scholarly journals Comprehensive analysis of histone-binding proteins with multi-angle light scattering

Methods ◽  
2020 ◽  
Vol 184 ◽  
pp. 93-101 ◽  
Author(s):  
Prithwijit Sarkar ◽  
Noushin Akhavantabib ◽  
Sheena D'Arcy
2018 ◽  
Vol 10 (21) ◽  
pp. 17756-17770 ◽  
Author(s):  
Zhi Shang ◽  
Liqiang Qian ◽  
Sha Liu ◽  
Xiaomin Niu ◽  
Zhi Qiao ◽  
...  

Epigenomics ◽  
2019 ◽  
Vol 11 (11) ◽  
pp. 1267-1282 ◽  
Author(s):  
Zupeng Luo ◽  
Zhiwang Zhang ◽  
Lina Tai ◽  
Lifang Zhang ◽  
Zheng Sun ◽  
...  

Aim: To assess the m6A methylome in mouse fatty liver induced by a high-fat diet (HFD). Materials & methods: MeRIP-seq was performed to identify differences in the m6A methylomes between the normal liver and fatty liver induced by an HFD. Results: As compared with the control group, the upmethylated coding genes upon feeding an HFD were primarily enriched in processes associated with lipid metabolism, while genes with downmethylation were enriched in processes associated with metabolism and translation. Furthermore, many RNA-binding proteins that potentially bind to differentially methylated m6A sites were mainly annotated in processes of RNA splicing. Conclusion: These findings suggest that differential m6A methylation may act on functional genes through RNA-binding proteins to regulate the metabolism of lipids in fatty liver disease.


2016 ◽  
Vol 64 (1) ◽  
pp. 52-58 ◽  
Author(s):  
Sakura Yoshida ◽  
Eriko Hori ◽  
Sakiko Ura ◽  
Mamoru Haratake ◽  
Takeshi Fuchigami ◽  
...  

Blood ◽  
2018 ◽  
Vol 132 (Supplement 1) ◽  
pp. 218-218
Author(s):  
Simon Timothy Abrams ◽  
Dunhao Su ◽  
Yasmina Sahraoui ◽  
Yasir Alhamdi ◽  
Guozheng Wang ◽  
...  

Abstract Background: Increased thrombin generation in vivo is pivotal to the development of disseminated intravascular coagulation (DIC). Typically, thrombin is generated when the prothrombinase complex, composed of activated factor X (FXa), activated co-factor V (FVa) and phospholipids, cleaves prothrombin in the presence of calcium. In critical illness, extensive cell death releases histones into the circulation, which can increase thrombin generation. However, the underlying pathophysiological mechanisms remains to be fully elucidated. Methods: In vitro: Isolation of histone-binding proteins with mass spectrometry analysis. Surface plasmon resonance binding studies, prothrombin cleavage and thrombin generation assays. In vivo: histone infusion mouse models (C57BL/6 mice) with or without prothrombin fragment F1+F2 infusion. Clinical: a prospective cohort of 129 adult intensive care unit patients (ICU) with sepsis and analysed for DIC. Results: Histone-conjugated Sepharose beads were used to pull down proteins from human plasma. Histone-binding proteins were subjected to 2D gel electrophoresis and sequenced by liquid chromatography-mass spectrometry. Prothrombin was the only coagulation factor identified. Histones directly bind to prothrombin (H3 [Kd = 6.8 x 107 M] and H4 [Kd = 7.0 x 107 M]), specifically prothrombin fragments F1+F2, to facilitate FXa-induced prothrombin cleavage and thrombin generation (H4 [12.25 ± 1.25 fold] and H3 [8.82 ± 0.67 fold]). FXa levels are the limiting factor of histone-enhanced thrombin generation since this process was inhibited in FX-deficient plasma unless exogenous FXa was added. Specifically, using either heparin or anti-histone antibodies to block histones, histone-prothrombin interactions, prothrombin cleavage and subsequent thrombin generation were significantly reduced. Unlike FVa which requires a phospholipid surface to form functional prothrombinase complexes, histones can substitute for FVa in the absence of phospholipids. The addition of histones to FV-deficient plasma restored thrombin generation, suggesting that histones can bypass FVa to induce thrombin generation. In vivo, infusion of histones into mice caused significant decreases in platelet counts and fibrinogen levels with elevations in thrombin-antithrombin complexes, D-dimer and prothrombin time in a dose-dependent manner. Pathological examination indicated intravascular thrombi with various organs, particularly in within lung tissues. These histone-induced DIC changes were significantly abrogated when prothrombin fragments F1+F2 were infused prior to histones to act as a decoy for binding of histones to circulating prothrombin. Analysis of DIC scores in ICU patients (n=129) with sepsis showed circulating histone levels to strongly correlate with DIC scores (r=0.446, p<0.0001). Conclusions: Histones can replace FVa in prothrombinase and not require phospholipid surfaces. This alternative histone-assembled prothrombinase can explain how thrombin could be generated and amplified away from cell surfaces to cause systemic dissemination of its effects and potentiate DIC. This study also identifies circulating histones as a potential target for therapeutic intervention in reducing DIC development and subsequent multi-organ failure in ICU patients. Disclosures No relevant conflicts of interest to declare.


