Pairs Of Cis Research Articles

Isomerization enhanced fluorescence brightness of benzobisthiadiazole-based NIR-II fluorophores for highly efficient fluorescence imaging: A theoretical perspective

As a cutting-edge technique, fluorescence imaging in the second near-infrared window (NIR-II) is vital for both biomedical research and clinical applications. However, its intravital imaging capacity has been restricted by the extremely limited brightness of NIR-II fluorophores. To address this challenge, we elucidated the inner mechanism of constructing high-performance NIR-II chromophores based on molecular isomer engineering from detailed computational investigations. Herein, three pairs of cis–trans isomers (cis-1, 2, 3 and trans-1, 2, 3) are designed by attaching amino, methoxyl and nitro moieties to different positions on the donor–acceptor-donor molecular skeleton with benzobisthiadiazole as the acceptor and triphenylamine as the donor. All the compounds feature efficient NIR-II emission ranging in 1000–1164 nm, and the photophysical characterizations are regulated by molecular isomer manipulation. Interestingly, fluorescence quantum yields of cis-isomers are higher than those of their trans-counterparts. These enhancements can be attributed to the significant reduction in non-radiative transition, as evidenced by the non-adiabatic excitation energy, non-adiabatic electron coupling and electron-vibration coupling. Meanwhile, fluorophores with nitro terminal group exhibit superior performance facilitated by the prominently intramolecular charge transfer. As a result, cis-3 achieves an optimal brightness maxima of 196.36 M−1 cm−1 at 632 nm. Notably, the energy gap and the hole-electron related H index are respectively identified as strongly relevant to the emission wavelength and brightness, making them capable of evaluating the feasibility of fluorophores as effective NIR-II candidates. These findings highlight the correlations between molecular geometry and luminescent properties, which will inspire more insights into the development of highly efficient NIR-II fluorophores through rational isomer engineering for biomedical applications.

Theory and simulations of light-induced self-assembly in colloids with quantum chemistry derived empirical potentials.

Light-induced self-assembly (LISA) is a non-invasive method for tuning material properties. Photoresponsive ligands coated on the surfaces of nanoparticles are often used to achieve LISA. We report simulation studies for a photoresponsive ligand, azobenzene dithiol (ADT), which switches from a trans-to-cis configuration on exposure to ultraviolet light, allowing self-assembly in ADT-coated gold nanoparticles (NPs). This is attributed to a higher dipole moment of cis-ADT over trans-ADT which leads to a dipole-dipole attraction facilitating self-assembly. Singh and Jha [Comput. Theor. Chem., 2021, 1206, 113492] used quantum-chemistry calculations to quantify the interaction energy of a pair of ADT ligands in their cis and trans conformations. The interaction energy between ligands was fit to a potential energy function of the Lennard-Jones (LJ) form having distinct exponents for attractive and repulsive contributions. Using this generalized equation for the ligand-ligand interaction energy, we calculated the total effective interaction energy between a pair of cis as well as trans ADT-coated NPs. Specifically, we calculated the effective interaction energies between cis/trans-NPs using discrete as well as continuous approaches. Given the limitations of experiments in probing individual ligand conformations, we also studied the effect of varying the functional ligand length on the interaction energy between NPs and identified the optimal functional ligand length to capture the steric and conformational effects. Finally, using the effective interaction energy, we obtained a generalized potential energy function, which was applied in Langevin dynamics simulations to capture self-assembly in NPs.

