Epigenomic Diversity in a Global Collection of Arabidopsis thaliana Accessions.

The epigenome orchestrates genome accessibility, functionality, and three-dimensional structure. Because epigenetic variation can impact transcription and thus phenotypes, it may contribute to adaptation. Here, we report 1,107 high-quality single-base resolution methylomes and 1,203 transcriptomes from the 1001 Genomes collection of Arabidopsis thaliana. Although the genetic basis of methylation variation is highly complex, geographic origin is a major predictor of genome-wide DNA methylation levels and of altered gene expression caused by epialleles. Comparison to cistrome and epicistrome datasets identifies associations between transcription factor binding sites, methylation, nucleotide variation, and co-expression modules. Physical maps for nine of the most diverse genomes reveal how transposons and other structural variants shape the epigenome, with dramatic effects on immunity genes. The 1001 Epigenomes Project provides a comprehensive resource for understanding how variation in DNA methylation contributes to molecular and non-molecular phenotypes in natural populations of the most studied model plant.

Spatiotemporal DNA methylome dynamics of the developing mouse fetus.

Cytosine DNA methylation is essential for mammalian development but understanding of its spatiotemporal distribution in the developing embryo remains limited1,2. Here, as part of the mouse Encyclopedia of DNA Elements (ENCODE) project, we profiled 168 methylomes from 12 mouse tissues or organs at 9 developmental stages from embryogenesis to adulthood. We identified 1,808,810 genomic regions that showed variations in CG methylation by comparing the methylomes of different tissues or organs from different developmental stages. These DNA elements predominantly lose CG methylation during fetal development, whereas the trend is reversed after birth. During late stages of fetal development, non-CG methylation accumulated within the bodies of key developmental transcription factor genes, coinciding with their transcriptional repression. Integration of genome-wide DNA methylation, histone modification and chromatin accessibility data enabled us to predict 461,141 putative developmental tissue-specific enhancers, the human orthologues of which were enriched for disease-associated genetic variants. These spatiotemporal epigenome maps provide a resource for studies of gene regulation during tissue or organ progression, and a starting point for investigating regulatory elements that are involved in human developmental disorders.

An atlas of dynamic chromatin landscapes in mouse fetal development.

The Encyclopedia of DNA Elements (ENCODE) project has established a genomic resource for mammalian development, profiling a diverse panel of mouse tissues at 8 developmental stages from 10.5 days after conception until birth, including transcriptomes, methylomes and chromatin states. Here we systematically examined the state and accessibility of chromatin in the developing mouse fetus. In total we performed 1,128 chromatin immunoprecipitation with sequencing (ChIP-seq) assays for histone modifications and 132 assay for transposase-accessible chromatin using sequencing (ATAC-seq) assays for chromatin accessibility across 72 distinct tissue-stages. We used integrative analysis to develop a unified set of chromatin state annotations, infer the identities of dynamic enhancers and key transcriptional regulators, and characterize the relationship between chromatin state and accessibility during developmental gene regulation. We also leveraged these data to link enhancers to putative target genes and demonstrate tissue-specific enrichments of sequence variants associated with disease in humans. The mouse ENCODE data sets provide a compendium of resources for biomedical researchers and achieve, to our knowledge, the most comprehensive view of chromatin dynamics during mammalian fetal development to date.

Author Correction: An atlas of dynamic chromatin landscapes in mouse fetal development.

An amendment to this paper has been published and can be accessed via a link at the top of the paper.

Expanded encyclopaedias of DNA elements in the human and mouse genomes.

The human and mouse genomes contain instructions that specify RNAs and proteins and govern the timing, magnitude, and cellular context of their production. To better delineate these elements, phase III of the Encyclopedia of DNA Elements (ENCODE) Project has expanded analysis of the cell and tissue repertoires of RNA transcription, chromatin structure and modification, DNA methylation, chromatin looping, and occupancy by transcription factors and RNA-binding proteins. Here we summarize these efforts, which have produced 5,992 new experimental datasets, including systematic determinations across mouse fetal development. All data are available through the ENCODE data portal (https://www.encodeproject.org), including phase II ENCODE1 and Roadmap Epigenomics2 data. We have developed a registry of 926,535 human and 339,815 mouse candidate cis-regulatory elements, covering 7.9 and 3.4% of their respective genomes, by integrating selected datatypes associated with gene regulation, and constructed a web-based server (SCREEN; http://screen.encodeproject.org) to provide flexible, user-defined access to this resource. Collectively, the ENCODE data and registry provide an expansive resource for the scientific community to build a better understanding of the organization and function of the human and mouse genomes.

