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The interphase genome is dynamically organized in the nucleus and decorated with chromatin-associated RNA (caRNA). It remains unclear whether the genome architecture modulates the spatial distribution of caRNA and vice versa. Here, we generate a resource of genome-wide RNA-DNA and DNA-DNA contact maps in human cells. These maps reveal the chromosomal domains demarcated by locally transcribed RNA, hereafter termed RNA-defined chromosomal domains. Further, the spreading of caRNA is constrained by the boundaries of topologically associating domains (TADs), demonstrating the role of the 3D genome structure in modulating the spatial distribution of RNA. Conversely, stopping transcription or acute depletion of RNA induces thousands of chromatin loops genome-wide. Activation or suppression of the transcription of specific genes suppresses or creates chromatin loops straddling these genes. Deletion of a specific caRNA-producing genomic sequence promotes chromatin loops that straddle the interchromosomal target sequences of this caRNA. These data suggest a feedback loop where the 3D genome modulates the spatial distribution of RNA, which in turn affects the dynamic 3D genome organization.

Chromatin-associated RNA (caRNA) has been proposed as a type of epigenomic modifier. Here, we test whether environmental stress can induce cellular dysfunction through modulating RNA-chromatin interactions. We induce endothelial cell (EC) dysfunction with high glucose and TNFα (H + T), that mimic the common stress in diabetes mellitus. We characterize the H + T-induced changes in gene expression by single cell (sc)RNA-seq, DNA interactions by Hi-C, and RNA-chromatin interactions by iMARGI. H + T induce inter-chromosomal RNA-chromatin interactions, particularly among the super enhancers. To test the causal relationship between H + T-induced RNA-chromatin interactions and the expression of EC dysfunction-related genes, we suppress the LINC00607 RNA. This suppression attenuates the expression of SERPINE1, a critical pro-inflammatory and pro-fibrotic gene. Furthermore, the changes of the co-expression gene network between diabetic and healthy donor-derived ECs corroborate the H + T-induced RNA-chromatin interactions. Taken together, caRNA-mediated dysregulation of gene expression modulates EC dysfunction, a crucial mechanism underlying numerous diseases.

RNA-chromatin interactions represent an important aspect of the transcriptional regulation of genes and transposable elements. However, analyses of chromatin-associated RNAs (caRNAs) are often limited to one caRNA at a time. Here, we describe the iMARGI (in situ mapping of RNA-genome interactome) technique, which is used to discover caRNAs and reveal their respective genomic interaction loci. iMARGI starts with in situ crosslinking and genome fragmentation, followed by converting each proximal RNA-DNA pair into an RNA-linker-DNA chimeric sequence. These chimeric sequences are subsequently converted into a sequencing library suitable for paired-end sequencing. A standardized bioinformatic software package, iMARGI-Docker, is provided to decode the paired-end sequencing data into caRNA-DNA interactions. Compared to its predecessor MARGI (mapping RNA-genome interactions), the number of input cells for iMARGI is 3-5 million (a 100-fold reduction), experimental time is reduced, and clear checkpoints have been established. It takes a few hours a day and a total of 8 d to complete the construction of an iMARGI sequencing library and 1 d to carry out data processing with iMARGI-Docker.

Fusion transcripts are used as biomarkers in companion diagnoses. Although more than 15,000 fusion RNAs have been identified from diverse cancer types, few common features have been reported. Here, we compared 16,410 fusion transcripts detected in cancer (from a published cohort of 9,966 tumor samples of 33 cancer types) with genome-wide RNA-DNA interactions mapped in two normal, noncancerous cell types [using iMARGI, an enhanced version of the mapping of RNA-genome interactions (MARGI) assay]. Among the top 10 most significant RNA-DNA interactions in normal cells, 5 colocalized with the gene pairs that formed fusion RNAs in cancer. Furthermore, throughout the genome, the frequency of a gene pair to exhibit RNA-DNA interactions is positively correlated with the probability of this gene pair to present documented fusion transcripts in cancer. To test whether RNA-DNA interactions in normal cells are predictive of fusion RNAs, we analyzed these in a validation cohort of 96 lung cancer samples using RNA sequencing (RNA-seq). Thirty-seven of 42 fusion transcripts in the validation cohort were found to exhibit RNA-DNA interactions in normal cells. Finally, by combining RNA-seq, single-molecule RNA FISH, and DNA FISH, we detected a cancer sample with EML4-ALK fusion RNA without forming the EML4-ALK fusion gene. Collectively, these data suggest an RNA-poise model, where spatial proximity of RNA and DNA could poise for the creation of fusion transcripts.