2009 ◽  
Vol 15 (1) ◽  
pp. 62-71 ◽  
Author(s):  
Tim J. Wigle ◽  
J. Martin Herold ◽  
Guillermo A. Senisterra ◽  
Masoud Vedadi ◽  
Dmitri B. Kireev ◽  
...  

The histone code comprises many posttranslational modifications that occur mainly in histone tail peptides. The identity and location of these marks are read by a variety of histone-binding proteins that are emerging as important regulators of cellular differentiation and development and are increasingly being implicated in numerous disease states. The authors describe the development of the first high-throughput screening assay for the discovery of inhibitors of methyl-lysine binding proteins that will be used to initiate a full-scale discovery effort for this broad target class. They focus on the development of an AlphaScreen™-based assay for malignant brain tumor (MBT) domain-containing proteins, which bind to the lower methylation states of lysine residues present in histone tail peptides. This assay takes advantage of the avidity of the AlphaScreen™ beads to clear the hurdle to assay development presented by the low micromolar binding constants of the histone binding proteins for their cognate peptides. The assay is applicable to other families of methyl-lysine binding proteins, and it has the potential to be used in screening efforts toward the discovery of novel small molecules with utility as research tools for cellular reprogramming and ultimately drug discovery.


1995 ◽  
Vol 206 (1) ◽  
pp. 260-265 ◽  
Author(s):  
M.A. Bonardi ◽  
E. Giovanetti ◽  
G. Legname ◽  
G. Fossati ◽  
G. Porro ◽  
...  

2021 ◽  
Vol 2021 (7) ◽  
Author(s):  
Marvin Zanke ◽  
Martin Hoferichter ◽  
Bastian Kubis

Abstract Estimating the contribution from axial-vector intermediate states to hadronic light-by-light scattering requires input on their transition form factors (TFFs). Due to the Landau–Yang theorem, any experiment sensitive to these TFFs needs to involve at least one virtual photon, which complicates their measurement. Phenomenologically, the situation is best for the f1(1285) resonance, for which information is available from e+e− → e+e−f1, f1 → 4π, f1 → ργ, f1 → ϕγ, and f1 → e+e−. We provide a comprehensive analysis of the f1 TFFs in the framework of vector meson dominance, including short-distance constraints, to determine to which extent the three independent TFFs can be constrained from the available experimental input — a prerequisite for improved calculations of the axial-vector contribution to hadronic light-by-light scattering. In particular, we focus on the process f1 → e+e−, evidence for which has been reported recently by SND for the first time, and discuss the impact that future improved measurements will have on the determination of the f1 TFFs.


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