In a myocardial ischemia-reperfusion injury ... Monoubiquitinated histone H2B lysine 120 (H2Bub1) is an epigenetic mark indicating active transcription of host genes. After ...
Direct measurement of the mechanical properties of a chromatin analog and the epigenetic effects of para-sulphonato-calix[4...
... known for epigenetic activity by interacting specifically with the lysine groups of histone proteins, was studied for its ... This can be compared to the effects of the histone proteins, H1, H2A, H3 where no changes in the mechanical properties of DNA ... Moskowitz, A. J. & Horwitz, S. M. Targeting histone deacetylases in T-cell lymphoma. Leukemia & Lymphoma 58, 1306-1319 (2017). ... Increasing concentrations of histone proteins H2A, H3, a 1:1 mix of histone proteins H3 and H4 and, finally, nucleosome, ...
HDNetDB: A Molecular Interaction Database for Network-Oriented Investigations into Huntington's Disease | Scientific Reports
Bardai, F. H., Price, V., Zaayman, M., Wang, L. & DMello, S. R. Histone deacetylase-1 (HDAC1) is a molecular switch between ... Histone deacetylase (HDAC) inhibitors targeting HDAC3 and HDAC1 ameliorate polyglutamine-elicited phenotypes in model systems ... Transcriptional modulator H2A histone family, member Y (H2AFY) marks Huntington disease activity in man and mouse. Proc Natl ... HDAC1 is a component of the histone deactylase complex and plays an important role in regulation of gene expression. It can act ...
Environmental influence in the brain, human welfare and mental health | Nature Neuroscience
Antidepressant actions of histone deacetylase inhibitors. J. Neurosci. 29, 11451-11460 (2009). ... Wang, H., Duclot, F., Liu, Y., Wang, Z. & Kabbaj, M. Histone deacetylase inhibitors facilitate partner preference formation in ...
Estrogen-related receptor gamma regulates mitochondrial and synaptic genes and modulates vulnerability to synucleinopathy | npj...
... and histone deacetylase binding (Fig. 7g). Top hits were identified by taking into consideration connectivity values within the ... ORCID: orcid.org/0000-0001-5814-94121,2 Show authors. npj Parkinsons Disease volume 8, Article number: 106 (2022) Cite this ... Esrrg+/+;L10+ and Esrrgfl/fl;L10+ mice were injected with 2 ul of AAV.rTH.PI.Cre.SV40 (AddGene) into the midbrain to cause ... At 3 months of age, 2 days following tamoxifen treatment, iSlc6a3Cre;Esrrg+/+ or iSlc6a3Cre;Esrrgfl/fl mice were injected with ...
Advances in epigenetics link genetics to the environment and disease | Nature
... acetyl-coenzyme A is the acetyl donor for histone acetylation; β-hydroxybutyrate inhibits class I histone deacetylases; and the ... For example, histone variants and histone modifications can influence local chromatin structure, either directly or indirectly ... These include mutations in DNA methylases and demethylases, histones144 and histone modifiers, and genes involved in chromatin ... Indeed, nucleosomes are subject to constant remodelling, histones are exchanged and all DNA and histone marks discovered so far ...
Microbiota metabolite short-chain fatty acid acetate promotes intestinal IgA response to microbiota which is mediated by GPR43 ...
SCFA have been shown to regulate host immune response through intracellular targets such as histone deacetylases (HDAC)41, 42, ... Although it has been shown that SCFA inhibit histone deacetylases in a GPR41- and GPR43-independent manner, a recent report ... Short-chain fatty acids induce both effector and regulatory T cells by suppression of histone deacetylases and regulation of ... SCFA can regulate cell function either by inhibiting histone deacetylase activity, thus, affecting gene transcription, or ...
Quantitative High-Throughput Profiling of Environmental Chemicals and Drugs that Modulate Farnesoid X Receptor | Scientific...
Additionally, ERα was reported to activate histone deacetylase 6 (HDAC6) to deacetylate tubulins in human breast cancer MCF-7 ... Association of estrogen receptor alpha and histone deacetylase 6 causes rapid deacetylation of tubulin in breast cancer cells. ... After 16 hours of incubation at 37°C/5% CO2, 1 μL of CCF4-AM substrate reagents was added to each well using a Bioraptr Flying ... INT-747 is being tested as a monotherapy in a Phase 3 clinical trial and as a combination therapy with UDCA in a Phase 2 ...