Synthesis, characterization, and anticancer activity of some mononuclear ruthenium(II) compounds

Mononuclear Ru-based compounds cis-RuII(dppm)2Cl2 (1) and trans-RuII(dppe)2Cl2 (4) were synthesized by treatment of RuIICl2(DMSO)4 with dppm or dppe, respectively (dppm = bis(diphenylphosphino) methane, dppe = 1,2-bis(diphenylphosphino) ethane, DMSO = dimethyl sulfoxide). Mononuclear Ru-based compounds trans-RuII(dppm)2Cl2 (2) and cis-RuII(dppe)2Cl2 (3) were obtained by reaction of RuIICl2(PPh3)3 with dppm or dppe, separately. These two pair of cis–trans isomers, cis/trans-RuII(dppm)2Cl2 and cis/trans-RuII(dppe)2Cl2, were characterized by electronic absorption spectra, infrared, elemental analysis, 1H NMR, 13C NMR, 31P NMR, and single-crystal X-ray diffraction analysis. Both the crystal structure data and electronic absorption spectra indicate that the cis-isomer is a more thermodynamically stable structure and has lower energy than the trans-isomer. The luminescence spectroscopic study and relative cell viability of 1–4 on HeLa cancer cells has been investigated.

Transcriptome analysis reveals potential function of long non-coding RNAs in 20-hydroxyecdysone regulated autophagy in Bombyx mori

Background20-hydroxyecdysone (20E) plays important roles in insect molting and metamorphosis. 20E-induced autophagy has been detected during the larval–pupal transition in different insects. In Bombyx mori, autophagy is induced by 20E in the larval fat body. Long non-coding RNAs (lncRNAs) function in various biological processes in many organisms, including insects. Many lncRNAs have been reported to be potential for autophagy occurrence in mammals, but it has not been investigated in insects.ResultsRNA libraries from the fat body of B. mori dissected at 2 and 6 h post-injection with 20E were constructed and sequenced, and comprehensive analysis of lncRNAs and mRNAs was performed. A total of 1035 lncRNAs were identified, including 905 lincRNAs and 130 antisense lncRNAs. Compared with mRNAs, lncRNAs had longer transcript length and fewer exons. 132 lncRNAs were found differentially expressed at 2 h post injection, compared with 64 lncRNAs at 6 h post injection. Thirty differentially expressed lncRNAs were common at 2 and 6 h post-injection, and were hypothesized to be associated with the 20E response. Target gene analysis predicted 6493 lncRNA-mRNA cis pairs and 42,797 lncRNA-mRNA trans pairs. The expression profiles of LNC_000560 were highly consistent with its potential target genes, Atg4B, and RNAi of LNC_000560 significantly decreased the expression of LNC_000560 and Atg4B. These results indicated that LNC_000560 was potentially involved in the 20E-induced autophagy of the fat body by regulating Atg4B.ConclusionsThis study provides the genome-wide identification and functional characterization of lncRNAs associated with 20E-induced autophagy in the fat body of B. mori. LNC_000560 and its potential target gene were identified to be related to 20-regulated autophagy in B. mori. These results will be helpful for further studying the regulatory mechanisms of lncRNAs in autophagy and other biological processes in this insect model.

Screening of long non-coding RNA related to CYP450s involved in biosynthesis of tanshinones

Tanshinones are abietane-type norditerpenoid quinones that make up the main bioactive ingredients of traditional Chinese medicine Salvia miltiorrhiza. Cytochrome CYP450 plays an important role in the post-structural modification of tanshinone biosynthesis pathway. Long non-coding RNA( lncRNA) have been defined as transcripts longer than 200 nucleotides,which have been functionally characterized in regulating the growth and development,secondary metabolism and stress of medicinal plants. In this study,we perform a comprehensive identification of lncRNAs in response to tanshinone metabolism induced by yeast extract( YE) and Ag~+ S. miltiorrhiza hairy roots. Deep RNA sequencing was used to identify a set of different 8 942 lncRNAs,of which 6 755 were intergenic lncRNAs. We predicted a total of 1 115 814 lncRNA-coding gene pairs,including 122 lncRNA-coding gene as cis pairs. The correlation analysis between lncRNA and CYP450 related to tanshinone biosynthesis was carried out and a total of 16 249 lncRNA-CYP450 target gene pairs were identified. Further analysis with functional known CYP76 AH1,CYP76 AH3 and CYP76 AK1 involved in tanshinone biosynthesis,we also identified a set of 216 target genes. These candidate genes will be the important target in the downstream regulation mechanism analysis of the tanshinone biosynthesis pathway.