Effects of hypoxic compound exercise to promote HIF-1α expression on cardiac pumping function, sleep activity behavior, and exercise capacity in Drosophila.

Alteration of HIF-1α expression levels under hypoxic conditions affects the sequence of its downstream target genes thereby producing different effects. In order to investigate whether the effect of hypoxic compound exercise (HE) on HIF-1α expression alters cardiac pumping function, myocardial structure, and exercise capacity, we developed a suitable model of hypoxic exercise using Drosophila, a model organism, and additionally investigated the effect of hypoxic compound exercise on nocturnal sleep and activity behavior. The results showed that hypoxic compound exercise at 6% oxygen concentration for five consecutive days, lasting 1 h per day, significantly improved the cardiac stress resistance of Drosophila. The hypoxic complex exercise promoted the whole-body HIF-1α expression in Drosophila, and improved the jumping ability, climbing ability, moving speed, and moving distance. The expression of HIF-1α in the heart was increased after hypoxic exercise, which made a closer arrangement of myofilaments, an increase in the diameter of cardiac tubules, and an increase in the pumping function of the heart. The hypoxic compound exercise improved the sleep quality of Drosophila by increasing its nocturnal sleep time, the number of deep sleeps, and decreasing its nocturnal awakenings and activities. Therefore, we conclude that hypoxic compound exercise promoted the expression of HIF-1α to enhance the exercise capacity and heart pumping function of Drosophila, and improved the quality of sleep.

High-Throughput Extracellular Matrix Proteomics of Human Lungs Enabled by Photocleavable Surfactant and diaPASEF.

The extracellular matrix (ECM) is a complex assembly of proteins that provide interstitial scaffolding and elastic recoil for human lungs. The pulmonary extracellular matrix is increasingly recognized as an independent bioactive entity, by creating biochemical and mechanical signals that influence disease pathogenesis, making it an attractive therapeutic target. However, the pulmonary ECM proteome ("matrisome") remains challenging to analyze by mass spectrometry due to its inherent biophysical properties and relatively low abundance. Here, we introduce a strategy designed for rapid and efficient characterization of the human pulmonary ECM using the photocleavable surfactant Azo. We coupled this approach with trapped ion mobility MS with diaPASEF to maximize the depth of matrisome coverage. Using this strategy, we identify nearly 400 unique matrisome proteins with excellent reproducibility that are known to be important in lung biology, including key core matrisome proteins.

Experiment and Computational Study on Pd-Catalyzed Methoxyiminoacyl-Directed γ-Alkoxylation of Alkylamides.

The direct alkoxylation of amides has been accomplished via methoxyiminoacyl (MIA)-mediated Pd-catalyzed C-H functionalization. A diverse array of alkylamide substrates is amenable to this protocol, providing γ-C(sp3)-alkoxylation of alkylamide derivatives with good to high efficiency. Two aspects of the research were completed to explore the reaction mechanism. On the one hand, the result of the kinetic isotopic effect experiment and control experiment indicated that reductive elimination is a rate-limiting step. On the other hand, density functional theory calculations demonstrated that a concerted Sn2 reductive elimination mechanism pathway is prior. Finally, the MIA group could be efficiently hydrogenated and protected in a one-pot procedure, which provides a short synthetic route to γ-methoxy amino acid derivatives.

Visible-light-promoted organic-dye-catalyzed sulfonylation/cyclization to access indolo[2,1-a]isoquinoline derivatives.

An efficient visible-light-promoted organic-dye-catalyzed radical cascade cyclization was developed for the rapid synthesis of sulfonyl-substituted indolo[2,1-a]isoquinolines and benzimidazo[2,1-a]isoquinolin-6(5H)-ones. Using the economical and environmentally benign Eosin B as the photocatalyst, a wide range of indolo[2,1-a]isoquinoline derivatives were obtained in moderate to good yields. Mechanistic studies indicate that a sulfonyl radical pathway is involved in this reaction. Compared with previous works, this protocol has the advantages of being metal- and base-free, using visible light as a traceless energy source, simple operation and mild reaction conditions, all of which make this methodology more attractive.

Metal- and additive-free radical-triggered nitration/cyclization to construct indolo[2,1-α]isoquinoline and benzimidazo[2,1-a]isoquinolin-6(5H)-one derivatives using t-BuONO as nitro reagents.

