Potential DNA Binding Research Articles

Porphyrin-Polymer as a Photosensitizer Prodrug for Antimicrobial Photodynamic Therapy and Biomolecule Binding Ability.

This study presents the development and characterization of a novel porphyrin-Jeffamine polymer conjugate designed to function as a photosensitizer prodrug for antimicrobial photodynamic therapy (aPDT). The conjugate features a photosensitive porphyrin unit covalently attached to a biocompatible polymer backbone, with enhanced solubility, stability, and bioavailability compared to those of the free porphyrin derivatives. The photophysical properties were studied using transient absorption spectroscopy spanning the fs-μs time scales in addition to emission studies. The production of reactive oxygen species upon photoactivation enabled effective bacterial cell killing. Spectroscopic studies confirmed strong binding of the conjugate to DNA through intercalation, likely disrupting DNA replication and transcription. Interaction studies with bovine serum albumin demonstrated substantial serum protein binding, which may positively impact the pharmacokinetics and biodistribution. Overall, this porphyrin-polymer conjugate offers a multifunctional theranostic platform, combining antimicrobial action with DNA and protein binding potential, positioning it as a promising candidate for aPDT and bioimaging applications.

In silico research on Novel Derivatives of N-(Acetylphenyl)-N-Ferrocenylmethyl-3-nitroaniline as DNA Binding Agents: Using Diverse Computational Methods, including Molecular Docking and ADME/Toxicity Assessment

This study presents an in silico investigation into the potential DNA binding properties of novel derivatives of N-(Acetylphenyl)-N-Ferrocenylmethylnitroaniline using different computational techniques, including molecular docking and ADME/Toxicity assessment, we explored the interaction between these derivatives and DNA. The results reveal promising candidates with strong binding affinities to DNA, substantiated by robust electrostatic interactions. Furthermore, our study sheds light on the ADME and toxicity profiles of these compounds, providing insights into their pharmacological potential. These findings offer valuable insights into the design and development of DNA-binding agents with potential applications in various biomedical fields.

Insights into the molecular mechanism of ParABS system in chromosome partition by HpParA and HpParB.

The ParABS system, composed of ParA (an ATPase), ParB (a DNA binding protein), and parS (a centromere-like DNA), regulates bacterial chromosome partition. The ParB-parS partition complex interacts with the nucleoid-bound ParA to form the nucleoid-adaptor complex (NAC). In Helicobacter pylori, ParA and ParB homologs are encoded as HpSoj and HpSpo0J (HpParA and HpParB), respectively. We determined the crystal structures of the ATP hydrolysis deficient mutant, HpParAD41A, and the HpParAD41A-DNA complex. We assayed the CTPase activity of HpParB and identified two potential DNA binding modes of HpParB regulated by CTP, one is the specific DNA binding by the DNA binding domain and the other is the non-specific DNA binding through the C-terminal domain under the regulation of CTP. We observed an interaction between HpParAD41A and the N-terminus fragment of HpParB (residue 1-10, HpParBN10) and determined the crystal structure of the ternary complex, HpParAD41A-DNA-HpParBN10 complex which mimics the NAC formation. HpParBN10 binds near the HpParAD41A dimer interface and is clamped by flexible loops, L23 and L34, through a specific cation-π interaction between Arg9 of HpParBN10 and Phe52 of HpParAD41A. We propose a molecular mechanism model of the ParABS system providing insight into chromosome partition in bacteria.