Elucidation of metabolite isomers of Leonurus japonicus and Leonurus cardiaca using discriminating metabolite isomerism strategy based on ultra-high performance liquid chromatography tandem quadrupole time-of-flight mass spectrometry

The isomer structural discrimination is a significant challenge in metabolome analysis based on ultrahigh performance liquid chromatography tandem high-resolution mass spectrometry (UHPLC-HRMS). In this study, a new discriminating metabolite isomerism strategy is proposed to elucidate the metabolome, especially the isomers, of Leonurus japonicus and Leonurus cardiaca. This strategy consists of three steps. First, the metabolite biosynthesis pathways are constructed based on a home-built compound database to rapidly profile the compounds of interest using the multiple diagnostic product ions (DPIs) screening analysis and binary comparison based on SUMPRODUCT function. Second, the fragmentation patterns (e.g. the high-resolution DPIs, DPI ratios) and chromatographic elution order are defined based on scattered reference chromatographic and mass spectrometry data, calculated lipophilicity parameters, molecular hydrogen bond analysis, and chemical reference standards. Finally, all discovered isomerisms are mapped with the defined applicable rules and the isomers are identified conveniently. Using this strategy, a total of 257 compounds were tentatively characterized, including 212 potential novel compounds and 67 pairs of cis-, trans-, and positional isomers of flavonoids, phenylethanoid glycosides, glucaric acids, novel quinic acids, and esters of fatty acids. Moreover, 56 characteristic markers were identified to discriminate these two herbal medicines. This strategy may significantly improve the efficiency and reliability of identifying isomers found in metabolite biosynthesis pathways.

Salviachinensines A-F, Antiproliferative Phenolic Derivatives from the Chinese Medicinal Plant Salvia chinensis.

Six new phenolic acid derivatives, salviachinensines A-F (1-6), together with 14 known compounds (7-20) were isolated from the Chinese medicinal plant Salvia chinensis. The structures of salviachinensines A-F (1-6) were elucidated by NMR spectroscopy, bioinspired chemical synthesis, ECD analysis, and quantum chemical calculation methods. Compounds 2 and 3 are a pair of cis- trans isomers, and compounds 5 and 6 a pair of epimers. The solvent-induced isomerization of compounds 5 and 6 and the hypothetical biogenetic pathway of compounds 1-6, as well as the antiproliferative property and the ability of 1 to induce apoptosis and arrest cell cycle progression of MOLM-13 cells, were also investigated.

Synthesis, characterization and photophysical properties of homoleptic platinum(II) complexes with 2,2′-biimidazole-based ligands

Eight pairs of cis–trans isomeric homoleptic platinum(II) complexes based on N-alkyl- or aryl-substituted 2,2′-biimidazole ligands were synthesized, and their photophysical properties were investigated. The cis and trans isomers readily interconvert at slightly elevated temperature, implying that the activation barrier for this process is low. Single crystal X-ray diffraction analysis revealed that the complexes have an ideal square-planar geometry. Their UV–Vis spectra showed lower energy absorption bands in the range of 345–378 nm, which are assigned to the typical MLCT mixed with LC transitions. In frozen glass solution at 77 K and also in the powder state, these complexes exhibit green emission ranging from 440 to 540 nm with photoluminescence quantum yields of 3.3–24.4%. The emitting excited state is dominated by 3ππ* character with some contributions from 3MLCT according to the excitation spectra.

Inducing the distinctly different fluorescence properties of a tetraphenylethene (TPE) derivative modified lanthanide nanowire upon the addition of a pair of cis- and trans-isomers of fatty acids.