An efficient metal- and additive-free nitro radical-triggered addition/cyclization of 2-aryl-N-acryloyl indoles/2-arylbenzimidazoles for the synthesis of nitro-substituted indolo[2,1-α]isoquinoline and benzimidazo[2,1-a]isoquinolin-6(5H)-one derivatives has been developed. The commercially available and low-cost t-BuONO was used as a nitro reagent. Due to mild reaction conditions, a variety of functional groups could be tolerated to give the corresponding products in moderate to good yields. Moreover, this nitration process could be scaled-up and the nitro group could be readily converted into the amino group, which may find applications in synthetic and medicinal chemistry.

Three-level nanogrooves by vibration-assisted fly-cutting for diffraction regulation and array output.

Integrating geometric and diffractive optics functions is urgently needed to develop compact equipment for integrating diffraction manipulation and arrayed outputs. In this Letter, a superimposed three-level-grooved surface is proposed to manipulate the diffraction of visible light and provide an array output. Structure design, vibration-assisted fly-cutting, finite-difference time-domain calculations, and diffraction tests are conducted to fabricate the three-level grooves and explore the diffraction mechanism. Nanogrooves with a period close to the middle wavelength of the spectrum primarily enhances the diffraction at low diffraction orders and angles because of resonance. Optical tests prove that these superimposed three-level nanogrooves have a large bandwidth when providing the array output and serving to control and transmit diffracted light. They also show stronger performance for manipulating low diffraction orders.

Methionine-Derived Organogels as Lubricant Additives Enhance the Continuity of the Oil Film through Dynamic Self-Healing Assembly.

(S)-2-((1-(Hexadecylamino)-4-(methylthio)-1-oxobutan-2-yl)carbamoyl)benzoic acid (HMTA) was efficiently synthesized and successfully applied as an additive to several types of blank lubricant oils. Initially, HMTA self-assembles to fibrous structures and traps blank lubricant oils to form gel lubricants. The prepared gel lubricants show thermo-reversible properties and enhanced lubricating performance by 3∼5-fold. X-ray photoelectron spectrometry of the metal surface and the quartz crystal microbalance illustrated that there are no obvious interactions between HMTA and the metal surface. The results of Fourier transform infrared spectroscopy and X-ray diffraction further confirm that inter/intro-molecular H-bonding interactions are the main driving force for the self-healing of HMTA. Finally, molecular dynamics (MD) simulations show that the number of noncovalent H-bonding interactions fluctuates with time, and this highly dynamic H-bonding network could regulate the self-assembly process and result in the self-healing property of the HMTA organogel, which is consistent with the results of the step-strain tests. Especially, the Hirshfeld independent gradient model method at the quantum level demonstrated that C8/C9 aromatics of 500SN have strong π-π stacking interactions with the aromatic heads of HMTA and van der Waals interactions with the hydrophobic tails of HMTA, which disrupt the self-assembly behavior of the 500SN model. Therefore, the calculation studies offer a rational explanation for the superior lubricant property of the PAO10 gel as compared to that for 500SN.

Pd-Catalyzed γ-Acetoxylation of Alkylamides: Structural Influence of Directing Groups.

Although direct acetoxylation and cyclization of alkylamide have been extensively reported, investigation of the structural influence of directing groups on selectivity is limited. Pd-catalyzed 2-methoxyiminoacyl (MIA) assisted γ-acetoxylation of alkylamides has been developed. Further DFT studies have demonstrated that the directing groups have a significant influence on the reductive elimination step. The strong electron-donating effect of the OMe group in MIA leads to the preferential formation of a five-membered cyclopalladium (OAc-Pd-C) complex, which favors the acetoxylation pathway.

Diffraction manipulation of visible light with submicron structures for structural coloration fabrication.

The structural coloration of glass induced by submicron structures is eco-friendly, ink-free, and has profound scientific significance. However, it is difficult to manufacture the submicron structures for glass optics due to the high hardness of glass and the miniature size of the microstructures. In this paper, the diffraction manipulation mechanism of groove shape to structural coloration and optimization theory are studied by establishing the theoretical and simulation mode. Moreover, a newly-developed axial-feed fly-cutting (AFC) technology and the PGM technology are introduced to precisely create the designed submicron V-shape grooves and structural color pattern on a Ni-P mold and then replicating them on a glass surface. Between these two kinds of typical submicron grooves that can be machined by mechanical cutting technology, it is found that the diffraction intensity and efficiency of V-shape grooves are higher than these of jagged-shape grooves, which indicates that V-shape grooves is more suitable to be used for structural coloration with high brightness. The structural color resolution is dramatically increased with the reduction of groove spacing and can be flexibly regulated by AFC, which significantly contributes to the structural coloration manufacturing. Structural pixel segments composed of submicron grooves are arranged row-by-row to form color patterns, and the letters of different colors are fabricated on the mold and transferred to the glass surface. Methods of optical diffraction manipulation, flexible manufacturing of submicron structures, and structural color image construction proposed in this paper for the production of a structural color pattern are beneficial to a wide range of fields.