Exploration of newly synthesized amantadine-thiourea conjugates for their DNA binding, anti-elastase, and anti-glioma potentials

Three newly synthesized amantadine thiourea conjugates namely MS-1 N-(((3 s,5 s,7 s)-adamantan-1-yl)carbamothioyl)benzamide, MS-2 N-(((3 s,5 s,7 s)-adamantan-1-yl)carbamothioyl)-4-methylbenzamide and MS-3 N-((3 s,5 s,7 s)-adamantan-1-ylcarbamothioyl)-4-chlorobenzamide were investigated for their structures, bindings (DNA/ elastase), and for their impact on healthy and cancerous cells. Theoretical (DFT/docking) and experimental {UV–visible (UV-), fluorescence (Flu-), and cyclic voltammetry (CV)} studies indicated binding interactions of each conjugate with DNA and elastase enzyme. Theoretically and experimentally calculated binding parameters for conjugate – DNA interaction revealed MS-3 – DNA to have most significant binding with comparatively greater values of binding parameters {(Kb/M−1: docking, 3.8 × 105; UV-, 5.95 × 103; Flu-,1.55 × 105; CV, 1.52 × 104), (∆G/ kJmol−1: docking, −32.09; UV-, −22.40; Flu-,-30.81; CV, −24.82)}. The docked structures, greater bindings site size values (n), and the trend in DNA viscosity changes in the presence of each conjugate concentration confirmed a mixed binding mode of interaction among them. Conjugate – elastase binding by docking agreed with the experimental anti-elastase findings. Cytotoxicity studies of each tested conjugate demonstrated greater cytotoxicity for cancerous (MG-U87) cells in comparison to control, while for the normal (HEK-293) cells the cytotoxicity was found comparatively low. Overall exploration suggested that MS-3 is the most effective candidate for DNA binding, anti-elastase, and for anti-glioma activities.

Insights on the nuclear shuttling of H2A-H2B histone chaperones

All cellular processes that involve the unwinding of DNA also lead to the systematic shuttling of histones. Histone shuttling across the nuclear membrane is facilitated by a class of proteins known as – histone chaperones. Histone chaperones are classified based on their binding to H3/H4 histones or H2A/H2B histones. During the shuttling process, two types of signals - NLS and NES are recognized by the nuclear transport proteins. However, this is the nuclear transport protein and the mechanism of signal recognition by the protein is still unknown. Thus, in this piece of work, the NLS and NES signals are predicted on important H2A/H2B binding histone chaperones. In addition, cellular localization and potential DNA binding regions of histone chaperones are predicted. Mapping of predicted regions on the histone chaperone’s structure suggested that the critical binding regions mainly lie on the disordered region of the histone chaperones. NLS and NES are present in the N- and C-terminal of the histone chaperones. Most histone chaperones contain bipartiate NLS signals. This article sheds light on the crucial aspect that in addition of being directly engaged in nucleosome synthesis and disassembly in vivo, histone chaperone also performs various specific roles via histone binding activity.

Green synthesis of ZnONps using Horse gram seed aqueous extract and its in vitro evaluation on antioxidant, antidiabetic, anticancer and DNA binding potential

The goal of this study was to access the green production of zinc oxide nanoparticles (G-ZnO NPs) using aqueous extract of horse gram seeds (Macrotyloma Uniflorum). The precursor to the extract ratio (2.5:1) and pH value (8.5), along with the zinc nitrate concentration (0.5 M), had an impact on the particle size and the green synthesized ZnO nanoparticles. UV Spectroscopy inspection revealed formation of G-ZnO NPs with absorption at 320 nm which is the characteristic absorption of G-ZnO NPs. FTIR, XRD, SEM, EDX and TEM were used to characterize the green synthesized ZnO NPs. The findings demonstrated that the presence of secondary metabolites in the seed extractstabilize and contribute in the production of G-ZnO NPs. A dose-dependent increase in antibacterial activity was seen in evaluation of these NPs against Klebsiella, Staphylococcus aureus, Escherichia coli, Pseudomonas aeruginosa. The antioxidant activity and antidiabetic activity for G-ZnO NPs was also noted to be concentration dependent. The synthesized nanoparticles are found to interact with CT-DNA to produce a hypochromic shift. Further the studies on the G-ZnONPs in MCF-7 cells using the MTT test demonstrated greater cellular inhibition. The results validate that the green synthesized ZnO-NPs from horse gram seed possess good biological activities and can be an excellent biologically derived potential material which could be used in the drug discovery from natural products.