A simple layer-by-layer approach has been developed to introduce a 3,5-dicarboxylphenoxy decorated tetraphenylethene derivative (denoted as TPE-2COOH) into a lanthanide nanowire. Interestingly, the aggregation-induced emission (AIE) was turned on by loading the negative TPE-2COOH on the positive surface of the nanowire via electrostatic interactions. More excitingly, these synthesized composite nanowires exhibit significantly different fluorescence properties in the presence of a pair of cis- and trans-isomers of fatty acids (oleic acid and elaidic acid). The obvious emission peak (382 nm) upon the addition of oleic acid (cis-configuration) was observed, which was consistent with that of the frozen diluted TPE-2COOH solution (1.95 × 10-10 mol L-1), demonstrating the occurrence of the monomer emission of TPE-2COOH. When the oleic acid with a special cis-configuration got close to the nanowire, it substituted some TPE-2COOH and arranged as cages on the surface to isolate the TPE-2COOH molecule, leading to the monomer emission. Different from such monomer emission induced by oleic acid, an attenuated aggregate emission was detected by the addition of its trans isomer elaidic acid, because it is almost impossible for the elaidic acid with a linear structure to form the cage-like shape on the surface during the substitution process. It was found for the first time that the fluorescence of such a TPE-based material can be controlled by the configuration of isomers. This discovery may provide a facile strategy to design and synthesize more promising candidates for TPE-based fluorescent sensors.

Effects of cytotoxic cis- and trans-diammine monochlorido platinum(II) complexes on selenium-dependent redox enzymes and DNA

Here we present the preparation of 14 pairs of cis- and trans-diammine monochlorido platinum(II) complexes, coordinated to heterocycles (i.e., imidazole, 2-methylimidazole and pyrazole) and linked to various acylhydrazones, which were designed as potential inhibitors of the selenium-dependent enzymes glutathione peroxidase 1 (GPx-1) and thioredoxin reductase 1 (TrxR-1). However, no inhibition of bovine GPx-1 and only weak inhibition of murine TrxR-1 was observed in in vitro assays. Nonetheless, the cis configured diammine monochlorido Pt(II) complexes exhibited cytotoxic and apoptotic properties on various human cancer cell lines, whereas the trans configured complexes generally showed weaker potency with a few exceptions. On the other hand, the trans complexes were generally more likely to lack cross-resistance to cisplatin than the cis analogues. Platinum was found bound to the nuclear DNA of cancer cells treated with representative Pt complexes, suggesting that DNA might be a possible target. Thus, detailed in vitro binding experiments with DNA were conducted. Interactions of the compounds with calf thymus DNA were investigated, including Pt binding kinetics, circular dichroism (CD) spectral changes, changes in DNA melting temperatures, unwinding of supercoiled plasmids and ethidium bromide displacement in DNA. The CD results indicate that the most active cis configured pyrazole-derived complex causes unique structural changes in the DNA compared to the other complexes as well as to those caused by cisplatin, suggesting a denaturation of the DNA structure. This may be important for the antiproliferative activity of this compound in the cancer cells.

A New Approach to Models of the 4,5-Dihydroxycyclopentenone Core of the Kodaistatins A-D: Elucidation of the Diol Configuration in Kodaistatin A.

The kodaistatins A-D are strongly anti-diabetic natural products from Aspergillus terreus that hold some promise of a novel diabetes cure. However, considerations of that kind face two drawbacks: 1) The kodaistatins A-D contain a heavily substituted pulvinone/cyclopentenone combination; 2) they are 1,2-diols, the 3D structures of which have not been assigned yet. However, we can exclude two of the four possible stereostructures. We conclude that kodaistatin A is a trans-, not a cis-diol from NMR comparisons with a pair of cis, trans-isomeric kodaistatin models, which we synthesized in 11 and 12 steps, respectively. The stereocenters of the diol moiety arose from stereocomplementary, highly diastereoselective aldol additions of a lithium enolate or the corresponding silyl ketene acetal. The cyclopentenone moieties stemmed from intramolecular aldol additions and ensuing dehydrations. The requisite enolates were obtained by the reduction of α-bromoketones with samarium diiodide.

