Selective Methylation Research Articles

The Putative Promoters of Germ Cell-specific Genes and <i>Nanog</i> are Hypomethylated in Chicken Sperm

Germ cell-specific genes such as Ddx4, Dnd1, and Dazl play critical roles in the proliferation and survival of germ cells. However, the methylation state of the promoter in mature germ cells is still unknown. Here, we investigated the methylation levels of these genes and the pluripotency marker gene Nanog in chicken sperm as compared with the Alb gene in the liver. CpG islands and/or promoter motifs such as TATA box, GC box and CAAT box were found within the putative promoter regions that we identified. By using the bisulfite reaction, CpG sites in the putative promoters were converted, and they were analyzed by sequencing. The putative promoters of Ddx4, Dnd1, Dazl and Nanog showed very low methylation levels in sperm, but they were highly methylated in the liver. Conversely, the Alb gene promoter was highly methylated in sperm and hypomethylated in the liver. However, no transcripts of Ddx4, Dnd1, Dazl and Nanog were detected in sperm or the liver. Also, no transcripts of Dnmt1 and Dnmt3a were detected in sperm. Our present results may indicate that these germ cell-specific genes and the pluripotency marker gene are ready to express any time after fertilization. Our findings showing that low methylation and selective DNA methylation of specific genes are present in chicken sperm contribute to our understanding of fertilization and embryogenesis of birds.

PIAS1 SUMO ligase regulates the self-renewal and differentiation of hematopoietic stem cells

The selective and temporal DNA methylation plays an important role in the self-renewal and differentiation of hematopoietic stem cells (HSCs), but the molecular mechanism that controls the dynamics of DNA methylation is not understood. Here, we report that the PIAS1 epigenetic pathway plays an important role in regulating HSC self-renewal and differentiation. PIAS1 is required for maintaining the quiescence of dormant HSCs and the long-term repopulating capacity of HSC. Pias1 disruption caused the abnormal expression of lineage-associated genes. Bisulfite sequencing analysis revealed the premature promoter demethylation of Gata1, a key myeloerythroid transcription factor and a PIAS1-target gene, in Pias1(-/-) HSCs. As a result, Pias1 disruption caused the inappropriate induction of Gata1 in HSCs and common lymphoid progenitors (CLPs). The expression of other myeloerythroid genes was also enhanced in CLPs and lineage-negative progenitors, with a concurrent repression of B cell-specific genes. Consistently, Pias1 disruption caused enhanced myeloerythroid, but reduced B lymphoid lineage differentiation. These results identify a novel role of PIAS1 in maintaining the quiescence of dormant HSCs and in the epigenetic repression of the myeloerythroid program.

Methyl Salicylate as a Selective Methylation Agent for the Esterification of Carboxylic Acids

Methyl salicylate is a selective and inexpensive methylating agent for the esterification of carboxylic acids with a wide range of functional group tolerance. The intramolecular hydrogen bonds between the carboxylate and hydroxyl groups in methyl salicylate are essential for the transformation. Allyl, benzyl, methallyl, and propargyl salicylates can also be used as alkylating agents for the preparation of the corresponding alkyl carboxylates.

Proof of cannabis administration by sensitive detection of 11‐nor‐Delta(9)‐tetrahydrocannabinol‐9‐carboxylic acid in hair using selective methylation and application of liquid chromatography‐ tandem and multistage mass spectrometry

The identification of 11-nor-Δ9-tetrahydrocannabinol-9-carboxylic acid (THCCOOH) in hair represents an exceptional forensic analytical challenge due to low target concentrations in a complex matrix. Several dedicated techniques [gas chromatography-negative chemical ionization-tandem mass spectrometry (GC-NCI-MS/MS) or GC-GC-MS couplings] were specifically introduced into forensic toxicology aiming to a selective and sensitive identification of THCCOOH in hair. The combination of liquid-chromatography (LC) and MS/MS gained an outstanding relevance in forensic toxicology (including the detection of cannabinoids). However, its application to hair matrix is characterized by a lack of specificity which is due to the unspecific decarboxylation as most abundant fragmentation reaction. Therefore, various chemical modifications of the carboxyl and/or phenolic hydroxyl groups were examined to improve the selectivity. The selective methylation of the 9-carboxyl-group proved to be the most efficient derivatization procedure. Hair extracts were redissolved in acetonitrile and after addition of few milligrams of solid sodium carbonate derivatized with 25 μL methyl iodide. The resulting THC-9-carboxymethylester was separated by conventional reverse phase LC and selectively detected using negative electrospray ionization by recording the fragmentation reactions 357➔325 and 357➔297. Resulting limits of quantification were below 100 fg/mg. A further significant improvement was achieved by application of the multistage MS3 fragmentation 357➔325➔297. To verify the validity of this procedure, a systematic quantitative comparison of THCCOOH concentrations in hair with data from a well established GC-NCI-MS/MS technique was performed. Both techniques proved to be in good accordance (R(2)=0.647, p = <0.001) and equally suitable for hair testing of THCCOOH.