Deciphering the calf thymus DNA binding potential of 5FU conjugated copper oxide nanoparticles along with its antiproliferative effects on liver cancer cells: A molecular, in silico, and in vitro approach

The current study accomplished 5-fluorouracil conjugated copper oxide nanoparticles (5FUcCuONPs) and assessed their DNA binding and antiproliferative capabilities using an array of in vitro techniques. The synthesized nanoparticles were characterized by UV-visible spectroscopy, dynamic light scattering, Fourier transform infrared spectroscopy, thermogravimetric analysis, and microscopic techniques. The DNA interaction analysis revealed that 5FUcCuONPs had a binding constant value in the range of 5.27 × 104 M−1, demonstrating an effective DNA binding interaction. The potency of the binding interactions was further corroborated by the Atomic Force Microscopic (AFM) analysis. Moreover, the intricate mechanism of the ligand-DNA interaction was investigated by molecular docking study, which revealed a binding energy of -6.3 kcal/mol. The 2D interaction plots of selected conformations revealed a network of hydrophobic and hydrogen bond interactions. Subsequent cell viability and the morphological study in HepG2 cells demonstrated the anticancer potential of 5FUcCuONPs with the IC50 value of 7.1μg/ml. This study demonstrates the DNA binding and therapeutic potential of 5-fluorouracil conjugated copper oxide nanoparticles, offering an intriguing alternative to combinatorial chemotherapy.

Identification and characterization of the Cyamopsis tetragonoloba transcription factor MYC (CtMYC) under drought stress

The MYC transcription factor (TF) has a variety of roles in abiotic stress responses of plants. In the present work, MYC TF named CtMYC (Cymopsis tetragonoloba) from guar plant, which is induced by drought stress, was identified. The mature leaves of guar were employed to detect the full-length CtMYC TF on the 8th day of drought stress. The CtMYC gene showed tissue-specific expression and up regulated under drought stress conditions as compared to the control and maximum expression was observed in mature leaves. Additionally, CtMYC TF was cloned and expressed in E. coli Rosetta cells and CtMYC protein was purified. The circular dichroism (CD) analysis revealed the presence of helical content and beta sheets and in the presence of genomic DNA the conformational changes were observed in secondary structure, which showed DNA binding potential of CtMYC. These results were analyzed by CD and fluorescence studies. In silico studies reveal the presence of conserved bHLH domain and DNA-binding amino acid residues His, Glu and Arg in CtMYC. This is first report on CtMYC TF with DNA binding potential that is responsive to drought. This study provides the structure and characterization of CtMYC TF and DNA binding ability in drought tolerance mechanism in guar.

Spectral studies, crystal structures, DNA binding, and anticancer potentials of Pd(II) complexes with iminophosphine ligands: Experimental and computational methods

Herein, we studied the synthesis and the biological properties of palladium(II) complexes derived from iminophosphine ligands DPPB-3-hydroxybenzohydrazone (DPPB-HBH), DPPB-4-phenylthiosemicarbazone (DPPB-PTSC), and DPPB-thiosemicarbazone (DPPB-TSC) (DPPB = 2-(diphenylphosphino)benzaldehyde) using theoretical and experimental methods. The molecular structures of [PdCl(DPPB-HBH)]Cl, [Pd(DPPB-HBH)2]Cl2·2CH3CN, [PdCl(DPPB-PTSC)], and [PdCl(DPPB-TSC)] were characterized by various spectroscopic techniques and X-ray crystallographic for [PdCl(DPPB-HBH)]Cl, [Pd(DPPB-HBH)2]Cl2·2CH3CN, and [PdCl(DPPB-PTSC)], confirming the distorted square-planar geometry for the palladium atoms. Complexes with the general formula [PdCl(Ligand)x] (x = 1) were employed to evaluate biological activities such as cytotoxicity against the MDA-MB-231 breast cancer cells and DNA binding ability. The results revealed the high cytotoxicity of the palladium complexes compared to the reference drug cisplatin (IC50 = 24.59 µg/mL), as well as their moderate binding ability to DNA through electrostatic interactions and groove binding. It was also found that [PdCl(DPPB-HBH)]Cl has the highest activity among others (IC50 = 9.3 µg/mL). Their interaction mode with DNA was investigated using molecular docking and NCI calculations, which showed complete agreement with the experimental results. Furthermore, quantum chemistry calculations were used to analyze the structure–activity relationship and introduce reactive sites, which determined the cause of the difference in the reactivity of the samples.