Energy resolved tandem mass spectrometry experiments for resolution of isobaric compounds: a case of cis/trans isomerism.

A series of N-alkanol-N-cyclohexanol amine aryl esters cis/trans isomers that showed high efficacy to reverse the acquired resistance of cancer cells during chemotherapeutic therapy (MDR mechanism) was studied. These compounds were two 1,4 cyclohexane cis/trans derivatives (named ELF26A and ELF26B, respectively), and their positional isomers (named ELF34A and ELF34B, respectively) where the aryl-moieties were exchanged. In order to evaluate the behaviour of these compounds during biological tests, a method based on liquid chromatography coupled with mass spectrometry (LC-MS), operating in tandem mass spectrometry (MS/MS) mode, was developed. A unique chromatographic method suitable to separate the two pairs of cis/trans isomers was not achieved and the MS/MS experiments of the different compounds was not always able to characterise the different isomers. Therefore, a system of linear equations of deconvolution analysis (LEDA) tool was proposed to determine the relative proportions of individual cis/trans isomers in the sample. Considering the pharmaceutical interest of the compounds under investigation, the analytical method developed was tested to be effective at the active concentration levels, corresponding to a concentration of ng mL-1 of compound in a processed sample. Precision and accuracy of the LEDA algorithm at three levels of relative concentrations of analytes were checked, i.e. low-level (about 25% in the mixture), mid-level (about 50% in the mixture) and high-level (about 70% in the mixture). Evaluation of performances of the algorithm proved that the accuracy (between 88.3% and 99.9%) and precision (between 2.0% and 3.7%) for simultaneous analysis of the mixtures of the four isomers is feasible. It is worth highlighting that the choice of characteristic product ions and optimal abundance ratios plays an important role in the application of the LEDA approach. Therefore, performing an investigation on the energetics of fragmentation pathway allowed the selection of the better product ions for each analyte in terms of both sensitivity of detection and specificity, i.e. the capability to distinguish between isomeric compounds. Finally, the developed approach was applied to determine the relative proportions of individual cis/trans isomers in spiked human plasma samples. The results obtained confirm the reliability of the proposed method in biological samples as well.

Synthesis and molecular structure of [Cu(NH3)4][Ni(CN)4]: A missing piece in the [Cu(NH3)n][Ni(CN)4] story

Reaction of CuCl2·2H2O and K2[Ni(CN)4]·2H2O in aqueous ammonia gave blue rod-like crystals of [Cu(NH3)4][Ni(CN)4]. An X-ray crystallographic reveals that square-planar anions and cations are weakly associated through coordination of a cis pair of cyanide ligands to copper, with one short and one long contact and thus the copper centre is best described as a square-based pyramid. Crystals lose ammonia readily upon removal from the solvent and this has been probed by TGA and DSC measurements. For comparison we have also re-determined the structure of the related ethylenediamine (en) complex [Cu(en)2][Ni(CN)4] at 150 K. This consists of a 1D chain in which a trans pair of cyanide ligands bind to copper such that the latter has an overall tetragonally distorted octahedral coordination geometry.

Cis and trans Isomers distinguished by imidazole N-alkylation after Debus-Radziszewski reaction starting from 2,7-di-tert-butyl-pyrene-4,5,9,10-tetraone

We report the design and synthesis of three new imidazo[5,4-f]2,7-di-tert-butyl-pyrene-imidazol derivatives prepared from 2,7-di-tert-butylpyrene-4,5,9,10-tetraone and respective aromatic aldehyde through Debus-Radziszewski reaction. It is noted that three pairs of cis and trans isomers (1–6) can be separated after double imidazole N-alkylation for the central fused imidazole/pyrene/imidazole core, because of their distinguishable molecular polarity and improved solubility. Successful separation of every cis and trans isomeric pair can be verified by the single-crystal structural and spectral proofs. To the best of our knowledge, the current study is the first structural and spectral investigation on the imidazole N-alkylation of imidazole/pyrene/imidazole based compounds after successful separation of cis and trans isomers.