Efficient Synthesis of 6-O-methyl-scutellarein from Scutellarin via Selective Methylation

Efficient Synthesis of 6-O-methyl-scutellarein from Scutellarin via Selective Methylation

Targeted DNA methylation by homology-directed repair in mammalian cells. Transcription reshapes methylation on the repaired gene

We report that homology-directed repair of a DNA double-strand break within a single copy Green Fluorescent Protein (GFP) gene in HeLa cells alters the methylation pattern at the site of recombination. DNA methyl transferase (DNMT)1, DNMT3a and two proteins that regulate methylation, Np95 and GADD45A, are recruited to the site of repair and are responsible for selective methylation of the promoter-distal segment of the repaired DNA. The initial methylation pattern of the locus is modified in a transcription-dependent fashion during the 15–20 days following repair, at which time no further changes in the methylation pattern occur. The variation in DNA modification generates stable clones with wide ranges of GFP expression. Collectively, our data indicate that somatic DNA methylation follows homologous repair and is subjected to remodeling by local transcription in a discrete time window during and after the damage. We propose that DNA methylation of repaired genes represents a DNA damage code and is source of variation of gene expression.

Selective Methylation of Amines with Carbon Dioxide and H2

In Kombination mit H2 entpuppt sich Kohlendioxid als effizientes und selektives Methylierungsreagens für aromatische und aliphatische Amine (siehe Schema; acac=Acetylacetonat, triphos=1,1,1-Tris(diphenylphosphanylmethyl)ethan). Eine Vielfalt funktionalisierter Amine, einschließlich 13C-markierter Wirkstoffe, wurde in guten Ausbeuten bei hoher Verträglichkeit mit funktionellen Gruppen erhalten.

Selective Methylation of Amines with Carbon Dioxide and H2

Selective Methylation of Amines with Carbon Dioxide and H₂

Process of p-Xylene Production by Highly Selective Methylation of Toluene

p-Xylene is an important industrial compound, and its demand has been increasing in recent years. It is mostly produced from cracking of naphtha, but there is a need for new and cost-effective meth...

Evolution of Structure and Mechanistic Divergence in Di-Domain Methyltransferases from Nematode Phosphocholine Biosynthesis

The phosphobase methylation pathway is the major route for supplying phosphocholine to phospholipid biosynthesis in plants, nematodes, and Plasmodium. In this pathway, phosphoethanolamine N-methyltransferase (PMT) catalyzes the sequential methylation of phosphoethanolamine to phosphocholine. In the PMT, one domain (MT1) catalyzes methylation of phosphoethanolamine to phosphomonomethylethanolamine and a second domain (MT2) completes the synthesis of phosphocholine. The X-ray crystal structures of the di-domain PMT from the parasitic nematode Haemonchus contortus (HcPMT1 and HcPMT2) reveal that the catalytic domains of these proteins are structurally distinct and allow for selective methylation of phosphobase substrates using different active site architectures. These structures also reveal changes leading to loss of function in the vestigial domains of the nematode PMT. Divergence of function in the two nematode PMTs provides two distinct antiparasitic inhibitor targets within the same essential metabolic pathway. The PMTs from nematodes, plants, and Plasmodium also highlight adaptable metabolic modularity in evolutionarily diverse organisms.

NMR methods for structural studies of large monomeric and multimeric proteins.

NMR structural studies of large monomeric and multimeric proteins face distinct challenges. In large monomeric proteins, the common occurrence of frequency degeneracies between residues impedes unambiguous assignment of NMR signals. To overcome this barrier, nonuniform sampling (NUS) is used to measure spectra with optimal resolution within reasonable time, new correlation maps resolve previous impasses in assignment strategies, and novel selective methyl labeling schemes provide additional structural probes without cluttering NMR spectra. These advances push the limits of NMR studies of large monomeric proteins. Large multimeric and multidomain proteins are studied by NMR when individual components can also be studied by NMR and have known structures. The structural properties of large assemblies are obtained by identifying binding surfaces, by orienting domains, and employing limited distance constraints. Segmental labeling and the combination of NMR with other methods have helped popularize NMR studies of such systems.