DNA Binding and Anticancer Properties of New Pd(II)-Phosphorus Schiff Base Metal Complexes.

DNA has become the target of metal complexes in cancer drug discovery. Due to the side effects of widely known cisplatin and its derivative compounds, alternative metal-based drug discovery studies are still ongoing. In this study, the DNA-binding ability of Pd(II) and Pt(II) complexes of four phosphorus Schiff base ligands and four hydrazonoic-phosphines are investigated by using in silico analyses. Phosphorus Schiff base-Pd(II) complexes encoded as B1 and B2 with the best DNA-binding potential are synthesized and characterized. The DNA-binding potentials of these two new Pd(II) complexes are also investigated experimentally, and their antitumor properties are demonstrated in vitro in A549, MCF7, HuH7, and HCT116 cancer cells. The mechanisms of these metal complexes that kill the cells mentioned above in different activities are elucidated by flow cytometry apoptosis analysis and colony formation analysis The in silico binding energies of these two new palladium complexes ΔG (B1): -4.51 and ΔG (B2): -6.04 kcal/mol, and their experimental DNA-binding constants were found as Kb (B1): 4.24 × 105, Kb (B2): 4.98 × 105). The new complexes, which show different antitumor effects in different cells, are the least effective in HuH7 liver cells, while they showed the best antitumor properties in HCT116 colon cancer cells.

Targeting aloe active compounds to c-KIT promoter G-quadruplex and comparative study of their anti proliferative property

Small molecules targeting G-quadruplex of oncogene promoter is considered as a promising anticancer therapeutics approach. Natural aloe compounds aloe emodin, and its glycoside derivative aloe emodin-8-glucoside and aloin have anticancer activity and also have potential DNA binding ability. These three compounds have promising binding ability towards quadruplex structures particularly c-KIT G-quadruplex. Here, this study demonstrates complete biophysical study of these compounds to c-KIT quadruplex structure. Aloe emodin showed highest binding stabilization with c-KIT which has been proved by absorbance, fluorescence, dye displacement, ITC and SPR studies. Moreover, comparative study of these compounds with HCT 116 cells line also agreed to their anti proliferative property which may be helpful to establish these aloe compounds as potential anticancer drugs. This study comprises a complete biophysical study along with their anti proliferative property and demonstrates aloe emodin as a potent c-KIT binding molecule.

Novel mycoplasma nucleomodulin MbovP475 decreased cell viability by regulating expression of CRYAB and MCF2L2

ABSTRACT Nucleomodulins are secreted bacterial proteins whose molecular targets are located in host cell nuclei. They are gaining attention as critical virulence factors that either modify the epigenetics of host cells or directly regulate host gene expression. Mycoplasma bovis is a major veterinary pathogen that secretes several potential virulence factors. The aim of this study was to determine whether any of their secreted proteins might function as nucleomodulins. After an initial in silico screening, the nuclear localization of the secreted putative lipoprotein MbovP475 of M. bovis was demonstrated in bovine macrophage cell line (BoMac) experimentally infected with M. bovis. Through combined application of ChIP-seq, Electrophoretic mobility shift assay (EMSA) and surface plasmon resonance (SPR) analysis, MbovP475 was determined to bind the promoter regions of the cell cycle central regulatory genes CRYAB and MCF2L2. MbovP475 has similar secondary structures with the transcription activator-like effectors (TALEs). Screening of various mutants affecting the potential DNA binding sites indicated that the residues 242NI243 within MbovP475 loop region of the helix-loop-helix domain were essential to its DNA binding activity, thereby contributing to decrease in BoMac cell viability. In conclusion, this is the first report to confirm M. bovis secretes a conserved TALE-like nucleomodulin that binds the promoters of CRYAB and MCF2L2 genes, and subsequently down-regulates their expression and decreases BoMac cell viability. Therefore, this study offers a new understanding of mycoplasma pathogenesis.