Strategies for developing DNA-encoded libraries beyond binding assays | Nature Chemistry
Identification of histone deacetylase (HDAC)-associated proteins with DNA-programmed affinity labeling. Angew. Chem. Int. Ed. ... Small-molecule positive allosteric modulators of the beta2-adrenoceptor isolated from DNA-encoded libraries. Mol. Pharmacol. 94 ... Agonists and antagonists of protease-activated receptor 2 discovered within a DNA-encoded chemical library using mutational ...
Cell Research
Structural basis of nucleosome deacetylation and DNA linker tightening by Rpd3S histone deacetylase complex *Shuqi Dong ... Now we are seeking 1-2 full-time, in-house scientific editors to join its editorial team. ...
Cell Research
Structural basis of nucleosome deacetylation and DNA linker tightening by Rpd3S histone deacetylase complex *Shuqi Dong ... Now we are seeking 1-2 full-time, in-house scientific editors to join its editorial team. ...
Context-dependent tumor-suppressive BMP signaling in diffuse intrinsic pontine glioma regulates stemness through epigenetic...
Moreover, we identified several drugs (including the histone deacetylase (HDAC) inhibitor Dacinostat) with antitumor efficacy ... Histone variant and cell context determine H3K27M reprogramming of the enhancer landscape and oncogenic state. Mol. Cell 76, ... Histone H3F3A and HIST1H3B K27M mutations define two subgroups of diffuse intrinsic pontine gliomas with different prognosis ... K27M mutation in histone H3.3 defines clinically and biologically distinct subgroups of pediatric diffuse intrinsic pontine ...
Genome wide analysis of the transition to pathogenic lifestyles in Magnaporthales fungi | Scientific Reports
0000118 histone deacetylase complex, GO:0051568 histone H3-K4 methylation), transcription and RNA processing (GO:0098781 ncRNA ... 0035267 NuA4 histone acetyltransferase complex), signaling and response to stimulus (GO:0009607 response to biotic stimulus, GO ... 0000414 regulation of histone H3-K36 methylation, GO:0035327 transcriptionally active chromatin, GO:0016233 telomere capping, ... 0051570 regulation of histone H3-K9 methylation, GO:0031618 nuclear pericentric heterochromatin, GO:0033562 co-transcriptional ...
PCAF-dependent epigenetic changes promote axonal regeneration in the central nervous system | Nature Communications
... promotes acetylation of histone 3 Lys 9 at the promoters of established key regeneration-associated genes following a ... Here we show through systematic epigenetic studies that the histone acetyltransferase p300/CBP-associated factor (PCAF) ... Recently, it has been shown that calcium influx ejects histone deacetylase 5 (HDAC5) from the DRG nucleus correlating to ... Histone codes are shaped by a peripheral not by a central lesion. Given that epigenetic changes are a rapid and dynamic way to ...
Cell Research
Structural basis of nucleosome deacetylation and DNA linker tightening by Rpd3S histone deacetylase complex *Shuqi Dong ... Now we are seeking 1-2 full-time, in-house scientific editors to join its editorial team. ...
The structure of the NuA4-Tip60 complex reveals the mechanism and importance of long-range chromatin modification | Nature...
The only essential histone acetyltransferase (HAT) in yeast, Esa1, is part of the 1-MDa NuA4 complex, which plays pivotal roles ... NuA4 has the unique capacity to acetylate histone targets located several nucleosomes away from its recruitment site. Neither ... Histone acetylation regulates most DNA transactions and is dynamically controlled by highly conserved enzymes. ... Structural insights into the assembly of the histone deacetylase-associated Sin3L/Rpd3L corepressor complex. Proc. Natl Acad. ...