Pyromellitic-Based Low Molecular Weight Gelators and Computational Studies of Intermolecular Interactions: A Potential Additive for Lubricant.

Low molecular weight gelators (LMWG) have been extensively explored in many research fields due to their unique reversible gel-sol transformation. Intermolecular interactions between LMWG are known as the main driving force for self-assembly. During this self-assembly process, individually analyzing the contribution difference between various intermolecular interactions is crucial to understand the gel properties. Herein, we report 2,5-bis(hexadecylcarbamoyl)terephthalic acid (BHTA) as a LMWG, which could efficiently form a stable organogel with n-hexadecane, diesel, liquid paraffin, and base lubricant oil at a relatively low concentration. To investigate the contribution difference of intermolecular interactions, we first finished FT-IR spectroscopy and XRD experiments. On the basis of the d-spacing, a crude simulation model was built and then subjected to molecular dynamics (MD) simulations. Then, we knocked out the energy contribution of the H-bonding interactions and π-π stacking, respectively, to evaluate the intermolecular interactions significantly influencing the stability of the gel system. MD simulations results suggest that the self-assembly of the aggregates was mainly driven by dense H-bonding interactions between carbonyl acid and amide moieties of BHTA, which is consistent with FT-IR data. Moreover, wave function analysis at a quantum level suggested these electrostatic interactions located in the middle of the BHTA molecule were surrounded by strong dispersion attraction originating from a hydrophobic environment. Furthermore, we also confirmed that 2 wt % BHTA was able to form gel lubricant with 150BS. The coefficient of friction (COF) data show that the gel lubricant has a better tribological performance than 150BS base lubricant oil. Finally, XPS was performed and offered valuable information about the lubrication mechanism during the friction.

MIA-Directed 2-Pyridione-Enabled Selective Ortho-C-H Arylation of Phenylalanine: A Mechanistic Study.

The 2-methoxyiminoacyl-mediated arylation of substituted phenylalanines has been examined. Selective monoarylation at the ortho position was achieved using pyridone ligands which decelerate the arylation process. Density functional theory (DFT) study of a continuous C-H arylation process that included the first and second arylation stage was performed. The computational result shows that the introduction of a pyridone ligand obviously disfavors the second arylation stage, which directly contributes to the selectivity between the mono/diarylated products. Furthermore, results of the kinetic isotope effect and a control experiment are agreed with DFT study.

Human body epigenome maps reveal noncanonical DNA methylation variation.

Understanding the diversity of human tissues is fundamental to disease and requires linking genetic information, which is identical in most of an individual's cells, with epigenetic mechanisms that could have tissue-specific roles. Surveys of DNA methylation in human tissues have established a complex landscape including both tissue-specific and invariant methylation patterns. Here we report high coverage methylomes that catalogue cytosine methylation in all contexts for the major human organ systems, integrated with matched transcriptomes and genomic sequence. By combining these diverse data types with each individuals' phased genome, we identified widespread tissue-specific differential CG methylation (mCG), partially methylated domains, allele-specific methylation and transcription, and the unexpected presence of non-CG methylation (mCH) in almost all human tissues. mCH correlated with tissue-specific functions, and using this mark, we made novel predictions of genes that escape X-chromosome inactivation in specific tissues. Overall, DNA methylation in several genomic contexts varies substantially among human tissues.

An alternative pluripotent state confers interspecies chimaeric competency.

Pluripotency, the ability to generate any cell type of the body, is an evanescent attribute of embryonic cells. Transitory pluripotent cells can be captured at different time points during embryogenesis and maintained as embryonic stem cells or epiblast stem cells in culture. Since ontogenesis is a dynamic process in both space and time, it seems counterintuitive that these two temporal states represent the full spectrum of organismal pluripotency. Here we show that by modulating culture parameters, a stem-cell type with unique spatial characteristics and distinct molecular and functional features, designated as region-selective pluripotent stem cells (rsPSCs), can be efficiently obtained from mouse embryos and primate pluripotent stem cells, including humans. The ease of culturing and editing the genome of human rsPSCs offers advantages for regenerative medicine applications. The unique ability of human rsPSCs to generate post-implantation interspecies chimaeric embryos may facilitate our understanding of early human development and evolution.