Cationic iridium(III) complexes with two carbene-based cyclometalating ligands: cis versus trans isomers.

A series of cationic iridium(III) complexes with two carbene-based cyclometalating ligands and five different N^N bipyridine and 1,10-phenanthroline ancillary ligands is presented. For the first time--in the frame of a rarely studied class of bis(heteroleptic) iridium complexes with two carbene-based cyclometalating ligands--a pair of cis and trans isomers has been isolated. All complexes (trans-1-5 and cis-3) were characterized by (1)H NMR, (13)C NMR, (31)P NMR, and HRMS (ESI-TOF); in addition, crystal structures of cis-3 and trans-4 are reported and discussed. Cyclic voltammetric studies show that the whole series exhibits highly reversible oxidation and reduction processes, suggesting promising potential for optoelectronic applications. Ground-state DFT and TD-DFT calculations nicely predict the blue shift experimentally observed in the room-temperature absorption and emission spectra of cis-3, compared to the trans complexes. In CH3CN, cis-3 displays a 4-fold increase in photoluminescence quantum yield (PLQY) with respect to trans-3, as a consequence of drastically slower nonradiative rate constant. By contrast, at 77 K, the emission properties of all the compounds, including the cis isomer, are much more similar, with a pronounced hypsochromic shift for the trans complexes. A similar behavior is found in solid state (1% w/w poly(methyl methacrylate) matrix), with all complexes displaying PLQY of ∼70-80%, comparable emission lifetimes (τ ≈ 1.3 μs), and a remarkable rigidochromic shift. To rationalize the more pronounced nonradiative deactivation (and smaller PLQY) observed for photoexcited trans complexes, comparative temperature-dependent emission studies in the range of 77-450 K for cis-3 and trans-3 were made in propylene glycol, showing that solvation effects are primarily responsible for the observed behavior.

Analysis of Seven-Membered Lactones by Computational NMR Methods: Proton NMR Chemical Shift Data are More Discriminating than Carbon

We report an NMR chemical shift study of conformationally challenging seven-membered lactones (1-11); computed and experimental data sets are compared. The computations involved full conformational analysis of each lactone, Boltzmann-weighted averaging of the chemical shifts across all conformers, and linear correction of the computed chemical shifts. DFT geometry optimizations [M06-2X/6-31+G(d,p)] and GIAO NMR chemical shift calculations [B3LYP/6-311+G(2d,p)] provided the computed chemical shifts. The corrected mean absolute error (CMAE), the average of the differences between the computed and experimental chemical shifts for each of the 11 lactones, is encouragingly small (0.02-0.08 ppm for (1)H or 0.8-2.2 ppm for (13)C). Three pairs of cis versus trans diastereomeric lactones were used to assess the ability of the method to distinguish between stereoisomers. The experimental shifts were compared with the computed shifts for each of the two possible isomers. We introduce the use of a "match ratio"--the ratio of the larger CMAE (worse fit) to the smaller CMAE (better fit). A greater match ratio value indicates better distinguishing ability. The match ratios are larger for proton data [2.4-4.0 (av = 3.2)] than for carbon [1.1-2.3 (av = 1.6)], indicating that the former provide a better basis for discriminating these diastereomers.