Extracellular sialyltransferase st6gal1 in breast tumor cell growth and invasiveness | Cancer Gene Therapy
Class I histone deacetylase inhibitor suppresses vasculogenic mimicry by enhancing the expression of tumor suppressor and anti- ... Regulation of histone acetylation in the nucleus by sphingosine-1-phosphate. Science. 2009;325:1254-7. ... 2: Functional ST6GAL-1 is variably expressed in breast cancer cells.. A mRNA levels of ST6GAL1 were determined from ER + and ... ST6GAL1 mRNA levels were also compared in different stages (stage 1, n = 178; stage 2, n = 610, stage 3, n = 245; stage 4, n = ...
Advances in the structure, mechanism and targeting of chemoresistance-linked ABC transporters | Nature Reviews Cancer
The selective class IIa histone deacetylase inhibitor TMP195 resensitizes ABCB1- and ABCG2-overexpressing multidrug-resistant ... Epigenetic regulation of MDR1 gene through post-translational histone modifications in prostate cancer. BMC Genomics 14, 898 ( ... Mechanistic basis of breast cancer resistance protein inhibition by new indeno[1,2-b]indoles. Sci. Rep. 11, 1788 (2021). ... Biological evaluation of non-basic chalcone CYB-2 as a dual ABCG2/ABCB1 inhibitor. Biochem. Pharmacol. 175, 113848 (2020). ...
Msh2 deficiency prevents in vivo somatic instability of the CAG repeat in Huntington disease transgenic mice | Nature Genetics
2,3,4,5,6. For longer repeat lengths, somatic instability of the repeat size has been observed both in human cases at autopsy7, ... 2,3,4,5. HD shows anticipation, in which subsequent generations display earlier disease onsets due to intergenerational repeat ... A selective inhibitor of histone deacetylase 3 prevents cognitive deficits and suppresses striatal CAG repeat expansions in ... Figure 2: Distribution of CAG repeats before and after the major GeneScan peak for various tissues from Msh2-/- and Msh2+/+ ...
Positioning of nucleosomes containing γ-H2AX precedes active DNA demethylation and transcription initiation | Nature...
... which are required by the histone chaperone FACT complex to incorporate nucleosomes containing the histone variant H2A.X. ... The order of DNA methylation and histone modifications during transcription remained unclear. Here the authors show that HMGA2 ... Chromatin-mediated regulation of transcription involves DNA methylation and histone modifications. However, the order of events ... Here we show that high-mobility group AT-hook 2 protein (HMGA2) induces DNA nicks at the transcription start site, ...
Mechanisms of mitochondrial respiratory adaptation | Nature Reviews Molecular Cell Biology
A role for the mitochondrial deacetylase Sirt3 in regulating energy homeostasis. Proc. Natl Acad. Sci. USA 105, 14447-14452 ( ... Narita, T., Weinert, B. T. & Choudhary, C. Functions and mechanisms of non-histone protein acetylation. Nat. Rev. Mol. Cell ... Succinate dehydrogenase is a direct target of sirtuin 3 deacetylase activity. PLoS ONE 6, e23295 (2011). ... Nature 598, 364-367 (2021). This article provides the first published structure of mammalian supercomplex III2 + IV and ...
Cellular senescence: when bad things happen to good cells | Nature Reviews Molecular Cell Biology
Munro, J., Barr, N. I., Ireland, H., Morrison, V. & Parkinson, E. K. Histone deacetylase inhibitors induce a senescence-like ... Minucci, S. & Pelicci, P. G. Histone deacetylase inhibitors and the promise of epigenetic (and more) treatments for cancer. ... Human fibroblast commitment to a senescence-like state in response to histone deacetylase inhibitors is cell cycle dependent. ... Funayama, R., Saito, M., Tanobe, H. & Ishikawa, F. Loss of linker histone H1 in cellular senescence. J. Cell Biol. 175, 869-880 ...
Axon-soma communication in neuronal injury | Nature Reviews Neuroscience
Cho, Y. & Cavalli, V. HDAC5 is a novel injury-regulated tubulin deacetylase controlling axon regeneration. EMBO J. 31, 3063- ... HDAC1 Expression, Histone Deacetylation, and Protective Role of Sodium Valproate in the Rat Dorsal Root Ganglia After Sciatic ... Figure 2: Retrograde signalling via the JUN kinase pathway after an axonal lesion.. ...