DeepZF: improved DNA-binding prediction of C2H2-zinc-finger proteins by deep transfer learning.

Cys2His2 zinc-finger (C2H2-ZF) proteins are the largest class of human transcription factors and hence play central roles in gene regulation and cell function. C2H2-ZF proteins are characterized by a DNA-binding domain containing multiple ZFs. A subset of the ZFs bind diverse DNA triplets. Despite their central roles, little is known about which of their ZFs are binding and how the DNA-binding preferences are encoded in the amino acid sequence of each ZF. We present DeepZF, a deep-learning-based pipeline for predicting binding ZFs and their DNA-binding preferences given only the amino acid sequence of a C2H2-ZF protein. To the best of our knowledge, we compiled the first in vivo dataset of binding and non-binding ZFs for training the first ZF-binding classifier. Our classifier, which is based on a novel protein transformer, achieved an average AUROC of 0.71. Moreover, we took advantage of both in vivo and in vitro datasets to learn the recognition code of ZF-DNA binding through transfer learning. Our newly developed model, which is the first to utilize deep learning for the task, achieved an average Pearson correlation greater than 0.94 over each of the three DNA binding positions. Together, DeepZF outperformed extant methods in the task of C2H2-ZF protein DNA-binding preferences prediction: it achieved an average Pearson correlation of 0.42 in motif similarity compared with an average correlation smaller than 0.1 achieved by extant methods. By applying established interpretability techniques, we show that DeepZF inferred biologically relevant binding principles, such as the effect of amino acid residue positions on ZF DNA-binding potential. DeepZF code, model, and results are available via github.com/OrensteinLab/DeepZF. Supplementary data are available at Bioinformatics online.

Transcriptional regulation of rice HSP101 promoter: Mitogen‐activated protein kinase‐mediated HSFA6a phosphorylation affects its stability and transactivation

AbstractHeat shock proteins (HSPs) and heat stress factors (HSFs) control the plant heat stress response to a large extent. HSP101 plays a decisive role in development of plant heat tolerance. We have previously shown that rice (Oryza sativa) cells contain 25 HSFs and among these, HSFA6a most predominantly binds to the HSP101 promoter and controls its transcript expression. This study shows that mitogen‐activated protein kinases (MAPKs), specifically MPK3, MPK4, and MPK6 phosphorylate HSFA6a. HSFA6a showed physical interaction with MPK3/MPK4, specifically in the nucleus and this interaction involved the C‐terminal end of HSFA6a. Four serine residues at positions Ser136, Ser141, Ser264, and Ser356 of HSFA6a are the putative sites of MAPK phosphorylation: we generated phospho‐mutant of HSFA6a by changing the serine residues to alanine either individually or all four together. The Hsp101 promoter binding potential of Ser136 mutant was enhanced while it declined for the other three phospho‐mutant HSFA6a forms. HSFA6a mutant lacking all the above four Ser residues exhibited reduced DNA binding and transactivation potential. We implicate the role of phosphorylation in the regulation of HSFA6a activity.

Exploration of DNA Binding Potential of Mononuclear Copper(II) Complex

Exploration of DNA Binding Potential of Mononuclear Copper(II) Complex

Ten-Eleven Translocation-3 CXXC domain is critical for postfertilization demethylation and expression of pluripotency genes in pig embryos†.

