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Precise dissection of DNA–protein interactions is essential for elucidating the recognition basis, dynamics and gene regulation mechanism. However, global profiling of weak and dynamic DNA–protein interactions remains a long-standing challenge. Here, we establish the light-induced lysine (K) enabled crosslinking (LIKE-XL) strategy for spatiotemporal and global profiling of DNA–protein interactions. Harnessing unique abilities to capture weak and transient DNA–protein interactions, we demonstrate that LIKE-XL enables the discovery of low-affinity transcription-factor/DNA interactions via sequence-specific DNA baits, determining the binding sites for transcription factors that have been previously unknown. More importantly, we successfully decipher the dynamics of the transcription factor subproteome in response to drug treatment in a time-resolved manner, and find downstream target transcription factors from drug perturbations, providing insight into their dynamic transcriptional networks. The LIKE-XL strategy offers a complementary method to expand the DNA–protein profiling toolbox and map accurate DNA–protein interactomes that were previously inaccessible via non-covalent strategies, for better understanding of protein function in health and disease.

Based on the typical similar repeat units (abcdefg)nof α-helical structure, the peptide H was designed to self-assemble into an organohydrogel in response to pH. Depending on the different pH, the proportions of secondary structure, microstructure, and mechanical properties of the gel were investigated. Circular dichroism (CD) and Fourier transform infrared (FT-IR) showed that the proportion of α-helical structure gradually increased to become dominant with the increase of pH. Combining transmission electron microscopy (TEM) and atomic force microscopy (AFM), it was found that the increase of the ordered α-helix structure promoted fiber formation. The further increase in pH changed the intermolecular forces, resulting in an increase in the α-helix content and the enhancement of helix–helix interaction, causing the gel fibers to converge into thicker and more dense ones. The temperature test showed the stable rheological properties of the organohydrogel between 20–60 °C. Drug release and cytotoxicity showed that the DOX-loaded organohydrogel could have a better release in an acidic environment, indicating its potential application as a drug local delivery carrier.

A protocol for the reaction of ketone or ester enolates with aza‐o‐quinodimethanes (aza‐o‐QMs) formed in situ is reported via a 1,4‐elimination in the presence of tetramethylammonium fluoride (TMAF). The reaction partners were reacted to provide a wide variety of substituted 2‐(tosylamino)dihydrochalcones in 45–97% yield in a single reaction sequence in one pot under mild condition. Additionally, various 2‐(tosylamino)dihydrochalcones could be easily converted to form diverse heterocycles. A protocolfor the formation of 2‐(tosylamino)dihydrochalcones is reported in which ketones and ester enolates and aza‐o‐quinone methides were generated in situ in a single reaction flask from silylated precursors using mild reaction conditions. The reported method provides rapid and efficient access to 2‐(tosylamino)dihydrochalcones derivatives with simple and readily available starting materials.

We developed a systematic approach to map human genetic networks by combinatorial CRISPR–Cas9 perturbations coupled to robust analysis of growth kinetics. We targeted all pairs of 73 cancer genes with dual guide RNAs in three cell lines, comprising 141,912 tests of interaction. Numerous therapeutically relevant interactions were identified, and these patterns replicated with combinatorial drugs at 75% precision. From these results, we anticipate that cellular context will be critical to synthetic-lethal therapies.

Though L-dopa is an effective drug for Parkinson’s disease, the usage of L-dopa in clinical treatment is limited for its physico-chemical properties which affect the bioavailability of L-dopa and increase the side effects of L-dopa. For improving the availability of L-dopa, L-dopa-L-His was synthesized by Fmoc solid-phase peptide synthesis, purified by reversed-phase HPLC and characterized by using 1H, 13C NMR and ESI-MS. The interaction of L-dopa-L-His and L-dopa with ctDNA has been investigated respectively by UV absorption and fluorescence spectroscopy. The results indicated that both L-dopa and L-dopa-L-His interacted with ctDNA through intercalative mode. The binding constant of L-dopa and Ldopa- L-His with ctDNA were 4.99x1010 L·mol-1·s-1 and 8.25x1011 L·mol-1·s-1, which showed a higher affinity of L-dopa- L-His to DNA for the imidazole side-chain. Meanwhile, compared with the free L-dopa, gel electrophoresis assay also demonstrated that the L-dopa-L-His interacted with plasmid DNA by stronger intercalation.

Obtaining fully functional cell types is a major challenge for drug discovery and regenerative medicine. Currently, a fundamental solution to this key problem is still lacking. Here, we show that functional human induced hepatocytes (hiHeps) can be generated from fibroblasts by overexpressing the hepatic fate conversion factors HNF1A, HNF4A, and HNF6along with the maturation factors ATF5, PROX1, and CEBPA. hiHeps express a spectrum of phase I and II drug-metabolizing enzymes and phase III drug transporters. Importantly, the metabolic activities of CYP3A4, CYP1A2, CYP2B6, CYP2C9, and CYP2C19 are comparable between hiHeps and freshly isolated primary human hepatocytes. Transplanted hiHeps repopulate up to 30% of the livers of Tet-uPA/Rag2−/−/γc−/−mice and secrete more than 300 μg/ml human ALBUMIN in vivo. Our data demonstrate that human hepatocytes with drug metabolic function can be generated by lineage reprogramming, thus providing a cell resource for pharmaceutical applications.

To identify whether Nestin-positve cells or Nestin-negative cells in pancreas enrich potential pancreatic stem/progenitor cells.

Understanding the effects of genetic perturbations on the cellular state has been challenging using traditional pooled screens, which typically rely on the delivery of a single perturbation per cell and unidimensional phenotypic readouts. Here, we use barcoded open reading frame overexpression libraries coupled with single-cell RNA sequencing to assay cell state and fitness, a technique we call SEUSS (scalable functional screening by sequencing). Using SEUSS, we perturbed hPSCs with a library of developmentally critical transcription factors (TFs) and assayed the impact of TF overexpression on fitness and transcriptomic states. We further leveraged the versatility of the ORF library approach to assay mutant genes and whole gene families. From the transcriptomic responses, we built genetic co-regulatory networks to identify altered gene modules and found that KLF4and SNAI2drive opposing effects along the epithelial-mesenchymal transition axis. From the fitness responses, we identified ETV2as a driver of reprogramming toward an endothelial-like state.

Background The usage of synonymous codons shows considerable variation among mammalian genes. How and why this usage is non-random are fundamental biological questions and remain controversial. It is also important to explore whether mammalian genes that are selectively expressed at different developmental stages bear different molecular features.Results In two models of mouse stem cell differentiation, we established correlations between codon usage and the patterns of gene expression. We found that the optimal codons exhibited variation (AT- or GC-ending codons) in different cell types within the developmental hierarchy. We also found that genes that were enriched (developmental-pivotal genes) or specifically expressed (developmental-specific genes) at different developmental stages had different patterns of codon usage and local genomic GC (GCg) content. Moreover, at the same developmental stage, developmental-specific genes generally used more GC-ending codons and had higher GCg content compared with developmental-pivotal genes. Further analyses suggest that the model of translational selection might be consistent with the developmental stage-related patterns of codon usage, especially for the AT-ending optimal codons. In addition, our data show that after human-mouse divergence, the influence of selective constraints is still detectable.Conclusion Our findings suggest that developmental stage-related patterns of gene expression are correlated with codon usage (GC3) and GCg content in stem cell hierarchies. Moreover, this paper provides evidence for the influence of natural selection at synonymous sites in the mouse genome and novel clues for linking the molecular features of genes to their patterns of expression during mammalian ontogenesis.