Selective Methylation of CpGs at Regulatory Binding Sites Controls NNAT Expression in Wilms Tumors

Aberrant expression of imprinted genes, such as those coding for the insulin-like growth factor 2 (IGF2) and neuronatin (NNAT), is a characteristic of a variety of embryonic neoplasms, including Wilms tumor (WT). In case of IGF2, it is generally accepted that loss of imprinting in a differentially methylated region of the IGF2/H19 locus results in biallelic expression and, thus, upregulation of the gene. In this study we examined methylation pattern at potential regulatory elements of the paternally expressed NNAT gene in a cohort of WT patients in order to further characterize the molecular mechanism causing overexpression of this regulatory gene. We demonstrate that transcriptional upregulation of NNAT in WT is grossly independent of the bladder cancer-associated protein (BLCAP) gene, an imprinted gene within the imprinted domain of the NNAT locus. However, expression of the BLCAP transcript isoform v2a formerly known to be selectively expressed from the paternal allele in brain was associated with high expression of NNAT. This contrasts the situation we found at the IGF2/H19 locus, which shows high overexpression of IGF2 and inversely correlated expression of the H19 gene in WT. An analysis of DNA methylation in two potential regulatory regions of the NNAT locus by pyrosequencing revealed significant hypomethylation of the tumors compared to normal kidney tissue. Interestingly, the difference in DNA methylation was highest at CpGs that were observed within three putative binding sites of the CCCTC-binding factor CTCF. Most importantly, hypomethylation of both NNAT regulatory regions is significantly associated with the upregulation of NNAT expression and the BLCAP_v2a transcript. Our data indicate that the methylation status of a not-yet-described regulatory element within the NNAT locus that contains four potential CTCF binding sites determines the expression level of NNAT and the nearby located BLCAP_v2a transcript, thereby suggesting a functional role in the aberrant upregulation of NNAT in WT.

Total Synthesis of the Phenolic Glycolipid Mycoside B and the Glycosylated p‐Hydroxybenzoic Acid Methyl Ester HBAD‐I, Virulence Markers of Mycobacterium tuberculosis

AbstractThe phenolic glycolipid mycoside B, present in Mycobacterium bovis and hypervirulent strains of Mycobacterium tuberculosis, has been synthesized for the first time. Multiple methyl groups were introduced by the extensive use of catalytic asymmetric 1,4‐addition reactions, asymmetric hydrogenation of a β‐keto ester afforded the basis for the central 1,3‐diol moiety, and introduction of the 2‐O‐methyl‐α‐L‐rhamnoside unit was achieved by stereoselective glycosylation with p‐iodophenol and subsequent Sonogashira coupling, providing a basis for the generation of analogues. In addition, the related monosaccharide HBAD‐I, present in the same species, has been efficiently synthesized for the first time by selective methylation of the hydroxy group at C‐2 of a rhamnoside.

Selective methylation of phloroglucinol in the presence of a glycoluril clip

Abstract Methylation of phloroglucinol was performed using dimethyl sulfate as the methylating agent in the presence and absence of a glycoluril clip. The results showed that the yield of the di-methylated product decreased significantly in the presence of a glycoluril clip (host), due to the formation of a host–guest complex between the clip and phloroglucinol. Also, the reaction was conducted with different quantities (mol %) of the host.

Semisynthesis, cytotoxicity, antiviral activity, and drug interaction liability of 7-O-methylated analogues of flavonolignans from milk thistle

Silymarin, an extract of the seeds of milk thistle (Silybum marianum), is used as an herbal remedy, particularly for hepatoprotection. The main chemical constituents in silymarin are seven flavonolignans. Recent studies explored the non-selective methylation of one flavonolignan, silybin B, and then tested those analogues for cytotoxicity and inhibition of both cytochrome P450 (CYP) 2C9 activity in human liver microsomes and hepatitis C virus infection in a human hepatoma (Huh7.5.1) cell line. In general, enhanced bioactivity was observed with the analogues. To further probe the biological consequences of methylation of the seven major flavonolignans, a series of 7-O-methylflavonolignans were generated. Optimization of the reaction conditions permitted selective methylation at the phenol in the 7-position in the presence of each metabolite’s 4–5 other phenolic and/or alcoholic positions without the use of protecting groups. These 7-O-methylated analogues, in parallel with the corresponding parent compounds, were evaluated for cytotoxicity against Huh7.5.1 cells; in all cases the monomethylated analogues were more cytotoxic than the parent compounds. Moreover, parent compounds that were relatively non-toxic and inactive or weak inhibitors of hepatitis C virus infection had enhanced cytotoxicity and anti-HCV activity upon 7-O-methylation. Also, the compounds were tested for inhibition of major drug metabolizing enzymes (CYP2C9, CYP3A4/5, UDP-glucuronsyltransferases) in pooled human liver or intestinal microsomes. Methylation of flavonolignans differentially modified inhibitory potency, with compounds demonstrating both increased and decreased potency depending upon the compound tested and the enzyme system investigated. In total, these data indicated that monomethylation modulates the cytotoxic, antiviral, and drug interaction potential of silymarin flavonolignans.