Enzymes of the ten-eleven translocation family are considered to play an important role in the regulation of DNA methylation patterns by converting 5-methylcytosine to 5-hydroxymethylcytosine. Known as a maternal transcript enriched in mature oocytes, ten-eleven translocation-3 (TET3) has been suggested to initiate DNA demethylation of the paternal genome in zygotes. Previous studies in mouse cells indicate that the N-terminal CXXC domain of TET3 is important in catalyzing the oxidation of 5-methylcytosine through its potential DNA binding ability; however, it is not clear whether the DNA binding capacity of CXXC domain is required for the 5-hydroxymethylcytosine conversion in mammalian embryos. Here, we identified TET3 isoforms in porcine oocytes and investigated the role of the oocyte specific TET3 isoform (pTET3L) in controlling postfertilization demethylation in porcine embryos. The pTET3L possessed sequences representing a known DNA binding domain, the CXXC, and injection of the TET3 CXXC fused with GFP into mature porcine oocytes resulted in exclusive localization of the GFP-CXXC in the pronuclei. The CXXC overexpression reduced the 5-methylcytosine level in zygotes and enhanced the DNA demethylation of the NANOG promoter in 2-cell stage embryos. Furthermore, there was an increase in the transcript abundance of NANOG and ESRRB in blastocysts developed from GFP-CXXC injected oocytes. Targeted knockdown of pTET3L resulted in the downregulation of pluripotency genes in subsequently developed blastocysts. The findings indicate that the CXXC domain of TET3 serves as a critical component for the postfertilization demethylation of porcine embryos and coordinates proper expression of pluripotency related genes in blastocysts.

Exploring the hydrogen-bonding interactions in the piperazinylethanol substituted homoleptic zinc(II)-dithiocarbamate and its diimine 2,2′-bipyridyl and 1,10-phenanthroline adducts, and their DNA binding studies

Keeping in view the significance of H-bonding hydroxyethyl substituent in the supramolecular organization of the compounds of general formula Zn(S2CNR1R2)2, herein we report synthesis and characterization (1H/13C NMR, FTIR, UV–Vis spectroscopy, CV, elemental analysis and single crystal XRD) of piperazinylethanol substituted complex [Zn{S2CN(CH2)4N(C2H4OH)}2]2 (1) and its 2,2′-bipyridyl (2) and 1,10-phenanthroline (3) adducts. Inferred from XRD data, these compounds show a variety of coordination geometries, i.e., Zn1-center (τ = 0.668) in (1) is more inclined towards trigonal-bipyramidal environment than the Zn2-center (τ = 0.567), whereas (2) and (3) exhibit distorted octa- and tetra-hedral geometries, respectively. Unlike the others, complex (2) co-crystallized with an uncoordinated 2,2′-bipyridyl ligand showing more stable trans-conformation of the N-atoms. Supramolecular data reveal pivotal role of the H-bonding interactions in the crystal packing, especially in (1) where (hydroxyethyl)OH···OH(hydroxyethyl) interaction sustains 3-D network. The interaction propagates in infinite open chain fashion and the network secures undulating topology. Adducts (2) and (3) also feature undulating topologies, however, OH···N H-bonding interaction plays the role to sustain 2- and 1-D networks, respectively. Other secondary bonding interactions, like CH···S, CH···π(aromatic), CH···O and π···π stacking etc. contribute to transform these 1- and 2-D architectures into 3-D aggregates. Compared to closely related systems, these compounds show enhanced H-bonding potential with less hydroxyethyl substituents per molecule, possibly due to the presence of sterically flexible piperazine ring. Further, their DNA-binding capability was assessed through multiple techniques (like UV–vis spectroscopy, CV and viscometry), which revealed promising DNA binding potential for these compounds.

Biological Activity of Solvent Extracts of Angelica archangelica Leaf and Stem

In the current study, extraction from the stem and leaf of the well-known Indian medicinal plant Angelica archangelica (A. Angelica) with the solvents of variable polarity such as water, methanol, ethyl acetate, and chloroform is reported. The presence of different secondary metabolites like terpenoid, flavonoid, glycosides, carbohydrates, resin, steroid, proteins, and tannin are confirmed by different phytochemical qualitative test for ethyl acetate, water, chloroform, and methanol extract. The difference in the composition of all the extracts is motivated to conduct the comparison of the biological potential of all extracts in the form of DNA cleavage, DNA binding, and antioxidant activity. It is observed that the methanolic extract is most potent among all which has high concentration of terpenoids. It has shown 95% DPPH scavenging activity and 62% DNA cleavage activity. Separation of terpenoids from methanolic extracts to hexane layer is conducted which proved the same as hexane layer has shown maximum DNA binding potential. Hexane layer has shown 52% DNA binding activity.