This paper investigates a nonlocal dispersal epidemic model under the multiple nonlocal distributed delays and nonlinear incidence effects. First, the minimal wave speed c ∗ and the basic reproduction number R 0 are defined, which determine the existence of traveling wave solutions. Second, with the help of the upper and lower solutions, Schauder's fixed point theorem, and limiting techniques, the traveling waves satisfying some asymptotic boundary conditions are discussed. Specifically, when ℛ 0 > 1 , for every speed c > c ∗ there exists a traveling wave solution satisfying the boundary conditions, and there is no such traveling wave solution for any 0 < c < c ∗ when ℛ 0 > 1 or c > 0 when ℛ 0 < 1. Finally, we analyze the effects of nonlocal time delay on the minimum wave speed. [ABSTRACT FROM AUTHOR]

Considering the importance of time delay phenomenon in disease transmission and the interdependence of time delay and spatial location, a reaction-diffusion SIR epidemic model with nonlocal time delay (or time-space time delay) is proposed and the travelling wave solutions are discussed. Specifically, we define the basic reproduction number $ \mathcal {R}_0 $ R0 and the critical wave speed $ c^* $ c∗. For every wave speed $ c\geq c^* $ c≥c∗, the existence of travelling wave solutions is studied by using the upper–lower solutions, the fixed-point theorem and some limit techniques when $ \mathcal {R}_0 \gt 1 $ R0>1. The nonexistence of travelling waves when $ \mathcal {R}_0 \gt 1 $ R0>1 for any $ 0 \lt c \lt c^* $ 0c>0 is also proved. Finally, the influence of time-delay on disease propagation, especially the critical wave speed, is discussed through analysis and simulations. [ABSTRACT FROM AUTHOR]

Methoxy poly(ethylene glycol)-block-poly(L-lactide) (MPEG-b-PLLA) has a wide range of applications in pharmaceuticals and biology, and its structure and morphology have been thoroughly studied. In the experiment, we synthesized MPEG-b-PLLA with different block lengths using the principle of ring-opening polymerization by controlling the amount of lactic acid added. The thermodynamic properties of copolymers and the crystallization properties of blends were studied separately. The crystallization kinetics of PDLA/MPEG-b-PLA and PLLA/MPEG-b-PLA composite films were studied using differential scanning calorimetry (DSC). The results indicate that the crystallization kinetics of composite films are closely related to the amount of block addition. The crystallinity of the sample first increases and then decreases with an increase in MPEG-b-PLLA content. These results were also confirmed in polarized optical microscope (POM) and wide-angle X-ray diffraction (WAXD) tests. When 3% MPEG-b-PLLA was added to the PDLA matrix, the blend exhibited the strongest crystallization performance. [ABSTRACT FROM AUTHOR]

BiFeO3/La0.7Sr0.3MnO3 (BFO/LSMO) epitaxial heterostructures were successfully synthesized by pulsed laser deposition on (001)-oriented SrTiO3 single-crystal substrates with Au top electrodes. Stable bipolar resistive switching characteristics regulated by ferroelectric polarization reversal was observed in the Au/BFO/LSMO heterostructures. The conduction mechanism was revealed to follow the Schottky emission model, and the Schottky barriers in high-resistance and low-resistance states were estimated based on temperature-dependent current–voltage curves. Further, the observed memristive behavior was interpreted via the modulation effect on the depletion region width and the Schottky barrier height caused by ferroelectric polarization reversal, combining with the oxygen vacancies migration near the BFO/LSMO interface. [ABSTRACT FROM AUTHOR]