A General Catalytic Methylation of Amines Using Carbon Dioxide

Putting CO2 to work: Carbon dioxide is shown to be a general and selective methylating reagent for secondary and primary, aromatic and aliphatic amines under reductive conditions. A variety of tertiary amines are obtained from CO2 and commercially available silanes in high yields with good tolerance to nitrile, olefin, ether, ester, and hydroxy groups.

Selective Methylation of NH-Containing Heterocycles and Sulfonamides Using N,N-Dimethylformamide Dimethylacetal Based on Calculated pKa Measurements

The use of <i>N</i>,<i>N</i>-dimethylformamide dimethylacetal (DMF-DMA) as a suitable methylating agent for the methylation of NH-containing groups and heterocycles has been investigated. Use of ReactArray and calculated p<i>K</i> _a measurements have allowed additional helpful information to be collated to determine optimum reaction conditions for a variety of substrates.

An efficient synthesis of LipidGreen and its derivatives via microwave assisted reaction and their live lipid imaging in zebrafish

We have developed an efficient synthesis of LipidGreen. The conversion is achieved by selective methylation with trimethylsilyldiazomethane, selective deprotection by BBr3 and an improved microwave-assisted C-allylation procedure. Using this route, we have synthesized novel LipidGreen derivatives, and evaluated their live imaging abilities in zebrafish. In this series, Compound 7 is the most active, which is at least 10 fold more potent than LipidGreen.

N-Heterocyclic Silylene (NHSi) Rhodium and Iridium Complexes: Synthesis, Structure, Reactivity, and Catalytic Ability

Reaction of the zwitterionic N-heterocyclic silylene (NHSi) 1 L′Si: (L′ = [HC(CMeNAr)(C(CH2)NAr)], Ar = 2,6-iPr2C6H3) with HCl at low temperatures affords the kinetically stable 1,4-addition product of 1, LSiCl (L = [HC(CMeNAr)2], Ar = 2,6-iPr2C6H3) (9a), which upon reaction with [Rh(Cl)cod]2 and [Ir(Cl)cod]2 (cod = 1,5-cyclooctadiene) selectively affords the NHSi complexes [L(Cl)Si:→Rh(Cl)cod] (10a) and [L(Cl)Si:→Ir(Cl)cod] (10b), respectively. The latter were employed as pre-catalysts in the catalytic reduction of amides in the presence of silanes. Remarkably, they show strikingly different activities and selectivities. While complex 10a yields selectively the C–O cleavage product, 10b affords both cleavage products (C–O and C–N). Moreover, the total conversion of the catalytic amide reduction with 10b is significantly higher than the conversion with a benchmark system [Ir(Cl)cod]2 highlighting the enhanced catalytic activity afforded by the coordination of the NHSi ligand. Introducing the hydride source Li[HBEt3] into the catalytic reactions retards the catalyst performance due to a competitive decomposition pathway. This appears to occur via a H-shift onto the cod ligand with concomitant liberation of cyclooctene, which is also presented. The different reactivity of 10a and 10b towards nucleophiles such as MeLi is also discussed. The reaction of 10a with MeLi affords an intractable array of products, while the reaction of 10b with one equivalent of MeLi selectively affords [L(Cl)Si:→Ir(CH3)cod] (14) with selective methylation at the Ir centre. The analogous reaction with two equivalents of 10b affords the double methylated product [L(CH3)Si:→Ir(CH3)cod] (15).

A simple structure fluorescent chemosensor for high selectivity and sensitivity of aluminum ions

Abstract A highly selective and sensitive fluorescent turn-on chemosensor methyl pyrazinylketone benzoyl hydrazone ( MPBH ) was synthesized by a facile one-step Schiff base reaction. MPBH which owns a quite simple structure showed a high selectivity for Al 3+ over other metal ions in ethanol. Due to the formation of a 1:1 complex between MPBH and the aluminum ions, a significant fluorescence enhancement with a turn-on ratio over 800-fold was achieved. The detection limit of MPBH for Al 3+ reached at 10 −7 M level.