Hsp70, sHsps and ubiquitin proteins modulate HsfA6a-mediated Hsp101 transcript expression in rice (Oryza sativa L.).

Hsp100 chaperones disaggregate the aggregated proteins and are vital for maintenance of protein homeostasis. The level of Hsp100 synthesised in the cells has a bearing on the survival of plants under heat stress. The Hsp100 transcription machinery is activated within minutes of the onset of heat stress. The heat shock factor HsfA6a plays a major role in the transcriptional regulation of the Hsp101 gene in rice plants. Through yeast-2-hybrid library screening, we identified small heat shock proteins (sHSPs), Hsp70 and ubiquitin as HsfA6a interacting proteins (HIPs). The bimolecular fluorescence complementation assays showed the physical interaction of HsfA6a with Hsp16.9A-CI and Hsp18.0-CII in the cytosolic region and with cHsp70-1 in the nucleus. With the Hsp101 promoter: reporter gene assays, using yeast cells and rice protoplasts, we show that CI-sHsps and CII-sHsps are negative regulators and Hsp70 positive regulator of the HsfA6a activity in modulation of Hsp101 transcription. We also noted that the HsfA6a interactors, Hsp70 and CI-sHsps and CII-sHsps, physically interact with each other. We noted that HsfA6a binds with the CI-sHsp and Hsp70 promoters, implying that HsfA6a has a role in transcriptional regulation of its interacting proteins. Furthermore, we noted that the mutation of the ubiquitin/sumoylation acceptor site lysine 10 to alanine (K10A) of HsfA6a enhanced its DNA binding potential on the Hsp101 promoter, implying that these modifiers are possibly involved in modulation of HsfA6a activity. Our work shows that Hsp70, CI-sHsps and CII-sHsp, and ubiquitin proteins coordinate with HsfA6a in mediating the Hsp101 transcription process in rice.

Genome-wide regulation of CpG methylation by ecCEBPα in acute myeloid leukemia

Background: Acute myeloid leukemia (AML) is a hematopoietic malignancy characterized by genetic and epigenetic aberrations that alter the differentiation capacity of myeloid progenitor cells. The transcription factor CEBPα is frequently mutated in AML patients leading to an increase in DNA methylation in many genomic locations. Previously, it has been shown that ecCEBPα (extra coding CEBPα) - a lncRNA transcribed in the same direction as CEBPα gene - regulates DNA methylation of CEBPα promoter in cis. Here, we hypothesize that ecCEBPα could participate in the regulation of DNA methylation in trans. Method: First, we retrieved the methylation profile of AML patients with mutated CEBPα locus from The Cancer Genome Atlas (TCGA). We then predicted the ecCEBPα secondary structure in order to check the potential of ecCEBPα to form triplexes around CpG loci and checked if triplex formation influenced CpG methylation, genome-wide. Results: Using DNA methylation profiles of AML patients with a mutated CEBPα locus, we show that ecCEBPα could interact with DNA by forming DNA:RNA triple helices and protect regions near its binding sites from global DNA methylation. Further analysis revealed that triplex-forming oligonucleotides in ecCEBPα are structurally unpaired supporting the DNA-binding potential of these regions. ecCEBPα triplexes supported with the RNA-chromatin co-localization data are located in the promoters of leukemia-linked transcriptional factors such as MLF2. Discussion: Overall, these results suggest a novel regulatory mechanism for ecCEBPα as a genome-wide epigenetic modulator through triple-helix formation which may provide a foundation for sequence-specific engineering of RNA for regulating methylation of specific genes.