Antcamphins A–L, Ergostanoids from Antrodia camphorata

Twelve ergostanoids, named antcamphins A-L (1-12), together with 20 known triterpenoids, were isolated from fruiting bodies of the medicinal fungus Antrodia camphorata. Compounds 1 and 2 represent the first examples of norergostanes isolated from A. camphorata, and compounds 3 and 4 are the first pair of cis-trans isomers of ergostane-type triterpenoids containing an aldehyde group. Compounds 5-12 are four pairs of C-25 epimers. The structures of 1-12 were elucidated on the basis of extensive spectroscopic data analysis including NMR and HRESIMS. Particularly, the absolute configurations at C-25 for 5-12 were determined by the modified Mosher's method. These triterpenoids exhibited weak cytotoxic activities against MDA-MB-231 breast cancer cells and A549 lung cancer cells, but did not inhibit the growth of normal cells in the sulforhodamine B assay.

Neolignanamides, Lignanamides, and Other Phenolic Compounds from the Root Bark of Lycium chinense

Seven new neolignanamides (1-7), including two pairs of cis- and trans-isomers, and a new lignanamide (8) were isolated from the EtOAc-soluble fraction of an EtOH extract of the root bark of Lycium chinense, together with 22 known phenolic compounds (9-30), four of which were obtained from the genus Lycium for the first time. Compounds 5, 6, and 7 are unusual dimers having a rare connection mode between the two cinnamic acid amide units, while compounds 6, 7, and 8 are the first naturally occurring dimers derived from two dissimilar cinnamic acid amides. The cinnamic acid amides, neolignanamides, and lignanamides possess moderate radical-scavenging activity against the DPPH (2,2-diphenyl-1-picrylhydrazyl) and superoxide radicals.

Thymidine glycol: the effect on DNA molecular structure and enzymatic processing

Thymine glycol (Tg) in DNA is a biologically active oxidative damage caused by ionizing radiation or oxidative stress. Due to chirality of C5 and C6 atoms, Tg exists as a mixture of two pairs of cis and trans diastereomers: 5R cis-trans pair (5R,6S; 5R,6R) and 5S cis-trans pair (5S,6R; 5S,6S). Of all the modified pyrimidine lesions that have been studied to date, only thymine glycol represents a strong block to high-fidelity DNA polymerases in vitro and is lethal in vivo. Here we describe the preparation of thymine glycol-containing oligonucleotides and the influence of the oxidized residue on the structure of DNA in different sequence contexts, thymine glycol being paired with either adenine or guanine. The effect of thymine glycol on biochemical processing of DNA, such as biosynthesis, transcription and repair in vitro and in vivo, is also reviewed. Special attention is paid to stereochemistry and 5R cis-trans epimerization of Tg, and their relation to the structure of DNA double helix and enzyme-mediated DNA processing. Described here are the comparative structure and properties of other forms of pyrimidine base oxidation, as well as the role of Tg in tandem lesions.

Epigenetic functions enriched in transcription factors binding to mouse recombination hotspots

The regulatory mechanism of recombination is a fundamental problem in genomics, with wide applications in genome-wide association studies, birth-defect diseases, molecular evolution, cancer research, etc. In mammalian genomes, recombination events cluster into short genomic regions called "recombination hotspots". Recently, a 13-mer motif enriched in hotspots is identified as a candidate cis-regulatory element of human recombination hotspots; moreover, a zinc finger protein, PRDM9, binds to this motif and is associated with variation of recombination phenotype in human and mouse genomes, thus is a trans-acting regulator of recombination hotspots. However, this pair of cis and trans-regulators covers only a fraction of hotspots, thus other regulators of recombination hotspots remain to be discovered. In this paper, we propose an approach to predicting additional trans-regulators from DNA-binding proteins by comparing their enrichment of binding sites in hotspots. Applying this approach on newly mapped mouse hotspots genome-wide, we confirmed that PRDM9 is a major trans-regulator of hotspots. In addition, a list of top candidate trans-regulators of mouse hotspots is reported. Using GO analysis we observed that the top genes are enriched with function of histone modification, highlighting the epigenetic regulatory mechanisms of recombination hotspots.